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Backblaze__b2-sdk-python-120

diff --git a/.travis.yml b/.travis.yml index 3e06cfe7..806c817e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -37,9 +37,9 @@ matrix: # Enable nightly without globally enabling sudo and xenial for other build jobs # disabled because nosetests is not supported on 3.9. We'll move to pytest. # disabled by commenting out because Travis does not listen to matrix.allow_failures.python = [pypy3, nightly] for some reason - #- python: nightly - # dist: xenial - # sudo: true + - python: nightly + #dist: xenial + #sudo: true - python: 3 os: osx diff --git a/README.md b/README.md index da6f4932..6b12564f 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,7 @@ b2sdk>=0.0.0,<1.0.0 * Make sync treat hidden files as deleted * Remove arrow warnings caused by https://github.com/crsmithdev/arrow/issues/612 +* Add a `list_file_versions` to buckets. ## 1.0.2 (2019-10-15) diff --git a/b2sdk/b2http.py b/b2sdk/b2http.py index 4fe5a172..c2230bb9 100644 --- a/b2sdk/b2http.py +++ b/b2sdk/b2http.py @@ -307,7 +307,12 @@ class B2Http(object): self._run_post_request_hooks('POST', url, headers, response) return response - response = _translate_and_retry(do_post, try_count, post_params) + try: + response = _translate_and_retry(do_post, try_count, post_params) + except B2RequestTimeout: + # this forces a token refresh, which is necessary if request is still alive + # on the server but has terminated for some reason on the client. See #79 + raise B2RequestTimeoutDuringUpload() # Decode the JSON that came back. If we've gotten this far, # we know we have a status of 200 OK. In this case, the body diff --git a/b2sdk/bucket.py b/b2sdk/bucket.py index 15d45f21..b95dd265 100644 --- a/b2sdk/bucket.py +++ b/b2sdk/bucket.py @@ -196,6 +196,36 @@ class Bucket(object): """ return self.api.list_parts(file_id, start_part_number, batch_size) + def list_file_versions(self, file_name, fetch_count=None): + """ + Lists all of the versions for a single file. + + :param str file_name: the name of the file to list. + :param int,None fetch_count: how many entries to list per API call or ``None`` to use the default. Acceptable values: 1 - 10000 + :rtype: generator[b2sdk.v1.FileVersionInfo] + """ + if fetch_count is not None and fetch_count <= 0: + # fetch_count equal to 0 means "use API default", which we don't want to support here + raise ValueError("unsupported fetch_count value") + start_file_name = file_name + start_file_id = None + session = self.api.session + while 1: + response = session.list_file_versions( + self.id_, start_file_name, start_file_id, fetch_count, file_name + ) + + for entry in response['files']: + file_version_info = FileVersionInfoFactory.from_api_response(entry) + if file_version_info.file_name != file_name: + # All versions for the requested file name have been listed. + return + yield file_version_info + start_file_name = response['nextFileName'] + start_file_id = response['nextFileId'] + if start_file_name is None: + return + def ls(self, folder_to_list='', show_versions=False, recursive=False, fetch_count=None): """ Pretend that folders exist and yields the information about the files in a folder. diff --git a/b2sdk/exception.py b/b2sdk/exception.py index 61d9fe5f..fdeb2d63 100644 --- a/b2sdk/exception.py +++ b/b2sdk/exception.py @@ -108,8 +108,9 @@ class BadJson(B2SimpleError): prefix = 'Bad request' -class BadUploadUrl(TransientErrorMixin, B2SimpleError): - pass +class BadUploadUrl(B2SimpleError): + def should_retry_upload(self): + return True class BrokenPipe(B2Error): @@ -209,6 +210,12 @@ class B2RequestTimeout(TransientErrorMixin, B2SimpleError): pass +class B2RequestTimeoutDuringUpload(B2RequestTimeout): + # if a timeout is hit during upload, it is not guaranteed that the the server has released the upload token lock already, so we'll use a new token + def should_retry_http(self): + return False + + class DestFileNewer(B2Error): def __init__(self, dest_file, source_file, dest_prefix, source_prefix): super(DestFileNewer, self).__init__() diff --git a/b2sdk/raw_simulator.py b/b2sdk/raw_simulator.py index 6b5a091d..50fa5ff4 100644 --- a/b2sdk/raw_simulator.py +++ b/b2sdk/raw_simulator.py @@ -510,8 +510,10 @@ class BucketSimulator(object): next_file_id = None for key in sorted(six.iterkeys(self.file_name_and_id_to_file)): (file_name, file_id) = key - if (start_file_name < - file_name) or (start_file_name == file_name and start_file_id <= file_id): + if (start_file_name < file_name) or ( + start_file_name == file_name and + (start_file_id == '' or int(start_file_id) <= int(file_id)) + ): file_sim = self.file_name_and_id_to_file[key] if prefix is not None and not file_name.startswith(prefix): break diff --git a/b2sdk/v1/exception.py b/b2sdk/v1/exception.py index cf149a68..7815a28f 100644 --- a/b2sdk/v1/exception.py +++ b/b2sdk/v1/exception.py @@ -18,6 +18,7 @@ from b2sdk.exception import B2HttpCallbackException from b2sdk.exception import B2HttpCallbackPostRequestException from b2sdk.exception import B2HttpCallbackPreRequestException from b2sdk.exception import B2RequestTimeout +from b2sdk.exception import B2RequestTimeoutDuringUpload from b2sdk.exception import B2SimpleError from b2sdk.exception import BadDateFormat from b2sdk.exception import BadFileInfo @@ -73,6 +74,7 @@ __all__ = ( 'B2HttpCallbackPostRequestException', 'B2HttpCallbackPreRequestException', 'B2RequestTimeout', + 'B2RequestTimeoutDuringUpload', 'B2SimpleError', 'BadDateFormat', 'BadFileInfo',

Backblaze/b2-sdk-python

6d35959ccfb06c3888702d91f3ce8d699f24f8e0

diff --git a/test/v0/test_exception.py b/test/v0/test_exception.py index 5bcb7fca..a90e5329 100644 --- a/test/v0/test_exception.py +++ b/test/v0/test_exception.py @@ -50,7 +50,7 @@ class TestExceptions(TestBase): try: raise BadUploadUrl('foo') except BadUploadUrl as e: - assert e.should_retry_http() + assert not e.should_retry_http() assert e.should_retry_upload() assert str(e) == 'Bad upload url: foo', str(e) diff --git a/test/v1/test_bucket.py b/test/v1/test_bucket.py index 0dcccab7..8f71157a 100644 --- a/test/v1/test_bucket.py +++ b/test/v1/test_bucket.py @@ -21,6 +21,7 @@ from .test_base import TestBase from .deps_exception import ( AlreadyFailed, B2Error, + B2RequestTimeoutDuringUpload, InvalidAuthToken, InvalidMetadataDirective, InvalidRange, @@ -303,6 +304,81 @@ class TestLs(TestCaseWithBucket): self.assertBucketContents(expected, '', show_versions=True) +class TestListVersions(TestCaseWithBucket): + def test_single_version(self): + data = six.b('hello world') + a_id = self.bucket.upload_bytes(data, 'a').id_ + b_id = self.bucket.upload_bytes(data, 'b').id_ + c_id = self.bucket.upload_bytes(data, 'c').id_ + + expected = [(a_id, 'a', 11, 'upload')] + actual = [ + (info.id_, info.file_name, info.size, info.action) + for info in self.bucket.list_file_versions('a') + ] + self.assertEqual(expected, actual) + + expected = [(b_id, 'b', 11, 'upload')] + actual = [ + (info.id_, info.file_name, info.size, info.action) + for info in self.bucket.list_file_versions('b') + ] + self.assertEqual(expected, actual) + + expected = [(c_id, 'c', 11, 'upload')] + actual = [ + (info.id_, info.file_name, info.size, info.action) + for info in self.bucket.list_file_versions('c') + ] + self.assertEqual(expected, actual) + + def test_multiple_version(self): + a_id1 = self.bucket.upload_bytes(six.b('first version'), 'a').id_ + a_id2 = self.bucket.upload_bytes(six.b('second version'), 'a').id_ + a_id3 = self.bucket.upload_bytes(six.b('last version'), 'a').id_ + + expected = [ + (a_id3, 'a', 12, 'upload'), (a_id2, 'a', 14, 'upload'), (a_id1, 'a', 13, 'upload') + ] + actual = [ + (info.id_, info.file_name, info.size, info.action) + for info in self.bucket.list_file_versions('a') + ] + self.assertEqual(expected, actual) + + def test_ignores_subdirectory(self): + data = six.b('hello world') + file_id = self.bucket.upload_bytes(data, 'a/b').id_ + self.bucket.upload_bytes(data, 'a/b/c') + + expected = [(file_id, 'a/b', 11, 'upload')] + actual = [ + (info.id_, info.file_name, info.size, info.action) + for info in self.bucket.list_file_versions('a/b') + ] + self.assertEqual(expected, actual) + + def test_all_versions_in_response(self): + data = six.b('hello world') + file_id = self.bucket.upload_bytes(data, 'a/b').id_ + self.bucket.upload_bytes(data, 'a/b/c') + + expected = [(file_id, 'a/b', 11, 'upload')] + actual = [ + (info.id_, info.file_name, info.size, info.action) + for info in self.bucket.list_file_versions('a/b', fetch_count=1) + ] + self.assertEqual(expected, actual) + + def test_bad_fetch_count(self): + try: + # Convert to a list to cause the generator to execute. + list(self.bucket.list_file_versions('a', fetch_count=0)) + self.fail('should have raised ValueError') + except ValueError as e: + self.assertEqual('unsupported fetch_count value', str(e)) + + class TestCopyFile(TestCaseWithBucket): def test_copy_without_optional_params(self): file_id = self._make_file() @@ -452,6 +528,11 @@ class TestUpload(TestCaseWithBucket): data = six.b('hello world') self.bucket.upload_bytes(data, 'file1') + def test_upload_timeout(self): + self.simulator.set_upload_errors([B2RequestTimeoutDuringUpload()]) + data = six.b('hello world') + self.bucket.upload_bytes(data, 'file1') + def test_upload_file_one_fatal_error(self): self.simulator.set_upload_errors([CanRetry(False)]) data = six.b('hello world') @@ -553,6 +634,18 @@ class TestUpload(TestCaseWithBucket): self._check_file_contents('file1', data) self.assertEqual("600: 200 400 600 closed", progress_listener.get_history()) + def test_upload_large_file_with_restricted_api_key(self): + self.simulator.key_id_to_key[self.account_id].name_prefix_or_none = 'path/to' + part_size = self.simulator.MIN_PART_SIZE + data = self._make_data(part_size * 3) + progress_listener = StubProgressListener() + file_info = self.bucket.upload_bytes( + data, 'path/to/file1', progress_listener=progress_listener + ) + self.assertEqual(len(data), file_info.size) + self._check_file_contents('path/to/file1', data) + self.assertEqual("600: 200 400 600 closed", progress_listener.get_history()) + def _start_large_file(self, file_name, file_info=None): if file_info is None: file_info = {} diff --git a/test/v1/test_exception.py b/test/v1/test_exception.py index a49969d8..2440a39f 100644 --- a/test/v1/test_exception.py +++ b/test/v1/test_exception.py @@ -50,7 +50,7 @@ class TestExceptions(TestBase): try: raise BadUploadUrl('foo') except BadUploadUrl as e: - assert e.should_retry_http() + assert not e.should_retry_http() assert e.should_retry_upload() assert str(e) == 'Bad upload url: foo', str(e)

No public API for getting a list of file ids for a filename In order to delete a file you need to know the file id of the version to delete but unless I'm missing something there is no straightforward way to list the different versions of a file with a given filename. `bucket.ls` exists but since it enforces a trailing `/` on the folder you pass the only way I can see right now to get this through the public API is to do something like this: ```python def get_file_ids(bucket, filename): for file_info, folder_name in bucket.ls(folder_to_list=os.path.dirname(filename), show_versions=True): if file_info.file_name == filename: yield file_info ``` Obviously this potentially wastes bandwidth by returning all files in the same "folder".

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

Backblaze__b2-sdk-python-121

diff --git a/b2sdk/v1/exception.py b/b2sdk/v1/exception.py index cf149a68..7815a28f 100644 --- a/b2sdk/v1/exception.py +++ b/b2sdk/v1/exception.py @@ -18,6 +18,7 @@ from b2sdk.exception import B2HttpCallbackException from b2sdk.exception import B2HttpCallbackPostRequestException from b2sdk.exception import B2HttpCallbackPreRequestException from b2sdk.exception import B2RequestTimeout +from b2sdk.exception import B2RequestTimeoutDuringUpload from b2sdk.exception import B2SimpleError from b2sdk.exception import BadDateFormat from b2sdk.exception import BadFileInfo @@ -73,6 +74,7 @@ __all__ = ( 'B2HttpCallbackPostRequestException', 'B2HttpCallbackPreRequestException', 'B2RequestTimeout', + 'B2RequestTimeoutDuringUpload', 'B2SimpleError', 'BadDateFormat', 'BadFileInfo',

Backblaze/b2-sdk-python

d1098c1d9d717a793872910edb314f0a26fa1f5d

diff --git a/test/v1/test_bucket.py b/test/v1/test_bucket.py index ec085c86..87c98d0f 100644 --- a/test/v1/test_bucket.py +++ b/test/v1/test_bucket.py @@ -21,6 +21,7 @@ from .test_base import TestBase from .deps_exception import ( AlreadyFailed, B2Error, + B2RequestTimeoutDuringUpload, InvalidAuthToken, InvalidMetadataDirective, InvalidRange, @@ -452,6 +453,11 @@ class TestUpload(TestCaseWithBucket): data = six.b('hello world') self.bucket.upload_bytes(data, 'file1') + def test_upload_timeout(self): + self.simulator.set_upload_errors([B2RequestTimeoutDuringUpload()]) + data = six.b('hello world') + self.bucket.upload_bytes(data, 'file1') + def test_upload_file_one_fatal_error(self): self.simulator.set_upload_errors([CanRetry(False)]) data = six.b('hello world')

400 bad_request more than one upload using auth token I have a loop uploading files locally to B2 cloud. After a few thousand uploads over a few hours, I get this error: `b2sdk.exception.UnknownError: Unknown error: 400 bad_request more than one upload using auth token 4_0021a87abca5e6b0000000005_018fe4f8_97f3ec_uplg_wANv-9n9ent4nLDoDI0yMFmZqeQ=` I feel like upload_local_file method should be able to handle renegotiating a new auth token on its own rather than failing as such.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

Backblaze__b2-sdk-python-163

diff --git a/.readthedocs.yml b/.readthedocs.yml index b4278123..7a1f282a 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -14,7 +14,7 @@ formats: all # Optionally set the version of Python and requirements required to build your docs python: - version: 3.9 + version: 3.8 install: - requirements: requirements.txt - method: pip diff --git a/CHANGELOG.md b/CHANGELOG.md index 8d0fd4e5..7a2a1214 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * Drop Python 2 and Python 3.4 support :tada: * Remove `--prefix` from `ls` (it didn't really work, use `folderName` argument) +### Fixed +* Allow to set an empty bucket info during the update + ## [1.1.4] - 2020-07-15 ### Added diff --git a/b2sdk/raw_api.py b/b2sdk/raw_api.py index 6aadbdb7..7c71450a 100644 --- a/b2sdk/raw_api.py +++ b/b2sdk/raw_api.py @@ -552,7 +552,7 @@ class B2RawApi(AbstractRawApi): lifecycle_rules=None, if_revision_is=None ): - assert bucket_info or bucket_type + assert bucket_info is not None or bucket_type is not None kwargs = {} if if_revision_is is not None: diff --git a/noxfile.py b/noxfile.py index a24483eb..a9f815f7 100644 --- a/noxfile.py +++ b/noxfile.py @@ -25,7 +25,7 @@ PY_PATHS = ['b2sdk', 'test', 'noxfile.py', 'setup.py'] REQUIREMENTS_FORMAT = ['yapf==0.27'] REQUIREMENTS_LINT = ['yapf==0.27', 'pyflakes==2.2.0', 'pytest==6.1.1', 'liccheck==0.4.7'] -REQUIREMENTS_TEST = ['pytest==6.1.1', 'pytest-cov==2.10.1'] +REQUIREMENTS_TEST = ['pytest==6.1.1', 'pytest-cov==2.10.1', 'pytest-mock==3.3.1'] REQUIREMENTS_BUILD = ['setuptools>=20.2'] nox.options.reuse_existing_virtualenvs = True

Backblaze/b2-sdk-python

c510c73820774958ba1cc11153bc1fe7668d675e

diff --git a/test/unit/v0/test_raw_api.py b/test/unit/v0/test_raw_api.py index 222fae4d..b1a8e03b 100644 --- a/test/unit/v0/test_raw_api.py +++ b/test/unit/v0/test_raw_api.py @@ -7,6 +7,7 @@ # License https://www.backblaze.com/using_b2_code.html # ###################################################################### +import pytest from .test_base import TestBase @@ -92,3 +93,27 @@ class TestRawAPIFilenames(TestBase): self._should_raise(u'foo/' + 251 * u'x', "segment too long") # So a segment of 125 two-byte chars plus one should also fail. self._should_raise(u'foo/' + 125 * TWO_BYTE_UNICHR + u'x', "segment too long") + + +class TestUpdateBucket: + """Test updating bucket.""" + + @pytest.fixture(autouse=True) + def init(self, mocker): + b2_http = mocker.MagicMock() + self.raw_api = B2RawApi(b2_http) + + def test_assertion_raises(self): + with pytest.raises(AssertionError): + self.raw_api.update_bucket('test', 'account_auth_token', 'account_id', 'bucket_id') + + @pytest.mark.parametrize('bucket_type,bucket_info', ((None, {}), ('allPublic', None))) + def test_assertion_not_raises(self, bucket_type, bucket_info): + self.raw_api.update_bucket( + 'test', + 'account_auth_token', + 'account_id', + 'bucket_id', + bucket_type=bucket_type, + bucket_info=bucket_info + ) diff --git a/test/unit/v1/test_raw_api.py b/test/unit/v1/test_raw_api.py index a0139740..1bf01dee 100644 --- a/test/unit/v1/test_raw_api.py +++ b/test/unit/v1/test_raw_api.py @@ -7,6 +7,7 @@ # License https://www.backblaze.com/using_b2_code.html # ###################################################################### +import pytest from .test_base import TestBase @@ -92,3 +93,27 @@ class TestRawAPIFilenames(TestBase): self._should_raise(u'foo/' + 251 * u'x', "segment too long") # So a segment of 125 two-byte chars plus one should also fail. self._should_raise(u'foo/' + 125 * TWO_BYTE_UNICHR + u'x', "segment too long") + + +class TestUpdateBucket: + """Test updating bucket.""" + + @pytest.fixture(autouse=True) + def init(self, mocker): + b2_http = mocker.MagicMock() + self.raw_api = B2RawApi(b2_http) + + def test_assertion_raises(self): + with pytest.raises(AssertionError): + self.raw_api.update_bucket('test', 'account_auth_token', 'account_id', 'bucket_id') + + @pytest.mark.parametrize('bucket_type,bucket_info', ((None, {}), ('allPublic', None))) + def test_assertion_not_raises(self, bucket_type, bucket_info): + self.raw_api.update_bucket( + 'test', + 'account_auth_token', + 'account_id', + 'bucket_id', + bucket_type=bucket_type, + bucket_info=bucket_info + )

should bucket.update() let me set my bucket_info to {}? Hi -- I'd like to set the bucket info on my bucket to not have any entries. To do that, I tried calling bucket.set_info() and got an assert. Here's a simple failing case: > b2_api = B2Api(InMemoryAccountInfo()) > b2_api.authorize_account(url, app_key_id, app_key) > bucket = b2_api.get_bucket_by_name("myBucket")) > > bucket.set_info({}) This triggers an assert on line 558, in update_bucket: > assert bucket_info or bucket_type I'm running on macOS 10.15.7. I'm using Python 3.8.6 installed with mac ports. i have the following b2 things installed with pip3: > $ pip3 list | grep b2 > b2 2.0.2 > b2sdk 1.1.4 Here's the stack trace that's generated: [stack.txt](https://github.com/Backblaze/b2-sdk-python/files/5337715/stack.txt) A similar thing happens when I use bucket.update(bucket_info={}), which ends up on the same place. I'm currently working around it by passing the bucket's type back in: > bucket.update(bucket_type=bucket.as_dict()['bucketType'], bucket_info={}, lifecycle_rules=[])

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

Backblaze__b2-sdk-python-305

diff --git a/CHANGELOG.md b/CHANGELOG.md index e75521aa..6c6565f8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 * Add pypy-3.8 to test matrix * Add support for unverified checksum upload mode * Add dedicated exception for unverified email +* Add a parameter to customize `sync_policy_manager` ### Fixed * Fix downloading files with unverified checksum diff --git a/b2sdk/sync/sync.py b/b2sdk/sync/sync.py index eb43eec5..8aa9dc3f 100644 --- a/b2sdk/sync/sync.py +++ b/b2sdk/sync/sync.py @@ -135,12 +135,13 @@ class Synchronizer: compare_version_mode=CompareVersionMode.MODTIME, compare_threshold=None, keep_days=None, + sync_policy_manager: SyncPolicyManager = POLICY_MANAGER, ): """ Initialize synchronizer class and validate arguments :param int max_workers: max number of workers - :param policies_manager: policies manager object + :param policies_manager: object which decides which files to process :param bool dry_run: test mode, does not actually transfer/delete when enabled :param bool allow_empty_source: if True, do not check whether source folder is empty :param b2sdk.v2.NewerFileSyncMode newer_file_mode: setting which determines handling for destination files newer than on the source @@ -148,6 +149,7 @@ class Synchronizer: :param b2sdk.v2.CompareVersionMode compare_version_mode: how to compare the source and destination files to find new ones :param int compare_threshold: should be greater than 0, default is 0 :param int keep_days: if keep_days_or_delete is `b2sdk.v2.KeepOrDeleteMode.KEEP_BEFORE_DELETE`, then this should be greater than 0 + :param SyncPolicyManager sync_policy_manager: object which decides what to do with each file (upload, download, delete, copy, hide etc) """ self.newer_file_mode = newer_file_mode self.keep_days_or_delete = keep_days_or_delete @@ -156,7 +158,8 @@ class Synchronizer: self.compare_threshold = compare_threshold or 0 self.dry_run = dry_run self.allow_empty_source = allow_empty_source - self.policies_manager = policies_manager + self.policies_manager = policies_manager # actually it should be called scan_policies_manager + self.sync_policy_manager = sync_policy_manager self.max_workers = max_workers self._validate() @@ -280,7 +283,7 @@ class Synchronizer: :param b2sdk.v2.AbstractFolder dest_folder: destination folder object :param int now_millis: current time in milliseconds :param b2sdk.v2.SyncReport reporter: reporter object - :param b2sdk.v2.SyncPolicyManager policies_manager: policies manager object + :param b2sdk.v2.ScanPolicyManager policies_manager: object which decides which files to process :param b2sdk.v2.AbstractSyncEncryptionSettingsProvider encryption_settings_provider: encryption setting provider """ if self.keep_days_or_delete == KeepOrDeleteMode.KEEP_BEFORE_DELETE and dest_folder.folder_type( @@ -358,7 +361,7 @@ class Synchronizer: delete = self.keep_days_or_delete == KeepOrDeleteMode.DELETE keep_days = self.keep_days - policy = POLICY_MANAGER.get_policy( + policy = self.sync_policy_manager.get_policy( sync_type, source_path, source_folder, diff --git a/b2sdk/v1/sync/sync.py b/b2sdk/v1/sync/sync.py index d7d306c7..75833605 100644 --- a/b2sdk/v1/sync/sync.py +++ b/b2sdk/v1/sync/sync.py @@ -37,10 +37,19 @@ class Synchronizer(v2.Synchronizer): compare_version_mode=v2.CompareVersionMode.MODTIME, compare_threshold=None, keep_days=None, + sync_policy_manager: v2.SyncPolicyManager = v2.POLICY_MANAGER, ): super().__init__( - max_workers, scan_wrap_if_necessary(policies_manager), dry_run, allow_empty_source, - newer_file_mode, keep_days_or_delete, compare_version_mode, compare_threshold, keep_days + max_workers, + scan_wrap_if_necessary(policies_manager), + dry_run, + allow_empty_source, + newer_file_mode, + keep_days_or_delete, + compare_version_mode, + compare_threshold, + keep_days, + sync_policy_manager, ) def make_folder_sync_actions(

Backblaze/b2-sdk-python

900df6b6921692cc8bc812c5d199b5989bdefcef

diff --git a/test/unit/sync/fixtures.py b/test/unit/sync/fixtures.py index 3ff871f0..a4861804 100644 --- a/test/unit/sync/fixtures.py +++ b/test/unit/sync/fixtures.py @@ -15,7 +15,7 @@ import pytest import apiver_deps from apiver_deps import AbstractFolder, B2Folder, LocalFolder, B2SyncPath, LocalSyncPath from apiver_deps import CompareVersionMode, NewerFileSyncMode, KeepOrDeleteMode -from apiver_deps import DEFAULT_SCAN_MANAGER, Synchronizer +from apiver_deps import DEFAULT_SCAN_MANAGER, POLICY_MANAGER, Synchronizer if apiver_deps.V <= 1: from apiver_deps import FileVersionInfo as VFileVersion @@ -112,6 +112,7 @@ def synchronizer_factory(): keep_days=None, compare_version_mode=CompareVersionMode.MODTIME, compare_threshold=None, + sync_policy_manager=POLICY_MANAGER, ): return Synchronizer( 1, @@ -123,6 +124,7 @@ def synchronizer_factory(): keep_days=keep_days, compare_version_mode=compare_version_mode, compare_threshold=compare_threshold, + sync_policy_manager=sync_policy_manager, ) return get_synchronizer diff --git a/test/unit/sync/test_sync.py b/test/unit/sync/test_sync.py index 6af85667..887d6152 100644 --- a/test/unit/sync/test_sync.py +++ b/test/unit/sync/test_sync.py @@ -12,7 +12,7 @@ from unittest import mock from enum import Enum from functools import partial -from apiver_deps import B2DownloadAction, B2UploadAction, B2CopyAction, AbstractSyncEncryptionSettingsProvider, UploadSourceLocalFile +from apiver_deps import UpPolicy, B2DownloadAction, B2UploadAction, B2CopyAction, AbstractSyncEncryptionSettingsProvider, UploadSourceLocalFile, SyncPolicyManager from apiver_deps_exception import DestFileNewer, InvalidArgument from b2sdk.utils import TempDir @@ -849,6 +849,25 @@ class TestSynchronizer: ) ] + def test_custom_sync_manager_policy(self, synchronizer_factory): + class MySyncPolicyManager(SyncPolicyManager): + def get_policy_class(self, sync_type, delete, keep_days): + return UpPolicy + + synchronizer = synchronizer_factory( + compare_version_mode=CompareVersionMode.SIZE, + keep_days_or_delete=KeepOrDeleteMode.DELETE, + sync_policy_manager=MySyncPolicyManager(), + ) + src = self.folder_factory('local', ('a.txt', [200], 11)) + dst = self.folder_factory('b2', ('a.txt', [100], 10)) + # normally_expected = [ + # 'b2_upload(/dir/a.txt, folder/a.txt, 200)', + # 'b2_delete(folder/a.txt, id_a_100, (old version))' + # ] + expected = ['b2_upload(/dir/a.txt, folder/a.txt, 200)'] + self.assert_folder_sync_actions(synchronizer, src, dst, expected) + class TstEncryptionSettingsProvider(AbstractSyncEncryptionSettingsProvider): def __init__(self, source_encryption_setting, destination_encryption_setting):

Custom sync policy? Is there a way to create a custom sync policy? I want to keep some files in the bucket unchanged even though the local counterpart has these files with a newer timestamp. I've tried with exclude regexes but that will treat the excluded files as missing and deletes them in the bucket.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

Backblaze__b2-sdk-python-433

diff --git a/CHANGELOG.md b/CHANGELOG.md index 03028df2..6b3a6531 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +### Fixed +* Fix ScanPoliciesManager support for compiled regexes + ### Infrastructure * Fix readthedocs build by updating to v2 configuration schema * Fix spellcheck erroring out on LICENSE file diff --git a/b2sdk/scan/policies.py b/b2sdk/scan/policies.py index e6a05396..349a76fd 100644 --- a/b2sdk/scan/policies.py +++ b/b2sdk/scan/policies.py @@ -43,7 +43,7 @@ class RegexSet: return any(c.match(s) is not None for c in self._compiled_list) -def convert_dir_regex_to_dir_prefix_regex(dir_regex): +def convert_dir_regex_to_dir_prefix_regex(dir_regex: str | re.Pattern) -> str: """ The patterns used to match directory names (and file names) are allowed to match a prefix of the name. This 'feature' was unintentional, but is @@ -65,8 +65,10 @@ def convert_dir_regex_to_dir_prefix_regex(dir_regex): either the regex ends in '$' or does not. :param dir_regex: a regular expression string or literal - :type dir_regex: str + :return: a regular expression string which matches the directory prefix """ + if isinstance(dir_regex, re.Pattern): + dir_regex = dir_regex.pattern if dir_regex.endswith('$'): return dir_regex[:-1] + r'/' else:

Backblaze/b2-sdk-python

f04cca5b9cf0a95ea9d292325bf2ed0f1ec97b7a

diff --git a/test/unit/scan/test_scan_policies.py b/test/unit/scan/test_scan_policies.py index fe79c9a4..2c6cd2fc 100644 --- a/test/unit/scan/test_scan_policies.py +++ b/test/unit/scan/test_scan_policies.py @@ -70,3 +70,15 @@ class TestScanPoliciesManager: } with pytest.raises(exception): ScanPoliciesManager(**kwargs) + + @pytest.mark.apiver(from_ver=2) + def test_re_pattern_argument_support(self): + kwargs = { + param: (re.compile(r".*"),) + for param in ( + "exclude_dir_regexes", + "exclude_file_regexes", + "include_file_regexes", + ) + } + ScanPoliciesManager(**kwargs)

passing compiled regex results in AttributeError I am using b2sdk-1.24.0. `b2sdk.v2.ScalPoliciesManager` accepts `Iterable[str | re.Pattern]` for `exclude_dir_regexes`. However, if `exclude_dir_regexes` contains an `re.Pattern` instance, an Attribute error results at `b2sdk/scan/policies.py:70` because `re.Pattern has no attribute 'endswith'`. When regex is `re.Pattern`, `regex.pattern.endswith` must be used.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

BelgianBiodiversityPlatform__python-dwca-reader-101

diff --git a/dwca/files.py b/dwca/files.py index a1bcd9a..bada8fa 100644 --- a/dwca/files.py +++ b/dwca/files.py @@ -6,7 +6,7 @@ from array import array from typing import List, Union, IO, Dict, Optional from dwca.descriptors import DataFileDescriptor -from dwca.rows import CoreRow, ExtensionRow +from dwca.rows import CoreRow, ExtensionRow, Row class CSVDataFile(object): @@ -105,11 +105,6 @@ class CSVDataFile(object): Creating this index can be time and memory consuming for large archives, so it's created on the fly at first access. """ - if self.file_descriptor.represents_corefile: - raise AttributeError( - "coreid_index is only available for extension data files" - ) - if self._coreid_index is None: self._coreid_index = self._build_coreid_index() @@ -120,14 +115,18 @@ class CSVDataFile(object): index = {} # type: Dict[str, array[int]] for position, row in enumerate(self): - tmp = ExtensionRow(row, position, self.file_descriptor) - index.setdefault(tmp.core_id, array('L')).append(position) + if self.file_descriptor.represents_corefile: + tmp = CoreRow(row, position, self.file_descriptor) + index.setdefault(tmp.id, array('L')).append(position) + else: + tmp = ExtensionRow(row, position, self.file_descriptor) + index.setdefault(tmp.core_id, array('L')).append(position) return index # TODO: For ExtensionRow and a specific field only, generalize ? # TODO: What happens if called on a Core Row? - def get_all_rows_by_coreid(self, core_id: int) -> List[ExtensionRow]: + def get_all_rows_by_coreid(self, core_id: int) -> List[Row]: """Return a list of :class:`dwca.rows.ExtensionRow` whose Core Id field match `core_id`.""" if core_id not in self.coreid_index: return [] diff --git a/dwca/star_record.py b/dwca/star_record.py new file mode 100644 index 0000000..6be17ff --- /dev/null +++ b/dwca/star_record.py @@ -0,0 +1,58 @@ +from dwca.files import CSVDataFile +from typing import List, Literal +import itertools + + +class StarRecordIterator(object): + """ Object used to iterate over multiple DWCA-files joined on the coreid + + :param files_to_join: a list of the `dwca.files.CSVDataFile`s we'd like to join. + May or may not include the core file (the core is not treated in a special way) + :param how: indicates the type of join. "inner" and "outer" correspond vaguely to + inner and full joins. The outer join includes rows that don't match on all files, + however, it doesn't create null fields to fill in when rows are missing in files. + Attempts to conform to pandas.DataFrame.merge API. + """ + def __init__(self, files_to_join: List[CSVDataFile], how: Literal["inner", "outer"] = "inner"): + self.files_to_join = files_to_join + + # gather the coreids we want to join over. + self.common_core = set(self.files_to_join[0].coreid_index) + for data_file in self.files_to_join[1:]: + # inner join: coreid must be in all files + if how == "inner": + self.common_core &= set(data_file.coreid_index) + # outer join: coreid may be in any files + elif how == "outer": + self.common_core |= set(data_file.coreid_index) + + # initialize iterator variables + self._common_core_iterator = iter(self.common_core) + self._cross_product_iterator = iter([]) + + + def __next__(self): + # the next combination of rows matching this coreid + next_positions = next(self._cross_product_iterator, None) + # we finished all the combinations for this coreid + if not next_positions: + # get the next coreid + self._current_coreid = next(self._common_core_iterator) + self._files_with_current_coreid = [ + csv_file for csv_file in self.files_to_join + if self._current_coreid in csv_file.coreid_index] + # this iterates over all combinations of rows matching a coreid from all files + self._cross_product_iterator = itertools.product( + *( + csv_file.coreid_index[self._current_coreid] + for csv_file in self._files_with_current_coreid + )) + # go back and try to iterate over the rows for the new coreid + return next(self) + # zip up this combination of rows from all of the files. + return ( + csv_file.get_row_by_position(position) for position, csv_file in zip(next_positions, self._files_with_current_coreid) + ) + + + def __iter__(self): return self

BelgianBiodiversityPlatform/python-dwca-reader

b5b2bea333527353c5fe05b22e01c347a890ac61

diff --git a/dwca/test/test_datafile.py b/dwca/test/test_datafile.py index d5d7841..3fc461b 100644 --- a/dwca/test/test_datafile.py +++ b/dwca/test/test_datafile.py @@ -31,9 +31,13 @@ class TestCSVDataFile(unittest.TestCase): with DwCAReader(sample_data_path("dwca-2extensions.zip")) as dwca: extension_files = dwca.extension_files + core_txt = dwca.core_file description_txt = extension_files[0] vernacular_txt = extension_files[1] + expected_core = {'1': array('L', [0]), '2': array('L', [1]), '3': array('L', [2]), '4': array('L', [3])} + assert core_txt.coreid_index == expected_core + expected_vernacular = {"1": array('L', [0, 1, 2]), "2": array('L', [3])} assert vernacular_txt.coreid_index == expected_vernacular diff --git a/dwca/test/test_star_record.py b/dwca/test/test_star_record.py new file mode 100644 index 0000000..c080595 --- /dev/null +++ b/dwca/test/test_star_record.py @@ -0,0 +1,55 @@ +from dwca.read import DwCAReader +from dwca.rows import CoreRow +from dwca.star_record import StarRecordIterator +from .helpers import sample_data_path +import pytest +import unittest + +class TestStarRecordIterator(unittest.TestCase): + + def test_inner_join(self): + + expected_inner_join = frozenset({ + frozenset({('1', 0, 'Description'), ('1', 0, 'Taxon'), ('1', 0, 'VernacularName')}), + frozenset({('1', 0, 'Description'), ('1', 0, 'Taxon'), ('1', 1, 'VernacularName')}), + frozenset({('1', 0, 'Description'), ('1', 0, 'Taxon'), ('1', 2, 'VernacularName')}), + frozenset({('1', 1, 'Description'), ('1', 0, 'Taxon'), ('1', 0, 'VernacularName')}), + frozenset({('1', 1, 'Description'), ('1', 0, 'Taxon'), ('1', 1, 'VernacularName')}), + frozenset({('1', 1, 'Description'), ('1', 0, 'Taxon'), ('1', 2, 'VernacularName')}) + }) + + with DwCAReader(sample_data_path("dwca-2extensions.zip")) as dwca: + star_records = StarRecordIterator(dwca.extension_files + [dwca.core_file], how="inner") + stars = [] + for star_record in star_records: + rows = [] + for row in star_record: + rows.append((row.id if isinstance(row, CoreRow) else row.core_id, row.position, row.rowtype.split('/')[-1])) + stars.append(frozenset(rows)) + + assert frozenset(stars) == expected_inner_join + + def test_outer_join(self): + + expected_outer_join = frozenset({ + frozenset({('4', 2, 'Description'), ('4', 3, 'Taxon')}), + frozenset({('1', 0, 'Description'), ('1', 0, 'Taxon'), ('1', 0, 'VernacularName')}), + frozenset({('1', 0, 'Description'), ('1', 0, 'Taxon'), ('1', 1, 'VernacularName')}), + frozenset({('1', 0, 'Description'), ('1', 0, 'Taxon'), ('1', 2, 'VernacularName')}), + frozenset({('1', 1, 'Description'), ('1', 0, 'Taxon'), ('1', 0, 'VernacularName')}), + frozenset({('1', 1, 'Description'), ('1', 0, 'Taxon'), ('1', 1, 'VernacularName')}), + frozenset({('1', 1, 'Description'), ('1', 0, 'Taxon'), ('1', 2, 'VernacularName')}), + frozenset({('3', 2, 'Taxon')}), + frozenset({('2', 1, 'Taxon'), ('2', 3, 'VernacularName')}) + }) + + with DwCAReader(sample_data_path("dwca-2extensions.zip")) as dwca: + star_records = StarRecordIterator(dwca.extension_files + [dwca.core_file], how="outer") + stars = [] + for star_record in star_records: + rows = [] + for row in star_record: + rows.append((row.id if isinstance(row, CoreRow) else row.core_id, row.position, row.rowtype.split('/')[-1])) + stars.append(frozenset(rows)) + + assert frozenset(stars) == expected_outer_join

Extend CSVDataFile to support hash index on Core file ### Description It would be useful to be able to generalize iterators over the type of record. AFAIK, there's nothing particularly special about the Core Record data-format-wise, so it should be possible to create iterator methods that apply arbitrarily to Core or Extension files. My particular use case is that I'm working on an iterator for JOINed files, and it's awkward to deal with the Core Record as a special entity, since nothing about the JOIN process requires knowledge of whether a file is Core or Extension. ### Deliverables: 1) Extend the CSVDataFile class to allow a hash index on the Core Record. - This seems like it's maybe a 3 line change in [`_build_coreid_index`](https://github.com/csbrown/python-dwca-reader/blob/master/dwca/files.py#L118) to just if/then over what kind of row it's inspecting. - Maybe also need to edit [some type hints](https://github.com/csbrown/python-dwca-reader/blob/master/dwca/files.py#L130) 2) Update the [`test_coreid_index`](https://github.com/csbrown/python-dwca-reader/blob/master/dwca/test/test_datafile.py#L30) test to also build an index on the Core Record.

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

Benardi__touvlo-47

diff --git a/README.md b/README.md index 5c8227a..75e7723 100644 --- a/README.md +++ b/README.md @@ -6,8 +6,8 @@ <p align="center"> - <a href="https://travis-ci.org/Benardi/touvlo"> - <img src="https://api.travis-ci.org/Benardi/touvlo.svg?branch=master" + <a href="https://travis-ci.com/Benardi/touvlo"> + <img src="https://api.travis-ci.com/Benardi/touvlo.svg?branch=master" alt="Build Status"/></a> <a href="https://touvlo.readthedocs.io/en/latest/?badge=latest"> <img src="https://readthedocs.org/projects/touvlo/badge/?version=latest" diff --git a/touvlo/supv/lin_rg.py b/touvlo/supv/lin_rg.py index df67ba3..a228801 100644 --- a/touvlo/supv/lin_rg.py +++ b/touvlo/supv/lin_rg.py @@ -5,8 +5,12 @@ .. moduleauthor:: Benardi Nunes <[email protected]> """ -from numpy import zeros, float64 -from numpy.linalg import inv, LinAlgError +from abc import ABC, abstractmethod + +from numpy import zeros, float64, ones, append, identity +from numpy.linalg import inv + +from touvlo.utils import BGD, SGD, MBGD # model hypothesis @@ -118,13 +122,196 @@ def normal_eqn(X, y): numpy.array: Optimized model parameters theta. """ n = X.shape[1] # number of columns - theta = zeros((n + 1, 1), dtype=float64) + theta = zeros((n, 1), dtype=float64) - try: - X_T = X.T - theta = inv(X_T.dot(X)).dot(X_T).dot(y) + X_T = X.T + theta = inv(X_T.dot(X)).dot(X_T).dot(y) - except LinAlgError: - pass + return theta + + +def reg_normal_eqn(X, y, _lambda): + """Produces optimal theta via normal equation. + + Args: + X (numpy.array): Features' dataset plus bias column. + y (numpy.array): Column vector of expected values. + _lambda (float): The regularization hyperparameter. + + Returns: + numpy.array: Optimized model parameters theta. + """ + n = X.shape[1] # number of columns, already has bias + theta = zeros((n, 1), dtype=float64) + L = identity(n) + L[0, 0] = 0 + X_T = X.T + + theta = inv(X_T.dot(X) + _lambda * L).dot(X_T).dot(y) return theta + + +class AbstractLinearRegression(ABC): + """Represents the definitons common to all Linear Regressions. + + Args: + theta (numpy.array): Column vector of model's parameters. + Defaults to None + + Attributes: + theta (numpy.array): Column vector of model's parameters. + """ + + def __init__(self, theta=None): + self.theta = theta + + def _add_bias_term(self, X): + m = len(X) + intercept = ones((m, 1), dtype=int) + X = append(intercept, X, axis=1) + return X + + def predict(self, X): + """Computes prediction vector. + + Args: + X (numpy.array): Features' dataset. + Returns: + numpy.array: vector with a prediction for each example. + """ + X = self._add_bias_term(X) + return predict(X, self.theta) + + @abstractmethod + def _normal_fit(self, X, y): + pass + + @abstractmethod + def _gradient_fit(self, grad_descent, X, y, alpha, num_iters): + pass + + def fit(self, X, y, strategy='BGD', alpha=0.1, + num_iters=100, **kwargs): + """Adjusts model parameters to training data. + + Args: + X (numpy.array): Features' dataset. + y (numpy.array): Column vector of expected values. + strategy (str) : Which optimization strategy should be employed: + + * 'BGD': Performs Batch Gradient Descent + * 'SGD': Performs Stochastic Gradient Descent + * 'MBGD': Performs Mini-Batch Gradient Descent + * 'normal_equation': Employs Normal Equation + alpha (float): Learning rate or _step size of the optimization. + num_iters (int): Number of times the optimization will be + performed. + + Returns: + None + """ + if isinstance(strategy, str) and strategy == 'BGD': + self._gradient_fit(BGD, X, y, alpha, num_iters, **kwargs) + + elif isinstance(strategy, str) and strategy == 'SGD': + self._gradient_fit(SGD, X, y, alpha, num_iters, **kwargs) + + elif isinstance(strategy, str) and strategy == 'MBGD': + self._gradient_fit(MBGD, X, y, alpha, num_iters, **kwargs) + + elif isinstance(strategy, str) and strategy == 'normal_equation': + self._normal_fit(X, y) + else: + raise ValueError( + ("'%s' (type '%s') was passed. " % (strategy, type(strategy)), + "The strategy parameter for the fit function should ", + "be 'BGD' or 'SGD' or 'MBGD' or 'normal_equation'.")) + + +class LinearRegression(AbstractLinearRegression): + """Represents an Unregularized Linear Regression model + + Args: + theta (numpy.array): Column vector of model's parameters. + Defaults to None + + Attributes: + theta (numpy.array): Column vector of model's parameters. + """ + + def __init__(self, theta=None): + super().__init__(theta) + + def _normal_fit(self, X, y): + X = self._add_bias_term(X) + self.theta = normal_eqn(X, y) + + def _gradient_fit(self, grad_descent, X, y, alpha, + num_iters, **kwargs): + if self.theta is None: + _, n = X.shape + self.theta = zeros((n + 1, 1), dtype=float64) + + X = self._add_bias_term(X) + self.theta = grad_descent(X, y, grad, self.theta, alpha, + num_iters, **kwargs) + + def cost(self, X, y): + """Computes the cost function J for Linear Regression. + + Args: + X (numpy.array): Features' dataset plus bias column. + y (numpy.array): Column vector of expected values. + + Returns: + float: Computed cost. + """ + X = self._add_bias_term(X) + return cost_func(X, y, self.theta) + + +class RidgeLinearRegression(AbstractLinearRegression): + """Represents a Ridge Linear Regression model + + Args: + theta (numpy.array): Column vector of model's parameters. + Defaults to None + _lambda (float): The regularization hyperparameter. + + Attributes: + theta (numpy.array): Column vector of model's parameters. + _lambda (float): The regularization hyperparameter. + """ + + def __init__(self, theta=None, _lambda=0): + super().__init__(theta) + self._lambda = _lambda + + def _normal_fit(self, X, y): + X = self._add_bias_term(X) + self.theta = reg_normal_eqn(X, y, self._lambda) + + def _gradient_fit(self, grad_descent, X, y, alpha, + num_iters, **kwargs): + if self.theta is None: + _, n = X.shape + self.theta = zeros((n + 1, 1), dtype=float64) + + X = self._add_bias_term(X) + self.theta = grad_descent(X, y, reg_grad, self.theta, alpha, + num_iters, _lambda=self._lambda, **kwargs) + + def cost(self, X, y, **kwargs): + """Computes the regularized cost function J for + Ridge Linear Regression. + + Args: + X (numpy.array): Features' dataset plus bias column. + y (numpy.array): Column vector of expected values. + + Returns: + float: Computed cost. + """ + X = self._add_bias_term(X) + return reg_cost_func(X, y, self.theta, self._lambda, **kwargs) diff --git a/touvlo/unsupv/kmeans.py b/touvlo/unsupv/kmeans.py index 7a9de32..0302a23 100644 --- a/touvlo/unsupv/kmeans.py +++ b/touvlo/unsupv/kmeans.py @@ -169,8 +169,7 @@ def elbow_method(X, K_values, max_iters, n_inits): n_inits (int): Number of random initialization. Returns: - (list(int), list(float)): A 2-tuple of K_values, a list of possible - numbers of centroids, and cost_values, a computed cost for each K. + (list(float)): a list of cost values for each K. """ cost_values = [] for K in K_values: @@ -178,4 +177,4 @@ def elbow_method(X, K_values, max_iters, n_inits): cost = cost_function(X, idx, centroids) cost_values.append(cost) - return K_values, cost_values + return cost_values

Benardi/touvlo

8eb6beaaf880527239a5a11524b10945e41175f8

diff --git a/tests/supv/test_lin_rg.py b/tests/supv/test_lin_rg.py index 001047e..4f452b3 100644 --- a/tests/supv/test_lin_rg.py +++ b/tests/supv/test_lin_rg.py @@ -3,9 +3,11 @@ import os import pytest from numpy.testing import assert_allclose from numpy import ones, zeros, float64, array, append, genfromtxt +from numpy.linalg import LinAlgError from touvlo.supv.lin_rg import (normal_eqn, cost_func, reg_cost_func, grad, - reg_grad, predict, h) + reg_grad, predict, h, LinearRegression, + RidgeLinearRegression, reg_normal_eqn) from touvlo.utils import numerical_grad TESTDATA1 = os.path.join(os.path.dirname(__file__), 'data1.csv') @@ -33,7 +35,7 @@ class TestLinearRegression: y = data1[:, -1:] X = data1[:, :-1] - m, n = X.shape + m, _ = X.shape intercept = ones((m, 1), dtype=int) X = append(intercept, X, axis=1) @@ -44,7 +46,7 @@ class TestLinearRegression: def test_normal_eqn_data2(self, data2): y = data2[:, -1:] X = data2[:, :-1] - m, n = X.shape + m, _ = X.shape intercept = ones((m, 1), dtype=int) X = append(intercept, X, axis=1) @@ -52,6 +54,81 @@ class TestLinearRegression: normal_eqn(X, y), rtol=0, atol=0.001) + def test_reg_normal_eqn_data1_1(self, data1): + + y = data1[:, -1:] + X = data1[:, :-1] + m, _ = X.shape + intercept = ones((m, 1), dtype=int) + X = append(intercept, X, axis=1) + _lambda = 0 + + assert_allclose([[-3.896], [1.193]], + reg_normal_eqn(X, y, _lambda), + rtol=0, atol=0.001) + + def test_reg_normal_eqn_data1_2(self, data1): + + y = data1[:, -1:] + X = data1[:, :-1] + m, _ = X.shape + intercept = ones((m, 1), dtype=int) + X = append(intercept, X, axis=1) + _lambda = 1 + + assert_allclose([[-3.889], [1.192]], + reg_normal_eqn(X, y, _lambda), + rtol=0, atol=0.001) + + def test_reg_normal_eqn_data2(self, data2): + y = data2[:, -1:] + X = data2[:, :-1] + m, _ = X.shape + intercept = ones((m, 1), dtype=int) + X = append(intercept, X, axis=1) + _lambda = 100 + + assert_allclose([[74104.492], [135.249], [-1350.731]], + reg_normal_eqn(X, y, _lambda), + rtol=0, atol=0.001) + + def test_normal_eqn_singular(self, data2): + y = array([[0], [0], [0]]) + X = array([[0, 0, 0], [0, 0, 0], [0, 0, 0]]) + m, _ = X.shape + intercept = ones((m, 1), dtype=int) + X = append(intercept, X, axis=1) + + with pytest.raises(LinAlgError) as excinfo: + normal_eqn(X, y) + msg = excinfo.value.args[0] + assert msg == ("Singular matrix") + + def test_reg_normal_eqn_singular1(self, data2): + y = array([[0], [0], [0]]) + X = array([[0, 0, 0], [0, 0, 0], [0, 0, 0]]) + m, _ = X.shape + intercept = ones((m, 1), dtype=int) + X = append(intercept, X, axis=1) + _lambda = 0 + + with pytest.raises(LinAlgError) as excinfo: + reg_normal_eqn(X, y, _lambda), + msg = excinfo.value.args[0] + assert msg == ("Singular matrix") + + def test_reg_normal_eqn_singular2(self, data2): + y = array([[0], [0], [0]]) + X = array([[0, 0, 0], [0, 0, 0], [0, 0, 0]]) + m, _ = X.shape + intercept = ones((m, 1), dtype=int) + X = append(intercept, X, axis=1) + _lambda = 0.1 + + assert_allclose([[0], [0], [0], [0]], + reg_normal_eqn(X, y, _lambda), + rtol=0, atol=0.001) + # COST FUNCTION def test_cost_func_data1_1(self, data1): @@ -505,7 +582,7 @@ class TestLinearRegression: def test_h_1(self): X = array([[3.5]]) - m, n = X.shape + m, _ = X.shape intercept = ones((m, 1), dtype=float64) X = append(intercept, X, axis=1) theta = array([[-3.6303], [1.1664]]) @@ -546,3 +623,288 @@ class TestLinearRegression: assert_allclose([[-0.2]], h(X, theta), rtol=0, atol=0.001) + +# LINEAR REGRESSION CLASS + + def test_LinearRegression_constructor1(self, data1): + theta = array([[1.], [0.6], [1.]]) + lr = LinearRegression(theta) + + assert_allclose(array([[1.], [0.6], [1.]]), + lr.theta, + rtol=0, atol=0.001) + + def test_LinearRegression_constructor2(self): + lr = LinearRegression() + + assert lr.theta is None + + def test_LinearRegression_cost_data1_1(self, data1): + y = data1[:, -1:] + X = data1[:, :-1] + _, n = X.shape + theta = ones((n + 1, 1), dtype=float64) + lr = LinearRegression(theta) + + assert_allclose([[10.266]], + lr.cost(X, y), + rtol=0, atol=0.001) + + def test_LinearRegression_normal_fit(self, data1): + y = data1[:, -1:] + X = data1[:, :-1] + lr = LinearRegression() + lr.fit(X, y, strategy="normal_equation") + + assert_allclose([[-3.896], [1.193]], + lr.theta, + rtol=0, atol=0.001) + + def test_LinearRegression_fit_BGD(self, data2): + y = data2[:, -1:] + X = data2[:, :-1] + lr = LinearRegression() + lr.fit(X, y, strategy="BGD", alpha=1, num_iters=1) + + assert_allclose([[340412.659], [764209128.191], [1120367.702]], + lr.theta, + rtol=0, atol=0.001) + + def test_LinearRegression_fit_SGD(self, err): + X = array([[0, 1, 2], [-1, 5, 3], [2, 0, 1]]) + y = array([[0.3], [1.2], [0.5]]) + lr = LinearRegression() + lr.fit(X, y, strategy="SGD", alpha=1, num_iters=1) + + assert_allclose(array([[2.3], [11.2], [-11.7], [-2.2]]), + lr.theta, + rtol=0, atol=0.001, equal_nan=False) + + def test_LinearRegression_fit_MBGD1(self, data2): + y = data2[:, -1:] + X = data2[:, :-1] + m = len(X) + lr = LinearRegression() + lr.fit(X, y, strategy="MBGD", alpha=1, num_iters=1, b=m) + + assert_allclose([[340412.659], [764209128.191], [1120367.702]], + lr.theta, + rtol=0, atol=0.001) + + def test_LinearRegression_fit_MBGD2(self, err): + X = array([[0, 1, 2], [-1, 5, 3], [2, 0, 1]]) + y = array([[0.3], [1.2], [0.5]]) + lr = LinearRegression() + lr.fit(X, y, strategy="MBGD", alpha=1, num_iters=1, b=1) + + assert_allclose(array([[2.3], [11.2], [-11.7], [-2.2]]), + lr.theta, + rtol=0, atol=0.001, equal_nan=False) + + def test_LinearRegression_predict(self): + X = array([[3.5]]) + theta = array([[-3.6303], [1.1664]]) + lr = LinearRegression(theta) + + assert_allclose([[0.4521]], + lr.predict(X), + rtol=0, atol=0.001) + +# RIDGE LINEAR REGRESSION CLASS + + def test_RidgeLinearRegression_constructor1(self, data1): + theta = ones((3, 1), dtype=float64) + lr = RidgeLinearRegression(theta, _lambda=13.50) + + assert lr._lambda == 13.50 + assert_allclose(array([[1.], [1.], [1.]]), + lr.theta, + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_constructor2(self): + lr = RidgeLinearRegression() + + assert lr.theta is None + assert lr._lambda == 0 + + def test_RidgeLinearRegression_cost_data1_1(self, data1): + y = data1[:, -1:] + X = data1[:, :-1] + _, n = X.shape + theta = ones((n + 1, 1), dtype=float64) + lr = RidgeLinearRegression(theta, _lambda=0) + + assert_allclose([[10.266]], + lr.cost(X, y), + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_cost_data1_2(self, data1): + + y = data1[:, -1:] + X = data1[:, :-1] + _, n = X.shape + theta = ones((n + 1, 1), dtype=float64) + lr = RidgeLinearRegression(theta, _lambda=100) + + assert_allclose([[10.781984]], + lr.cost(X, y), + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_cost_data2_1(self, data2): + y = data2[:, -1:] + X = data2[:, :-1] + _, n = X.shape + theta = ones((n + 1, 1), dtype=float64) + lr = RidgeLinearRegression(theta, _lambda=0) + + assert_allclose([[64828197300.798]], + lr.cost(X, y), + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_cost_data2_2(self, data2): + y = data2[:, -1:] + X = data2[:, :-1] + _, n = X.shape + theta = ones((n + 1, 1), dtype=float64) + lr = RidgeLinearRegression(theta, _lambda=1000000) + + assert_allclose([[64828218577.393623]], + lr.cost(X, y), + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_normal_fit_data1_1(self, data1): + y = data1[:, -1:] + X = data1[:, :-1] + lr = RidgeLinearRegression(_lambda=0) + lr.fit(X, y, strategy="normal_equation") + + assert_allclose([[-3.896], [1.193]], + lr.theta, + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_normal_fit_data1_2(self, data1): + y = data1[:, -1:] + X = data1[:, :-1] + lr = RidgeLinearRegression(_lambda=1) + lr.fit(X, y, strategy="normal_equation") + + assert_allclose([[-3.889], [1.192]], + lr.theta, + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_fit_BGD1(self, data2): + y = data2[:, -1:] + X = data2[:, :-1] + lr = RidgeLinearRegression(_lambda=0) + lr.fit(X, y, strategy="BGD", alpha=1, num_iters=1) + + assert_allclose([[340412.659], [764209128.191], [1120367.702]], + lr.theta, + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_fit_BGD2(self, data1): + y = data1[:, -1:] + X = data1[:, :-1] + _, n = X.shape + theta = ones((n + 1, 1), dtype=float64) + lr = RidgeLinearRegression(theta, _lambda=100) + + lr.fit(X, y, strategy="BGD", alpha=1, num_iters=1) + + assert_allclose([[-2.321], [-24.266]], + lr.theta, + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_fit_SGD1(self, err): + X = array([[0, 1, 2], [-1, 5, 3], [2, 0, 1]]) + y = array([[0.3], [1.2], [0.5]]) + lr = RidgeLinearRegression(_lambda=0) + lr.fit(X, y, strategy="SGD", alpha=1, num_iters=1) + + assert_allclose(array([[2.3], [11.2], [-11.7], [-2.2]]), + lr.theta, + rtol=0, atol=0.001, equal_nan=False) + + def test_RidgeLinearRegression_fit_SGD2(self, err): + X = array([[0, 1, 2], [-1, 5, 3], [2, 0, 1]]) + y = array([[0.3], [1.2], [0.5]]) + lr = RidgeLinearRegression(_lambda=10) + lr.fit(X, y, strategy="SGD", alpha=1, num_iters=1) + + assert_allclose(array([[8.3], [-0.8], [132.3], [123.8]]), + lr.theta, + rtol=0, atol=0.001, equal_nan=False) + + def test_RidgeLinearRegression_fit_MBGD1(self, data2): + y = data2[:, -1:] + X = data2[:, :-1] + m = len(X) + lr = RidgeLinearRegression(_lambda=0) + lr.fit(X, y, strategy="MBGD", alpha=1, num_iters=1, b=m) + + assert_allclose([[340412.659], [764209128.191], [1120367.702]], + lr.theta, + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_fit_MBGD2(self, err): + X = array([[0, 1, 2], [-1, 5, 3], [2, 0, 1]]) + y = array([[0.3], [1.2], [0.5]]) + lr = RidgeLinearRegression(_lambda=0) + lr.fit(X, y, strategy="MBGD", alpha=1, num_iters=1, b=1) + + assert_allclose(array([[2.3], [11.2], [-11.7], [-2.2]]), + lr.theta, + rtol=0, atol=0.001, equal_nan=False) + + def test_RidgeLinearRegression_fit_MBGD3(self, data1): + y = data1[:, -1:] + X = data1[:, :-1] + m, n = X.shape + theta = ones((n + 1, 1), dtype=float64) + lr = RidgeLinearRegression(theta, _lambda=100) + lr.fit(X, y, strategy="MBGD", alpha=1, num_iters=1, b=m) + + assert_allclose([[-2.321], [-24.266]], + lr.theta, + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_fit_MBGD4(self, data1): + X = array([[0, 1, 2], [-1, 5, 3], [2, 0, 1]]) + y = array([[0.3], [1.2], [0.5]]) + lr = RidgeLinearRegression(_lambda=10) + lr.fit(X, y, strategy="MBGD", alpha=1, num_iters=1, b=1) + + assert_allclose(array([[8.3], [-0.8], [132.3], [123.8]]), + lr.theta, + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_fit_unknown(self, data1): + X = array([[0, 1, 2], [-1, 5, 3], [2, 0, 1]]) + y = array([[0.3], [1.2], [0.5]]) + lr = RidgeLinearRegression(_lambda=10) + + with pytest.raises(ValueError) as excinfo: + lr.fit(X, y, strategy="oompa_loompa") + + msg = excinfo.value.args[0] + assert msg == ("'oompa_loompa' (type '<class 'str'>') was passed. ", + 'The strategy parameter for the fit function should ', + "be 'BGD' or 'SGD' or 'MBGD' or 'normal_equation'.") + + def test_RidgeLinearRegression_predict1(self): + X = array([[3.5]]) + theta = array([[-3.6303], [1.1664]]) + lr = RidgeLinearRegression(theta) + + assert_allclose([[0.4521]], + lr.predict(X), + rtol=0, atol=0.001) + + def test_RidgeLinearRegression_predict2(self): + X = array([[3.5]]) + theta = array([[-3.6303], [1.1664]]) + lr = RidgeLinearRegression(theta, _lambda=10) + + assert_allclose([[0.4521]], + lr.predict(X), + rtol=0, atol=0.001) diff --git a/tests/test_utils.py b/tests/test_utils.py index f59f102..2671f02 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -5,7 +5,7 @@ from numpy import array, cos, sin, exp from numpy.testing import assert_allclose from touvlo.utils import (numerical_grad, g_grad, BGD, SGD, - MBGD, mean_normlztn) + MBGD, mean_normlztn, feature_normalize) class TestLogisticRegression: @@ -386,3 +386,20 @@ class TestLogisticRegression: assert_allclose(Y_mean, array([[4.5], [3], [4], [3], [3]]), rtol=0, atol=0.001, equal_nan=False) + + def test_feature_normalize(self, err): + X = array([[1.5, 8., 7.5], [1., 6., 9.]]) + X_norm, mu, sigma = feature_normalize(X) + + assert_allclose(array([1.25, 7, 8.25]), + mu, + rtol=0, atol=0.001, equal_nan=False) + + assert_allclose(array([0.35355339, 1.41421356, 1.06066017]), + sigma, + rtol=0, atol=0.001, equal_nan=False) + + assert_allclose(array([[0.707, 0.707, -0.707], + [-0.707, -0.707, 0.707]]), + X_norm, + rtol=0, atol=0.001, equal_nan=False) diff --git a/tests/unsupv/test_kmeans.py b/tests/unsupv/test_kmeans.py index eec059d..189d62a 100644 --- a/tests/unsupv/test_kmeans.py +++ b/tests/unsupv/test_kmeans.py @@ -5,7 +5,7 @@ from numpy.testing import assert_allclose, assert_almost_equal from touvlo.unsupv.kmeans import (find_closest_centroids, euclidean_dist, compute_centroids, init_centroids, cost_function, run_kmeans, - run_intensive_kmeans) + run_intensive_kmeans, elbow_method) class TestKmeans: @@ -180,3 +180,16 @@ class TestKmeans: assert all(idx < K) assert all(idx > -1) assert len(centroids) == K + + def test_elbow_method(self): + X = array([[5.89562, 2.89844], [5.61754, 2.59751], [5.63176, 3.04759], + [5.50259, 3.11869], [6.48213, 2.55085], [7.30279, 3.38016], + [6.99198, 2.98707], [4.82553, 2.77962], [6.11768, 2.85476], + [0.94049, 5.71557]]) + max_iters = 6 + n_inits = 1 + K_values = [1, 2, 3, 4] + + cost_values = elbow_method(X, K_values, max_iters, n_inits) + + assert all(cost >= 0 for cost in cost_values)

Add classes for existing Linear Regression implementations #### Description Add classes to encapsulate existing Ridge and Unregularized Linear Regression implementations. #### Files * `touvlo/supv/lin_rg.py` - Existing linear regression module * `tests/supv/test_lin_rg.py` - Test suite for linear regression module #### Tasks Include specific tasks in the order they need to be done in. Include links to specific lines of code where the task should happen at. - [x] Add classes for Ridge and Unregularized Linear Regression - [x] Add unit tests for new classes - [x] Add documentation for new classes

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

BlueBrain__NeuroM-1001

diff --git a/CHANGELOG.rst b/CHANGELOG.rst index de024a1..4d0b572 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -3,6 +3,15 @@ Changelog Version 3.2.0 ------------- + +- Fix ``neurom.features.bifurcation.partition_asymmetry`` Uylings variant to not throw + for bifurcations with leaves. +- Fix ``neurom.features.neurite.principal_direction_extents`` to remove duplicate points + when calculated. +- Add ``neurom.features.morphology.volume_density`` feature so that it is calculated + correctly when the entire morphology is taken into account instead of summing the per + neurite volume densities. +- Add support for py39 and py310 testing. - Fix ``neurom.features.morphology.sholl_frequency`` to return an empty list when a neurite_type that is not present in the morphology is specified. - Fix ``neurom.features.morphology.trunk_origin_radii`` to warn and use only the root diff --git a/neurom/features/bifurcation.py b/neurom/features/bifurcation.py index 65db001..6c628d1 100644 --- a/neurom/features/bifurcation.py +++ b/neurom/features/bifurcation.py @@ -115,12 +115,13 @@ def partition_asymmetry(bif_point, uylings=False): n = float(sum(1 for _ in bif_point.children[0].ipreorder())) m = float(sum(1 for _ in bif_point.children[1].ipreorder())) - c = 0 - if uylings: - c = 2 - if n + m <= c: - raise NeuroMError('Partition asymmetry cant be calculated by Uylings because the sum of' - 'terminal tips is less than 2.') + + if n == m == 1: + # By definition the asymmetry A(1, 1) is zero + return 0.0 + + c = 2.0 if uylings else 0.0 + return abs(n - m) / abs(n + m - c)

BlueBrain/NeuroM

127d6fd45167b3cf2ae6d41c51ad241846d082dc

diff --git a/tests/features/test_bifurcation.py b/tests/features/test_bifurcation.py index 530a4c4..f2eea4c 100644 --- a/tests/features/test_bifurcation.py +++ b/tests/features/test_bifurcation.py @@ -80,8 +80,7 @@ def test_partition_asymmetry(): assert bf.partition_asymmetry(root) == 0.5 assert bf.partition_asymmetry(root.children[0]) == 0.0 assert bf.partition_asymmetry(root, True) == 1.0 - with pytest.raises(NeuroMError, match='Uylings'): - bf.partition_asymmetry(root.children[0], True) + assert bf.partition_asymmetry(root.children[0], True) == 0.0 leaf = root.children[0].children[0] assert_raises(NeuroMError, bf.partition_asymmetry, leaf)

Is `partition_asymmetry` with `Uylings` variant usable? I find peculiar the implementation of the **Uylings variant** of for the partition asymmetry: https://github.com/BlueBrain/NeuroM/blob/127d6fd45167b3cf2ae6d41c51ad241846d082dc/neurom/features/bifurcation.py#L102-L124 because all bifurcation points the children of which are leaves will have downstream counts `n,m = (1, 1)`, therefore all morphs would fail the check. Am I missing a use case where this could work? @mgeplf @lidakanari @arnaudon @adrien-berchet

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

BlueBrain__NeuroM-1002

diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 4d0b572..21e19fe 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,6 +4,7 @@ Changelog Version 3.2.0 ------------- +- Fix warning system so that it doesn't change the pre-existing warnings configuration - Fix ``neurom.features.bifurcation.partition_asymmetry`` Uylings variant to not throw for bifurcations with leaves. - Fix ``neurom.features.neurite.principal_direction_extents`` to remove duplicate points diff --git a/neurom/__init__.py b/neurom/__init__.py index 90290b5..2b2f24a 100644 --- a/neurom/__init__.py +++ b/neurom/__init__.py @@ -55,7 +55,6 @@ Examples: >>> mapping = lambda n : len(n.points) >>> n_points = [n for n in nm.iter_neurites(pop, mapping, filter)] """ - from neurom.core.dataformat import COLS from neurom.core.types import NeuriteType, NeuriteIter, NEURITES as NEURITE_TYPES from neurom.core.morphology import graft_morphology, iter_neurites, iter_sections, iter_segments @@ -63,6 +62,7 @@ from neurom.core.morphology import graft_morphology, iter_neurites, iter_section from neurom.features import get from neurom.io.utils import MorphLoader, load_morphology, load_morphologies from neurom.io.utils import load_neuron, load_neurons +from neurom.exceptions import NeuroMDeprecationWarning APICAL_DENDRITE = NeuriteType.apical_dendrite BASAL_DENDRITE = NeuriteType.basal_dendrite diff --git a/neurom/exceptions.py b/neurom/exceptions.py index fac38b2..7eba4c8 100644 --- a/neurom/exceptions.py +++ b/neurom/exceptions.py @@ -35,3 +35,7 @@ class NeuroMError(Exception): class ConfigError(NeuroMError): """Exception class for configuration data in apps errors.""" + + +class NeuroMDeprecationWarning(DeprecationWarning): + """NeuroM deprecation warning for users.""" diff --git a/neurom/utils.py b/neurom/utils.py index 5ccf9a8..e8786f3 100644 --- a/neurom/utils.py +++ b/neurom/utils.py @@ -35,13 +35,12 @@ from functools import wraps import numpy as np from neurom.core.dataformat import COLS +from neurom.exceptions import NeuroMDeprecationWarning def warn_deprecated(msg): """Issue a deprecation warning.""" - warnings.simplefilter('always', DeprecationWarning) - warnings.warn(msg, category=DeprecationWarning, stacklevel=2) - warnings.simplefilter('default', DeprecationWarning) + warnings.warn(msg, category=NeuroMDeprecationWarning, stacklevel=3) def deprecated(fun_name=None, msg=""):

BlueBrain/NeuroM

f57feb2f40c287f644b53da671f7b63cf7a8aef9

diff --git a/tests/test_utils.py b/tests/test_utils.py index f01a172..a8dd018 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -29,11 +29,20 @@ """Test neurom.utils.""" import json import warnings +from copy import deepcopy import numpy as np from neurom import utils as nu import pytest +from neurom.exceptions import NeuroMDeprecationWarning + + +def test_warn_deprecated(): + + with pytest.warns(NeuroMDeprecationWarning, match="foo"): + nu.warn_deprecated(msg="foo") + def test_deprecated(): @nu.deprecated(msg='Hello')

Inappropriate `warnings.simplefilter` in `neurom.utils.warn_deprecated` `warnings.simplefilter` is used to enforce that a deprecation warning is shown: https://github.com/BlueBrain/NeuroM/blob/c570a2faa18f4e417fcdb743f6487beee0c60c3e/neurom/utils.py#L40-L44 This is problematic for several reasons * It's not the business of a library to configure how the warnings are shown * There is no way for the library user to easily disable those warnings * By calling `warnings.simplefilter` `neurom` modifies the global state and has the side-effect of permanently setting ` warnings.simplefilter('default', DeprecationWarning)`. E.g ```py import warnings import neurom as nm print("before:", warnings.filters) nm.load_neuron(some_path) # this triggers the warning `neurom.io.utils.load_neuron` is deprecated print("after:", warnings.filters) ``` output: ``` before: [] after: [('default', None, <class 'DeprecationWarning'>, None, 0), ('always', None, <class 'DeprecationWarning'>, None, 0)] ``` I would strongly advocate for removing the two `warnings.simplefilter` lines. P.S.: since `warnings.warn` is wrapped into `warn_deprecated` setting `stacklevel=3` should be considered.

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

BlueBrain__NeuroM-1008

diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 540b7e2..80313f9 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,6 +4,7 @@ Changelog Version 3.2.0 ------------- +- Fix ``neurom.morphmath.principal_direction_extent`` to calculate correctly the pca extent. - Fix ``neurom.features.neurite.segment_taper_rates`` to return signed taper rates. - Fix warning system so that it doesn't change the pre-existing warnings configuration - Fix ``neurom.features.bifurcation.partition_asymmetry`` Uylings variant to not throw diff --git a/neurom/morphmath.py b/neurom/morphmath.py index b01c516..41e090d 100644 --- a/neurom/morphmath.py +++ b/neurom/morphmath.py @@ -462,17 +462,17 @@ section_length = path_distance def principal_direction_extent(points): """Calculate the extent of a set of 3D points. - The extent is defined as the maximum distance between - the projections on the principal directions of the covariance matrix - of the points. + The extent is defined as the maximum distance between the projections on the principal + directions of the covariance matrix of the points. - Parameter: - points : a 2D numpy array of points + Args: + points : a 2D numpy array of points with 2 or 3 columns for (x, y, z) Returns: extents : the extents for each of the eigenvectors of the cov matrix - eigs : eigenvalues of the covariance matrix - eigv : respective eigenvectors of the covariance matrix + + Note: + Direction extents are not ordered from largest to smallest. """ # pca can be biased by duplicate points points = np.unique(points, axis=0) @@ -483,14 +483,8 @@ def principal_direction_extent(points): # principal components _, eigv = pca(points) - extent = np.zeros(3) - - for i in range(eigv.shape[1]): - # orthogonal projection onto the direction of the v component - scalar_projs = np.sort(np.array([np.dot(p, eigv[:, i]) for p in points])) - extent[i] = scalar_projs[-1] - - if scalar_projs[0] < 0.: - extent -= scalar_projs[0] + # for each eigenvector calculate the scalar projection of the points on it (n_points, n_eigv) + scalar_projections = points.dot(eigv) - return extent + # and return the range of the projections (abs(max - min)) along each column (eigenvector) + return np.ptp(scalar_projections, axis=0)

BlueBrain/NeuroM

fdf9f78be79508e34c0349936e233c184279c955

diff --git a/tests/features/test_get_features.py b/tests/features/test_get_features.py index 6661b89..a78efa7 100644 --- a/tests/features/test_get_features.py +++ b/tests/features/test_get_features.py @@ -793,18 +793,18 @@ def test_section_term_radial_distances(): def test_principal_direction_extents(): m = nm.load_morphology(SWC_PATH / 'simple.swc') principal_dir = features.get('principal_direction_extents', m) - assert_allclose(principal_dir, [14.736052694538641, 12.105102672688004]) + assert_allclose(principal_dir, [10.99514 , 10.997688]) # test with a realistic morphology m = nm.load_morphology(DATA_PATH / 'h5/v1' / 'bio_neuron-000.h5') p_ref = [ - 1672.969491, - 142.437047, - 224.607978, - 415.50613, - 429.830081, - 165.954097, - 346.832825, + 1210.569727, + 38.493958, + 147.098687, + 288.226628, + 330.166506, + 152.396521, + 293.913857 ] p = features.get('principal_direction_extents', m) assert_allclose(p, p_ref, rtol=1e-6) diff --git a/tests/test_morphmath.py b/tests/test_morphmath.py index 0188ccf..6119f7b 100644 --- a/tests/test_morphmath.py +++ b/tests/test_morphmath.py @@ -29,6 +29,7 @@ from math import fabs, pi, sqrt import numpy as np +from numpy import testing as npt from neurom import morphmath as mm from neurom.core.dataformat import Point from numpy.random import uniform @@ -532,3 +533,59 @@ def test_spherical_coordinates(): new_elevation, new_azimuth = mm.spherical_from_vector(vect) assert np.allclose([elevation, azimuth], [new_elevation, new_azimuth]) + + +def test_principal_direction_extent(): + + # test with points on a circle with radius 0.5, and center at 0.0 + circle_points = np.array([ + [ 5.0e-01, 0.0e+00, 0.0e+00], + [ 4.7e-01, 1.6e-01, 0.0e+00], + [ 3.9e-01, 3.1e-01, 0.0e+00], + [ 2.7e-01, 4.2e-01, 0.0e+00], + [ 1.2e-01, 4.8e-01, 0.0e+00], + [-4.1e-02, 5.0e-01, 0.0e+00], + [-2.0e-01, 4.6e-01, 0.0e+00], + [-3.4e-01, 3.7e-01, 0.0e+00], + [-4.4e-01, 2.4e-01, 0.0e+00], + [-5.0e-01, 8.2e-02, 0.0e+00], + [-5.0e-01, -8.2e-02, 0.0e+00], + [-4.4e-01, -2.4e-01, 0.0e+00], + [-3.4e-01, -3.7e-01, 0.0e+00], + [-2.0e-01, -4.6e-01, 0.0e+00], + [-4.1e-02, -5.0e-01, 0.0e+00], + [ 1.2e-01, -4.8e-01, 0.0e+00], + [ 2.7e-01, -4.2e-01, 0.0e+00], + [ 3.9e-01, -3.1e-01, 0.0e+00], + [ 4.7e-01, -1.6e-01, 0.0e+00], + [ 5.0e-01, -1.2e-16, 0.0e+00] + ]) + + npt.assert_allclose( + mm.principal_direction_extent(circle_points), + [1., 1., 0.], atol=1e-6, + ) + + # extent should be invariant to translations + npt.assert_allclose( + mm.principal_direction_extent(circle_points + 100.), + [1., 1., 0.], atol=1e-6, + ) + npt.assert_allclose( + mm.principal_direction_extent(circle_points - 100.), + [1., 1., 0.], atol=1e-6, + ) + + cross_3D_points = np.array([ + [-5.2, 0.0, 0.0], + [ 4.8, 0.0, 0.0], + [ 0.0,-1.3, 0.0], + [ 0.0, 4.7, 0.0], + [ 0.0, 0.0,-11.2], + [ 0.0, 0.0, 0.8], + ]) + + npt.assert_allclose( + sorted(mm.principal_direction_extent(cross_3D_points)), + [6.0, 10.0, 12.0], atol=0.1, + )

Bug in principal direction extent There is a bug in the calculation of the principal direction extents: https://github.com/BlueBrain/NeuroM/blob/fdf9f78be79508e34c0349936e233c184279c955/neurom/morphmath.py#L462-L496 At the point where the most negative value is subtracted from the entire extent: ```python if scalar_projs[0] < 0.: extent -= scalar_projs[0] ``` It shouldn't subtract from the entire extent, rather from the i-th component `extent[i]`. Failing test example with points on a circle with radius `0.5`, and center at `0.0`: ```python from neurom.morphmath import principal_direction_extent from numpy import testing as npt def test_principal_direction_extent(): circle_points = np.array([ [ 5.0e-01, 0.0e+00, 0.0e+00], [ 4.7e-01, 1.6e-01, 0.0e+00], [ 3.9e-01, 3.1e-01, 0.0e+00], [ 2.7e-01, 4.2e-01, 0.0e+00], [ 1.2e-01, 4.8e-01, 0.0e+00], [-4.1e-02, 5.0e-01, 0.0e+00], [-2.0e-01, 4.6e-01, 0.0e+00], [-3.4e-01, 3.7e-01, 0.0e+00], [-4.4e-01, 2.4e-01, 0.0e+00], [-4.9e-01, 8.2e-02, 0.0e+00], [-4.9e-01, -8.2e-02, 0.0e+00], [-4.4e-01, -2.4e-01, 0.0e+00], [-3.4e-01, -3.7e-01, 0.0e+00], [-2.0e-01, -4.6e-01, 0.0e+00], [-4.1e-02, -5.0e-01, 0.0e+00], [ 1.2e-01, -4.8e-01, 0.0e+00], [ 2.7e-01, -4.2e-01, 0.0e+00], [ 3.9e-01, -3.1e-01, 0.0e+00], [ 4.7e-01, -1.6e-01, 0.0e+00], [ 5.0e-01, -1.2e-16, 0.0e+00] ]) npt.assert_allclose( principal_direction_extent(circle_points), [1., 1., 0.], ) ``` Which returns instead `[1.49, 1.0, 0.0]`. Thanks, @lidakanari for finding that there is something wrong with the principal direction extent function. @arnaudon @adrien-berchet

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

BlueBrain__NeuroM-1017

diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 1a4feec..8606975 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -4,6 +4,8 @@ Changelog Version 3.2.0 ------------- +- ``neurom.features.neurite.principal_direction_extents`` directions correspond to extents + ordered in a descending order. - Add features ``neurom.features.morphology.(aspect_ration, circularity, shape_factor)``` - Fix ``neurom.morphmath.principal_direction_extent`` to calculate correctly the pca extent. - Fix ``neurom.features.neurite.segment_taper_rates`` to return signed taper rates. diff --git a/neurom/features/neurite.py b/neurom/features/neurite.py index 0439d88..6aac5e9 100644 --- a/neurom/features/neurite.py +++ b/neurom/features/neurite.py @@ -446,7 +446,12 @@ def section_end_distances(neurite): @feature(shape=(...,)) def principal_direction_extents(neurite, direction=0): - """Principal direction extent of neurites in morphologies.""" + """Principal direction extent of neurites in morphologies. + + Note: + Principal direction extents are always sorted in descending order. Therefore, + by default the maximal principal direction extent is returned. + """ return [morphmath.principal_direction_extent(neurite.points[:, COLS.XYZ])[direction]] diff --git a/neurom/morphmath.py b/neurom/morphmath.py index 248c2e9..45f0700 100644 --- a/neurom/morphmath.py +++ b/neurom/morphmath.py @@ -479,7 +479,7 @@ def principal_direction_extent(points): extents : the extents for each of the eigenvectors of the cov matrix Note: - Direction extents are not ordered from largest to smallest. + Direction extents are ordered from largest to smallest. """ # pca can be biased by duplicate points points = np.unique(points, axis=0) @@ -488,13 +488,17 @@ def principal_direction_extent(points): points -= np.mean(points, axis=0) # principal components - _, eigv = pca(points) + _, eigenvectors = pca(points) # for each eigenvector calculate the scalar projection of the points on it (n_points, n_eigv) - scalar_projections = points.dot(eigv) + scalar_projections = points.dot(eigenvectors) - # and return the range of the projections (abs(max - min)) along each column (eigenvector) - return np.ptp(scalar_projections, axis=0) + # range of the projections (abs(max - min)) along each column (eigenvector) + extents = np.ptp(scalar_projections, axis=0) + + descending_order = np.argsort(extents)[::-1] + + return extents[descending_order] def convex_hull(points):

BlueBrain/NeuroM

dc54aa8566d59ba08aefb3457412b23297903f49

diff --git a/tests/features/test_get_features.py b/tests/features/test_get_features.py index 6b480c8..20372b9 100644 --- a/tests/features/test_get_features.py +++ b/tests/features/test_get_features.py @@ -798,18 +798,46 @@ def test_principal_direction_extents(): # test with a realistic morphology m = nm.load_morphology(DATA_PATH / 'h5/v1' / 'bio_neuron-000.h5') - p_ref = [ - 1210.569727, - 38.493958, - 147.098687, - 288.226628, - 330.166506, - 152.396521, - 293.913857 - ] - p = features.get('principal_direction_extents', m) - assert_allclose(p, p_ref, rtol=1e-6) + assert_allclose( + features.get('principal_direction_extents', m, direction=0), + [ + 1210.569727, + 117.988454, + 147.098687, + 288.226628, + 330.166506, + 152.396521, + 293.913857, + ], + atol=1e-6 + ) + assert_allclose( + features.get('principal_direction_extents', m, direction=1), + [ + 851.730088, + 99.108911, + 116.949436, + 157.171734, + 137.328019, + 20.66982, + 67.157249, + ], + atol=1e-6 + ) + assert_allclose( + features.get('principal_direction_extents', m, direction=2), + [ + 282.961199, + 38.493958, + 40.715183, + 94.061625, + 51.120255, + 10.793167, + 62.808188 + ], + atol=1e-6 + ) def test_total_width(): diff --git a/tests/test_morphmath.py b/tests/test_morphmath.py index 181aaf8..43bb4dc 100644 --- a/tests/test_morphmath.py +++ b/tests/test_morphmath.py @@ -587,8 +587,8 @@ def test_principal_direction_extent(): ]) npt.assert_allclose( - sorted(mm.principal_direction_extent(cross_3D_points)), - [6.0, 10.0, 12.0], atol=0.1, + mm.principal_direction_extent(cross_3D_points), + [12.0, 10.0, 6.0], atol=0.1, )

Maximal direction extent @lidakanari , asked for a maximal direction extent feature in https://github.com/BlueBrain/NeuroM/pull/1008#issuecomment-1073704148 There are two ways to achieve this: 1. Add a new feature that will return the maximum of the principal direction extents. 2. Order the existing principal_direction_extent feature from max to min. The max extent would then be equal to `principal_direction_extent(direction=0)` @arnaudon , @adrien-berchet, @mgeplf

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

BlueBrain__NeuroM-1064

diff --git a/neurom/features/__init__.py b/neurom/features/__init__.py index 1970d49..bf80af0 100644 --- a/neurom/features/__init__.py +++ b/neurom/features/__init__.py @@ -40,7 +40,9 @@ Examples: import inspect import operator from enum import Enum -from functools import partial, reduce +from functools import partial, reduce, wraps + +import numpy as np from neurom.core import Morphology, Neurite, Population from neurom.core.morphology import iter_neurites @@ -226,6 +228,8 @@ def _register_feature(namespace: NameSpace, name, func, shape): def feature(shape, namespace: NameSpace, name=None): """Feature decorator to automatically register the feature in the appropriate namespace. + This decorator also ensures that the results of the features are casted to built-in types. + Arguments: shape(tuple): the expected shape of the feature values namespace(string): a namespace, see :class:`NameSpace` @@ -233,8 +237,26 @@ def feature(shape, namespace: NameSpace, name=None): """ def inner(func): - _register_feature(namespace, name or func.__name__, func, shape) - return func + @wraps(func) + def scalar_wrapper(*args, **kwargs): + res = func(*args, **kwargs) + try: + return res.tolist() + except AttributeError: + return res + + @wraps(func) + def matrix_wrapper(*args, **kwargs): + res = func(*args, **kwargs) + return np.array(res).tolist() + + if shape == (): + decorated_func = scalar_wrapper + else: + decorated_func = matrix_wrapper + + _register_feature(namespace, name or func.__name__, decorated_func, shape) + return decorated_func return inner

BlueBrain/NeuroM

8bddfc93ca6f4434e3db3ec124534fa8bde45bc9

diff --git a/tests/features/test_features.py b/tests/features/test_features.py new file mode 100644 index 0000000..42f3ec5 --- /dev/null +++ b/tests/features/test_features.py @@ -0,0 +1,98 @@ +"""Miscelaneous tests of features.""" +from pathlib import Path +from itertools import chain + +import numpy as np +import pytest +from numpy import testing as npt + +import neurom as nm +from neurom import features + + [email protected] +def DATA_PATH(): + return Path(__file__).parent.parent / "data" + + [email protected] +def SWC_PATH(DATA_PATH): + return DATA_PATH / "swc" + + [email protected] +def MORPHOLOGY(SWC_PATH): + return nm.load_morphology(SWC_PATH / "test_morph.swc") + + [email protected] +def NEURITE(MORPHOLOGY): + return MORPHOLOGY.neurites[0] + + [email protected] +def SECTION(NEURITE): + return NEURITE.sections[0] + + [email protected] +def NRN_FILES(DATA_PATH): + return [ + DATA_PATH / "h5/v1" / f for f in ("Neuron.h5", "Neuron_2_branch.h5", "bio_neuron-001.h5") + ] + + [email protected] +def POP(NRN_FILES): + return nm.load_morphologies(NRN_FILES) + + +def _check_nested_type(data): + """Check that the given data contains only built-in types. + + The data should either be an int or float, or a list or tuple of ints or floats. + """ + if isinstance(data, (list, tuple)): + for i in data: + _check_nested_type(i) + else: + assert isinstance(data, (int, float)) + + [email protected]( + "feature_name", + [ + pytest.param(name, id=f"Test type of {name} neurite feature") + for name in features._NEURITE_FEATURES + ], +) +def test_neurite_feature_types(feature_name, NEURITE): + """Test neurite features.""" + res = features._NEURITE_FEATURES.get(feature_name)(NEURITE) + _check_nested_type(res) + + [email protected]( + "feature_name", + [ + pytest.param(name, id=f"Test type of {name} morphology feature") + for name in features._MORPHOLOGY_FEATURES + ], +) +def test_morphology_feature_types(feature_name, MORPHOLOGY): + """Test morphology features.""" + res = features._MORPHOLOGY_FEATURES.get(feature_name)(MORPHOLOGY) + _check_nested_type(res) + + [email protected]( + "feature_name", + [ + pytest.param(name, id=f"Test type of {name} population feature") + for name in features._POPULATION_FEATURES + ], +) +def test_population_feature_types(feature_name, POP): + """Test population features.""" + res = features._POPULATION_FEATURES.get(feature_name)(POP) + _check_nested_type(res) diff --git a/tests/features/test_neurite.py b/tests/features/test_neurite.py index fee2ce3..c31cf3b 100644 --- a/tests/features/test_neurite.py +++ b/tests/features/test_neurite.py @@ -133,7 +133,7 @@ def test_section_end_distances(): def test_section_partition_pairs(): part_pairs = [neurite.partition_pairs(s) for s in SIMPLE.neurites] - assert part_pairs == [[(1.0, 1.0)], [(1.0, 1.0)]] + assert part_pairs == [[[1.0, 1.0]], [[1.0, 1.0]]] def test_section_bif_radial_distances():

Features should return consistent types The `NeuroM.features.*` functions return inconsistent types. For example, `segment_taper_rates` returns a list of `floats` while `section_taper_rates` returns a list of `numpy.float32`. This can be annoying to process results (e.g. it's harder to dump the results to JSON strings or stuff like that). I suggest we make all the types consistent, like casting all the results to built-in Python types. WDYT @eleftherioszisis @mgeplf ? If you agree I can work on this.

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

BlueBrain__NeuroM-1073

diff --git a/neurom/features/morphology.py b/neurom/features/morphology.py index 69098cb..4b2c4de 100644 --- a/neurom/features/morphology.py +++ b/neurom/features/morphology.py @@ -63,6 +63,13 @@ from neurom.morphmath import convex_hull feature = partial(feature, namespace=NameSpace.NEURON) +def _assert_soma_center(morph): + if morph.soma.center is None: + raise NeuroMError( + f"The morphology named '{morph.name}' has no soma so the feature can not be computed." + ) + + def _map_neurites(function, morph, neurite_type): return list( iter_neurites(morph, mapfun=function, filt=is_type(neurite_type)) @@ -132,6 +139,8 @@ def trunk_origin_azimuths(morph, neurite_type=NeuriteType.all): The range of the azimuth angle [-pi, pi] radians """ + _assert_soma_center(morph) + def azimuth(neurite): """Azimuth of a neurite trunk.""" return morphmath.azimuth_from_vector( @@ -151,6 +160,8 @@ def trunk_origin_elevations(morph, neurite_type=NeuriteType.all): The range of the elevation angle [-pi/2, pi/2] radians """ + _assert_soma_center(morph) + def elevation(neurite): """Elevation of a section.""" return morphmath.elevation_from_vector( @@ -163,6 +174,8 @@ def trunk_origin_elevations(morph, neurite_type=NeuriteType.all): @feature(shape=(...,)) def trunk_vectors(morph, neurite_type=NeuriteType.all): """Calculate the vectors between all the trunks of the morphology and the soma center.""" + _assert_soma_center(morph) + def vector_to_root_node(neurite): return morphmath.vector(neurite.root_node.points[0], morph.soma.center) @@ -496,6 +509,7 @@ def sholl_crossings(morph, neurite_type=NeuriteType.all, center=None, radii=None '`sholl_crossings` input error. If `center` or `radii` is not set then `morph` is ' \ 'expected to be an instance of Morphology and have a soma.' if center is None: + _assert_soma_center(morph) center = morph.soma.center if radii is None: radii = [morph.soma.radius] @@ -525,6 +539,7 @@ def sholl_frequency(morph, neurite_type=NeuriteType.all, step_size=10, bins=None If a `neurite_type` is specified and there are no trees corresponding to it, an empty list will be returned. """ + _assert_soma_center(morph) neurite_filter = is_type(neurite_type) if bins is None: @@ -701,6 +716,7 @@ def length_fraction_above_soma(morph, neurite_type=NeuriteType.all, up="Y"): Returns: The fraction of neurite length that lies on the right of the soma along the given axis. """ + _assert_soma_center(morph) axis = up.upper() if axis not in {"X", "Y", "Z"}: diff --git a/neurom/features/population.py b/neurom/features/population.py index 98cbd4d..dfd0a7e 100644 --- a/neurom/features/population.py +++ b/neurom/features/population.py @@ -47,6 +47,7 @@ from neurom.core.dataformat import COLS from neurom.core.types import NeuriteType from neurom.core.types import tree_type_checker as is_type from neurom.features import feature, NameSpace +from neurom.features.morphology import _assert_soma_center from neurom.features.morphology import sholl_crossings feature = partial(feature, namespace=NameSpace.POPULATION) @@ -78,7 +79,8 @@ def sholl_frequency(morphs, neurite_type=NeuriteType.all, step_size=10, bins=Non for n in m.neurites if neurite_filter(n)) bins = np.arange(min_soma_edge, min_soma_edge + max_radii, step_size) - return np.array([ - sholl_crossings(m, neurite_type, m.soma.center, bins) - for m in morphs - ]).sum(axis=0) + def _sholl_crossings(morph): + _assert_soma_center(morph) + return sholl_crossings(morph, neurite_type, morph.soma.center, bins) + + return np.array([_sholl_crossings(m) for m in morphs]).sum(axis=0)

BlueBrain/NeuroM

276c7b2bc925d6d61078018d0c3accf8fd59499f

diff --git a/tests/features/test_morphology.py b/tests/features/test_morphology.py index 2337c83..3bd49d5 100644 --- a/tests/features/test_morphology.py +++ b/tests/features/test_morphology.py @@ -33,6 +33,7 @@ import warnings from io import StringIO from pathlib import Path +import morphio import numpy as np import pytest from morphio import PointLevel, SectionType @@ -44,9 +45,9 @@ from numpy.testing import assert_array_equal from neurom import morphmath from neurom import NeuriteType, load_morphology, AXON, BASAL_DENDRITE -from neurom.core import Morphology +from neurom.core import Morphology, Population from neurom.exceptions import NeuroMError -from neurom.features import morphology, section +from neurom.features import morphology, population, section DATA_PATH = Path(__file__).parent.parent / 'data' @@ -725,3 +726,26 @@ def test_unique_projected_points(): morphology._unique_projected_points(morph, "airplane", NeuriteType.all) assert len(morphology._unique_projected_points(morph, "yz", NeuriteType.apical_dendrite)) == 0 + + +def test_missing_soma(): + NRN_missing_soma = load_morphology(SWC_PATH / 'Single_apical_no_soma.swc') + + with pytest.raises(NeuroMError): + morphology.trunk_origin_elevations(NRN_missing_soma) + with pytest.raises(NeuroMError): + morphology.trunk_origin_azimuths(NRN_missing_soma) + with pytest.raises(NeuroMError): + morphology.trunk_origin_elevations(NRN_missing_soma) + with pytest.raises(NeuroMError): + morphology.trunk_vectors(NRN_missing_soma) + with pytest.raises(NeuroMError): + morphology.sholl_crossings(NRN_missing_soma) + with pytest.raises(NeuroMError): + morphology.sholl_frequency(NRN_missing_soma) + with pytest.raises(NeuroMError): + morphology.length_fraction_above_soma(NRN_missing_soma) + + POP_missing_soma = Population([NRN_missing_soma]) + with pytest.raises(NeuroMError): + population.sholl_frequency(POP_missing_soma)

Raise more informative error when a morph has no soma Some morphology files have no soma, which NeuroM is able to load. But when one compute features on such morphology, one may get obscure errors. For example: ```python nm.get("trunk_angles", neuron, neurite_type=nm.core.types.NeuriteType.basal_dendrite) ``` will raise the following error on a morphology without soma: ```python File neurom/features/__init__.py:150, in get(feature_name, obj, **kwargs) 135 def get(feature_name, obj, **kwargs): 136 """Obtain a feature from a set of morphology objects. 137 138 Features can be either Neurite, Morphology or Population features. For Neurite features see (...) 148 List|Number: feature value as a list or a single number. 149 """ --> 150 return _get_feature_value_and_func(feature_name, obj, **kwargs)[0] File neurom/features/__init__.py:110, in _get_feature_value_and_func(feature_name, obj, **kwargs) 108 if feature_name in _MORPHOLOGY_FEATURES: 109 feature_ = _MORPHOLOGY_FEATURES[feature_name] --> 110 res = feature_(obj, **kwargs) 111 elif feature_name in _NEURITE_FEATURES: 112 feature_ = _NEURITE_FEATURES[feature_name] File neurom/features/morphology.py:202, in trunk_angles(morph, neurite_type, coords_only, sort_along, consecutive_only) 172 @feature(shape=(...,)) 173 def trunk_angles( 174 morph, (...) 178 consecutive_only=True, 179 ): 180 """Calculate the angles between all the trunks of the morph. 181 182 By default, the angles are defined on the x-y plane and the trees are sorted from the y axis (...) 200 only the angle with the next trunk is returned for each trunk. 201 """ --> 202 vectors = np.array(trunk_vectors(morph, neurite_type=neurite_type)) 203 # In order to avoid the failure of the process in case the neurite_type does not exist 204 if len(vectors) == 0: File neurom/features/morphology.py:169, in trunk_vectors(morph, neurite_type) 166 def vector_to_root_node(neurite): 167 return morphmath.vector(neurite.root_node.points[0], morph.soma.center) --> 169 return _map_neurites(vector_to_root_node, morph, neurite_type) File neurom/features/morphology.py:67, in _map_neurites(function, morph, neurite_type) 66 def _map_neurites(function, morph, neurite_type): ---> 67 return list( 68 iter_neurites(morph, mapfun=function, filt=is_type(neurite_type)) 69 ) File neurom/features/morphology.py:167, in trunk_vectors.<locals>.vector_to_root_node(neurite) 166 def vector_to_root_node(neurite): --> 167 return morphmath.vector(neurite.root_node.points[0], morph.soma.center) File neurom/morphmath.py:60, in vector(p1, p2) 50 def vector(p1, p2): 51 """Compute vector between two 3D points. 52 53 Args: (...) 58 3-vector from p1 - p2 59 """ ---> 60 return np.subtract(p1[COLS.XYZ], p2[COLS.XYZ]) TypeError: 'NoneType' object is not subscriptable ``` which is not really helpful for users. I suggest we add some checkers to raise more understandable errors.

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

BlueBrain__NeuroM-990

diff --git a/CHANGELOG.rst b/CHANGELOG.rst index f852163..de024a1 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -3,10 +3,18 @@ Changelog Version 3.2.0 ------------- +- Fix ``neurom.features.morphology.sholl_frequency`` to return an empty list when a + neurite_type that is not present in the morphology is specified. +- Fix ``neurom.features.morphology.trunk_origin_radii`` to warn and use only the root + section for the calculation of the path distances. Edge cases from the combination + of ``min_length_filter`` and ``max_length_filter`` are addressed. +- Fix ``neurom.features.morphology.sholl_frequency`` to use soma center in distance + calculation, instead of using the origin. - Add ``neurom.features.morphology.trunk_angles_inter_types`` and ``neurom.features.morphology.trunk_angles_from_vector`` features, make ``neurom.features.morphology.trunk_angles`` more generic and add length filter to ``neurom.features.morphology.trunk_origin_radii``. +- Deprecate python3.6 - Add doc on spherical coordinates. Version 3.1.0 diff --git a/neurom/features/morphology.py b/neurom/features/morphology.py index 405816d..2aded0e 100644 --- a/neurom/features/morphology.py +++ b/neurom/features/morphology.py @@ -515,16 +515,24 @@ def sholl_frequency(morph, neurite_type=NeuriteType.all, step_size=10, bins=None in steps of `step_size`. Each segment of the morphology is tested, so a neurite that bends back on itself, and crosses the same Sholl radius will get counted as having crossed multiple times. + + If a `neurite_type` is specified and there are no trees corresponding to it, an empty + list will be returned. """ neurite_filter = is_type(neurite_type) if bins is None: min_soma_edge = morph.soma.radius - max_radii = max( + + max_radius_per_neurite = [ np.max(np.linalg.norm(n.points[:, COLS.XYZ] - morph.soma.center, axis=1)) for n in morph.neurites if neurite_filter(n) - ) - bins = np.arange(min_soma_edge, min_soma_edge + max_radii, step_size) + ] + + if not max_radius_per_neurite: + return [] + + bins = np.arange(min_soma_edge, min_soma_edge + max(max_radius_per_neurite), step_size) return sholl_crossings(morph, neurite_type, morph.soma.center, bins)

BlueBrain/NeuroM

d120263701bd2de8fb6f8ea6c655b9ec8a0a99ce

diff --git a/tests/features/test_get_features.py b/tests/features/test_get_features.py index 312edaf..61d3119 100644 --- a/tests/features/test_get_features.py +++ b/tests/features/test_get_features.py @@ -717,6 +717,10 @@ def test_sholl_frequency(): assert features.get('sholl_frequency', m, step_size=5.0) == [0, 1, 1, 1] + # check that if there is no neurite of a specific type, an empty list is returned + assert features.get('sholl_frequency', m, neurite_type=NeuriteType.axon) == [] + + def test_bifurcation_partitions(): assert_allclose(features.get('bifurcation_partitions', POP)[:10], [19., 17., 15., 13., 11., 9., 7., 5., 3., 1.])

`sholl_frequency` fails if `neurite_type` not in morphology ```python import neurom m = neurom.load_morphology( """ 1 1 0 0 0 0.5 -1 2 3 -1 0 0 0.1 1 3 3 -2 0 0 0.1 2 4 3 -3 0 0 0.1 3 """", reader="swc" ) neurom.get("sholl_frequency", step_size=1, neurite_type=neurom.NeuriteType.axon) ``` throws: ```python --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Input In [40], in <module> ----> 1 get("sholl_frequency", m, step_size=1, neurite_type=neurom.NeuriteType.axon) File ~/Projects/BBP/NEUROM/venv3.8-test/lib/python3.8/site-packages/neurom/features/__init__.py:150, in get(feature_name, obj, **kwargs) 135 def get(feature_name, obj, **kwargs): 136 """Obtain a feature from a set of morphology objects. 137 138 Features can be either Neurite, Morphology or Population features. For Neurite features see (...) 148 List|Number: feature value as a list or a single number. 149 """ --> 150 return _get_feature_value_and_func(feature_name, obj, **kwargs)[0] File ~/Projects/BBP/NEUROM/venv3.8-test/lib/python3.8/site-packages/neurom/features/__init__.py:110, in _get_feature_value_and_func(feature_name, obj, **kwargs) 108 if feature_name in _MORPHOLOGY_FEATURES: 109 feature_ = _MORPHOLOGY_FEATURES[feature_name] --> 110 res = feature_(obj, **kwargs) 111 elif feature_name in _NEURITE_FEATURES: 112 feature_ = _NEURITE_FEATURES[feature_name] File ~/Projects/BBP/NEUROM/venv3.8-test/lib/python3.8/site-packages/neurom/features/morphology.py:293, in sholl_frequency(morph, neurite_type, step_size, bins) 291 if bins is None: 292 min_soma_edge = morph.soma.radius --> 293 max_radii = max(np.max(np.linalg.norm(n.points[:, COLS.XYZ], axis=1)) 294 for n in morph.neurites if neurite_filter(n)) 295 bins = np.arange(min_soma_edge, min_soma_edge + max_radii, step_size) 297 return sholl_crossings(morph, morph.soma.center, bins, neurite_type) ValueError: max() arg is an empty sequence ``` I can think of two possible solutions here: 1. Return a [0] bin count. 2. Raise a meaningful error which will inform the user that the `neurite_type` provided is not present in the morphology Note: This error takes place only when bins are not provided. It tries to get the max of the points that belong to neurites of that type but finds none. @lidakanari @arnaudon @adrien-berchet

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

BlueBrain__atlas-densities-25

diff --git a/atlas_densities/densities/fitting.py b/atlas_densities/densities/fitting.py index af117c5..775bdc4 100644 --- a/atlas_densities/densities/fitting.py +++ b/atlas_densities/densities/fitting.py @@ -177,7 +177,8 @@ def compute_average_intensity( Compute the average of `intensity` within the volume defined by `volume_mask`. If `slices` is a non-empty list of slice indices along the x-axis, then the average is - restricted to the subvolume of `volume_mask` enclosed by these slices. + restricted to the subvolume of `volume_mask` enclosed by these slices. Slices indices outside + the `volume_mask` will be ignored. Args: intensity: a float array of shape (W, H, D) where W, H and D are integer dimensions. @@ -196,7 +197,9 @@ def compute_average_intensity( restricted_mask = volume_mask else: restricted_mask = np.zeros_like(volume_mask) - restricted_mask[slices] = True + # remove slices indices outside the volume_mask + slices_ = [slice_ for slice_ in slices if 0 <= slice_ < volume_mask.shape[0]] + restricted_mask[slices_] = True restricted_mask = np.logical_and(restricted_mask, volume_mask) if np.any(restricted_mask):

BlueBrain/atlas-densities

9bfda2ba2827a9b8fc5e2201f91eeb63b528aa76

diff --git a/tests/densities/test_fitting.py b/tests/densities/test_fitting.py index 4338969..8d1e8b5 100644 --- a/tests/densities/test_fitting.py +++ b/tests/densities/test_fitting.py @@ -219,6 +219,10 @@ def test_compute_average_intensity(): assert np.allclose(actual, 0.3 / 2.0) actual = tested.compute_average_intensity(intensity, volume_mask, slices=[1]) assert np.allclose(actual, 0.1 / 2.0) + actual = tested.compute_average_intensity(intensity, volume_mask, slices=[-1, 1, 3]) + assert np.allclose(actual, 0.1 / 2.0) + actual = tested.compute_average_intensity(intensity, volume_mask, slices=[-1, 3]) + assert actual == 0 def test_compute_average_intensities(hierarchy_info):

Check slices position during fitting For the fitting of the densities, the user can provide a list of coronal positions that corresponds to the original ISH slices in a separate file. There is no tests in atlas_densities/densities/fitting.py to check if these positions are in range of the annotation volume shape. Suggestion: add at line 199: ``` slices = np.delete(slices, np.array(slices) >= volume_mask.shape[0]) slices = np.delete(slices, np.array(slices) < 0) ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

BlueBrain__atlas-densities-61

diff --git a/README.rst b/README.rst index 8b8cc3b..8479266 100644 --- a/README.rst +++ b/README.rst @@ -10,8 +10,8 @@ The outcome of this project is a list of volumetric files that provides cell typ for each voxel of the mouse brain volume. The BBP Cell Atlas is the first model required to reconstruct BBP circuits of the mouse brain. -The tools implementation is based on the methods of `Eroe et al. (2018)`_, `Rodarie et al. (2021)`_, -and `Roussel et al. (2021)`_. +The tools implementation is based on the methods of `Eroe et al. (2018)`_, `Rodarie et al. (2022)`_, +and `Roussel et al. (2022)`_. The source code was originally written by Csaba Eroe, Dimitri Rodarie, Hugo Dictus, Lu Huanxiang, Wojciech Wajerowicz, Jonathan Lurie, and Yann Roussel. @@ -53,7 +53,7 @@ Note: Depending on the size and resolution of the atlas, it can happen that some Reference atlases ----------------- -Most the pipeline steps rely on the following AIBS reference datasets (see `Rodarie et al. (2021)`_ for more +Most the pipeline steps rely on the following AIBS reference datasets (see `Rodarie et al. (2022)`_ for more details on the different versions of these datasets): * A Nissl volume @@ -161,7 +161,7 @@ ISH datasets for inhibitory/excitatory neurons In `Eroe et al. (2018)`_ (i.e., BBP Cell Atlas version 1), the excitatory neurons are distinguished from the inhibitory neurons using the Nrn1 and GAD67 (or GAD1) genetic marker. -In `Rodarie et al. (2021)`_ (i.e., BBP Cell Atlas version 2), the authors used parvalbumin (Pvalb), +In `Rodarie et al. (2022)`_ (i.e., BBP Cell Atlas version 2), the authors used parvalbumin (Pvalb), somatostatin (SST), vasoactive intestinal peptide (VIP) and gabaergic (GAD1) markers (see also `fit_average_densities_ccfv2_config.yaml`_). @@ -207,7 +207,7 @@ The files `glia.nrrd`, `oligodendrocyte.nrrd`, `microglia.nrrd`, `astrocyte.nrrd Extract literature neuron type densities estimates -------------------------------------------------- -In `Rodarie et al. (2021)`_, the authors collected density estimates from the literature for +In `Rodarie et al. (2022)`_, the authors collected density estimates from the literature for inhibitory neurons. Some estimates are in a format that can not be directly used by the pipeline (e.g., counts instead of densities). This part of the pipeline integrates the literature values into csv files, that will be used later on for the fitting. @@ -216,7 +216,7 @@ Format literature review files ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ We compile here the cell density estimates related to measurements of `Kim et al. (2017)`_ density -file (`mmc3.xlsx`_) and `Rodarie et al. (2021)`_ literature +file (`mmc3.xlsx`_) and `Rodarie et al. (2022)`_ literature review file (`gaba_papers.xlsx`_) into a single CSV file. Regions known to be purely excitatory or inhibitory (in terms of neuron composition) are also listed in a separate CSV file. @@ -237,6 +237,13 @@ Convert literature measurements into average densities Compute and save average cell densities based on literature measurements and Cell Atlas data (e.g., region volumes). +WARNING: +Different versions of the annotation atlas or the hierarchy file might have different sets brain +regions (see `Rodarie et al. (2022)`_ for more details). The region names used by the literature +measurements might therefore have no match in these datasets. +Regions from the measurements that are not in the hierarchy or do not appear in the annotations will +be ignored. A warning message will display these regions, allowing us to review them. + .. code-block:: bash atlas-densities cell-densities measurements-to-average-densities \ @@ -252,7 +259,7 @@ Fit transfer functions from mean region intensity to neuron density ------------------------------------------------------------------- We fit here transfer functions that describe the relation between mean ISH expression in regions of -the mouse brain and literature regional density estimates (see `Rodarie et al. (2021)`_ for more +the mouse brain and literature regional density estimates (see `Rodarie et al. (2022)`_ for more details). This step leverages AIBS ISH marker datasets (in their expression form, see also `fit_average_densities_ccfv2_config.yaml`_) and the previously computed literature density values. @@ -281,7 +288,7 @@ Compute inhibitory/excitatory neuron densities ---------------------------------------------- The neuron subtypes are here distinguished from each other using either the pipeline from -`Eroe et al. (2018)`_ (BBP Cell Atlas version 1) or `Rodarie et al. (2021)`_ (BBP Cell Atlas version +`Eroe et al. (2018)`_ (BBP Cell Atlas version 1) or `Rodarie et al. (2022)`_ (BBP Cell Atlas version 2). BBP Cell Atlas version 1 @@ -321,8 +328,8 @@ Compute ME-types densities from a probability map ------------------------------------------------- Morphological and Electrical type densities of inhibitory neurons in the isocortex can be estimated -using Roussel et al.'s pipeline. This pipeline produces a mapping from inhibitory neuron molecular -types (here PV, SST, VIP and GAD67) to ME-types defined in `Markram et al. (2015)`_. +using `Roussel et al. (2022)`_'s pipeline. This pipeline produces a mapping from inhibitory neuron +molecular types (here PV, SST, VIP and GAD67) to ME-types defined in `Markram et al. (2015)`_. The following command creates neuron density nrrd files for the me-types listed in a probability mapping csv file (see also `mtypes_probability_map_config.yaml`_). @@ -431,8 +438,8 @@ Copyright © 2022 Blue Brain Project/EPFL .. _`Eroe et al. (2018)`: https://www.frontiersin.org/articles/10.3389/fninf.2018.00084/full .. _`Kim et al. (2017)`: https://www.sciencedirect.com/science/article/pii/S0092867417310693 .. _`Markram et al. (2015)`: https://www.cell.com/cell/fulltext/S0092-8674(15)01191-5 -.. _`Rodarie et al. (2021)`: https://www.biorxiv.org/content/10.1101/2021.11.20.469384v2 -.. _`Roussel et al. (2021)`: https://www.biorxiv.org/content/10.1101/2021.11.24.469815v1 +.. _`Rodarie et al. (2022)`: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010739 +.. _`Roussel et al. (2022)`: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010058 .. _`BBP Cell Atlas`: https://portal.bluebrain.epfl.ch/resources/models/cell-atlas/ .. _cgal-pybind: https://github.com/BlueBrain/cgal-pybind .. _`DeepAtlas`: https://github.com/BlueBrain/Deep-Atlas diff --git a/atlas_densities/app/cell_densities.py b/atlas_densities/app/cell_densities.py index 019145e..f60a87b 100644 --- a/atlas_densities/app/cell_densities.py +++ b/atlas_densities/app/cell_densities.py @@ -621,6 +621,12 @@ def compile_measurements( @app.command() @common_atlas_options [email protected]( + "--region-name", + type=str, + default="root", + help="Name of the root region in the hierarchy", +) @click.option( "--cell-density-path", type=EXISTING_FILE_PATH, @@ -654,6 +660,7 @@ def compile_measurements( def measurements_to_average_densities( annotation_path, hierarchy_path, + region_name, cell_density_path, neuron_density_path, measurements_path, @@ -666,6 +673,10 @@ def measurements_to_average_densities( `neuron_density_path`) are used to compute average cell densities in every AIBS region where sufficient information is available. + Measurements from regions which are not in the provided brain region hierarchy or not in the + provided annotation volume will be ignored. A warning with all ignored lines from the + measurements file will be displayed. + The different cell types (e.g., PV+, SST+, VIP+ or overall inhibitory neurons) and brain regions under consideration are prescribed by the input measurements. @@ -709,6 +720,7 @@ def measurements_to_average_densities( region_map = RegionMap.load_json(hierarchy_path) L.info("Loading measurements ...") measurements_df = pd.read_csv(measurements_path) + L.info("Measurement to average density: started") average_cell_densities_df = measurement_to_average_density( region_map, @@ -718,6 +730,7 @@ def measurements_to_average_densities( overall_cell_density.raw, neuron_density.raw, measurements_df, + region_name, ) remove_non_density_measurements(average_cell_densities_df) @@ -735,7 +748,7 @@ def measurements_to_average_densities( "--region-name", type=str, default="root", - help="Name of the region in the hierarchy", + help="Name of the root region in the hierarchy", ) @click.option( "--neuron-density-path", @@ -822,6 +835,10 @@ def fit_average_densities( `neuron_density_path` is used to compute the average density of inhibitory neurons (a.k.a gad67+) in every homogenous region of type "inhibitory". + Regions from the literature values and homogenous regions which are not in the provided brain + region hierarchy or not in the provided annotation volume will be ignored. A warning with all + ignored lines from the measurements file will be displayed. + Our linear fitting of density values relies on the assumption that the average cell density (number of cells per mm^3) of a cell type T in a brain region R depends linearly on the average intensity of a gene marker of T. The conversion factor is a constant which depends only @@ -932,7 +949,7 @@ def fit_average_densities( "--region-name", type=str, default="root", - help="Name of the region in the hierarchy", + help="Name of the root region in the hierarchy", ) @click.option( "--neuron-density-path", diff --git a/atlas_densities/densities/fitting.py b/atlas_densities/densities/fitting.py index 1fa8dc6..14428ad 100644 --- a/atlas_densities/densities/fitting.py +++ b/atlas_densities/densities/fitting.py @@ -29,6 +29,7 @@ from scipy.optimize import curve_fit from tqdm import tqdm from atlas_densities.densities import utils +from atlas_densities.densities.measurement_to_density import remove_unknown_regions from atlas_densities.exceptions import AtlasDensitiesError, AtlasDensitiesWarning if TYPE_CHECKING: # pragma: no cover @@ -625,6 +626,9 @@ def linear_fitting( # pylint: disable=too-many-arguments _check_homogenous_regions_sanity(homogenous_regions) hierarchy_info = utils.get_hierarchy_info(region_map, root=region_name) + remove_unknown_regions(average_densities, region_map, annotation, hierarchy_info) + remove_unknown_regions(homogenous_regions, region_map, annotation, hierarchy_info) + L.info("Creating a data frame from known densities ...") densities = create_dataframe_from_known_densities( hierarchy_info["brain_region"].to_list(), average_densities diff --git a/atlas_densities/densities/measurement_to_density.py b/atlas_densities/densities/measurement_to_density.py index 49b8777..65170e4 100644 --- a/atlas_densities/densities/measurement_to_density.py +++ b/atlas_densities/densities/measurement_to_density.py @@ -11,6 +11,7 @@ more than 40 scientific articles. Densities are expressed in number of cells per mm^3. """ +import warnings from typing import Set, Tuple, Union import numpy as np @@ -20,6 +21,7 @@ from tqdm import tqdm from voxcell import RegionMap # type: ignore from atlas_densities.densities.utils import compute_region_volumes, get_hierarchy_info +from atlas_densities.exceptions import AtlasDensitiesWarning def get_parent_region(region_name: str, region_map: RegionMap) -> Union[str, None]: @@ -255,7 +257,59 @@ def cell_count_per_slice_to_density( measurements[mask_50um] = cell_counts_per_slice -def measurement_to_average_density( +def remove_unknown_regions( + measurements: "pd.DataFrame", + region_map: RegionMap, + annotation: AnnotationT, + hierarchy_info: "pd.DataFrame", +): + """ + Drop lines from the measurements dataframe which brain regions are not in the AIBS brain region + hierarchy or not in the annotation volume. + The data frame `measurements` is modified in place. + + Args: + measurements: dataframe whose columns are described in + :func:`atlas_densities.app.densities.compile_measurements`. + region_map: RegionMap object to navigate the brain regions hierarchy. + annotation: int array of shape (W, H, D) holding the annotation of the whole AIBS + mouse brain. (The integers W, H and D are the dimensions of the array). + hierarchy_info: data frame returned by + :func:`atlas_densities.densities.utils.get_hierarchy_info`. + """ + pd.set_option("display.max_colwidth", None) + indices_ids = measurements.index[ + ~measurements["brain_region"].isin(hierarchy_info["brain_region"]) + ] + if len(indices_ids) > 0: + warnings.warn( + "The following lines in the measurements dataframe have no equivalent in the " + "brain region hierarchy: \n" + f"{measurements.loc[indices_ids, 'brain_region'].to_string()}", + AtlasDensitiesWarning, + ) + measurements.drop(indices_ids, inplace=True) + + u_regions = np.unique(annotation) + u_regions = np.delete(u_regions, 0) # don't take 0, i.e: outside of the brain + u_regions = [ + region_map.get(u_region, "name", with_ascendants=True) + for u_region in u_regions + if region_map.find(u_region, "id") + ] + u_regions = np.unique([elem for row in u_regions for elem in row]) # flatten + + indices_ann = measurements.index[~measurements["brain_region"].isin(u_regions)] + if len(indices_ann) > 0: + warnings.warn( + "The following lines in the measurements dataframe have no equivalent in the " + f"annotation volume: \n{measurements.loc[indices_ann, 'brain_region'].to_string()}", + AtlasDensitiesWarning, + ) + measurements.drop(indices_ann, inplace=True) + + +def measurement_to_average_density( # pylint: disable=too-many-arguments region_map: RegionMap, annotation: AnnotationT, voxel_dimensions: Tuple[float, float, float], @@ -263,6 +317,7 @@ def measurement_to_average_density( cell_density: FloatArray, neuron_density: FloatArray, measurements: "pd.DataFrame", + root_region: str = "Basic cell groups and regions", ) -> "pd.DataFrame": """ Compute average cell densities in AIBS brain regions based on experimental `measurements`. @@ -274,9 +329,6 @@ def measurement_to_average_density( (or if several cell density computations are possible from measurements of different articles), the output cell density of the region is the average of the possible cell densities. - The region names in `measurements` which are not compliant with the AIBS nomenclature (1.json) - are ignored. - Args: region_map: RegionMap object to navigate the brain regions hierarchy. annotation: int array of shape (W, H, D) holding the annotation of the whole AIBS @@ -291,6 +343,7 @@ def measurement_to_average_density( in that voxel expressed in number of neurons per mm^3. measurements: dataframe whose columns are described in :func:`atlas_densities.app.densities.compile_measurements`. + root_region: name of the root region in the brain region hierarchy. Returns: dataframe of the same format as `measurements` but where all measurements of type @@ -298,10 +351,8 @@ def measurement_to_average_density( type "cell density". Densities are expressed in number of cells per mm^3. """ - # Filter out non-AIBS compliant region names - hierarchy_info = get_hierarchy_info(region_map) - indices = measurements.index[~measurements["brain_region"].isin(hierarchy_info["brain_region"])] - measurements = measurements.drop(indices) + hierarchy_info = get_hierarchy_info(region_map, root_region) + remove_unknown_regions(measurements, region_map, annotation, hierarchy_info) # Replace NaN standard deviations by measurement values nan_mask = measurements["standard_deviation"].isna() diff --git a/atlas_densities/version.py b/atlas_densities/version.py index 907cbe3..90cc3fc 100644 --- a/atlas_densities/version.py +++ b/atlas_densities/version.py @@ -1,4 +1,4 @@ """version""" -from pkg_resources import get_distribution # type: ignore +import importlib.metadata -VERSION = get_distribution("atlas_densities").version +VERSION = importlib.metadata.version("atlas_densities") diff --git a/doc/source/conf.py b/doc/source/conf.py index 885f797..4014bef 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -11,8 +11,7 @@ import os import sys -from pkg_resources import get_distribution - +import importlib.metadata # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the @@ -52,7 +51,7 @@ project = 'atlas-densities' # built documents. # # The short X.Y version. -version = get_distribution(project).version +version = importlib.metadata.version(project) # The full version, including alpha/beta/rc tags. release = version

BlueBrain/atlas-densities

67d273c11bcb85dd7a5132dbaf879f88effba112

diff --git a/tests/app/test_cell_densities.py b/tests/app/test_cell_densities.py index ddc894d..df2d5dc 100644 --- a/tests/app/test_cell_densities.py +++ b/tests/app/test_cell_densities.py @@ -271,6 +271,8 @@ def _get_measurements_to_average_densities_result(runner, hierarchy_path, measur hierarchy_path, "--annotation-path", "annotation.nrrd", + "--region-name", + "Basic cell groups and regions", "--cell-density-path", "cell_density.nrrd", "--neuron-density-path", diff --git a/tests/densities/test_measurement_to_density.py b/tests/densities/test_measurement_to_density.py index 2c6bdb8..440d918 100644 --- a/tests/densities/test_measurement_to_density.py +++ b/tests/densities/test_measurement_to_density.py @@ -20,6 +20,11 @@ def region_map(): return RegionMap.from_dict(get_hierarchy()) [email protected] +def annotations(): + return np.array([[[0, 10710, 10710, 10711, 10711, 0]]], dtype=int) + + @pytest.fixture def cell_densities(): densities = np.array([5.0 / 9.0, 4.0 / 8.0, 1.0 / 3.0, 1.0 / 3.0, 1.0 / 3.0]) @@ -55,6 +60,37 @@ def volumes(voxel_volume=2): ) +def test_remove_unknown_regions(region_map, annotations): + measurements = pd.DataFrame( + { + "brain_region": [ + "Lobule Ii", + "Lobule II, granular layer", + "Lobule II, molecular layer", + ], + "measurement": [0.722, 28118.0, 31047], + "standard_deviation": [0.722, 6753.9, 5312], + "measurement_type": ["volume", "cell count", "cell count"], + "measurement_unit": ["mm^3", "number of cells", "number of cells"], + "source_title": ["Article 1", "Article 2", "Article 1"], + } + ) + tested.remove_unknown_regions(measurements, region_map, annotations, get_hierarchy_info()) + expected = pd.DataFrame( + { + "brain_region": [ + "Lobule II, molecular layer", + ], + "measurement": [31047.0], + "standard_deviation": [5312.0], + "measurement_type": ["cell count"], + "measurement_unit": ["number of cells"], + "source_title": ["Article 1"], + } + ) + pdt.assert_frame_equal(measurements.reset_index(drop=True), expected) + + def test_cell_count_to_density(region_map, volumes): measurements = pd.DataFrame( {

Exception in fitting due to regions in json hierarchy but not in the annotations volume On master branch, when running the cell atlas pipeline with the CCFv3 annotation atlas, the following command: ``` atlas-densities cell-densities fit-average-densities \ --hierarchy-path=data/1.json \ --annotation-path=data/ccfv3/annotation_25.nrrd \ --neuron-density-path=data/ccfv3/density_volumes/neuron_density.nrrd \ --average-densities-path=data/ccfv3/measurements/lit_densities.csv \ --homogenous-regions-path=data/ccfv3/measurements/homogeneous_regions.csv \ --gene-config-path=atlas_densities/app/data/markers/fit_average_densities_ccfv2_config.yaml \ --fitted-densities-output-path=data/ccfv3/first_estimates/first_estimates.csv \ --fitting-maps-output-path=data/ccfv3/first_estimates/fitting.json ``` This fails with the following exception: ``` Traceback (most recent call last): File "Workspace/venv/bin/atlas-densities", line 8, in <module> sys.exit(cli()) File "Workspace/abt/atlas-densities/atlas_densities/app/cli.py", line 24, in cli app() File "Workspace/venv/lib/python3.10/site-packages/click/core.py", line 1130, in __call__ return self.main(*args, **kwargs) File "Workspace/venv/lib/python3.10/site-packages/click/core.py", line 1055, in main rv = self.invoke(ctx) File "Workspace/venv/lib/python3.10/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "Workspace/venv/lib/python3.10/site-packages/click/core.py", line 1657, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "Workspace/venv/lib/python3.10/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "Workspace/venv/lib/python3.10/site-packages/click/core.py", line 760, in invoke return __callback(*args, **kwargs) File "Workspace/venv/lib/python3.10/site-packages/atlas_commons/app_utils.py", line 47, in wrapper function(*args, **kw) File "Workspace/abt/atlas-densities/atlas_densities/app/cell_densities.py", line 906, in fit_average_densities fitted_densities_df, fitting_maps = linear_fitting( File "Workspace/abt/atlas-densities/atlas_densities/densities/fitting.py", line 624, in linear_fitting _check_average_densities_sanity(average_densities) File "Workspace/abt/atlas-densities/atlas_densities/densities/fitting.py", line 514, in _check_average_densities_sanity raise AtlasDensitiesError( atlas_densities.exceptions.AtlasDensitiesError: `average_densities` has a NaN measurement or a NaN standard deviation for the following entries: brain_region ... specimen_age 3050 Entorhinal area, lateral part, layer 2a ... 8- to 14-week-old 3051 Entorhinal area, lateral part, layer 2b ... 8- to 14-week-old ``` These lines are part of the `lit_densities.csv` and contain no mean values. These lines have been generated when creating the `lit_densities.csv` (command `atlas-densities cell-densities measurements-to-average-densities`) from `gaba_papers.xlsx`. The regions associated with these lines exist in the brain region hierarchy but do not appear in the CCFv3 annotation atlas: ```python import numpy as np from voxcell import RegionMap, VoxelData region_map = RegionMap.load_json("data/1.json") annotation = VoxelData.load_nrrd("data/ccfv3/annotation_25.nrrd").raw # Same for the other layer. region_map.find("Entorhinal area, lateral part, layer 2a", "name") # {715} region_map.is_leaf_id(715) # True np.count_nonzero(annotation==715) # 0 ``` The regions having no volume, every literature values based on them will be stored as NaNs in the final `lit_densities.csv`. The question is when/how should we solve this issue: - When preparing the literature data? Every literature value that do not appear in the annotations should not be stored in the literature file (test with a set of unique ids from the annotations) - When writing in the literature file? Lines with NaNs should not be stored. - When reading the literature file during fitting? Lines with NaNs should be ignored.

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

BlueBrain__atlas-splitter-12

diff --git a/atlas_splitter/utils.py b/atlas_splitter/utils.py index 66186d0..95407d8 100644 --- a/atlas_splitter/utils.py +++ b/atlas_splitter/utils.py @@ -9,6 +9,9 @@ from atlas_splitter.exceptions import AtlasSplitterError HierarchyDict = Dict[str, Any] +MIN_CUSTOM_ID = 1_000_000_000 +MAX_CUSTOM_ID = 4_000_000_000 + def get_isocortex_hierarchy(allen_hierachy: HierarchyDict): """ @@ -61,13 +64,23 @@ def id_from_acronym(region_map: RegionMap, acronym: str) -> int: if region_id_set: [region_id] = region_id_set else: # acronym not present in hierarchy, generating a corresponding id - sha = hashlib.sha256() - sha.update(acronym.encode("utf-8")) - region_id = int(str(int(sha.hexdigest(), 16))[0:10]) - + region_id = _hash_derived_id(acronym) return region_id +def _hash_derived_id(acronym: str) -> int: + """Create an id from the acronym's sha256 digest. + + Notes: + The id is generated in the [MIN_CUSTOM_ID, MAX_CUSTOM_ID] interval for two reasons: + - Be outside the current ids range + - Fit within the range of uint32 annotation dtype + """ + sha = hashlib.sha256(acronym.encode("utf-8")) + integer = int.from_bytes(sha.digest(), "big") + return MIN_CUSTOM_ID + integer % (MAX_CUSTOM_ID - MIN_CUSTOM_ID) + + def _assert_is_leaf_node(node) -> None: """ Raises an AtalasSplitterError if `node` is not a leaf node.

BlueBrain/atlas-splitter

18932cbeb9dd4f0e38c0fae362a072e1d325d433

diff --git a/tests/barrel_splitter/test_somatosensory_barrels.py b/tests/barrel_splitter/test_somatosensory_barrels.py index 4f5ee74..e8d2a93 100644 --- a/tests/barrel_splitter/test_somatosensory_barrels.py +++ b/tests/barrel_splitter/test_somatosensory_barrels.py @@ -46,10 +46,11 @@ def test_layer_ids(): names = ["region1", "region2", "region3"] layers = ["layer1", "layer2"] result = tested.layer_ids(region_map, names, layers) + expected = { - "region1": {"region1": 5293416420, "layer1": 1111509459, "layer2": 8291842637}, - "region2": {"region2": 9197100151, "layer1": 1048759989, "layer2": 8562892645}, - "region3": {"region3": 2807168083, "layer1": 2207162267, "layer2": 3619321798}, + "region1": {"region1": 3631290122, "layer1": 2267454475, "layer2": 1012379119}, + "region2": {"region2": 1722831506, "layer1": 3787876483, "layer2": 1416363748}, + "region3": {"region3": 1193141608, "layer1": 3031486657, "layer2": 3890489924}, } assert result == expected diff --git a/tests/layer_splitter/test_isocortex_layer_23.py b/tests/layer_splitter/test_isocortex_layer_23.py index fd89f49..f4a1c04 100644 --- a/tests/layer_splitter/test_isocortex_layer_23.py +++ b/tests/layer_splitter/test_isocortex_layer_23.py @@ -91,7 +91,7 @@ def test_edit_hierarchy(): "parent_structure_id": 219, }, { - "id": 2438771567, + "id": 2906756445, "acronym": "MO3", "name": "Somatomotor areas, Layer 3", "children": [], @@ -109,7 +109,6 @@ def test_edit_hierarchy(): ids_to_reuse, region_map, ) - assert isocortex_hierarchy == expected_hierarchy diff --git a/tests/test_app_barrel_splitter.py b/tests/test_app_barrel_splitter.py index eccb9b1..ec913c7 100644 --- a/tests/test_app_barrel_splitter.py +++ b/tests/test_app_barrel_splitter.py @@ -19,24 +19,24 @@ output_bfd = { 1070, 1998, 1999, - 6808354304, - 4625922081, - 9632197987, - 6740949287, - 4025629096, - 1028864429, - 1132763284, - 1135236927, - 1569938381, - 4159694229, - 5965588094, - 7178447226, - 7758245998, - 7766041724, - 7882359060, - 8701962317, - 8773083888, - 9288923888, + 1050271831, + 1419828837, + 1541598958, + 1561898146, + 1669999094, + 1742227897, + 1779524838, + 1914058509, + 1941812702, + 2061835172, + 2112620658, + 2190770412, + 2321675771, + 2491030215, + 3335143301, + 3364575989, + 3625413550, + 3951617891, } @@ -74,4 +74,4 @@ def test_split_barrels(): barrel_cortex_ids = output_region_map.find("SSp-bfd", attr="acronym", with_descendants=True) - assert barrel_cortex_ids == set(output_bfd) + assert barrel_cortex_ids == output_bfd diff --git a/tests/test_utils.py b/tests/test_utils.py index 8921641..b385e65 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -2,6 +2,7 @@ import json from pathlib import Path +import numpy as np import numpy.testing as npt import pytest from voxcell import RegionMap @@ -59,14 +60,25 @@ def test_id_from_acronym(region_map): # existing region -> existing id res1 = tested.id_from_acronym(region_map, "VISp1") + _assert_within_integer_type_range(res1, np.uint32) assert region_map.get(res1, attr="acronym") == "VISp1" - # new regeion -> non-existing id - res2 = tested.id_from_acronym(region_map, "MontyPython") + # new region -> non-existing id + res2 = tested.id_from_acronym(region_map, "VISPXXX") + _assert_within_integer_type_range(res2, np.uint32) with pytest.raises(VoxcellError, match="Region ID not found"): region_map.get(res2, attr="acronym") +def _assert_within_integer_type_range(value, int_dtype): + info = np.iinfo(int_dtype) + check = info.min <= value < info.max + assert check, ( + f"Value not within dtype '{int_dtype.__name__}' range: " + f"{info.min} <= {value} < {info.max}" + ) + + def test_create_id_generator(region_map): id_generator = tested.create_id_generator(region_map)

`atlas-splitter split-isocortex-layer-23` outputs an annotation volume with region IDs not present in the output hierarchy Occurred with ``` cd /gpfs/bbp.cscs.ch/data/project/proj84/atlas_pipeline_runs/2024-03-12T15:01:39 atlas-splitter --version atlas-splitter, version 0.1.3 atlas-splitter split-isocortex-layer-23 \ --hierarchy-path hierarchy.json \ --annotation-path annotation_ccfv3.nrrd \ --direction-vectors-path direction_vectors/direction_vectors_isocortex_ccfv3.nrrd \ --output-hierarchy-path hierarchy_ccfv3_l23split.json \ --output-annotation-path annotation_ccfv3_l23split.nrrd ``` 49 regions in the output annotation volume are not found in the output hierarchy: [74352560, 96323749, 117943286, 144508775, 146617060, 156558204, 215093570, 259388834, 373656076, 410200320, 586135081, 740752775, 775557082, 940760025, 972952746, 976342702, 990831169, 1160972157, 1174775454, 1209880404, 1324692064, 1361664772, 1622995831, 1635953398, 1636706498, 1735586154, 1776372845, 1797874319, 2278275862, 2357063861, 2655117045, 2927565312, 3204811968, 3232181544, 3373402385, 3402245361, 3447123322, 3484927447, 3561909895, 3670850531, 3743715038, 3840653638, 3903157542, 3965686099, 4108857031, 4207091109, 4219725843, 4256935451, 4261721241]

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

Bogdanp__dramatiq_sqs-13

diff --git a/dramatiq_sqs/broker.py b/dramatiq_sqs/broker.py index 6ce094a..d9a2b8f 100644 --- a/dramatiq_sqs/broker.py +++ b/dramatiq_sqs/broker.py @@ -68,6 +68,7 @@ class SQSBroker(dramatiq.Broker): retention: int = MAX_MESSAGE_RETENTION, dead_letter: bool = False, max_receives: int = MAX_RECEIVES, + tags: Optional[Dict[str, str]] = None, **options, ) -> None: super().__init__(middleware=middleware) @@ -80,6 +81,7 @@ class SQSBroker(dramatiq.Broker): self.queues: Dict[str, Any] = {} self.dead_letter: bool = dead_letter self.max_receives: int = max_receives + self.tags: Optional[Dict[str, str]] = tags self.sqs: Any = boto3.resource("sqs", **options) def consume(self, queue_name: str, prefetch: int = 1, timeout: int = 30000) -> dramatiq.Consumer: @@ -104,11 +106,22 @@ class SQSBroker(dramatiq.Broker): "MessageRetentionPeriod": self.retention, } ) + if self.tags: + self.sqs.meta.client.tag_queue( + QueueUrl=self.queues[queue_name].url, + Tags=self.tags + ) + if self.dead_letter: dead_letter_queue_name = f"{prefixed_queue_name}_dlq" dead_letter_queue = self.sqs.create_queue( QueueName=dead_letter_queue_name ) + if self.tags: + self.sqs.meta.client.tag_queue( + QueueUrl=dead_letter_queue.url, + Tags=self.tags + ) redrive_policy = { "deadLetterTargetArn": dead_letter_queue.attributes["QueueArn"], "maxReceiveCount": str(self.max_receives)

Bogdanp/dramatiq_sqs

69129e07c25be9aca5f5466c92ae7f6463926f65

diff --git a/tests/conftest.py b/tests/conftest.py index c961ed5..afd5441 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -26,6 +26,9 @@ def broker(): Pipelines(), Retries(min_backoff=1000, max_backoff=900000, max_retries=96), ], + tags={ + "owner": "dramatiq_sqs_tests", + }, ) dramatiq.set_broker(broker) yield broker diff --git a/tests/test_broker.py b/tests/test_broker.py index 6183803..077a70c 100644 --- a/tests/test_broker.py +++ b/tests/test_broker.py @@ -6,6 +6,7 @@ import pytest from botocore.stub import Stubber from dramatiq_sqs import SQSBroker +from dramatiq_sqs.broker import MAX_MESSAGE_RETENTION def test_can_enqueue_and_process_messages(broker, worker, queue_name): @@ -158,3 +159,28 @@ def test_creates_dead_letter_queue(): with stubber: broker.declare_queue("test") stubber.assert_no_pending_responses() + + +def test_tags_queues_on_create(): + # Given that I have an SQS broker with tags + broker = SQSBroker( + namespace="dramatiq_sqs_tests", + tags={"key1": "value1", "key2": "value2"} + ) + + # And I've stubbed out all the relevant API calls + stubber = Stubber(broker.sqs.meta.client) + stubber.add_response("create_queue", {"QueueUrl": ""}) + stubber.add_response("tag_queue", {}, { + "QueueUrl": "", + "Tags": { + "key1": "value1", + "key2": "value2" + } + }) + + # When I create a queue + # Then the queue should have the specified tags + with stubber: + broker.declare_queue("test") + stubber.assert_no_pending_responses()

Allow tagging of queues on creation Tagging AWS resources is really useful to keep track of which resources belong to which application, and to track things like costs on a per-application basis. Currently the SQS broker doesn't allow tags to be set on the queue, but this would be useful functionality to have. I'm happy to contribute the PR for this if you're 👍 with it.

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

BraeWebb__allocate-10

diff --git a/README.md b/README.md index 551f73a..1fddaa2 100644 --- a/README.md +++ b/README.md @@ -50,7 +50,27 @@ The typical command run, assuming `tutors.csv`, `sessions.csv` and `availability allocate tutors.csv sessions.csv availability.csv ``` -## Examples +The `--stub` flag generates template `tutors.csv` and `sessions.csv` files from an availability spreadsheet. +*Note* Ensure that the tutors.csv and sessions.csv files are empty first. +```bash +allocate --stub tutors.csv sessions.csv availability.csv +``` + +The `--doodle` flag tells the tool to parse the availability CSV file as if it is an export from doodle. +```bash +allocate --doodle tutors.csv sessions.csv doodle_export.csv +``` + +The `--update-availability` flag causes the output to be an availability CSV with the allocations removed from each tutors availability. +An example usage might look like the below, in this case we first get the allocations and place them in `allocations.csv` +We then update the availability and run availability again and place it in `extras.csv` +```bash +allocate tutors.csv sessions.csv availability.csv > allocations.csv +allocate --update-availability tutors.csv sessions.csv availability.csv > updated_availability.csv +allocate tutors.csv sessions.csv updated_availability > extras.csv +``` + +## Example 1 The following tables represent the 3 example CSV files that come with the project. ### tutors.csv @@ -96,6 +116,45 @@ Brae,T02,T04,P01,P03,P04,P05 Emily,T03,P02,P04 ``` + +## Example 2 +This is an example of how to generate an allocation from doodle along with an extras allocation for weeks with extra tutors. + +Starting with a CSV file exported from doodle like the one below, named `doodle.csv` +| "Poll ""Sample Doodle Availability""" | | | | | | | | | | +|---|---|---|---|---|---|---|---|---|---| +| https://doodle\.com/poll/v7scx5pzwgeu3m2y | | | | | | | | | | +| | | | | | | | | | | +| | February 2020 | | | | | | | | | +| | Tue 4 | | | Wed 5 | | | Thu 6 | Fri 7 | | +| | 11:00 AM – 1:00 PM | 1:00 PM – 3:00 PM | 3:00 PM – 5:00 PM | 8:00 AM – 9:00 AM | 9:00 AM – 10:00 AM | 12:00 PM – 2:00 PM | 9:00 AM – 11:00 AM | 11:00 AM – 12:00 PM | 12:00 PM – 1:00 PM | +| Brae | OK | | OK | | OK | OK | OK | | OK | +| Henry | OK | OK | OK | OK | | | OK | | | +| Emily | | OK | | | OK | OK | | OK | OK | +| Count | 2 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | + +The first thing we do is generate `tutors.csv` and `sessions.csv` files from the availability: +```bash +allocate --stub --doodle tutors.csv sessions.csv doodle.csv +``` + +Once this is completed we open the `tutors.csv` and `sessions.csv` files and fill out the required details. + +After filling out details in those spreadsheets, we perform the first allocations. +```bash +allocate --doodle tutors.csv sessions.csv doodle.csv +``` + +This will provide us the allocation for regular weeks. If we want allocations for extra weeks, we first need to update the tutors availabilities based on the first round of allocations. +```bash +allocate --update-availability --doodle tutors.csv sessions.csv doodle.csv > updated_availability.csv +``` + +We can then generate allocations for weeks with extra tutors (edit the sessions.csv file as required) +```bash +allocate tutors.csv sessions.csv updated_availability.csv +``` + ## Support You are most welcome to use this in your courses to allocate tutors. If you want to use this in your course but need assistance and would like to ask any questions please email <[email protected]>. diff --git a/allocate/allocation.py b/allocate/allocation.py index c6f72a4..e23edfc 100644 --- a/allocate/allocation.py +++ b/allocate/allocation.py @@ -2,10 +2,10 @@ import csv import sys import pprint import argparse -from typing import Dict, List +from typing import Dict, List, Iterable, Any from allocate.solver import validate_availability, Engine -from allocate.model import Tutor, Session +from allocate.model import Tutor, Session, TimeSlot from allocate.csvalidator import CSVModel from allocate.availability import Availability @@ -49,8 +49,33 @@ def stub_files(tutors: str, sessions: str, availability: str, writer.writerow(["", session.day, session.start, session.duration, "", ""]) -def run_allocation(tutors: str, sessions: str, availability: str, - doodle: bool = False, json: bool = False): +def new_availability(sessions: Iterable[Session], availability: Availability, + solution: Dict[str, Any]): + session_map = {session.id: TimeSlot(session.day.value, session.start_time, + session.duration) + for session in sessions} + + for tutor, allocated in solution.items(): + for session in allocated: + slot = session_map[session] + availability.set_available(tutor, slot, False) + + print(availability.to_csv()) + + +def run_allocation(tutors: Iterable[Tutor], sessions: Iterable[Session], + availability: Availability): + matrix = availability.to_matrix(tutors, sessions) + + for message in validate_availability(matrix): + print(message) + + engine = Engine(tutors, sessions, matrix) + return engine.solve() + + +def load_data(tutors: str, sessions: str, availability: str, + doodle: bool = False): tutor_model = CSVModel(Tutor) tutor_model.load(tutors, allow_defaults=True) @@ -61,23 +86,34 @@ def run_allocation(tutors: str, sessions: str, availability: str, availability_data = Availability.from_doodle(availability) else: availability_data = Availability.from_csv(availability) - availability_matrix = availability_data.to_matrix(tutor_model, session_model) - for message in validate_availability(availability_matrix): - print(message) + return tutor_model, session_model, availability_data + + +def output_results(solution, json: bool = False): + if json: + pprint.pprint(solution) + else: + solution_to_csv(solution, sys.stdout) + - engine = Engine(tutor_model, session_model, availability_matrix) - solution = engine.solve() +def run(tutors: str, sessions: str, availability: str, + doodle: bool = False, update_availability: bool = False, + json: bool = False): + data = load_data(tutors, sessions, availability, + doodle=doodle) + + solution = run_allocation(*data) if solution is None: print("No allocation was found because the allocation is infeasible.") print("Please ensure that a valid allocation is possible based on tutor availability.") print("If you think something is wrong, contact Brae at [email protected]") + + if update_availability: + new_availability(data[1], data[2], solution) else: - if json: - pprint.pprint(solution) - else: - solution_to_csv(solution, sys.stdout) + output_results(solution, json=json) def main(): @@ -91,6 +127,8 @@ def main(): parser.add_argument('availability', type=str, help='CSV file of tutors availabilities to sessions') + parser.add_argument('--update-availability', action='store_true', + help='Allocate tutors and print the availability spreadsheet with allocation applied') parser.add_argument('--doodle', action='store_true', help='Parse the input availability table as a doodle export') parser.add_argument('--stub', action='store_true', @@ -104,8 +142,9 @@ def main(): stub_files(args.tutors, args.sessions, args.availability, doodle=args.doodle) else: - run_allocation(args.tutors, args.sessions, args.availability, - doodle=args.doodle, json=args.json) + run(args.tutors, args.sessions, args.availability, + doodle=args.doodle, update_availability=args.update_availability, + json=args.json) if __name__ == '__main__': diff --git a/allocate/availability.py b/allocate/availability.py index 90eac30..ee261b5 100644 --- a/allocate/availability.py +++ b/allocate/availability.py @@ -51,7 +51,7 @@ class Availability: return instance - def get_available_slots(self, tutor: str) -> Iterable[TimeSlot]: + def get_available_slots(self, tutor: str) -> List[TimeSlot]: """Get the time slots a tutor is available""" return self._tutors_to_times[tutor] @@ -59,6 +59,16 @@ class Availability: """Determine if a tutor is available at the given timeslot""" return session in self.get_available_slots(tutor) + def set_available(self, tutor: str, session: TimeSlot, available: bool): + """Set a tutor as (un)available for a timeslot""" + slots = self.get_available_slots(tutor) + if available: + if session not in slots: + slots.append(session) + else: + if session in slots: + slots.remove(session) + @property def tutors(self) -> Iterable[str]: """All the tutors in this availability"""

BraeWebb/allocate

f45769c8814ba399349f5feaa1f0a4511f32b4d4

diff --git a/tests/allocation_test.py b/tests/allocation_test.py index 8b0eb87..807fc57 100644 --- a/tests/allocation_test.py +++ b/tests/allocation_test.py @@ -3,7 +3,7 @@ import os from unittest import TestCase from contextlib import redirect_stdout -from allocate.allocation import run_allocation, stub_files +from allocate.allocation import run, stub_files class AllocationTest(TestCase): @@ -29,6 +29,13 @@ Henry,,,,,,""" ,Fri,11,1,, ,Fri,12,1,,""" + EXPECTED_UPDATED_AVAILABILITY = """,Tue,Tue,Tue,Wed,Wed,Wed,Thu,Fri,Fri +,11,13,15,8,9,12,9,11,12 +,2,2,2,1,1,2,2,1,1 +Brae,,,,,1,,,, +Henry,,,,,,,,, +Emily,,,,,,,,,1""" + def test_sample_allocation(self): """Tests to ensure standard allocation works as expected @@ -36,8 +43,8 @@ Henry,,,,,,""" """ output = io.StringIO() with redirect_stdout(output): - run_allocation("sample_tutors.csv", "sample_sessions.csv", - "sample_availability.csv") + run("sample_tutors.csv", "sample_sessions.csv", + "sample_availability.csv") self.assertEqual(output.getvalue().split(), AllocationTest.EXPECTED_ALLOCATION.split(), @@ -51,8 +58,8 @@ Henry,,,,,,""" """ output = io.StringIO() with redirect_stdout(output): - run_allocation("sample_tutors.csv", "sample_sessions.csv", - "sample_doodle.csv", doodle=True) + run("sample_tutors.csv", "sample_sessions.csv", + "sample_doodle.csv", doodle=True) self.assertEqual(output.getvalue().split(), AllocationTest.EXPECTED_ALLOCATION.split(), @@ -95,6 +102,19 @@ Henry,,,,,,""" AllocationTest.EXPECTED_SESSIONS_STUB.split(), "Session stub file does not match") + def test_update_availability(self): + """Tests that the --update-availability flag works as expected. + + allocate --update-availability sample_tutors.csv sample_sessions.csv sample_availability.csv""" + output = io.StringIO() + with redirect_stdout(output): + run("sample_tutors.csv", "sample_sessions.csv", + "sample_availability.csv", update_availability=True) + + self.assertEqual(output.getvalue().split(), + AllocationTest.EXPECTED_UPDATED_AVAILABILITY.split(), + "Updated availability output does not match") + @classmethod def tearDownClass(cls): os.remove("stub_tutors.csv")

Compositional Allocations Allow for composition allocations by exporting an updated availability sheet based on an allocation run. This would allow for a regular allocation to be generated for normal weeks and then an additional 'overflow' allocation to be generated when more tutors are required. Example usage: ```bash allocate --update-availability tutors.csv sessions.csv allocation.csv > new_allocation.csv ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

BraeWebb__allocate-7

diff --git a/README.md b/README.md index 5f97814..7d8a697 100644 --- a/README.md +++ b/README.md @@ -92,8 +92,8 @@ allocate tutors.csv sessions.csv availability.csv ``` ``` Henry,T01,P01,P02,P03,P05 -Brae,T04,P01,P03,P04,P05 -Emily,T02,T03,P02,P04 +Brae,T02,T04,P01,P03,P04,P05 +Emily,T03,P02,P04 ``` ## Support diff --git a/allocate/allocation.py b/allocate/allocation.py index 4559ede..cf9989f 100644 --- a/allocate/allocation.py +++ b/allocate/allocation.py @@ -7,7 +7,7 @@ from typing import Dict, List from allocate.solver import validate_availability, Engine from allocate.model import Tutor, Session from allocate.csvalidator import CSVModel -from allocate.doodle import parse_doodle_hack +from allocate.doodle import parse_doodle_to_stub, parse_doodle_hack def solution_to_csv(solution: Dict[str, List[str]], output): @@ -20,6 +20,31 @@ def solution_to_csv(solution: Dict[str, List[str]], output): writer.writerow([name, *sessions]) +def stub_files(tutors: str, sessions: str, availability: str): + """Write out stub files for tutors and sessions based on the + given availability file.""" + tutors_names, sessions_details = parse_doodle_to_stub(availability) + + with open(tutors, 'x') as file: + writer = csv.writer(file) + + # write header + writer.writerow(Tutor.__annotations__.keys()) + columns = len(Tutor.__annotations__) + # write tutor names + for tutor in sorted(tutors_names): + writer.writerow([tutor] + ["" for _ in range(columns - 1)]) + + with open(sessions, 'x') as file: + writer = csv.writer(file) + + # write header + writer.writerow(Session.__annotations__.keys()) + # write session names + for session in sessions_details: + writer.writerow(["", session.day, session.start, session.duration, "", ""]) + + def run_allocation(tutors: str, sessions: str, availability: str, json: bool = False): tutor_model = CSVModel(Tutor) @@ -58,12 +83,17 @@ def main(): parser.add_argument('availability', type=str, help='CSV file of tutors availabilities to sessions') + parser.add_argument('--stub', action='store_true', + help='Write to the tutor and session files a stub table generated by the allocations file') parser.add_argument('--json', action="store_true", help='Output solution as a JSON object instead of default') args = parser.parse_args() - run_allocation(args.tutors, args.sessions, args.availability, json=args.json) + if args.stub: + stub_files(args.tutors, args.sessions, args.availability) + else: + run_allocation(args.tutors, args.sessions, args.availability, json=args.json) if __name__ == '__main__': diff --git a/allocate/doodle.py b/allocate/doodle.py index b6914d5..885ffeb 100644 --- a/allocate/doodle.py +++ b/allocate/doodle.py @@ -75,6 +75,8 @@ def _assign_columns_timeslots(days: Iterable[str], times: Iterable[str]): return columns +# TODO: Abstract the 3 functions below + def parse_doodle(filename: str) -> Dict[str, List[TimeSlot]]: """Parse a Doodle CSV to create a dictionary that maps a tutor name to a list of all their available time slots. @@ -105,6 +107,33 @@ def parse_doodle(filename: str) -> Dict[str, List[TimeSlot]]: return dict(availabilities) +def parse_doodle_to_stub(filename: str) -> Tuple[Iterable[str], Iterable[TimeSlot]]: + """Parse a Doodle CSV to create the lists of tutors and list of sessions + in the availability file. + """ + with open(filename, 'r') as file: + reader = iter(csv.reader(file)) + + # skip the first 4 rows since it is just doodle garbage + reader = islice(reader, 4, None) + + day_row = next(reader) + time_row = next(reader) + days = _assign_columns_timeslots(day_row, time_row) + + tutors = set() + sessions = days.values() + for row in reader: + name = row[0] + # last row is always a count of availabilities for a timeslot + if name == "Count": + break + + tutors.add(name) + + return tutors, sessions + + def parse_doodle_hack(filename: str, tutors: Iterable[Tutor], sessions: Iterable[Session]) \ -> Dict[Tuple[Tutor, Session], bool]: diff --git a/allocate/model.py b/allocate/model.py index 8c0b007..ceea073 100644 --- a/allocate/model.py +++ b/allocate/model.py @@ -28,6 +28,6 @@ class Session: id: str day: Day start_time: int + duration: int = 1 lower_tutor_count: int = 1 upper_tutor_count: int = 1 - duration: int = 1

BraeWebb/allocate

7194a80b506dead1a37482c8c0f36f94a1387ab0

diff --git a/tests/allocation_test.py b/tests/allocation_test.py index 56dfbec..ec34031 100644 --- a/tests/allocation_test.py +++ b/tests/allocation_test.py @@ -1,16 +1,39 @@ import io +import os from unittest import TestCase from contextlib import redirect_stdout -from allocate.allocation import run_allocation +from allocate.allocation import run_allocation, stub_files class AllocationTest(TestCase): + """Allocation tests works as a quick system sanity test""" + EXPECTED_ALLOCATION = """Henry,T01,P01,P02,P03,P05 Brae,T04,P01,P03,P04,P05 Emily,T02,T03,P02,P04""" + EXPECTED_TUTORS_STUB = """name,is_junior,pref_contig,lower_hr_limit,upper_hr_limit,daily_max,session_preference +Brae,,,,,, +Emily,,,,,, +Henry,,,,,,""" + + EXPECTED_SESSIONS_STUB = """id,day,start_time,duration,lower_tutor_count,upper_tutor_count +,Tue,11,2,, +,Tue,13,2,, +,Tue,15,2,, +,Wed,8,1,, +,Wed,9,1,, +,Wed,12,2,, +,Thu,9,2,, +,Fri,11,1,, +,Fri,12,1,,""" + def test_sample_allocation(self): + """Tests to ensure standard allocation works as expected + + allocate sample_tutors.csv sample_sessions.csv sample_doodle.csv + """ output = io.StringIO() with redirect_stdout(output): run_allocation("sample_tutors.csv", "sample_sessions.csv", @@ -19,3 +42,26 @@ Emily,T02,T03,P02,P04""" self.assertEqual(output.getvalue().split(), AllocationTest.EXPECTED_ALLOCATION.split(), "Allocation output does not match") + + def test_stub_generation(self): + """Tests to ensure that stubs are generated from availability + appropriately + + allocate --stub stub_tutors.csv stub_sessions.csv sample_doodle.csv + """ + stub_files("stub_tutors.csv", "stub_sessions.csv", "sample_doodle.csv") + + with open("stub_tutors.csv") as file: + self.assertEqual([line.strip() for line in file.readlines()], + AllocationTest.EXPECTED_TUTORS_STUB.split(), + "Tutor stub file does not match") + + with open("stub_sessions.csv") as file: + self.assertEqual([line.strip() for line in file.readlines()], + AllocationTest.EXPECTED_SESSIONS_STUB.split(), + "Session stub file does not match") + + @classmethod + def tearDownClass(cls): + os.remove("stub_tutors.csv") + os.remove("stub_sessions.csv")

Stub Tutors and Sessions Ability to use an availability file to create empty files with the list of sessions and tutors filled out. ```bash allocate --stub tutors.csv sessions.csv availability.csv ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

BraeWebb__allocate-8

diff --git a/README.md b/README.md index 7d8a697..551f73a 100644 --- a/README.md +++ b/README.md @@ -74,17 +74,17 @@ The following tables represent the 3 example CSV files that come with the projec | P05 | 2 | 2 | Thu | 9 | 2 | ### availabilities.csv -| "Poll ""Sample Doodle Availability""" | | | | | | | | | | -|---|---|---|---|---|---|---|---|---|---| -| https://doodle\.com/poll/v7scx5pzwgeu3m2y | | | | | | | | | | -| | | | | | | | | | | -| | February 2020 | | | | | | | | | -| | Tue 4 | | | Wed 5 | | | Thu 6 | Fri 7 | | -| | 11:00 AM – 1:00 PM | 1:00 PM – 3:00 PM | 3:00 PM – 5:00 PM | 8:00 AM – 9:00 AM | 9:00 AM – 10:00 AM | 12:00 PM – 2:00 PM | 9:00 AM – 11:00 AM | 11:00 AM – 12:00 PM | 12:00 PM – 1:00 PM | -| Brae | OK | | OK | | OK | OK | OK | | OK | -| Henry | OK | OK | OK | OK | | | OK | | | -| Emily | | OK | | | OK | OK | | OK | OK | -| Count | 2 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | +The first row is the day of the week of a session, second row represents the +time of day in 24 hours and the third row is the duration of the session. +Anything but a 1 in the availability cell of each tutor is treated as unavailable. + +| | Tue | Tue | Tue | Wed | Wed | Wed | Thu | Fri | Fri | +|-------|-----|-----|-----|-----|-----|-----|-----|-----|-----| +| | 11 | 13 | 15 | 8 | 9 | 12 | 9 | 11 | 12 | +| | 2 | 2 | 2 | 1 | 1 | 2 | 2 | 1 | 1 | +| Brae | 1 | | 1 | | 1 | 1 | 1 | | 1 | +| Henry | 1 | 1 | 1 | 1 | | | 1 | | | +| Emily | | 1 | | | 1 | 1 | | 1 | 1 | With the above files available in the current working directory, execution of the following command will produce the allocation below ```bash diff --git a/allocate/allocation.py b/allocate/allocation.py index cf9989f..c6f72a4 100644 --- a/allocate/allocation.py +++ b/allocate/allocation.py @@ -7,7 +7,7 @@ from typing import Dict, List from allocate.solver import validate_availability, Engine from allocate.model import Tutor, Session from allocate.csvalidator import CSVModel -from allocate.doodle import parse_doodle_to_stub, parse_doodle_hack +from allocate.availability import Availability def solution_to_csv(solution: Dict[str, List[str]], output): @@ -20,10 +20,14 @@ def solution_to_csv(solution: Dict[str, List[str]], output): writer.writerow([name, *sessions]) -def stub_files(tutors: str, sessions: str, availability: str): +def stub_files(tutors: str, sessions: str, availability: str, + doodle: bool = False): """Write out stub files for tutors and sessions based on the given availability file.""" - tutors_names, sessions_details = parse_doodle_to_stub(availability) + if doodle: + availability_data = Availability.from_doodle(availability) + else: + availability_data = Availability.from_csv(availability) with open(tutors, 'x') as file: writer = csv.writer(file) @@ -32,7 +36,7 @@ def stub_files(tutors: str, sessions: str, availability: str): writer.writerow(Tutor.__annotations__.keys()) columns = len(Tutor.__annotations__) # write tutor names - for tutor in sorted(tutors_names): + for tutor in sorted(availability_data.tutors): writer.writerow([tutor] + ["" for _ in range(columns - 1)]) with open(sessions, 'x') as file: @@ -41,24 +45,28 @@ def stub_files(tutors: str, sessions: str, availability: str): # write header writer.writerow(Session.__annotations__.keys()) # write session names - for session in sessions_details: + for session in availability_data.sessions: writer.writerow(["", session.day, session.start, session.duration, "", ""]) def run_allocation(tutors: str, sessions: str, availability: str, - json: bool = False): + doodle: bool = False, json: bool = False): tutor_model = CSVModel(Tutor) tutor_model.load(tutors, allow_defaults=True) session_model = CSVModel(Session) session_model.load(sessions, allow_defaults=True) - availability_data = parse_doodle_hack(availability, tutor_model, session_model) + if doodle: + availability_data = Availability.from_doodle(availability) + else: + availability_data = Availability.from_csv(availability) + availability_matrix = availability_data.to_matrix(tutor_model, session_model) - for message in validate_availability(availability_data): + for message in validate_availability(availability_matrix): print(message) - engine = Engine(tutor_model, session_model, availability_data) + engine = Engine(tutor_model, session_model, availability_matrix) solution = engine.solve() if solution is None: @@ -83,6 +91,8 @@ def main(): parser.add_argument('availability', type=str, help='CSV file of tutors availabilities to sessions') + parser.add_argument('--doodle', action='store_true', + help='Parse the input availability table as a doodle export') parser.add_argument('--stub', action='store_true', help='Write to the tutor and session files a stub table generated by the allocations file') parser.add_argument('--json', action="store_true", @@ -91,9 +101,11 @@ def main(): args = parser.parse_args() if args.stub: - stub_files(args.tutors, args.sessions, args.availability) + stub_files(args.tutors, args.sessions, args.availability, + doodle=args.doodle) else: - run_allocation(args.tutors, args.sessions, args.availability, json=args.json) + run_allocation(args.tutors, args.sessions, args.availability, + doodle=args.doodle, json=args.json) if __name__ == '__main__': diff --git a/allocate/availability.py b/allocate/availability.py new file mode 100644 index 0000000..90eac30 --- /dev/null +++ b/allocate/availability.py @@ -0,0 +1,135 @@ +"""Handles saving and loading of an availability file""" +import io +import csv +from collections import defaultdict +from typing import Dict, Iterable, Tuple, List, Mapping + +from allocate.model import Tutor, Session, TimeSlot +from allocate.doodle import parse_doodle_to_stub, parse_doodle + + +class Availability: + """Availability represents the times a tutor indicates they are available.""" + + def __init__(self): + self._tutors_to_times: Mapping[str, List[TimeSlot]] = {} + self._all_slots: Iterable[TimeSlot] = [] + + @classmethod + def from_doodle(cls, doodle_file: str): + """Load an availability from a doodle CSV file""" + instance = cls() + instance._tutors_to_times = parse_doodle(doodle_file) + instance._all_slots = parse_doodle_to_stub(doodle_file)[1] + return instance + + @classmethod + def from_csv(cls, filename: str): + """Load an availability from a regular availability CSV file""" + instance = cls() + + with open(filename, 'r') as file: + reader = iter(csv.reader(file)) + + day_row = next(reader)[1:] + time_row = map(int, next(reader)[1:]) + duration_row = map(int, next(reader)[1:]) + + days = [TimeSlot(*slot) for slot in zip(day_row, time_row, duration_row)] + + availabilities: Mapping[str, List[TimeSlot]] = defaultdict(list) + for row in reader: + name = row[0] + + # add every availability timeslot + for column, status in enumerate(row): + if status == "1": + availabilities[name].append(days[column - 1]) + + instance._tutors_to_times = availabilities + instance._all_slots = days + + return instance + + def get_available_slots(self, tutor: str) -> Iterable[TimeSlot]: + """Get the time slots a tutor is available""" + return self._tutors_to_times[tutor] + + def is_available(self, tutor: str, session: TimeSlot) -> bool: + """Determine if a tutor is available at the given timeslot""" + return session in self.get_available_slots(tutor) + + @property + def tutors(self) -> Iterable[str]: + """All the tutors in this availability""" + return self._tutors_to_times.keys() + + @property + def sessions(self) -> Iterable[TimeSlot]: + """All the sessions in this availability""" + return self._all_slots + + def write(self, filename: str): + """Write the availability information to a CSV file""" + with open(filename, 'w') as file: + file.write(self.to_csv()) + + def to_matrix(self, tutors: Iterable[Tutor], sessions: Iterable[Session])\ + -> Dict[Tuple[Tutor, Session], bool]: + matrix = {} + session_map = {TimeSlot(session.day.value, session.start_time, + session.duration): session for session in sessions} + + for slot, session in session_map.items(): + for tutor in tutors: + matrix[(tutor, session)] = self.is_available(tutor.name, slot) + + return matrix + + def to_csv(self) -> str: + """Convert the availability information to a CSV file format""" + # calculate the index of each time slow + columns = {} + current_column = 1 + for session in self._all_slots: + columns[session] = current_column + current_column += 1 + + output = io.StringIO() + writer = csv.writer(output) + + # write the columns for each time slot + data = [(session.day, session.start, session.duration) + for session in self._all_slots] + for slot_row in zip(*data): + writer.writerow(("",) + slot_row) + + # write in availabilities + blank_row = [""] + ["" for _ in self._all_slots] + for name, times in self._tutors_to_times.items(): + row = blank_row[:] + row[0] = name + + for available_slot in times: + slot_index = columns[available_slot] + row[slot_index] = "1" + + writer.writerow(row) + + return output.getvalue() + + +def main(): + availability = Availability.from_doodle("sample_doodle.csv") + availability.write("tmp.csv") + + written = Availability.from_csv("tmp.csv") + + print(written.to_csv() == availability.to_csv()) + + import os + os.remove("tmp.csv") + + +if __name__ == "__main__": + main() diff --git a/allocate/doodle.py b/allocate/doodle.py index 885ffeb..850fe63 100644 --- a/allocate/doodle.py +++ b/allocate/doodle.py @@ -4,20 +4,11 @@ that other programs are able to parse with relative ease. """ import csv -from typing import Dict, Iterable, Tuple, List -from dataclasses import dataclass +from typing import Mapping, Iterable, Tuple, List from collections import defaultdict from itertools import islice -from allocate.model import Tutor, Session - - -@dataclass(eq=True, frozen=True) -class TimeSlot: - """Data class used to represent a class that occupied a time slot""" - day: str - start: int - duration: int +from allocate.model import TimeSlot def _hour_from_time(time: str) -> int: @@ -75,9 +66,9 @@ def _assign_columns_timeslots(days: Iterable[str], times: Iterable[str]): return columns -# TODO: Abstract the 3 functions below +# TODO: Abstract the 2 functions below -def parse_doodle(filename: str) -> Dict[str, List[TimeSlot]]: +def parse_doodle(filename: str) -> Mapping[str, List[TimeSlot]]: """Parse a Doodle CSV to create a dictionary that maps a tutor name to a list of all their available time slots. """ @@ -91,7 +82,7 @@ def parse_doodle(filename: str) -> Dict[str, List[TimeSlot]]: time_row = next(reader) days = _assign_columns_timeslots(day_row, time_row) - availabilities: Dict[str, List[TimeSlot]] = defaultdict(list) + availabilities: Mapping[str, List[TimeSlot]] = defaultdict(list) for row in reader: name = row[0] @@ -134,44 +125,5 @@ def parse_doodle_to_stub(filename: str) -> Tuple[Iterable[str], Iterable[TimeSlo return tutors, sessions -def parse_doodle_hack(filename: str, tutors: Iterable[Tutor], - sessions: Iterable[Session]) \ - -> Dict[Tuple[Tutor, Session], bool]: - """Parse a Doodle CSV to create a dictionary that maps a tutor name - to a list of all their available time slots. - - Hacked version to support the way the allocation engine requires. - """ - tutor_map = {tutor.name: tutor for tutor in tutors} - session_map = {TimeSlot(session.day.value, session.start_time, - session.duration): session for session in sessions} - - with open(filename, 'r') as file: - reader = iter(csv.reader(file)) - - # skip the first 4 rows since it is just doodle garbage - reader = islice(reader, 4, None) - - day_row = next(reader) - time_row = next(reader) - days = _assign_columns_timeslots(day_row, time_row) - - availabilities: Dict[Tuple[Tutor, Session], bool] = {} - for row in reader: - name = row[0] - - # last row is always a count of availabilities for a timeslot - if name == "Count": - break - - # add every availability timeslot - for column, status in islice(enumerate(row), 1, None): - tutor = tutor_map[name] - session = session_map[days[column]] - availabilities[(tutor, session)] = status == "OK" - - return availabilities - - if __name__ == "__main__": print(parse_doodle("sample_doodle.csv")) diff --git a/allocate/model.py b/allocate/model.py index ceea073..c928e6c 100644 --- a/allocate/model.py +++ b/allocate/model.py @@ -2,6 +2,17 @@ from enum import Enum from dataclasses import dataclass +@dataclass(eq=True, frozen=True) +class TimeSlot: + """Data class used to represent a class that occupied a time slot. + + This is practically used as a Session when the id of the session is unknown. + """ + day: str + start: int + duration: int + + @dataclass(eq=True, frozen=True) class Tutor: name: str diff --git a/sample_availability.csv b/sample_availability.csv new file mode 100644 index 0000000..c52ac09 --- /dev/null +++ b/sample_availability.csv @@ -0,0 +1,6 @@ +,Tue,Tue,Tue,Wed,Wed,Wed,Thu,Fri,Fri +,11,13,15,8,9,12,9,11,12 +,2,2,2,1,1,2,2,1,1 +Brae,1,,1,,1,1,1,,1 +Henry,1,1,1,1,,,1,, +Emily,,1,,,1,1,,1,1

BraeWebb/allocate

b1af498fa349c77f77ac88ac6ec1b9c42aae3557

diff --git a/tests/allocation_test.py b/tests/allocation_test.py index ec34031..8b0eb87 100644 --- a/tests/allocation_test.py +++ b/tests/allocation_test.py @@ -32,12 +32,27 @@ Henry,,,,,,""" def test_sample_allocation(self): """Tests to ensure standard allocation works as expected - allocate sample_tutors.csv sample_sessions.csv sample_doodle.csv + allocate sample_tutors.csv sample_sessions.csv sample_availability.csv """ output = io.StringIO() with redirect_stdout(output): run_allocation("sample_tutors.csv", "sample_sessions.csv", - "sample_doodle.csv") + "sample_availability.csv") + + self.assertEqual(output.getvalue().split(), + AllocationTest.EXPECTED_ALLOCATION.split(), + "Allocation output does not match") + + def test_sample_allocation_doodle(self): + """Tests to ensure standard allocation works as expected with + a doodle file + + allocate --doodle sample_tutors.csv sample_sessions.csv sample_doodle.csv + """ + output = io.StringIO() + with redirect_stdout(output): + run_allocation("sample_tutors.csv", "sample_sessions.csv", + "sample_doodle.csv", doodle=True) self.assertEqual(output.getvalue().split(), AllocationTest.EXPECTED_ALLOCATION.split(), @@ -47,9 +62,9 @@ Henry,,,,,,""" """Tests to ensure that stubs are generated from availability appropriately - allocate --stub stub_tutors.csv stub_sessions.csv sample_doodle.csv + allocate --stub stub_tutors.csv stub_sessions.csv sample_availability.csv """ - stub_files("stub_tutors.csv", "stub_sessions.csv", "sample_doodle.csv") + stub_files("stub_tutors.csv", "stub_sessions.csv", "sample_availability.csv") with open("stub_tutors.csv") as file: self.assertEqual([line.strip() for line in file.readlines()], @@ -61,7 +76,28 @@ Henry,,,,,,""" AllocationTest.EXPECTED_SESSIONS_STUB.split(), "Session stub file does not match") + def test_stub_generation_doodle(self): + """Tests to ensure that stubs are generated from availability + appropriately from doodle files + + allocate --stub --doodle stub_tutors.csv stub_sessions.csv sample_doodle.csv + """ + stub_files("stub_tutors_doodle.csv", "stub_sessions_doodle.csv", + "sample_doodle.csv", doodle=True) + + with open("stub_tutors_doodle.csv") as file: + self.assertEqual([line.strip() for line in file.readlines()], + AllocationTest.EXPECTED_TUTORS_STUB.split(), + "Tutor stub file does not match") + + with open("stub_sessions_doodle.csv") as file: + self.assertEqual([line.strip() for line in file.readlines()], + AllocationTest.EXPECTED_SESSIONS_STUB.split(), + "Session stub file does not match") + @classmethod def tearDownClass(cls): os.remove("stub_tutors.csv") + os.remove("stub_tutors_doodle.csv") os.remove("stub_sessions.csv") + os.remove("stub_sessions_doodle.csv")

Availabilities Format The only accepted format for availabilities at the moment is the output of a doodle poll. This format is kind of gross and it would be better to have a standard availability format with the ability to accept the doodle format being optional. With standard availability format: ```bash allocate tutors.csv sessions.csv availability.csv ``` With a doodle availability format (functions the same as the current system): ```bash allocate --doodle tutors.csv sessions.csv availability.csv ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

BurnzZ__scrapy-loader-upkeep-3

diff --git a/README.rst b/README.rst index 6fb0e87..3112d48 100644 --- a/README.rst +++ b/README.rst @@ -58,8 +58,8 @@ This only works for the following ``ItemLoader`` methods: - ``add_xpath()`` - ``replace_xpath()`` -Spider Example -~~~~~~~~~~~~~~ +Basic Spider Example +~~~~~~~~~~~~~~~~~~~~ This is taken from the `examples/ <https://github.com/BurnzZ/scrapy-loader-upkeep/tree/master/examples>`_ directory. @@ -83,6 +83,77 @@ This should output in the stats: In this example, we could see that the **1st css** rule for the ``quote`` field has had instances of not being matched at all during the scrape. +New Feature +~~~~~~~~~~~ + +As with the example above, we're limited only to the positional context of when +the ``add_css()``, ``add_xpath()``, etc were called during the execution. + +There will be cases where developers will be maintaining a large spider with a +lot of different parsers to handle varying layouts in the site. It would make +sense to have a better context to what a parser does or is for. + +A new optional ``name`` parameter is supported to provide more context around a +given parser. This supports the two (2) main types of creating fallback parsers: + +1. **multiple calls** + +.. code-block:: python + + loader.add_css('NAME', 'h1::text', name='Name from h1') + loader.add_css('NAME', 'meta[value="title"]::attr(content)', name="Name from meta tag") + +would result in something like: + +.. code-block:: python + + { ... + 'parser/QuotesItemLoader/NAME/css/1/Name from h1': 8, + 'parser/QuotesItemLoader/NAME/css/1/Name from h1/missing': 2, + 'parser/QuotesItemLoader/NAME/css/2/Name from meta tag': 7, + 'parser/QuotesItemLoader/NAME/css/2/Name from meta tag/missing': 3, + ... + } + +2. **grouped parsers in a single call** + +.. code-block:: python + + loader.add_css( + 'NAME', + [ + 'h1::text', + 'meta[value="title"]::attr(content)', + ], + name='NAMEs at the main content') + loader.add_css( + 'NAME', + [ + 'footer .name::text', + 'div.page-end span.name::text', + ], + name='NAMEs at the bottom of the page') + +would result in something like: + +.. code-block:: python + + { ... + 'parser/QuotesItemLoader/NAME/css/1/NAMEs at the main content': 8, + 'parser/QuotesItemLoader/NAME/css/1/NAMEs at the main content/missing': 2, + 'parser/QuotesItemLoader/NAME/css/2/NAMEs at the main content': 7, + 'parser/QuotesItemLoader/NAME/css/2/NAMEs at the main content/missing': 3, + 'parser/QuotesItemLoader/NAME/css/3/NAMEs at the bottom of the page': 8, + 'parser/QuotesItemLoader/NAME/css/3/NAMEs at the bottom of the page/missing': 2, + 'parser/QuotesItemLoader/NAME/css/4/NAMEs at the bottom of the page': 7, + 'parser/QuotesItemLoader/NAME/css/4/NAMEs at the bottom of the page/missing': 3, + ... + } + +The latter is useful in grouping fallback parsers together if they are quite +related in terms of layout/arrangement in the page. + + Requirements ~~~~~~~~~~~~ Python 3.6+ diff --git a/examples/README.rst b/examples/README.rst index fc57fdb..037f806 100644 --- a/examples/README.rst +++ b/examples/README.rst @@ -1,5 +1,12 @@ Contains examples of using the ``scrapy-loader-upkeep`` package inside Scrapy. +A symlink has been included in the example project dir in order to read the +source code. Run the following in order to test these out: + +.. code-block:: bash + + $ python3 -m scrapy crawl <spider_name> + Simple Example ~~~~~~~~~~~~~~ @@ -41,3 +48,24 @@ This should output in the stats: 'parser/QuotesItemLoader/quote/css/2': 10 ... } + + +Example using 'name' feature +~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: bash + + $ scrapy crawl quotestoscrape_use_name + +This should output in the stats: + +.. code-block:: python + + 2019-06-16 14:32:32 [scrapy.statscollectors] INFO: Dumping Scrapy stats: + { ... + 'parser/QuotesItemLoader/author/css/1/basic author class': 10, + 'parser/QuotesItemLoader/quote/css/1/Quotes inside the box/missing': 10, + 'parser/QuotesItemLoader/quote/css/2/Quotes inside the box': 10, + 'parser/QuotesItemLoader/tags/css/1/underneath the author text': 10, + ... + } diff --git a/scrapy_loader_upkeep/loader.py b/scrapy_loader_upkeep/loader.py index cb47f96..805b3ce 100644 --- a/scrapy_loader_upkeep/loader.py +++ b/scrapy_loader_upkeep/loader.py @@ -79,6 +79,9 @@ class ItemLoader(ItemLoaderOG): selector_type = selector.__name__ # either 'css' or 'xpath' + # The optional arg in methods like `add_css()` for context in stats + name = kw.get('name') + # For every call of `add_css()` and `add_xpath()` this is incremented. # We'll use it as the base index of the position of the logged stats. index = self.field_tracker[f'{field_name}_{selector_type}'] @@ -87,10 +90,12 @@ class ItemLoader(ItemLoaderOG): for position, rule in enumerate(arg_to_iter(selector_rules), index): parsed_data = selector(rule).getall() values.append(parsed_data) - self.write_to_stats(field_name, parsed_data, position, selector_type) + self.write_to_stats(field_name, parsed_data, position, + selector_type, name=name) return flatten(values) - def write_to_stats(self, field_name, parsed_data, position, selector_type): + def write_to_stats(self, field_name, parsed_data, position, selector_type, + name=None): """Responsible for logging the parser rules usage. NOTES: It's hard to easily denote which parser rule hasn't produced any @@ -111,6 +116,9 @@ class ItemLoader(ItemLoaderOG): f"parser/{self.loader_name}/{field_name}/{selector_type}/{position}" ) + if name: + parser_label += f'/{name}' + if parsed_data in (None, []): parser_label += "/missing"

BurnzZ/scrapy-loader-upkeep

0b36309d1c9ea814e097e06e9d7220cfef6e6f9e

diff --git a/examples/quotestoscrape/items.py b/examples/quotestoscrape/items.py index 360d6f0..2eac930 100644 --- a/examples/quotestoscrape/items.py +++ b/examples/quotestoscrape/items.py @@ -3,3 +3,4 @@ import scrapy class QuotesToScrapeItem(scrapy.Item): quote = scrapy.Field() author = scrapy.Field() + tags = scrapy.Field() diff --git a/examples/quotestoscrape/spiders/quotestoscrape.py b/examples/quotestoscrape/spiders/quotestoscrape.py index 04dd31e..da8ff0e 100644 --- a/examples/quotestoscrape/spiders/quotestoscrape.py +++ b/examples/quotestoscrape/spiders/quotestoscrape.py @@ -5,7 +5,7 @@ from ..loader import QuotesItemLoader class BaseExampleSpider(scrapy.Spider): - start_urls = ['http://quotes.toscrape.com/'] + start_urls = ["http://quotes.toscrape.com/"] class QuotesToScrapeSimpleSpider(BaseExampleSpider): @@ -22,18 +22,17 @@ class QuotesToScrapeSimpleSpider(BaseExampleSpider): been successfully matched. """ - name = 'quotestoscrape_simple' - + name = "quotestoscrape_simple" def parse(self, response): """Notice that in order for this enhanced ItemLoader package to work, we'll need to inject the stats API into it. """ - for quote_div in response.css('div.quote'): + for quote_div in response.css("div.quote"): loader = QuotesItemLoader(selector=quote_div, stats=self.crawler.stats) - loader.add_css('quote', '.quote > span[itemprop="text"]::text') - loader.add_css('author', '.author::text') + loader.add_css("quote", '.quote > span[itemprop="text"]::text') + loader.add_css("author", ".author::text") yield loader.load_item() @@ -50,20 +49,58 @@ class QuotesToScrapeHasMissingSpider(BaseExampleSpider): } """ - name = 'quotestoscrape_has_missing' + name = "quotestoscrape_has_missing" + + def parse(self, response): + """Notice that in order for this enhanced ItemLoader package to work, + we'll need to inject the stats API into it. + """ + + for quote_div in response.css("div.quote"): + loader = QuotesItemLoader(selector=quote_div, stats=self.crawler.stats) + loader.add_css( + "quote", + [ + # This first parser rule doesn't exist at all. + ".this-quote-does-not-exist span::text", + '.quote > span[itemprop="text"]::text', + ], + ) + loader.add_css("author", ".author::text") + yield loader.load_item() + + +class QuotesToScrapeUseName(BaseExampleSpider): + """Demonstrates the new feature of naming the parsers using the 'name' param. + + 2019-06-16 14:32:32 [scrapy.statscollectors] INFO: Dumping Scrapy stats: + { ... + 'parser/QuotesItemLoader/author/css/1/basic author class': 10, + 'parser/QuotesItemLoader/quote/css/1/Quotes inside the box/missing': 10, + 'parser/QuotesItemLoader/quote/css/2/Quotes inside the box': 10, + 'parser/QuotesItemLoader/tags/css/1/underneath the author text': 10, + ... + } + """ + name = "quotestoscrape_use_name" def parse(self, response): """Notice that in order for this enhanced ItemLoader package to work, we'll need to inject the stats API into it. """ - for quote_div in response.css('div.quote'): + for quote_div in response.css("div.quote"): loader = QuotesItemLoader(selector=quote_div, stats=self.crawler.stats) - loader.add_css('quote', [ - # This first parser rule doesn't exist at all. - '.this-quote-does-not-exist span::text', - '.quote > span[itemprop="text"]::text' - ]) - loader.add_css('author', '.author::text') + loader.add_css( + "quote", + [ + # This first parser rule doesn't exist at all. + ".this-quote-does-not-exist span::text", + '.quote > span[itemprop="text"]::text', + ], + name="Quotes inside the box", + ) + loader.add_css("author", ".author::text", name="basic author class") + loader.add_css("tags", ".tag::text", name="underneath the author text") yield loader.load_item() diff --git a/tests/test_loader.py b/tests/test_loader.py index 2a3672b..92a7f58 100644 --- a/tests/test_loader.py +++ b/tests/test_loader.py @@ -50,9 +50,9 @@ def test_get_selector_values(): loader.write_to_stats.assert_has_calls( [ - mock.call(field_name, parsed_data, 1, "css"), - mock.call(field_name, parsed_data, 2, "css"), - mock.call(field_name, parsed_data, 3, "css"), + mock.call(field_name, parsed_data, 1, "css", name=None), + mock.call(field_name, parsed_data, 2, "css", name=None), + mock.call(field_name, parsed_data, 3, "css", name=None), ] ) @@ -205,16 +205,36 @@ def test_multiple_1(loader): mock.call("parser/TestItemLoader/title/css/3"), ] ) + assert loader.stats.inc_value.call_count == 3 -def test_multiple_2(loader): - loader.add_css('title', 'h2::text') - loader.add_xpath('title', '//article/h2/text()') +def test_multiple_1_with_name(loader): + loader.add_css('title', 'h2::text', name='title from h2') + loader.add_css('title', [ + 'article h2::text', + 'article .product-title::text', + ], name='title from article') + loader.stats.inc_value.assert_has_calls( + [ + mock.call("parser/TestItemLoader/title/css/1/title from h2"), + mock.call("parser/TestItemLoader/title/css/2/title from article"), + mock.call("parser/TestItemLoader/title/css/3/title from article"), + ] + ) + assert loader.stats.inc_value.call_count == 3 + + +def test_multiple_2_with_name(loader): + loader.add_css('title', 'h2::text', name='title from h2') + loader.add_xpath('title', '//article/h2/text()', name='title from article') loader.add_css('title', 'article .product-title::text') + loader.add_xpath('title', '//aside/h1/text()', name='title from aside') loader.stats.inc_value.assert_has_calls( [ - mock.call("parser/TestItemLoader/title/css/1"), - mock.call("parser/TestItemLoader/title/xpath/1"), + mock.call("parser/TestItemLoader/title/css/1/title from h2"), + mock.call("parser/TestItemLoader/title/xpath/1/title from article"), mock.call("parser/TestItemLoader/title/css/2"), + mock.call("parser/TestItemLoader/title/xpath/2/title from aside/missing"), ] ) + assert loader.stats.inc_value.call_count == 4

Allow paths to be named When having several amounts of xpaths for each field, is really difficult to determine which one was added firsts, specially when there are different workflows on the code. To make easier the task to identify the paths on the stats, it would be great if we could name them. For example: ```python loader.add_css('NAME', 'h1::text', name='Name from h1') loader.add_css('NAME', 'meta[value="title"]::attr(content)', name="Name from meta tag") ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

ByteInternet__pip-install-privates-20

diff --git a/pip_install_privates/install.py b/pip_install_privates/install.py index db7eee3..acc62b1 100644 --- a/pip_install_privates/install.py +++ b/pip_install_privates/install.py @@ -100,7 +100,8 @@ are also stripped of the -e flag. If no token is given, private URLs will be kept, including the -e flag (otherwise they can't be installed at all). """) - parser.add_argument('--token', '-t', help='Your Personal Access Token for private GitHub repositories') + parser.add_argument('--token', '-t', help='Your Personal Access Token for private GitHub repositories', + default=os.environ.get('GITHUB_TOKEN')) parser.add_argument('req_file', help='path to the requirements file to install') args = parser.parse_args() diff --git a/setup.py b/setup.py index 950654e..2df3987 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ def readfile(filename): setup( name='pip_install_privates', - version='0.5.1', + version='0.5.2', description='Install pip packages from private repositories without an ssh agent', long_description=readfile('README.rst'), long_description_content_type='text/x-rst',

ByteInternet/pip-install-privates

f92dabd7a3d4b2cca677ded7f2073162dd5349e2

diff --git a/tests/unit/test_commandline.py b/tests/unit/test_commandline.py index b694c25..eba89c5 100644 --- a/tests/unit/test_commandline.py +++ b/tests/unit/test_commandline.py @@ -40,6 +40,21 @@ class TestCommandLine(TestCase): self.mock_collect.assert_called_once_with('requirements.txt', transform_with_token='my-token') + def test_uses_github_token_environment_variable_if_no_token_supplied(self): + with patch.dict('pip_install_privates.install.os.environ', {'GITHUB_TOKEN': 'my-token'}): + with patch.object(sys, 'argv', ['pip-install', 'requirements.txt']): + install() + + self.mock_collect.assert_called_once_with('requirements.txt', + transform_with_token='my-token') + + def test_uses_none_if_no_token_supplied_and_no_github_token_defined_as_environment_variable(self): + with patch.object(sys, 'argv', ['pip-install', 'requirements.txt']): + install() + + self.mock_collect.assert_called_once_with('requirements.txt', + transform_with_token=None) + def test_commandline_requires_requirements_file(self): with patch('sys.stderr', new_callable=StringIO): with patch.object(sys, 'argv', ['pip-install']):

Environment variable GITHUB_TOKEN is ignored If `--token` isn't provided on invocation while environment variable `GITHUB_TOKEN` is defined, the environment variable's value should be used as the access token.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

CMakePP__CMinx-57

diff --git a/.gitignore b/.gitignore index 79c016b..43ea2ec 100644 --- a/.gitignore +++ b/.gitignore @@ -27,6 +27,7 @@ examples/sphinx/build # Python virtual environment venv/ virt_env/ +Pipfile* # Python3 __pycache__ __pycache__/ diff --git a/cminx/parser/aggregator.py b/cminx/parser/aggregator.py index e9334a1..4a14a70 100755 --- a/cminx/parser/aggregator.py +++ b/cminx/parser/aggregator.py @@ -198,6 +198,8 @@ class DocumentationAggregator(CMakeListener): cleaned_lines.append(cleaned_line) cleaned_lines[-1] = cleaned_lines[-1].rstrip("#]") cleaned_doc = "\n".join(cleaned_lines) + if cleaned_doc.startswith("\n"): + cleaned_doc = cleaned_doc[1:] command = ctx.command_invocation().Identifier().getText().lower() if f"process_{command}" in dir(self): getattr(self, f"process_{command}")(ctx, cleaned_doc) diff --git a/cminx/rstwriter.py b/cminx/rstwriter.py index e15298e..d023bbc 100755 --- a/cminx/rstwriter.py +++ b/cminx/rstwriter.py @@ -214,7 +214,7 @@ class Paragraph(object): def build_text_string(self): """ Populates Paragraph.text_string with the - RST string cooresponding to this paragraph + RST string corresponding to this paragraph """ self.text_string = "\n".join([self.prefix + text for text in self.text.split("\n")]) @@ -237,7 +237,7 @@ class Field(object): def build_field_string(self): """ Populates Field.field_string with the - RST string cooresponding to this field + RST string corresponding to this field """ self.field_string = f"\n{self.prefix}:{self.field_name}: {self.field_text}" @@ -539,6 +539,9 @@ class Directive(RSTWriter): for option in self.options: document_string += f"{option}\n" + if len(self.document) > 1: + document_string += "\n" + for element in self.document[1:]: document_string += f"{element}\n" return document_string

CMakePP/CMinx

9bde06f9c97a278e14d4c8f438fd0ad538d28526

diff --git a/tests/examples/sphinx/source/example.rst b/tests/examples/sphinx/source/example.rst index acfa2e1..7a0ee3a 100644 --- a/tests/examples/sphinx/source/example.rst +++ b/tests/examples/sphinx/source/example.rst @@ -7,7 +7,7 @@ example.cmake .. function:: say_hi_to(person me) - + This function has very basic documentation. This function's description stays close to idealized formatting and does not do @@ -22,9 +22,9 @@ example.cmake .. function:: macro_say_hi(person) + .. warning:: This is a macro, and so does not introduce a new scope. - This macro says hi. This documentation uses a differing format, but is still processed correctly. @@ -35,7 +35,7 @@ example.cmake .. data:: MyList - + This is an example of variable documentation. This variable is a list of string values. @@ -46,7 +46,7 @@ example.cmake .. data:: MyString - + This is another example of variable documentation. This variable is a string variable. @@ -58,9 +58,9 @@ example.cmake .. function:: message("hello") + .. warning:: This is a generic command invocation. It is not a function or macro definition. - This is a generic command invocation. It will be documented as well, but with an admonition stating it is an invocation and not a definition. diff --git a/tests/examples/sphinx/source/example_prefix.rst b/tests/examples/sphinx/source/example_prefix.rst index 784809d..3cd49f1 100644 --- a/tests/examples/sphinx/source/example_prefix.rst +++ b/tests/examples/sphinx/source/example_prefix.rst @@ -7,7 +7,7 @@ prefix.example.cmake .. function:: say_hi_to(person me) - + This function has very basic documentation. This function's description stays close to idealized formatting and does not do @@ -22,9 +22,9 @@ prefix.example.cmake .. function:: macro_say_hi(person) + .. warning:: This is a macro, and so does not introduce a new scope. - This macro says hi. This documentation uses a differing format, but is still processed correctly. @@ -35,7 +35,7 @@ prefix.example.cmake .. data:: MyList - + This is an example of variable documentation. This variable is a list of string values. @@ -46,7 +46,7 @@ prefix.example.cmake .. data:: MyString - + This is another example of variable documentation. This variable is a string variable. @@ -58,9 +58,9 @@ prefix.example.cmake .. function:: message("hello") + .. warning:: This is a generic command invocation. It is not a function or macro definition. - This is a generic command invocation. It will be documented as well, but with an admonition stating it is an invocation and not a definition. diff --git a/tests/test_samples/corr_rst/advanced_function.rst b/tests/test_samples/corr_rst/advanced_function.rst index f801a4a..588460d 100644 --- a/tests/test_samples/corr_rst/advanced_function.rst +++ b/tests/test_samples/corr_rst/advanced_function.rst @@ -7,7 +7,7 @@ advanced_function.cmake .. function:: advanced_say_hi_to(me) - + Variation of say_hi_to, which takes lists of people and cats to say hi to. This function is basically the same as ``say_hi_to``, but accounts for the diff --git a/tests/test_samples/corr_rst/basic_function.rst b/tests/test_samples/corr_rst/basic_function.rst index a7bfa45..4d34f54 100644 --- a/tests/test_samples/corr_rst/basic_function.rst +++ b/tests/test_samples/corr_rst/basic_function.rst @@ -7,7 +7,7 @@ basic_function.cmake .. function:: say_hi_to(person) - + This function has very basic documentation. This function's description stays close to idealized formatting and does not do diff --git a/tests/test_samples/corr_rst/basic_macro.rst b/tests/test_samples/corr_rst/basic_macro.rst index 9892a39..6d41c6f 100644 --- a/tests/test_samples/corr_rst/basic_macro.rst +++ b/tests/test_samples/corr_rst/basic_macro.rst @@ -8,9 +8,9 @@ basic_macro.cmake .. function:: macro_say_hi(person) + .. warning:: This is a macro, and so does not introduce a new scope. - This macro says hi. This documentation uses a differing format, but is still processed correctly. diff --git a/tests/test_samples/corr_rst/ct_test.rst b/tests/test_samples/corr_rst/ct_test.rst index 656dff1..e1faac6 100644 --- a/tests/test_samples/corr_rst/ct_test.rst +++ b/tests/test_samples/corr_rst/ct_test.rst @@ -8,18 +8,18 @@ ct_test.cmake .. function:: test1(EXPECTFAIL) + .. warning:: This is a CMakeTest test definition, do not call this manually. - This is how you document a CMakeTest test. .. function:: section1(EXPECTFAIL) + .. warning:: This is a CMakeTest section definition, do not call this manually. - And this is how you document a CMakeTest section. diff --git a/tests/test_samples/corr_rst/index.rst b/tests/test_samples/corr_rst/index.rst index 26415d1..b6250b0 100644 --- a/tests/test_samples/corr_rst/index.rst +++ b/tests/test_samples/corr_rst/index.rst @@ -5,6 +5,7 @@ .. toctree:: :maxdepth: 2 + basic_macro basic_function quickstart diff --git a/tests/test_samples/corr_rst/quickstart.rst b/tests/test_samples/corr_rst/quickstart.rst index 50881a2..403a9ff 100644 --- a/tests/test_samples/corr_rst/quickstart.rst +++ b/tests/test_samples/corr_rst/quickstart.rst @@ -7,7 +7,7 @@ quickstart.cmake .. function:: quickstart(param0) - + A brief description. A more detailed description, must be separated from the brief by at least diff --git a/tests/test_samples/corr_rst/variable.rst b/tests/test_samples/corr_rst/variable.rst index 5d292d8..c14d09b 100644 --- a/tests/test_samples/corr_rst/variable.rst +++ b/tests/test_samples/corr_rst/variable.rst @@ -7,7 +7,7 @@ variable.cmake .. data:: MyList - + This is an example of variable documentation. This variable is a list of string values. diff --git a/tests/test_samples/test_samples.py b/tests/test_samples/test_samples.py index 66ee5b3..baa83d6 100644 --- a/tests/test_samples/test_samples.py +++ b/tests/test_samples/test_samples.py @@ -49,4 +49,4 @@ class TestSamples(unittest.TestCase): generated_path = os.path.join(self.output_dir, file_name) corr_path = os.path.join(self.corr_dir, file_name) diff = helpers.diff_files(generated_path, corr_path) - self.assertTrue(diff == "") + self.assertEqual(diff, "") diff --git a/tests/unit_tests/rst_validator.py b/tests/unit_tests/rst_validator.py index aeb1288..c12ce63 100755 --- a/tests/unit_tests/rst_validator.py +++ b/tests/unit_tests/rst_validator.py @@ -216,7 +216,7 @@ class RSTValidator: if ad[0].astext() != to_validate.document[1].text: self.fail( - "Parsed admonition text does not match original admonition text" + f"Parsed admonition text ({ad[0].astext()}) does not match original admonition text ({to_validate.document[1].text}" ) def process_image(self, img: image, to_validate: Directive): diff --git a/tests/unit_tests/test_init.py b/tests/unit_tests/test_init.py index 0cd26b3..4673c44 100755 --- a/tests/unit_tests/test_init.py +++ b/tests/unit_tests/test_init.py @@ -23,7 +23,8 @@ import cminx import helpers class TestInit(unittest.TestCase): - """ Tests the functions found in __init__.py + """ + Tests the functions found in __init__.py """ def setUp(self): @@ -84,7 +85,7 @@ class TestInit(unittest.TestCase): self.assertTrue(is_file, "Output file does not exist") diff = helpers.diff_files(self.output_file, context.corr_example_rst) - self.assertTrue(diff == "") + self.assertEqual(diff, "") def test_recursive_prefix(self): """Tests the use of CMinx in recursive mode with a prefix""" @@ -100,8 +101,7 @@ class TestInit(unittest.TestCase): self.assertTrue(is_file, "Output file does not exist") diff = helpers.diff_files(self.output_file, context.corr_example_prefix_rst) - - self.assertTrue(diff == "") + self.assertEqual(diff, "") if __name__ == '__main__': unittest.main() diff --git a/tests/unit_tests/test_rstwriter.py b/tests/unit_tests/test_rstwriter.py index b0c9cff..0acdc36 100755 --- a/tests/unit_tests/test_rstwriter.py +++ b/tests/unit_tests/test_rstwriter.py @@ -102,6 +102,21 @@ class TestRSTWriter(unittest.TestCase): self.assertTrue(text in str(self.writer), f"Subsection text was not included") self.assertTrue(self.validator.validate(), self.validator.failures) + def test_directive(self): + dir_type = "attention" + + opts = {"name" : "attention"} + dir_text = "This is an attention admonition" + + directive = self.writer.directive(dir_type) + for opt_type, opt_val in opts.items(): + directive.option(opt_type, opt_val) + + directive.text(dir_text) + + self.assertTrue(dir_type in str(self.writer), f"Directive {dir_type} was not included") + self.assertTrue(self.validator.validate(), self.validator.failures) + def test_write(self): self.writer.write_to_file(self.file) with open(self.file, "w") as f:

Toctree directive does not have necessary blank line between options and elements ## Describe the bug When running CMinx on a directory containing documented CMake functions, the `toctree` directives within the generated `index.rst` files generated are invalid, resulting in many `WARNING: Error in "toctree" directive: invalid option block.` warnings that make the API documentation generated by CMinx unable to be traversed on the documentation website. This appears to be because there is not a blank line between the directive options and elements. For example, ```rst .. toctree:: :maxdepth: 2 file1 file2 ``` (what CMinx generates currently) fails, while ```rst .. toctree:: :maxdepth: 2 file1 file2 ``` succeeds. ## To Reproduce Steps to reproduce the behavior: 1. Create a directory with a CMake file in it, for example `reproduce/test.cmake`. 2. Add a documented function to the CMake file, for example ```cmake #[[[ # Test function for CMinx. #]] function(test_function) message("-- in function") endfunction() ``` 4. Run CMinx on the directory. ```bash cminx "reproduce/test.cmake" -o "build/api_docs" -r ``` 6. Set up a Sphinx documentation directory. 7. Copy the documentation files generated by CMinx into the Sphinx documentation source, ensuring it is included in an `index.rst` file. 8. Try to build the documentation and see `WARNING: Error in "toctree" directive: invalid option block.` errors for the `toctree` directives in the generated `index.rst` files. 9. If you try to host the resulting HTML documentation, the API links on the documentation website will not exist. 10. Add a blank line between the options and elements of the `toctree` directive in the generated `index.rst` file, and the build will work. ## Expected behavior The `toctree` directives in CMinx-generated `index.rst` files should have a blank line between the options and elements. ## Additional context I poked around in CMinx and around [L541](https://github.com/CMakePP/CMinx/blob/master/cminx/rstwriter.py#L541) in `rstwriter.py` seems to be the issue. I added `document_string += f"\n"` to L541 and the `index.rst` files were generated properly. I don't know if this breaks anything else though, so further testing is probably needed.

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CODAIT__exchange-metadata-converter-38

diff --git a/setup.py b/setup.py index 1e62eb5..afb9bf4 100644 --- a/setup.py +++ b/setup.py @@ -22,7 +22,7 @@ with open('README.md') as readme: setup( name='exchange-metadata-converter', packages=find_packages(), - version='0.0.8', + version='0.0.9', license='Apache-2.0', description='exchange metadata converters', long_description=README, diff --git a/templates/dlf_out.yaml b/templates/dlf_out.yaml index b440965..0e8427a 100644 --- a/templates/dlf_out.yaml +++ b/templates/dlf_out.yaml @@ -14,7 +14,7 @@ apiVersion: com.ie.ibm.hpsys/v1alpha1 kind: Dataset metadata: - name: '{{name}}' + name: '{{id}}' labels: version: '{{version}}' spec:

CODAIT/exchange-metadata-converter

c306552b0a2fc25f868cfc7daee7b26a1c99f31b

diff --git a/tests/test_dlf.py b/tests/test_dlf.py index 9e37f60..e593f79 100644 --- a/tests/test_dlf.py +++ b/tests/test_dlf.py @@ -48,7 +48,7 @@ class TestDLF(unittest.TestCase): 'com.ie.ibm.hpsys/v1alpha1') self.assertEqual(out_dict['kind'], 'Dataset') self.assertEqual(out_dict['metadata']['name'], - self.in_yamls['name']) + self.in_yamls['id']) self.assertEqual(out_dict['metadata']['labels']['version'], self.in_yamls['version']) self.assertEqual(out_dict['spec']['type'],

Non-compliant metadata.name in the generated DLF YAML The `metadata.name` in the generated DLF YAML does not comply with the Kubernetes spec for DNS-1123 subdomain names. ```JSON { "kind": "Status", "apiVersion": "v1", "metadata": {}, "status": "Failure", "message": "Dataset.com.ie.ibm.hpsys \"Finance Proposition Bank\" is invalid: metadata.name: Invalid value: \"Finance Proposition Bank\": a DNS-1123 subdomain must consist of lower case alphanumeric characters, '-' or '.', and must start and end with an alphanumeric character (e.g. 'example.com', regex used for validation is '[a-z0-9]([-a-z0-9]*[a-z0-9])?(\\.[a-z0-9]([-a-z0-9]*[a-z0-9])?)*')", "reason": "Invalid", "details": { "name": "Finance Proposition Bank", "group": "com.ie.ibm.hpsys", "kind": "Dataset", "causes": [ { "reason": "FieldValueInvalid", "message": "Invalid value: \"Finance Proposition Bank\": a DNS-1123 subdomain must consist of lower case alphanumeric characters, '-' or '.', and must start and end with an alphanumeric character (e.g. 'example.com', regex used for validation is '[a-z0-9]([-a-z0-9]*[a-z0-9])?(\\.[a-z0-9]([-a-z0-9]*[a-z0-9])?)*')", "field": "metadata.name" } ] }, "code": 422 } ``` @ptitzler

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CORE-GATECH-GROUP__serpent-tools-34

diff --git a/serpentTools/__init__.py b/serpentTools/__init__.py index 87c984c..bf0e5d3 100644 --- a/serpentTools/__init__.py +++ b/serpentTools/__init__.py @@ -5,13 +5,14 @@ ROOT_DIR = os.path.dirname(__file__) from serpentTools import settings # List TODOS/feature requests here for now -# Compatability +# Compatibility # TODO: Python 2 support # TODO: Test compatibility with earlier numpy releases # Usage/scripting # TODO: Update rc with dictionary # TODO: Update rc with yaml file into dictionary # TODO: Capture materials with underscores for depletion +# TODO: Find a way to capture some or all of log messages for testing from ._version import get_versions __version__ = get_versions()['version'] diff --git a/serpentTools/objects/materials.py b/serpentTools/objects/materials.py index 43e3db8..49e2ff4 100644 --- a/serpentTools/objects/materials.py +++ b/serpentTools/objects/materials.py @@ -3,7 +3,7 @@ import numpy from matplotlib import pyplot - +from serpentTools.settings import messages from serpentTools.objects import _NamedObject @@ -62,6 +62,7 @@ class DepletedMaterial(_NamedObject): List of strings corresponding to the raw data from the file """ newName = self._convertVariableName(variable) + messages.debug('Adding {} data to {}'.format(newName, self.name)) if isinstance(rawData, str): scratch = [float(item) for item in rawData.split()] else: diff --git a/serpentTools/parsers/depletion.py b/serpentTools/parsers/depletion.py index 2f31b49..c053805 100644 --- a/serpentTools/parsers/depletion.py +++ b/serpentTools/parsers/depletion.py @@ -37,22 +37,15 @@ class DepletionReader(MaterialReader): def __init__(self, filePath): MaterialReader.__init__(self, filePath, 'depletion') self._matPatterns = self._makeMaterialRegexs() - self.matchMatNVar = r'[A-Z]{3}_([0-9a-zA-Z]*)_([A-Z]*_?[A-Z]*)' - """ - Captures material name and variable from string:: + self._matchMatNVar = r'[A-Z]{3}_([0-9a-zA-Z]*)_([A-Z]*_?[A-Z]*)' + # Captures material name and variable from string + # MAT_fuel1_ADENS --> ('fuel1', 'ADENS') + # MAT_fUeL1g_ING_TOX --> ('fUeL1', 'ING_TOX') - MAT_fuel1_ADENS --> ('fuel1', 'ADENS') - MAT_fUeL1g_ING_TOX --> ('fUeL1', 'ING_TOX') - - """ - self.matchTotNVar = r'[A-Z]{3}_([A-Z]*_?[A-Z]*)' - """ - Captures variables for total block from string:: - - TOT_ADENS --> ('ADENS', ) - ING_TOX --> ('ING_TOX', ) - - """ + self._matchTotNVar = r'[A-Z]{3}_([A-Z]*_?[A-Z]*)' + # Captures variables for total block from string:: + # TOT_ADENS --> ('ADENS', ) + # ING_TOX --> ('ING_TOX', ) def _makeMaterialRegexs(self): """Return the patterns by which to find the requested materials.""" @@ -64,7 +57,7 @@ class DepletionReader(MaterialReader): def read(self): """Read through the depletion file and store requested data.""" - messages.info('Preparing to read {}'.format(self.filePath)) + messages.debug('Preparing to read {}'.format(self.filePath)) keys = ['MAT', 'TOT'] if self.settings['processTotal'] else ['MAT'] keys.extend(self.settings['metadataKeys']) separators = ['\n', '];'] @@ -75,7 +68,7 @@ class DepletionReader(MaterialReader): elif (('TOT' in chunk[0] and self.settings['processTotal']) or 'MAT' in chunk[0]): self._addMaterial(chunk) - messages.info('Done reading depletion file') + messages.debug('Done reading depletion file') messages.debug(' found {} materials'.format(len(self.materials))) def _addMetadata(self, chunk): @@ -100,13 +93,13 @@ class DepletionReader(MaterialReader): def _addMaterial(self, chunk): """Add data from a MAT chunk.""" - name, variable = self._getGroupsFromChunk(self.matchMatNVar, chunk) + name, variable = self._getGroupsFromChunk(self._matchMatNVar, chunk) if any([re.match(pat, name) for pat in self._matPatterns]): self._processChunk(chunk, name, variable) def _addTotal(self, chunk): """Add data from a TOT chunk""" - variable = self._getGroupsFromChunk(self.matchTotNVar, chunk) + variable = self._getGroupsFromChunk(self._matchTotNVar, chunk) self._processChunk(chunk, 'total', variable) def _getGroupsFromChunk(self, regex, chunk): @@ -120,7 +113,9 @@ class DepletionReader(MaterialReader): if variable not in self.settings['materialVariables']: pass if name not in self.materials: + messages.debug('Adding material {}...'.format(name)) self.materials[name] = DepletedMaterial(self, name) + messages.debug(' added') if len(chunk) == 1: # single line values, e.g. volume or burnup cleaned = self._cleanSingleLine(chunk) else: diff --git a/serpentTools/settings/messages.py b/serpentTools/settings/messages.py index a639526..54faeef 100644 --- a/serpentTools/settings/messages.py +++ b/serpentTools/settings/messages.py @@ -7,7 +7,8 @@ See Also * https://www.python.org/dev/peps/pep-0391/ """ - +import functools +import warnings import logging from logging.config import dictConfig @@ -19,11 +20,10 @@ class SerpentToolsException(Exception): LOG_OPTS = ['critical', 'error', 'warning', 'info', 'debug'] - loggingConfig = { 'version': 1, 'formatters': { - 'brief': {'format': '%(levelname)-8s: %(name)-15s: %(message)s'}, + 'brief': {'format': '%(levelname)-8s: %(name)-12s: %(message)s'}, 'precise': { 'format': '%(asctime)s %(name)-12s %(levelname)-8s %(message)s' } @@ -74,8 +74,42 @@ def updateLevel(level): """Set the level of the logger.""" if level.lower() not in LOG_OPTS: __logger__.setLevel('INFO') - warning('Logger option {} not in options. Set to warning.') - return 'warning' + warning('Logger option {} not in options. Set to info.'.format(level)) + return 'info' else: __logger__.setLevel(level.upper()) return level + + +def depreciated(f): + """Display a warning indicating a function will be depreciated.""" + + @functools.wraps(f) + def decoratedFunc(*args, **kwargs): + msg = 'Call to depreciated function {}'.format(f.__name__) + warning(msg) + _updateFilterAlert(msg, DeprecationWarning) + return f(*args, **kwargs) + + return decoratedFunc + + +def willChange(changeMsg): + """Inform the user that some functionality may change.""" + + def decorate(f): + @functools.wraps(f) + def decoratedFunc(*args, **kwargs): + warning(changeMsg) + _updateFilterAlert(changeMsg, FutureWarning) + return f(*args, **kwargs) + + return decoratedFunc + + return decorate + + +def _updateFilterAlert(msg, category): + warnings.simplefilter('always', category) + warnings.warn(msg, category=category, stacklevel=3) + warnings.simplefilter('default', category)

CORE-GATECH-GROUP/serpent-tools

4db24e02a2491d3a6f0b7ffe1609d24175ebda7d

diff --git a/serpentTools/tests/test_settings.py b/serpentTools/tests/test_settings.py index e094205..f57fe77 100644 --- a/serpentTools/tests/test_settings.py +++ b/serpentTools/tests/test_settings.py @@ -2,6 +2,7 @@ import unittest from serpentTools import settings +from serpentTools.settings.messages import depreciated, willChange class DefaultSettingsTester(unittest.TestCase): @@ -99,5 +100,30 @@ class RCTester(unittest.TestCase): self.assertSetEqual(expected, actual) +class MessagingTester(unittest.TestCase): + """Class to test the messaging framework.""" + + def test_futureDecorator(self): + """Verify that the future decorator doesn't break""" + + @willChange('This function will be updated in the future, ' + 'but will still exist') + def demoFuture(x, val=5): + return x + val + + self.assertEqual(7, demoFuture(2)) + self.assertEqual(7, demoFuture(2, 5)) + + def test_depreciatedDecorator(self): + """Verify that the depreciated decorator doesn't break things""" + + @depreciated + def demoFunction(x, val=5): + return x + val + + self.assertEqual(7, demoFunction(2)) + self.assertEqual(7, demoFunction(2, 5)) + + if __name__ == '__main__': unittest.main()

Add more message types Add some future/depreciated warnings that can either piggy back off the [python builtin warnings](https://docs.python.org/2/library/warnings.html) but also conform to our messaging methodology

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

CORE-GATECH-GROUP__serpent-tools-35

diff --git a/serpentTools/objects/containers.py b/serpentTools/objects/containers.py new file mode 100644 index 0000000..ff8f941 --- /dev/null +++ b/serpentTools/objects/containers.py @@ -0,0 +1,144 @@ +""" +Supporting object that will be used by the branching reader and +results reader to store data for a single homogenized universe at a single +instance in time. +""" + +from serpentTools.objects import SupportingObject +from serpentTools.settings import messages + + +class HomogUniv(SupportingObject): + """ + Class for storing homogenized universe specifications and retrieving them + + Parameters + ---------- + -container: str + name of the parser + -name: str + name of the universe + -bu: float + burnup value + -step: float + temporal step + -day: float + depletion day + + Attributes + ---------- + -name: str + name of the universe + -bu: float + burnup value + -step: float + temporal step + -day: float + depletion day + + """ + + def __init__(self, container, name, bu, step, day): + SupportingObject.__init__(self, container) + self.name = name + self.bu = bu + self.step = step + self.day = day + # Dictionaries: + self.b1Exp = {} + self.infExp = {} + self.b1Unc = {} + self.infUnc = {} + self.metaData = {} + + def addData(self, variableName, variableValue, uncertainty=False): + """ + Sets the value of the variable and, optionally, the associate s.d. + + Parameters + ---------- + variableName: str + Variable Name + variableValue: str/tuple/list + Variable Value + uncertainty: bool + Boolean Variable- set to True in order to retrieve the + uncertainty associated to the expected values + + Notes: + --------- + Raises a warning if the value of the variable is overwritten + + """ + + # 1. Check the input type + variableName = SupportingObject._convertVariableName(variableName) + if not isinstance(uncertainty, bool): + raise TypeError('The variable uncertainty has type %s.\n ...' + 'It should be boolean.', type(uncertainty)) + # 2. Pointer to the proper dictionary + setter = self._lookup(variableName, uncertainty) + # 3. Check if variable is already present. Then set the variable. + if variableName in setter: + messages.warning( + "The variable {} will be overwritten".format(variableName)) + setter[variableName] = variableValue + + def get(self, variableName, uncertainty=False): + """ + Gets the value of the variable VariableName from the dictionaries + + Parameters + ---------- + variableName: str + Variable Name + uncertainty: bool + Boolean Variable- set to True in order to retrieve the + uncertainty associated to the expected values + + Returns + ------- + x: str/tuple/list + Variable Value + dx: str/tuple/list + Associated uncertainty + + """ + # 1. Check the input values + if not isinstance(uncertainty, bool): + raise TypeError('The variable uncertainty has type %s.\n ...' + 'It should be boolean.', type(uncertainty)) + # 2. Pointer to the proper dictionary + setter = self._lookup(variableName, False) + if variableName not in setter: + raise KeyError( + "Variable {} absent from expected value dictionary".format( + variableName)) + x = setter.get(variableName) + # 3. Return the value of the variable + if not uncertainty: + return x + if setter is self.metaData: + messages.warning('No uncertainty is associated to metadata') + return x + setter = self._lookup(variableName, True) + if variableName not in setter: + raise KeyError( + "Variable {} absent from uncertainty dictionary".format( + variableName)) + dx = setter.get(variableName) + return x, dx + + def _lookup(self, variableName, uncertainty): + if "inf" in variableName: + if not uncertainty: + return self.infExp + else: + return self.infUnc + elif "b1" in variableName: + if not uncertainty: + return self.b1Exp + else: + return self.b1Unc + else: + return self.metaData

CORE-GATECH-GROUP/serpent-tools

0c0c57f55bd6632c7015406087b9cee12315ebed

diff --git a/serpentTools/tests/test_branching.py b/serpentTools/tests/test_branching.py index 0d4881d..6693d98 100644 --- a/serpentTools/tests/test_branching.py +++ b/serpentTools/tests/test_branching.py @@ -11,7 +11,7 @@ REF_FILE = os.path.join(TEST_ROOT, 'ref_branch.txt') class BranchTester(unittest.TestCase): - """Classs for testing the branching coefficient file reader.""" + """Class for testing the branching coefficient file reader.""" @classmethod def setUpClass(cls): diff --git a/serpentTools/tests/test_container.py b/serpentTools/tests/test_container.py new file mode 100644 index 0000000..32321f2 --- /dev/null +++ b/serpentTools/tests/test_container.py @@ -0,0 +1,86 @@ +"""Test the container object. """ + +import unittest +from serpentTools.objects import containers +from serpentTools.parsers import DepletionReader + + +class HomogenizedUniverseTester(unittest.TestCase): + """ Class to test the Homogenized Universe """ + + @classmethod + def setUpClass(cls): + cls.univ = containers.HomogUniv(DepletionReader(None), 'dummy', 0, 0, 0) + cls.Exp = {} + cls.Unc = {} + # Data definition + cls.Exp = {'B1_1': 1, 'B1_2': [1, 2], 'B1_3': [1, 2, 3], + 'INF_1': 3, 'INF_2': [4, 5], 'INF_3': [6, 7, 8], + 'MACRO_E': (.1, .2, .3, .1, .2, .3), 'Test_1': 'ciao'} + cls.Unc = {'B1_1': 1e-1, 'B1_2': [1e-1, 2e-1], 'B1_3': [1e-1, 2e-1, + 3e-1], + 'INF_1': 3e-1, 'INF_2': [4e-1, 5e-1], 'INF_3': [6e-1, 7e-1, + 8e-1], + 'MACRO_E': (.1e-1, .2e-1, .3e-1, .1e-1, .2e-1, .3e-1), + 'Test_1': 'addio'} + + # Partial dictionaries + cls.b1Exp = {'b11': 1, 'b12': [1, 2], 'b13': [1, 2, 3]} + cls.b1Unc = {'b11': (1, 0.1), 'b12': ([1, 2], [.1, .2]), 'b13': + ([1, 2, 3], [.1, .2, .3])} + cls.infExp = {'inf1': 3, 'inf2': [4, 5], 'inf3': [6, 7, 8]} + cls.infUnc = {'inf1': (3, .3), 'inf2': ([4, 5], [.4, .5]), 'inf3': + ([6, 7, 8], [.6, .7, .8])} + cls.meta = {'macroE': (.1e-1, .2e-1, .3e-1, .1e-1, .2e-1, .3e-1), + 'test1': 'addio'} + # Use addData + for kk in cls.Exp: + cls.univ.addData(kk, cls.Exp[kk], False) + for kk in cls.Unc: + cls.univ.addData(kk, cls.Unc[kk], True) + + def test_getB1Exp(self): + """ Get Expected vales from B1 dictionary""" + d = {} + # Comparison + for kk in self.univ.b1Exp: + d[kk] = self.univ.get(kk, False) + self.assertDictEqual(self.b1Exp, d) + + def test_getB1Unc(self): + """ Get Expected vales and associated uncertainties from B1 dictionary + """ + d = {} + # Comparison + for kk in self.univ.b1Exp: + d[kk] = self.univ.get(kk, True) + self.assertDictEqual(self.b1Unc, d) + + def test_getInfExp(self): + """ Get Expected vales from Inf dictionary""" + d = {} + # Comparison + for kk in self.univ.infExp: + d[kk] = self.univ.get(kk, False) + self.assertDictEqual(self.infExp, d) + + def test_getInfUnc(self): + """ Get Expected vales and associated uncertainties from Inf dictionary + """ + d = {} + # Comparison + for kk in self.univ.infUnc: + d[kk] = self.univ.get(kk, True) + self.assertDictEqual(self.infUnc, d) + + def test_getMeta(self): + """ Get metaData from corresponding dictionary""" + d = {} + # Comparison + for kk in self.univ.metaData: + d[kk] = self.univ.get(kk, False) + self.assertDictEqual(self.meta, d) + + +if __name__ == '__main__': + unittest.main()

Support: Homogenized Universe Object Implement a supporting object that will be used by the branching reader and results reader that stores data for a single homogenized universe at a single instance in time. ## Requirements 1. Should store the universe number, and, optionally, day, burnup, and burnup step for this instance. Optional because for a problem with no burnup, those values will not be present in the file. 1. Simple methods to add and get variable data, that will be sent from the readers. ## Optional 1. Output the data with some template engine like [Jinja2](http://jinja.pocoo.org/) or [Mako](http://www.makotemplates.org/) ## Holding up #6 #7

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

CORE-GATECH-GROUP__serpent-tools-4

diff --git a/serpentTools/__init__.py b/serpentTools/__init__.py index 8af8d0f..d38090d 100644 --- a/serpentTools/__init__.py +++ b/serpentTools/__init__.py @@ -1,7 +1,7 @@ from serpentTools import settings from serpentTools import parsers -__version__ = '0.1.1' +__version__ = '0.1.2' # List TODOS/feature requests here for now # Messages/Errors diff --git a/serpentTools/objects/__init__.py b/serpentTools/objects/__init__.py index 42ee6c0..8f2e2cd 100644 --- a/serpentTools/objects/__init__.py +++ b/serpentTools/objects/__init__.py @@ -146,8 +146,18 @@ class DepletedMaterial(_SupportingObject): AttributeError If the names of the isotopes have not been obtained and specific isotopes have been requested + KeyError + If at least one of the days requested is not present """ - returnX = timePoints is None + if timePoints is not None: + returnX = False + timeCheck = self._checkTimePoints(xUnits, timePoints) + if any(timeCheck): + raise KeyError('The following times were not present in file {}' + '\n{}'.format(self._container.filePath, + ', '.join(timeCheck))) + else: + returnX = True if names and 'names' not in self._container.metadata: raise AttributeError('Parser {} has not stored the isotope names.' .format(self._container)) @@ -164,6 +174,12 @@ class DepletedMaterial(_SupportingObject): return yVals, xVals return yVals + def _checkTimePoints(self, xUnits, timePoints): + valid = self[xUnits] + badPoints = [str(time) for time in timePoints if time not in valid] + return badPoints + + def _getXSlice(self, xUnits, timePoints): allX = self[xUnits] if timePoints is not None: diff --git a/serpentTools/parsers/branching.py b/serpentTools/parsers/branching.py index 6817810..8efd2f1 100644 --- a/serpentTools/parsers/branching.py +++ b/serpentTools/parsers/branching.py @@ -1,9 +1,9 @@ """Parser responsible for reading the ``*coe.m`` files""" -from serpentTools.parsers import _BaseReader +from serpentTools.objects.readers import BaseReader -class BranchingReader(_BaseReader): +class BranchingReader(BaseReader): """ Parser responsible for reading and working with automated branching files. diff --git a/serpentTools/parsers/bumat.py b/serpentTools/parsers/bumat.py index 70ead0a..27c155b 100644 --- a/serpentTools/parsers/bumat.py +++ b/serpentTools/parsers/bumat.py @@ -1,9 +1,9 @@ """Parser responsible for reading the ``*bumat<n>.m`` files""" -from serpentTools.parsers import _MaterialReader +from serpentTools.objects.readers import MaterialReader -class BumatReader(_MaterialReader): +class BumatReader(MaterialReader): """ Parser responsible for reading and working with burned material files. diff --git a/serpentTools/parsers/detector.py b/serpentTools/parsers/detector.py index ea40920..9c4c33c 100644 --- a/serpentTools/parsers/detector.py +++ b/serpentTools/parsers/detector.py @@ -1,9 +1,9 @@ """Parser responsible for reading the ``*det<n>.m`` files""" -from serpentTools.parsers import _BaseReader +from serpentTools.objects.readers import BaseReader -class DetectorReader(_BaseReader): +class DetectorReader(BaseReader): """ Parser responsible for reading and working with detector files. diff --git a/serpentTools/parsers/fissionMatrix.py b/serpentTools/parsers/fissionMatrix.py index 58af81d..3923415 100644 --- a/serpentTools/parsers/fissionMatrix.py +++ b/serpentTools/parsers/fissionMatrix.py @@ -1,9 +1,9 @@ """Parser responsible for reading the ``*fmtx<n>.m`` files""" -from serpentTools.parsers import _BaseReader +from serpentTools.objects.readers import BaseReader -class FissionMatrixReader(_BaseReader): +class FissionMatrixReader(BaseReader): """ Parser responsible for reading and working with fission matrix files. diff --git a/serpentTools/parsers/results.py b/serpentTools/parsers/results.py index f33b68c..ae4f1ef 100644 --- a/serpentTools/parsers/results.py +++ b/serpentTools/parsers/results.py @@ -1,9 +1,9 @@ """Parser responsible for reading the ``*res.m`` files""" -from serpentTools.parsers import _BaseReader +from serpentTools.objects.readers import BaseReader -class ResultsReader(_BaseReader): +class ResultsReader(BaseReader): """ Parser responsible for reading and working with result files.

CORE-GATECH-GROUP/serpent-tools

606a90d665a15a16c437dd1fb72ef014aa480142

diff --git a/serpentTools/tests/test_depletion.py b/serpentTools/tests/test_depletion.py index 0574305..d7f6d52 100644 --- a/serpentTools/tests/test_depletion.py +++ b/serpentTools/tests/test_depletion.py @@ -156,6 +156,17 @@ class DepletedMaterialTester(_DepletionTestHelper): names=['Xe135']) numpy.testing.assert_equal(actualDays, self.reader.metadata['days']) + def test_getXY_raisesError_badTime(self): + """Verify that a ValueError is raised for non-present requested days.""" + badDays = [-1, 0, 50] + with self.assertRaises(KeyError): + self.material.getXY('days', 'adens', timePoints=badDays) + + def test_fetchData(self): + """Verify that key errors are raised when bad data are requested.""" + with self.assertRaises(KeyError): + _ = self.material['fake units'] + if __name__ == '__main__': unittest.main()

`getXY` for `DepletedMaterial` raises unhelpful value error if days missing from object If a depleted material is asked to get some quantity for days that are not present, the following error is raised: ``` File "C:\Users\ajohnson400\AppData\Local\Continuum\Anaconda3\lib\site-packages\serpenttools-0.1.1rc0-py3.5.egg\serpentTools\objects\__init__.py", line 162, in getXY else allY[rowId][:]) ValueError: could not broadcast input array from shape (19) into shape (0) ``` The value of `colIndices` is an empty list for this case.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

CS-SI__eodag-405

diff --git a/eodag/plugins/download/aws.py b/eodag/plugins/download/aws.py index 3202c76a..fe7d3573 100644 --- a/eodag/plugins/download/aws.py +++ b/eodag/plugins/download/aws.py @@ -253,11 +253,17 @@ class AwsDownload(Download): bucket_names_and_prefixes = [self.get_bucket_name_and_prefix(product)] # add complementary urls - for complementary_url_key in product_conf.get("complementary_url_key", []): - bucket_names_and_prefixes.append( - self.get_bucket_name_and_prefix( - product, product.properties[complementary_url_key] + try: + for complementary_url_key in product_conf.get("complementary_url_key", []): + bucket_names_and_prefixes.append( + self.get_bucket_name_and_prefix( + product, product.properties[complementary_url_key] + ) ) + except KeyError: + logger.error( + "complementary_url_key %s is missing in %s properties" + % (complementary_url_key, product.properties["id"]) ) # authenticate @@ -566,13 +572,18 @@ class AwsDownload(Download): def check_manifest_file_list(self, product_path): """Checks if products listed in manifest.safe exist""" - manifest_path = [ + manifest_path_list = [ os.path.join(d, x) for d, _, f in os.walk(product_path) for x in f if x == "manifest.safe" - ][0] - safe_path = os.path.dirname(manifest_path) + ] + if len(manifest_path_list) == 0: + raise FileNotFoundError( + f"No manifest.safe could be found in {product_path}" + ) + else: + safe_path = os.path.dirname(manifest_path_list[0]) root = etree.parse(os.path.join(safe_path, "manifest.safe")).getroot() for safe_file in root.xpath("//fileLocation"): @@ -587,13 +598,18 @@ class AwsDownload(Download): """Add missing dirs to downloaded product""" try: logger.debug("Finalize SAFE product") - manifest_path = [ + manifest_path_list = [ os.path.join(d, x) for d, _, f in os.walk(product_path) for x in f if x == "manifest.safe" - ][0] - safe_path = os.path.dirname(manifest_path) + ] + if len(manifest_path_list) == 0: + raise FileNotFoundError( + f"No manifest.safe could be found in {product_path}" + ) + else: + safe_path = os.path.dirname(manifest_path_list[0]) # create empty missing dirs auxdata_path = os.path.join(safe_path, "AUX_DATA") @@ -868,7 +884,7 @@ class AwsDownload(Download): auth=None, downloaded_callback=None, progress_callback=None, - **kwargs + **kwargs, ): """ download_all using parent (base plugin) method @@ -878,5 +894,5 @@ class AwsDownload(Download): auth=auth, downloaded_callback=downloaded_callback, progress_callback=progress_callback, - **kwargs + **kwargs, ) diff --git a/eodag/resources/providers.yml b/eodag/resources/providers.yml index 0dc859d4..2b792b94 100644 --- a/eodag/resources/providers.yml +++ b/eodag/resources/providers.yml @@ -1718,7 +1718,7 @@ platformSerialIdentifier: '$.id.`split(_, 0, -1)`' polarizationMode: '$.id.`sub(/.{14}([A-Z]{2}).*/, \\1)`' productPath: | - $.properties."sentinel:product_id".`sub(/([S2AB]{3})_MSIL1C_([0-9]{4})(0?)([1-9]+)([0-9]{2})(T.*)/, products/\\2/\\4/\\5/\\1_MSIL1C_\\2\\3\\4\\5\\6)` + $.properties."sentinel:product_id".`sub(/([S2AB]{3})_MSIL1C_([0-9]{4})([0-9]{2})([0-9]{2})(T.*)/, products/\\2/\\3/\\4/\\1_MSIL1C_\\2\\3\\4\\5)`.`sub(/\/0+/, \/)` tilePath: | $.assets.info.href.`sub(/.*/sentinel-s2-l1c\/(tiles\/.*)\/tileInfo\.json/, \\1)` S2_MSI_L2A: @@ -1728,7 +1728,7 @@ platformSerialIdentifier: '$.id.`split(_, 0, -1)`' polarizationMode: '$.id.`sub(/.{14}([A-Z]{2}).*/, \\1)`' productPath: | - $.properties."sentinel:product_id".`sub(/([S2AB]{3})_MSIL2A_([0-9]{4})(0?)([1-9]+)([0-9]{2})(T.*)/, products/\\2/\\4/\\5/\\1_MSIL2A_\\2\\3\\4\\5\\6)` + $.properties."sentinel:product_id".`sub(/([S2AB]{3})_MSIL2A_([0-9]{4})([0-9]{2})([0-9]{2})(T.*)/, products/\\2/\\3/\\4/\\1_MSIL2A_\\2\\3\\4\\5)`.`sub(/\/0+/, \/)` tilePath: | $.assets.info.href.`sub(/.*/sentinel-s2-l2a\/(tiles\/.*)\/tileInfo\.json/, \\1)` L8_OLI_TIRS_C1L1:

CS-SI/eodag

d9f16f411fdf5eb6ad752f984782dd06ed882dc8

diff --git a/tests/units/test_search_plugins.py b/tests/units/test_search_plugins.py index 405451a8..47ced2e6 100644 --- a/tests/units/test_search_plugins.py +++ b/tests/units/test_search_plugins.py @@ -297,3 +297,50 @@ class TestSearchPluginODataV4Search(BaseSearchPluginTest): self.assertEqual(estimate, self.onda_products_count) self.assertEqual(len(products), number_of_products) self.assertIsInstance(products[0], EOProduct) + + +class TestSearchPluginStacSearch(BaseSearchPluginTest): + @mock.patch("eodag.plugins.search.qssearch.StacSearch._request", autospec=True) + def test_plugins_search_stacsearch_mapping_earthsearch(self, mock__request): + """The metadata mapping for earth_search should return well formatted results""" # noqa + + geojson_geometry = self.search_criteria_s2_msi_l1c["geometry"].__geo_interface__ + + mock__request.return_value = mock.Mock() + mock__request.return_value.json.side_effect = [ + { + "context": {"page": 1, "limit": 2, "matched": 1, "returned": 2}, + }, + { + "features": [ + { + "id": "foo", + "geometry": geojson_geometry, + "properties": { + "sentinel:product_id": "S2B_MSIL1C_20201009T012345_N0209_R008_T31TCJ_20201009T123456", + }, + }, + { + "id": "bar", + "geometry": geojson_geometry, + "properties": { + "sentinel:product_id": "S2B_MSIL1C_20200910T012345_N0209_R008_T31TCJ_20200910T123456", + }, + }, + ] + }, + ] + + search_plugin = self.get_search_plugin(self.product_type, "earth_search") + + products, estimate = search_plugin.query( + page=1, items_per_page=2, auth=None, **self.search_criteria_s2_msi_l1c + ) + self.assertEqual( + products[0].properties["productPath"], + "products/2020/10/9/S2B_MSIL1C_20201009T012345_N0209_R008_T31TCJ_20201009T123456", + ) + self.assertEqual( + products[1].properties["productPath"], + "products/2020/9/10/S2B_MSIL1C_20200910T012345_N0209_R008_T31TCJ_20200910T123456", + )

finalize_s2_safe_product: Fails when missing manifest.safe When downloading some products on `earth_search`, I have a problem when converting the product format to `.SAFE`:   It seems some L2A products are arriving without the `manifest.safe` file 😓 Environment: Python version: Python 3.7.12 EODAG version: eodag (Earth Observation Data Access Gateway): version 2.3.4

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CS-SI__eodag-586

diff --git a/eodag/api/product/_product.py b/eodag/api/product/_product.py index 777b3026..a0a3d78c 100644 --- a/eodag/api/product/_product.py +++ b/eodag/api/product/_product.py @@ -221,15 +221,30 @@ class EOProduct(object): """ self.downloader = downloader self.downloader_auth = authenticator + # resolve locations and properties if needed with downloader configuration - self.location = self.location % vars(self.downloader.config) - self.remote_location = self.remote_location % vars(self.downloader.config) + location_attrs = ("location", "remote_location") + for location_attr in location_attrs: + try: + setattr( + self, + location_attr, + getattr(self, location_attr) % vars(self.downloader.config), + ) + except ValueError as e: + logger.debug( + f"Could not resolve product.{location_attr} ({getattr(self, location_attr)})" + f" in register_downloader: {str(e)}" + ) + for k, v in self.properties.items(): if isinstance(v, str): try: self.properties[k] = v % vars(self.downloader.config) - except TypeError: - pass + except (TypeError, ValueError) as e: + logger.debug( + f"Could not resolve {k} property ({v}) in register_downloader: {str(e)}" + ) def download( self,

CS-SI/eodag

3465afe00a492e73bfd517f19c409ba21196f85f

diff --git a/tests/units/test_eoproduct.py b/tests/units/test_eoproduct.py index ed716125..81bdd00f 100644 --- a/tests/units/test_eoproduct.py +++ b/tests/units/test_eoproduct.py @@ -453,3 +453,84 @@ class TestEOProduct(EODagTestCase): # progress bar finished self.assertEqual(progress_callback.n, progress_callback.total) self.assertGreater(progress_callback.total, 0) + + def test_eoproduct_register_downloader(self): + """eoproduct.register_donwloader must set download and auth plugins""" + product = self._dummy_product() + + self.assertIsNone(product.downloader) + self.assertIsNone(product.downloader_auth) + + downloader = mock.MagicMock() + downloader_auth = mock.MagicMock() + + product.register_downloader(downloader, downloader_auth) + + self.assertEqual(product.downloader, downloader) + self.assertEqual(product.downloader_auth, downloader_auth) + + def test_eoproduct_register_downloader_resolve_ok(self): + """eoproduct.register_donwloader must resolve locations and properties""" + downloadable_product = self._dummy_downloadable_product( + product=self._dummy_product( + properties=dict( + self.eoproduct_props, + **{ + "downloadLink": "%(base_uri)s/is/resolved", + "otherProperty": "%(outputs_prefix)s/also/resolved", + }, + ) + ) + ) + self.assertEqual( + downloadable_product.location, + f"{downloadable_product.downloader.config.base_uri}/is/resolved", + ) + self.assertEqual( + downloadable_product.remote_location, + f"{downloadable_product.downloader.config.base_uri}/is/resolved", + ) + self.assertEqual( + downloadable_product.properties["downloadLink"], + f"{downloadable_product.downloader.config.base_uri}/is/resolved", + ) + self.assertEqual( + downloadable_product.properties["otherProperty"], + f"{downloadable_product.downloader.config.outputs_prefix}/also/resolved", + ) + + def test_eoproduct_register_downloader_resolve_ignored(self): + """eoproduct.register_donwloader must ignore unresolvable locations and properties""" + with self.assertLogs(level="DEBUG") as cm: + downloadable_product = self._dummy_downloadable_product( + product=self._dummy_product( + properties=dict( + self.eoproduct_props, + **{ + "downloadLink": "%257B/cannot/be/resolved", + "otherProperty": "%/%s/neither/resolved", + }, + ) + ) + ) + self.assertEqual(downloadable_product.location, "%257B/cannot/be/resolved") + self.assertEqual( + downloadable_product.remote_location, "%257B/cannot/be/resolved" + ) + self.assertEqual( + downloadable_product.properties["downloadLink"], + "%257B/cannot/be/resolved", + ) + self.assertEqual( + downloadable_product.properties["otherProperty"], + "%/%s/neither/resolved", + ) + + needed_logs = [ + f"Could not resolve product.location ({downloadable_product.location})", + f"Could not resolve product.remote_location ({downloadable_product.remote_location})", + f"Could not resolve downloadLink property ({downloadable_product.properties['downloadLink']})", + f"Could not resolve otherProperty property ({downloadable_product.properties['otherProperty']})", + ] + for needed_log in needed_logs: + self.assertTrue(any(needed_log in log for log in cm.output))

percent variables parsing error in product location If product location contains some percent variables, it may conflict with `register_downloader()` internal parsing mechanism and raise: ``` Traceback (most recent call last): File "/usr/local/lib/python3.8/dist-packages/eodag/api/core.py", line 1474, in _do_search eo_product.register_downloader( File "/usr/local/lib/python3.8/dist-packages/eodag/api/product/_product.py", line 224, in register_downloader self.location = self.location % vars(self.downloader.config) ValueError: unsupported format character 'B' (0x42) at index 72 2022-12-19 16:27:20,206 - eodag.core - ERROR - Error while searching on provider foo (ignored): Traceback (most recent call last): File "/usr/local/lib/python3.8/dist-packages/eodag/api/core.py", line 1474, in _do_search eo_product.register_downloader( File "/usr/local/lib/python3.8/dist-packages/eodag/api/product/_product.py", line 224, in register_downloader self.location = self.location % vars(self.downloader.config) ValueError: unsupported format character 'B' (0x42) at index 72 ``` Reproductible as: ```py "https://example.com/%257B" % ({}) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In [26], line 1 ----> 1 "https://example.com/%257B" % ({}) ValueError: unsupported format character 'B' (0x42) at index 24 ``` - [ ] Intercept error, log a warning and ignore this step if it occurs

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CS-SI__eodag-592

diff --git a/eodag/api/product/metadata_mapping.py b/eodag/api/product/metadata_mapping.py index e449a643..3f014290 100644 --- a/eodag/api/product/metadata_mapping.py +++ b/eodag/api/product/metadata_mapping.py @@ -302,7 +302,10 @@ def format_metadata(search_param, *args, **kwargs): @staticmethod def convert_csv_list(values_list): - return ",".join([str(x) for x in values_list]) + if isinstance(values_list, list): + return ",".join([str(x) for x in values_list]) + else: + return values_list @staticmethod def convert_remove_extension(string): diff --git a/eodag/plugins/search/qssearch.py b/eodag/plugins/search/qssearch.py index 6595d429..dda336da 100644 --- a/eodag/plugins/search/qssearch.py +++ b/eodag/plugins/search/qssearch.py @@ -33,6 +33,7 @@ from eodag.api.product.metadata_mapping import ( get_metadata_path, get_metadata_path_value, get_search_param, + mtd_cfg_as_jsonpath, properties_from_json, properties_from_xml, ) @@ -214,19 +215,19 @@ class QueryStringSearch(Search): for product_type_result in result: # providers_config extraction - mapping_config = { - k: (None, cached_parse(v)) - for k, v in self.config.discover_product_types[ - "generic_product_type_parsable_properties" - ].items() - } - mapping_config["generic_product_type_id"] = ( - None, - cached_parse( + mapping_config = {} + mapping_config = mtd_cfg_as_jsonpath( + dict( self.config.discover_product_types[ - "generic_product_type_id" - ] + "generic_product_type_parsable_properties" + ], + **{ + "generic_product_type_id": self.config.discover_product_types[ + "generic_product_type_id" + ] + }, ), + mapping_config, ) extracted_mapping = properties_from_json( @@ -244,15 +245,52 @@ class QueryStringSearch(Search): ), ) # product_types_config extraction - mapping_config = { - k: (None, cached_parse(v)) - for k, v in self.config.discover_product_types[ + mapping_config = {} + mapping_config = mtd_cfg_as_jsonpath( + self.config.discover_product_types[ "generic_product_type_parsable_metadata" - ].items() - } + ], + mapping_config, + ) conf_update_dict["product_types_config"][ generic_product_type_id ] = properties_from_json(product_type_result, mapping_config) + + # update keywords + keywords_fields = [ + "instrument", + "platform", + "platformSerialIdentifier", + "processingLevel", + "keywords", + ] + keywords_values_str = ",".join( + [generic_product_type_id] + + [ + str( + conf_update_dict["product_types_config"][ + generic_product_type_id + ][kf] + ) + for kf in keywords_fields + if conf_update_dict["product_types_config"][ + generic_product_type_id + ][kf] + != NOT_AVAILABLE + ] + ) + keywords_values_str = keywords_values_str.replace( + ", ", "," + ).replace(" ", "-") + keywords_values_str = re.sub( + r"[\[\]'\"]", "", keywords_values_str + ) + keywords_values_str = ",".join( + set(keywords_values_str.split(",")) + ) + conf_update_dict["product_types_config"][ + generic_product_type_id + ]["keywords"] = keywords_values_str except KeyError as e: logger.warning( "Incomplete %s discover_product_types configuration: %s", diff --git a/eodag/resources/stac_provider.yml b/eodag/resources/stac_provider.yml index 3018f52c..22981b82 100644 --- a/eodag/resources/stac_provider.yml +++ b/eodag/resources/stac_provider.yml @@ -38,11 +38,11 @@ search: productType: '$.id' generic_product_type_parsable_metadata: abstract: '$.description' - instrument: '$.summaries.instruments' - platform: '$.summaries.constellation' - platformSerialIdentifier: '$.summaries.platform' + instrument: '{$.summaries.instruments#csv_list}' + platform: '{$.summaries.constellation#csv_list}' + platformSerialIdentifier: '{$.summaries.platform#csv_list}' processingLevel: '$.summaries."processing:level"' - keywords: '$.keywords' + keywords: '{$.keywords#csv_list}' license: '$.license' title: '$.title' missionStartDate: '$.extent.temporal.interval[0][0]'

CS-SI/eodag

870580e4565e533838a1b3c1b2acd2edd335de11

diff --git a/tests/units/test_search_plugins.py b/tests/units/test_search_plugins.py index ca6c2456..b25b7ea7 100644 --- a/tests/units/test_search_plugins.py +++ b/tests/units/test_search_plugins.py @@ -187,6 +187,50 @@ class TestSearchPluginQueryStringSearch(BaseSearchPluginTest): "The FOO collection", ) + @mock.patch( + "eodag.plugins.search.qssearch.QueryStringSearch._request", autospec=True + ) + def test_plugins_search_querystringseach_discover_product_types_keywords( + self, mock__request + ): + """QueryStringSearch.discover_product_types must return a dict with well formatted keywords""" + # One of the providers that has a QueryStringSearch Search plugin and keywords configured + provider = "astraea_eod" + search_plugin = self.get_search_plugin(self.product_type, provider) + + mock__request.return_value = mock.Mock() + mock__request.return_value.json.return_value = { + "collections": [ + { + "id": "foo_collection", + "keywords": ["foo", "bar"], + "summaries": { + "instruments": ["baz"], + "constellation": "qux,foo", + "platform": ["quux", "corge", "bar"], + "processing:level": "grault", + }, + }, + ] + } + conf_update_dict = search_plugin.discover_product_types() + keywords_list = conf_update_dict["product_types_config"]["foo_collection"][ + "keywords" + ].split(",") + + self.assertEqual(len(keywords_list), 8) + for k in [ + "foo_collection", + "foo", + "bar", + "baz", + "qux", + "quux", + "corge", + "grault", + ]: + self.assertIn(k, keywords_list) + class TestSearchPluginPostJsonSearch(BaseSearchPluginTest): def setUp(self):

Add keywords to discovered product types Automatically add default keywords to discovered product types to help finding them using [guess_product_type()](https://eodag.readthedocs.io/en/stable/api_reference/core.html#eodag.api.core.EODataAccessGateway.guess_product_type). See also [Guess a product type documentation](https://eodag.readthedocs.io/en/stable/notebooks/api_user_guide/4_search.html#Guess-a-product-type)

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CS-SI__eodag-927

diff --git a/docs/_static/product_types_information.csv b/docs/_static/product_types_information.csv index 21b10020..61464555 100644 --- a/docs/_static/product_types_information.csv +++ b/docs/_static/product_types_information.csv @@ -28,10 +28,10 @@ CLMS_GLO_GDMP_333M,"Gross dry matter Productivity (GDMP) is an indication of the CLMS_GLO_LAI_333M,"LAI was defined by CEOS as half the developed area of the convex hull wrapping the green canopy elements per unit horizontal ground. This definition allows accounting for elements which are not flat such as needles or stems. LAI is strongly non linearly related to reflectance. Therefore, its estimation from remote sensing observations will be scale dependant over heterogeneous landscapes. When observing a canopy made of different layers of vegetation, it is therefore mandatory to consider all the green layers. This is particularly important for forest canopies where the understory may represent a very significant contribution to the total canopy LAI. The derived LAI corresponds therefore to the total green LAI, including the contribution of the green elements of the understory. The product at 333m resolution is provided in Near Real Time and consolidated in the next six periods. ","OLCI,PROBA-V",Sentinel-3,,,"Land,Leaf-area-index,LAI,OLCI,PROBA-V,Sentinel-3",,proprietary,Global 10-daily Leaf Area Index 333m,2014-01-10T00:00:00Z,,,,,,,,,,,,,,,,,,,,,available CLMS_GLO_NDVI_1KM_LTS,"The Normalized Difference Vegetation Index (NDVI) is a proxy to quantify the vegetation amount. It is defined as NDVI=(NIR-Red)/(NIR+Red) where NIR corresponds to the reflectance in the near infrared band, and Red to the reflectance in the red band. The time series of dekadal (10-daily) NDVI 1km version 2 observations over the period 1999-2017 is used to calculate Long Term Statistics (LTS) for each of the 36 10-daily periods (dekads) of the year. The calculated LTS include the minimum, median, maximum, average, standard deviation and the number of observations in the covered time series period. These LTS can be used as a reference for actual NDVI observations, which allows evaluating whether vegetation conditions deviate from a 'normal' situation. ","VEGETATION,PROBA-V",SPOT,,,"Land,NDVI,LTS,SPOT,VEGETATION,PROBA-V",,proprietary,"Normalized Difference Vegetation Index: global Long Term Statistics (raster 1km) - version 2, Apr 2019",1999-01-01T00:00:00Z,,,,,,,,,,,,,,,,,,,,,available CLMS_GLO_NDVI_333M,"The Normalized Difference Vegetation Index (NDVI) is a proxy to quantify the vegetation amount. It is defined as NDVI=(NIR-Red)/(NIR+Red) where NIR corresponds to the reflectance in the near infrared band, and Red to the reflectance in the red band. It is closely related to FAPAR and is little scale dependant. ",PROBA-V,,,,"Land,NDVI,PROBA-V",,proprietary,Global 10-daily Normalized Difference Vegetation Index 333M,2014-01-01T00:00:00Z,,,,,,,,,,,,,,,,,,,,,available -COP_DEM_GLO30_DGED,"Defence Gridded Elevation Data (DGED) formatted Copernicus DEM GLO-30 data. The Copernicus Digital Elevation Model is a Digital Surface Model (DSM) that represents the surface of the Earth including buildings, infrastructure and vegetation. The Copernicus DEM is provided in 3 different instances: EEA-10, GLO-30 and GLO-90. GLO-30 provides worldwide coverage at 30 meters.Data were acquired through the TanDEM-X mission between 2011 and 2015. The datasets were made available for use in 2019 and will be maintained until 2026. ",,TerraSAR,,,"TerraSAR,TanDEM-X,DEM,surface,GLO-30,DSM,GDGED",ALTIMETRIC,proprietary,Copernicus DEM GLO-30 DGED,2010-06-21T00:00:00Z,,,,,,available,,,,,,,,,,,,,,,available -COP_DEM_GLO30_DTED,"Digital Terrain Elevation Data (DTED) formatted Copernicus DEM GLO-30 data. The Copernicus Digital Elevation Model is a Digital Surface Model (DSM) that represents the surface of the Earth including buildings, infrastructure and vegetation. The Copernicus DEM is provided in 3 different instances: EEA-10, GLO-30 and GLO-90. GLO-30 provides worldwide coverage at 30 meters.Data were acquired through the TanDEM-X mission between 2011 and 2015. The datasets were made available for use in 2019 and will be maintained until 2026. ",,TerraSAR,,,"TerraSAR,TanDEM-X,DEM,surface,GLO-30,DSM,DTED",ALTIMETRIC,proprietary,Copernicus DEM GLO-30 DTED,2010-06-21T00:00:00Z,,,,,,available,,,,,,,,,,,,,,, -COP_DEM_GLO90_DGED,"Defence Gridded Elevation Data (DGED) formatted Copernicus DEM GLO-90 data. The Copernicus Digital Elevation Model is a Digital Surface Model (DSM) that represents the surface of the Earth including buildings, infrastructure and vegetation. The Copernicus DEM is provided in 3 different instances: EEA-10, GLO-30 and GLO-90. GLO-90 provides worldwide coverage at 90 meters.Data were acquired through the TanDEM-X mission between 2011 and 2015. The datasets were made available for use in 2019 and will be maintained until 2026. ",,TerraSAR,,,"TerraSAR,TanDEM-X,DEM,surface,GLO-90,DSM,GDGED",ALTIMETRIC,proprietary,Copernicus DEM GLO-90 DGED,2010-06-21T00:00:00Z,,,,,,available,,,,,,,,,,,,,,,available -COP_DEM_GLO90_DTED,"Digital Terrain Elevation Data (DTED) formatted Copernicus DEM GLO-90 data. The Copernicus Digital Elevation Model is a Digital Surface Model (DSM) that represents the surface of the Earth including buildings, infrastructure and vegetation. The Copernicus DEM is provided in 3 different instances: EEA-10, GLO-30 and GLO-90. GLO-90 provides worldwide coverage at 90 meters.Data were acquired through the TanDEM-X mission between 2011 and 2015. The datasets were made available for use in 2019 and will be maintained until 2026. ",,TerraSAR,,,"TerraSAR,TanDEM-X,DEM,surface,GLO-90,DSM,DTED",ALTIMETRIC,proprietary,Copernicus DEM GLO-90 DTED,2010-06-21T00:00:00Z,,,,,,available,,,,,,,,,,,,,,, +COP_DEM_GLO30_DGED,"Defence Gridded Elevation Data (DGED) formatted Copernicus DEM GLO-30 data. The Copernicus Digital Elevation Model is a Digital Surface Model (DSM) that represents the surface of the Earth including buildings, infrastructure and vegetation. The Copernicus DEM is provided in 3 different instances: EEA-10, GLO-30 and GLO-90. GLO-30 provides worldwide coverage at 30 meters.Data were acquired through the TanDEM-X mission between 2011 and 2015. The datasets were made available for use in 2019 and will be maintained until 2026. ",,TerraSAR,,,"TerraSAR,TanDEM-X,DEM,surface,GLO-30,DSM,GDGED",ALTIMETRIC,proprietary,Copernicus DEM GLO-30 DGED,2010-06-21T00:00:00Z,,,,,,available,available,,,,,,,,,,,,,,available +COP_DEM_GLO30_DTED,"Digital Terrain Elevation Data (DTED) formatted Copernicus DEM GLO-30 data. The Copernicus Digital Elevation Model is a Digital Surface Model (DSM) that represents the surface of the Earth including buildings, infrastructure and vegetation. The Copernicus DEM is provided in 3 different instances: EEA-10, GLO-30 and GLO-90. GLO-30 provides worldwide coverage at 30 meters.Data were acquired through the TanDEM-X mission between 2011 and 2015. The datasets were made available for use in 2019 and will be maintained until 2026. ",,TerraSAR,,,"TerraSAR,TanDEM-X,DEM,surface,GLO-30,DSM,DTED",ALTIMETRIC,proprietary,Copernicus DEM GLO-30 DTED,2010-06-21T00:00:00Z,,,,,,available,available,,,,,,,,,,,,,, +COP_DEM_GLO90_DGED,"Defence Gridded Elevation Data (DGED) formatted Copernicus DEM GLO-90 data. The Copernicus Digital Elevation Model is a Digital Surface Model (DSM) that represents the surface of the Earth including buildings, infrastructure and vegetation. The Copernicus DEM is provided in 3 different instances: EEA-10, GLO-30 and GLO-90. GLO-90 provides worldwide coverage at 90 meters.Data were acquired through the TanDEM-X mission between 2011 and 2015. The datasets were made available for use in 2019 and will be maintained until 2026. ",,TerraSAR,,,"TerraSAR,TanDEM-X,DEM,surface,GLO-90,DSM,GDGED",ALTIMETRIC,proprietary,Copernicus DEM GLO-90 DGED,2010-06-21T00:00:00Z,,,,,,available,available,,,,,,,,,,,,,,available +COP_DEM_GLO90_DTED,"Digital Terrain Elevation Data (DTED) formatted Copernicus DEM GLO-90 data. The Copernicus Digital Elevation Model is a Digital Surface Model (DSM) that represents the surface of the Earth including buildings, infrastructure and vegetation. The Copernicus DEM is provided in 3 different instances: EEA-10, GLO-30 and GLO-90. GLO-90 provides worldwide coverage at 90 meters.Data were acquired through the TanDEM-X mission between 2011 and 2015. The datasets were made available for use in 2019 and will be maintained until 2026. ",,TerraSAR,,,"TerraSAR,TanDEM-X,DEM,surface,GLO-90,DSM,DTED",ALTIMETRIC,proprietary,Copernicus DEM GLO-90 DTED,2010-06-21T00:00:00Z,,,,,,available,available,,,,,,,,,,,,,, EEA_DAILY_SSM_1KM,"Surface Soil Moisture (SSM) is the relative water content of the top few centimetres soil, describing how wet or dry the soil is in its topmost layer, expressed in percent saturation. It is measured by satellite radar sensors and allows insights in local precipitation impacts and soil conditions. SSM is a key driver of water and heat fluxes between the ground and the atmosphere, regulating air temperature and humidity. Moreover, in its role as water supply, it is vital to vegetation health. Vice versa, SSM is very sensitive to external forcing in the form of precipitation, temperature, solar irradiation, humidity, and wind. SSM is thus both an integrator of climatic conditions and a driver of local weather and climate, and plays a major role in global water-, energy- and carbon- cycles. Knowledge on the dynamics of soil moisture is important in the understanding of processes in many environmental and socio-economic fields, e.g., its impact on vegetation vitality, crop yield, droughts or exposure to flood threats. ","C-SAR,Metop ASCAT",Sentinel-1,,,"SSM,C-SAR,Metop-ASCAT,Sentinel-1",RADAR,proprietary,"Surface Soil Moisture: continental Europe daily (raster 1km) - version 1, Apr 2019",2015-01-01T00:00:00Z,,,,,,,,,,,,,,,,,,,,,available EEA_DAILY_SWI_1KM,"The Soil Water Index (SWI) quantifies the moisture condition at various depths in the soil. It is mainly driven by the precipitation via the process of infiltration. Soil moisture is a very heterogeneous variable and varies on small scales with soil properties and drainage patterns. Satellite measurements integrate over relative large-scale areas, with the presence of vegetation adding complexity to the interpretation. Soil moisture is a key parameter in numerous environmental studies including hydrology, meteorology and agriculture, and is recognized as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS). The SWI product provides daily information about moisture conditions in different soil layers. It includes a quality flag (QFLAG) indicating the availability of SSM measurements for SWI calculations, and a Surface State Flag (SSF) indicating frozen or snow covered soils. ","C-SAR,Metop ASCAT",Sentinel-1,,,"SWI,QFLAG,SSF,C-SAR,Metop-ASCAT,Sentinel-1",RADAR,proprietary,"Soil Water Index: continental Europe daily (raster 1km) - version 1, Apr 2019",2015-01-01T00:00:00Z,,,,,,,,,,,,,,,,,,,,,available EEA_DAILY_VI,"Vegetation Indices (VI) comprises four daily vegetation indices (PPI, NDVI, LAI and FAPAR) and quality information, that are part of the Copernicus Land Monitoring Service (CLMS) HR-VPP product suite. The 10m resolution, daily updated Plant Phenology Index (PPI), Normalized Difference Vegetation Index (NDVI), Leaf Area Index (LAI) and Fraction of Absorbed Photosynthetically Active Radiation (fAPAR) are derived from Copernicus Sentinel-2 satellite observations. They are provided together with a related quality indicator (QFLAG2) that flags clouds, shadows, snow, open water and other areas where the VI retrieval is less reliable. These Vegetation Indices are made available as a set of raster files with 10 x 10m resolution, in UTM/WGS84 projection corresponding to the Sentinel-2 tiling grid, for those tiles that cover the EEA38 countries and the United Kingdom and for the period from 2017 until today, with daily updates. The Vegetation Indices are part of the pan-European High Resolution Vegetation Phenology and Productivity (HR-VPP) component of the Copernicus Land Monitoring Service (CLMS). ",,Sentinel-2,"S2A, S2B",,"Land,Plant-phenology-index,Phenology,Vegetation,Sentinel-2,S2A,S2B",RADAR,proprietary,"Vegetation Indices, daily, UTM projection",,,,,,,,,,,,,,,,,,,,,,available diff --git a/docs/getting_started_guide/configure.rst b/docs/getting_started_guide/configure.rst index ac0559c5..4601b6ae 100644 --- a/docs/getting_started_guide/configure.rst +++ b/docs/getting_started_guide/configure.rst @@ -137,6 +137,7 @@ Core configuration using environment variables Some EODAG core settings can be overriden using environment variables: +* ``EODAG_CFG_DIR`` customized configuration directory in place of ``~/.config/eodag`` * ``EODAG_CFG_FILE`` for defining the desired path to the `user configuration file\ <https://eodag.readthedocs.io/en/stable/getting_started_guide/configure.html#yaml-user-configuration-file>`_ * ``EODAG_LOCS_CFG_FILE`` for defining the desired path to the diff --git a/eodag/api/core.py b/eodag/api/core.py index bcd5d3e5..81a69d27 100644 --- a/eodag/api/core.py +++ b/eodag/api/core.py @@ -21,6 +21,7 @@ import logging import os import re import shutil +import tempfile from operator import itemgetter from typing import ( TYPE_CHECKING, @@ -129,8 +130,27 @@ class EODataAccessGateway: self.product_types_config_md5 = obj_md5sum(self.product_types_config.source) self.providers_config = load_default_config() - self.conf_dir = os.path.join(os.path.expanduser("~"), ".config", "eodag") - makedirs(self.conf_dir) + env_var_cfg_dir = "EODAG_CFG_DIR" + self.conf_dir = os.getenv( + env_var_cfg_dir, + default=os.path.join(os.path.expanduser("~"), ".config", "eodag"), + ) + try: + makedirs(self.conf_dir) + except OSError as e: + logger.debug(e) + tmp_conf_dir = os.path.join(tempfile.gettempdir(), ".config", "eodag") + logger.warning( + f"Cannot create configuration directory {self.conf_dir}. " + + f"Falling back to temporary directory {tmp_conf_dir}." + ) + if os.getenv(env_var_cfg_dir) is None: + logger.warning( + "You can set the path of the configuration directory " + + f"with the environment variable {env_var_cfg_dir}" + ) + self.conf_dir = tmp_conf_dir + makedirs(self.conf_dir) self._plugins_manager = PluginManager(self.providers_config) # use updated providers_config

CS-SI/eodag

72e7a48eba23f7debb89903f31d67555b53fcbce

diff --git a/tests/units/test_core.py b/tests/units/test_core.py index f5f118c4..46fc1bed 100644 --- a/tests/units/test_core.py +++ b/tests/units/test_core.py @@ -22,6 +22,7 @@ import json import logging import os import shutil +import tempfile import unittest import uuid from pathlib import Path @@ -1178,6 +1179,20 @@ class TestCoreConfWithEnvVar(TestCoreBase): class TestCoreInvolvingConfDir(unittest.TestCase): + @classmethod + def setUpClass(cls): + super(TestCoreInvolvingConfDir, cls).setUpClass() + cls.dag = EODataAccessGateway() + # mock os.environ to empty env + cls.mock_os_environ = mock.patch.dict(os.environ, {}, clear=True) + cls.mock_os_environ.start() + + @classmethod + def tearDownClass(cls): + super(TestCoreInvolvingConfDir, cls).tearDownClass() + # stop os.environ + cls.mock_os_environ.stop() + def setUp(self): super(TestCoreInvolvingConfDir, self).setUp() self.dag = EODataAccessGateway() @@ -1194,14 +1209,15 @@ class TestCoreInvolvingConfDir(unittest.TestCase): except OSError: shutil.rmtree(old_path) - def execution_involving_conf_dir(self, inspect=None): + def execution_involving_conf_dir(self, inspect=None, conf_dir=None): """Check that the path(s) inspected (str, list) are created after the instantation of EODataAccessGateway. If they were already there, rename them (.old), instantiate, check, delete the new files, and restore the existing files to there previous name.""" if inspect is not None: + if conf_dir is None: + conf_dir = os.path.join(os.path.expanduser("~"), ".config", "eodag") if isinstance(inspect, str): inspect = [inspect] - conf_dir = os.path.join(os.path.expanduser("~"), ".config", "eodag") olds = [] currents = [] for inspected in inspect: @@ -1233,6 +1249,49 @@ class TestCoreInvolvingConfDir(unittest.TestCase): """The core object must create a locations config file and a shp dir in standard user config location on instantiation""" # noqa self.execution_involving_conf_dir(inspect=["locations.yml", "shp"]) + def test_read_only_home_dir(self): + # standard directory + home_dir = os.path.join(os.path.expanduser("~"), ".config", "eodag") + self.execution_involving_conf_dir(inspect="eodag.yml", conf_dir=home_dir) + + # user defined directory + user_dir = os.path.join(os.path.expanduser("~"), ".config", "another_eodag") + os.environ["EODAG_CFG_DIR"] = user_dir + self.execution_involving_conf_dir(inspect="eodag.yml", conf_dir=user_dir) + shutil.rmtree(user_dir) + del os.environ["EODAG_CFG_DIR"] + + # fallback temporary folder + def makedirs_side_effect(dir): + if dir == os.path.join(os.path.expanduser("~"), ".config", "eodag"): + raise OSError("Mock makedirs error") + else: + return makedirs(dir) + + with mock.patch( + "eodag.api.core.makedirs", side_effect=makedirs_side_effect + ) as mock_makedirs: + # backup temp_dir if exists + temp_dir = temp_dir_old = os.path.join( + tempfile.gettempdir(), ".config", "eodag" + ) + if os.path.exists(temp_dir): + temp_dir_old = f"{temp_dir}.old" + shutil.move(temp_dir, temp_dir_old) + + EODataAccessGateway() + expected = [unittest.mock.call(home_dir), unittest.mock.call(temp_dir)] + mock_makedirs.assert_has_calls(expected) + self.assertTrue(os.path.exists(temp_dir)) + + # restore temp_dir + if temp_dir_old != temp_dir: + try: + shutil.rmtree(temp_dir) + except OSError: + os.unlink(temp_dir) + shutil.move(temp_dir_old, temp_dir) + class TestCoreGeometry(TestCoreBase): @classmethod

EODataAccessGateway constructor fails on AWS Lambda **Describe the bug** `makedirs` [invocation](https://github.com/CS-SI/eodag/blob/develop/eodag/api/core.py#L98) within the EODataAccessGateway constructor causes `OSError: [Errno 30] Read-only file system` when run on AWS Lambda **Code To Reproduce** CLI commands or Python code snippet to reproduce the bug. Please use maximum verbosity using: ```py from aws_lambda_powertools.logging import Logger from aws_lambda_powertools.tracing import Tracer from eodag import EODataAccessGateway logger = Logger() tracer = Tracer() @tracer.capture_lambda_handler @logger.inject_lambda_context def lambda_handler(event, context): EODataAccessGateway() ``` **Output** Compete output obtained with maximal verbosity. ``` [ERROR] OSError: [Errno 30] Read-only file system: '/home/sbx_user1051' Traceback (most recent call last): File "/opt/python/aws_lambda_powertools/tracing/tracer.py", line 305, in decorate response = lambda_handler(event, context, **kwargs) File "/opt/python/aws_lambda_powertools/logging/logger.py", line 438, in decorate return lambda_handler(event, context, *args, **kwargs) File "/var/task/<my file, my line>, in lambda_handler EODataAccessGateway() File "/opt/python/eodag/api/core.py", line 91, in __init__ makedirs(self.conf_dir) File "/opt/python/eodag/utils/__init__.py", line 496, in makedirs os.makedirs(dirpath) File "/var/lang/lib/python3.9/os.py", line 215, in makedirs makedirs(head, exist_ok=exist_ok) File "/var/lang/lib/python3.9/os.py", line 215, in makedirs makedirs(head, exist_ok=exist_ok) File "/var/lang/lib/python3.9/os.py", line 225, in makedirs mkdir(name, mode) ``` **Environment:** - Python version: 3.9 - EODAG version: 2.5.2 - Runtime: AWS Lambda **Additional context** File system on AWS Lambda is read-only. It has "ephemeral storage" that could be accessed in `/tmp` ([1](https://aws.amazon.com/blogs/aws/aws-lambda-now-supports-up-to-10-gb-ephemeral-storage/), [2](https://aws.amazon.com/blogs/aws/aws-lambda-now-supports-up-to-10-gb-ephemeral-storage/)), however this class does not accept any configuration to where to point to `makedirs`. The workaround that heavily relies on the [current implementation](https://github.com/CS-SI/eodag/blob/develop/eodag/api/core.py#L97) is to change `$HOME` env var before invoking the constructor. But it is barely acceptable and extremely inconvenient, since this variable is used by many tools locally and in automated tools along the way.

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CSCfi__swift-browser-ui-41

diff --git a/docs/source/_static/api.yml b/docs/source/_static/api.yml index a46ecf9b..720d80bf 100644 --- a/docs/source/_static/api.yml +++ b/docs/source/_static/api.yml @@ -156,11 +156,34 @@ paths: get: tags: - API Endpoints - summary: Get container or object(s) metadata. + summary: Get container metadata. parameters: - name: container in: query - description: The container the metadata of which is to be queried, or the container in which the queried objects are. + description: The container the metadata of which is to be queried. + schema: + type: string + example: test-container-1 + responses: + 200: + description: OK + content: + application/json: + schema: + $ref: '#/components/schemas/Meta' + 403: + description: Unauthorized + 404: + description: Not Found + /bucket/object/meta: + get: + tags: + - API Endpoints + summary: Get object(s) metadata. + parameters: + - name: container + in: query + description: The container in which the queried objects are. schema: type: string example: test-container-1 @@ -181,7 +204,6 @@ paths: description: Unauthorized 404: description: Not Found - components: schemas: diff --git a/swift_browser_ui/api.py b/swift_browser_ui/api.py index 6490830a..c4b2b00e 100644 --- a/swift_browser_ui/api.py +++ b/swift_browser_ui/api.py @@ -263,7 +263,46 @@ async def get_object_metadata(conn, meta_cont, meta_obj): raise aiohttp.web.HTTPNotFound() -async def get_metadata(request): +async def get_metadata_bucket(request): + """Get metadata for a container.""" + session = api_check(request) + request.app['Log'].info( + 'API cal for project listing from {0}, sess: {1} :: {2}'.format( + request.remote, + session, + time.ctime(), + ) + ) + + # Get required variables from query string + meta_cont = ( + request.query['container'] + if 'container' in request.query.keys() + else None + ) + conn = request.app['Creds'][session]['ST_conn'] + # Get container listing if no object list was specified + ret = conn.stat(meta_cont) + + if not ret['success']: + raise aiohttp.web.HTTPNotFound() + + # Strip any unnecessary information from the metadata headers + ret['headers'] = dict(filter( + lambda i: "x-container-meta" in i[0], + ret['headers'].items() + )) + ret['headers'] = { + k.replace("x-container-meta-", ""): v + for k, v in ret['headers'].items() + } + + return aiohttp.web.json_response( + [ret['container'], ret['headers']] + ) + + +async def get_metadata_object(request): """Get metadata for a container or for an object.""" session = api_check(request) request.app['Log'].info( @@ -295,26 +334,6 @@ async def get_metadata(request): conn = request.app['Creds'][session]['ST_conn'] - # Get container listing if no object list was specified - if not meta_obj: - ret = conn.stat(meta_cont) - - if not ret['success']: - raise aiohttp.web.HTTPNotFound() - - # Strip any unnecessary information from the metadata headers - ret['headers'] = dict(filter( - lambda i: "x-container-meta" in i[0], - ret['headers'].items() - )) - ret['headers'] = { - k.replace("x-container-meta-", ""): v - for k, v in ret['headers'].items() - } - - return aiohttp.web.json_response( - [ret['container'], ret['headers']] - ) # Otherwise get object listing (object listing won't need to throw an # exception here incase of a failure – the function handles that) return aiohttp.web.json_response( diff --git a/swift_browser_ui/server.py b/swift_browser_ui/server.py index fc6c9af6..481324fd 100644 --- a/swift_browser_ui/server.py +++ b/swift_browser_ui/server.py @@ -19,7 +19,7 @@ from .login import sso_query_end from .login import token_rescope from .api import list_buckets, list_objects, download_object, os_list_projects from .api import get_os_user, get_os_active_project -from .api import get_metadata, get_project_metadata +from .api import get_metadata_object, get_metadata_bucket, get_project_metadata from .api import swift_list_shared_objects from .settings import setd from .middlewares import error_middleware @@ -116,7 +116,8 @@ async def servinit(): aiohttp.web.get('/api/username', get_os_user), aiohttp.web.get('/api/projects', os_list_projects), aiohttp.web.get('/api/project/active', get_os_active_project), - aiohttp.web.get('/api/bucket/meta', get_metadata), + aiohttp.web.get('/api/bucket/meta', get_metadata_bucket), + aiohttp.web.get('/api/bucket/object/meta', get_metadata_object), aiohttp.web.get('/api/project/meta', get_project_metadata), ])

CSCfi/swift-browser-ui

941a02a58da7335438f2cd91bb5765a84e8cf687

diff --git a/tests/unit/test_api.py b/tests/unit/test_api.py index e4888a19..ac566f9b 100644 --- a/tests/unit/test_api.py +++ b/tests/unit/test_api.py @@ -13,7 +13,8 @@ from swiftclient.service import SwiftError from swift_browser_ui.api import get_os_user, os_list_projects from swift_browser_ui.api import swift_list_buckets, swift_list_objects from swift_browser_ui.api import swift_download_object -from swift_browser_ui.api import get_metadata +from swift_browser_ui.api import get_metadata_object +from swift_browser_ui.api import get_metadata_bucket from swift_browser_ui.api import get_project_metadata from swift_browser_ui.api import get_os_active_project from swift_browser_ui.settings import setd @@ -210,7 +211,7 @@ class APITestClass(asynctest.TestCase): # Set up the query string self.request.query["container"] = "test-container-0" - resp = await get_metadata(self.request) + resp = await get_metadata_bucket(self.request) resp = json.loads(resp.text) expected = [ # nosec @@ -248,7 +249,7 @@ class APITestClass(asynctest.TestCase): self.request.query["container"] = "test-container-0" self.request.query["object"] = objkey - resp = await get_metadata(self.request) + resp = await get_metadata_object(self.request) resp = json.loads(resp.text) expected = [[ objkey, {"obj-example": "example"} @@ -285,7 +286,7 @@ class APITestClass(asynctest.TestCase): self.request.query["container"] = "test-container-0" self.request.query["object"] = objkey - resp = await get_metadata(self.request) + resp = await get_metadata_object(self.request) resp = json.loads(resp.text) expected = [[ # nosec @@ -330,7 +331,7 @@ class APITestClass(asynctest.TestCase): "%s,%s,%s,%s,%s" % tuple([i["name"] for i in objs]) ) - resp = await get_metadata(self.request) + resp = await get_metadata_object(self.request) resp = json.loads(resp.text) comp = [

Split container and object metadata API request #### Description Container and object metadata would be more intuitive when queried from separate API endpoints. Proposal to split /bucket/meta -> /bucket/meta & /bucket/object/meta to make the API more intuitive. (inspired by PR #34) #### DoD (Definition of Done) Metadata API is refactored to contain separate endpoints for objects and for containers. #### Testing Unit tests for the split API functions.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

CTFd__CTFd-1802

diff --git a/CTFd/forms/config.py b/CTFd/forms/config.py index aee30b12..51ba3d56 100644 --- a/CTFd/forms/config.py +++ b/CTFd/forms/config.py @@ -33,8 +33,15 @@ class AccountSettingsForm(BaseForm): "Account Email Whitelist", description="Comma-seperated email domains which users can register under (e.g. ctfd.io, gmail.com, yahoo.com)", ) + team_creation = SelectField( + "Team Creation", + description="Control whether users can create their own teams (Teams mode only)", + choices=[("true", "Enabled"), ("false", "Disabled")], + default="true", + ) team_size = IntegerField( - widget=NumberInput(min=0), description="Amount of users per team" + widget=NumberInput(min=0), + description="Amount of users per team (Teams mode only)", ) verify_emails = SelectField( "Verify Emails", diff --git a/CTFd/teams.py b/CTFd/teams.py index 1d0a2e0d..1b99d6af 100644 --- a/CTFd/teams.py +++ b/CTFd/teams.py @@ -191,6 +191,12 @@ def new(): infos = get_infos() errors = get_errors() + if bool(get_config("team_creation", default=True)) is False: + abort( + 403, + description="Team creation is currently disabled. Please join an existing team.", + ) + user = get_current_user_attrs() if user.team_id: errors.append("You are already in a team. You cannot join another.") diff --git a/CTFd/themes/admin/templates/configs/accounts.html b/CTFd/themes/admin/templates/configs/accounts.html index dc518087..32ebdde5 100644 --- a/CTFd/themes/admin/templates/configs/accounts.html +++ b/CTFd/themes/admin/templates/configs/accounts.html @@ -2,7 +2,8 @@ {% set verify_emails = "true" if verify_emails == True else "false" %} {% set name_changes = "true" if name_changes == True else "false" %} - {% with form = Forms.config.AccountSettingsForm(verify_emails=verify_emails, name_changes=name_changes, team_disbanding=team_disbanding) %} + {% set team_creation = "true" if team_creation == True else "false" %} + {% with form = Forms.config.AccountSettingsForm(verify_emails=verify_emails, name_changes=name_changes, team_disbanding=team_disbanding, team_creation=team_creation) %} <form method="POST" autocomplete="off" class="w-100"> <div class="form-group"> @@ -21,6 +22,14 @@ </small> </div> + <div class="form-group"> + {{ form.team_creation.label }} + {{ form.team_creation(class="form-control", value=team_creation) }} + <small class="form-text text-muted"> + {{ form.team_creation.description }} + </small> + </div> + <div class="form-group"> {{ form.team_size.label }} {{ form.team_size(class="form-control", value=team_size) }}

CTFd/CTFd

abdc366bb78e8a734b0525ffcaab85e7c6d9177d

diff --git a/tests/teams/test_teams.py b/tests/teams/test_teams.py index eb09e762..333c2e05 100644 --- a/tests/teams/test_teams.py +++ b/tests/teams/test_teams.py @@ -179,3 +179,31 @@ def test_team_size_limit(): resp = r.get_data(as_text=True) assert len(Teams.query.filter_by(id=team_id).first().members) == 2 destroy_ctfd(app) + + +def test_team_creation_disable(): + app = create_ctfd(user_mode="teams") + with app.app_context(): + register_user(app) + with login_as_user(app) as client: + # Team creation page should be available + r = client.get("/teams/new") + assert r.status_code == 200 + + # Disable team creation in config + set_config("team_creation", False) + + # Can't access the public team creation page + r = client.get("/teams/new") + assert r.status_code == 403 + + # User should be blocked from creating teams as well + with client.session_transaction() as sess: + data = { + "name": "team_name", + "password": "password", + "nonce": sess.get("nonce"), + } + r = client.post("/teams/new", data=data) + assert r.status_code == 403 + destroy_ctfd(app)

Feature request: disable team creation I have a use case where the teams are manually created and the students receive the teamname+passcode. Team creation should be disabled so that they only can join an existing team.

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CTFd__CTFd-2269

diff --git a/CTFd/themes/admin/templates/config.html b/CTFd/themes/admin/templates/config.html index 3fae030e..1e097069 100644 --- a/CTFd/themes/admin/templates/config.html +++ b/CTFd/themes/admin/templates/config.html @@ -23,6 +23,9 @@ <li class="nav-item"> <a class="nav-link rounded-0" href="#accounts" role="tab" data-toggle="tab">Accounts</a> </li> + <li class="nav-item"> + <a class="nav-link rounded-0" href="#pages" role="tab" data-toggle="tab">Pages</a> + </li> <li class="nav-item"> <a class="nav-link rounded-0" href="#fields" role="tab" data-toggle="tab">Custom Fields</a> </li> @@ -73,6 +76,8 @@ {% include "admin/configs/accounts.html" %} + {% include "admin/configs/pages.html" %} + {% include "admin/configs/fields.html" %} {% include "admin/configs/mlc.html" %} diff --git a/CTFd/themes/admin/templates/configs/pages.html b/CTFd/themes/admin/templates/configs/pages.html new file mode 100644 index 00000000..972f425c --- /dev/null +++ b/CTFd/themes/admin/templates/configs/pages.html @@ -0,0 +1,14 @@ +<div role="tabpanel" class="tab-pane config-section" id="pages"> + <form method="POST" enctype="multipart/form-data"> + <div class="form-group"> + <label> + Robots.txt + <small class="form-text text-muted"> + The robots.txt file contains instructions that suggest to bots which webpages they can and cannot access + </small> + </label> + <textarea class="form-control" id="theme-footer" name="robots_txt" rows="7">{{ robots_txt or "User-agent: *\nDisallow: /admin\n" }}</textarea> + </div> + <button type="submit" class="btn btn-md btn-primary float-right">Update</button> + </form> +</div> diff --git a/CTFd/utils/initialization/__init__.py b/CTFd/utils/initialization/__init__.py index 8e0c376c..7379b36e 100644 --- a/CTFd/utils/initialization/__init__.py +++ b/CTFd/utils/initialization/__init__.py @@ -204,6 +204,7 @@ def init_request_processors(app): "views.themes", "views.files", "views.healthcheck", + "views.robots", ): return else: diff --git a/CTFd/views.py b/CTFd/views.py index d94cecf3..8876bab8 100644 --- a/CTFd/views.py +++ b/CTFd/views.py @@ -2,7 +2,15 @@ import os from flask import Blueprint, abort from flask import current_app as app -from flask import redirect, render_template, request, send_file, session, url_for +from flask import ( + make_response, + redirect, + render_template, + request, + send_file, + session, + url_for, +) from flask.helpers import safe_join from jinja2.exceptions import TemplateNotFound from sqlalchemy.exc import IntegrityError @@ -514,3 +522,11 @@ def healthcheck(): if check_config() is False: return "ERR", 500 return "OK", 200 + + [email protected]("/robots.txt") +def robots(): + text = get_config("robots_txt", "User-agent: *\nDisallow: /admin\n") + r = make_response(text, 200) + r.mimetype = "text/plain" + return r

CTFd/CTFd

68da00900a792fffae8e563198abe8045d33c0a9

diff --git a/tests/test_views.py b/tests/test_views.py index 3b814940..55da66bf 100644 --- a/tests/test_views.py +++ b/tests/test_views.py @@ -451,3 +451,19 @@ def test_user_can_access_files_if_view_after_ctf(): rmdir(directory) destroy_ctfd(app) + + +def test_robots_txt(): + """Does the robots.txt page work""" + app = create_ctfd() + with app.app_context(): + with app.test_client() as client: + r = client.get("/robots.txt") + assert r.status_code == 200 + assert r.get_data(as_text=True) == "User-agent: *\nDisallow: /admin\n" + set_config("robots_txt", "testing") + with app.test_client() as client: + r = client.get("/robots.txt") + assert r.status_code == 200 + assert r.get_data(as_text=True) == "testing" + destroy_ctfd(app)

Controlling static content like robots.txt Some users seem to wish to be able to control things like their robots.txt. Is this something that we could implement in CTFd? Perhaps as a type of Page with a custom reponse type?

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CTFd__CTFd-2333

diff --git a/CTFd/api/v1/hints.py b/CTFd/api/v1/hints.py index 0ee60fa3..8d347fd9 100644 --- a/CTFd/api/v1/hints.py +++ b/CTFd/api/v1/hints.py @@ -9,7 +9,8 @@ from CTFd.api.v1.schemas import APIDetailedSuccessResponse, APIListSuccessRespon from CTFd.constants import RawEnum from CTFd.models import Hints, HintUnlocks, db from CTFd.schemas.hints import HintSchema -from CTFd.utils.decorators import admins_only, authed_only, during_ctf_time_only +from CTFd.utils.decorators import admins_only, during_ctf_time_only +from CTFd.utils.decorators.visibility import check_challenge_visibility from CTFd.utils.helpers.models import build_model_filters from CTFd.utils.user import get_current_user, is_admin @@ -105,7 +106,7 @@ class HintList(Resource): @hints_namespace.route("/<hint_id>") class Hint(Resource): @during_ctf_time_only - @authed_only + @check_challenge_visibility @hints_namespace.doc( description="Endpoint to get a specific Hint object", responses={ @@ -117,11 +118,23 @@ class Hint(Resource): }, ) def get(self, hint_id): - user = get_current_user() hint = Hints.query.filter_by(id=hint_id).first_or_404() + user = get_current_user() + + # We allow public accessing of hints if challenges are visible and there is no cost or prerequisites + # If there is a cost or a prereq we should block the user from seeing the hint + if user is None: + if hint.cost or hint.prerequisites: + return ( + { + "success": False, + "errors": {"cost": ["You must login to unlock this hint"]}, + }, + 403, + ) - if hint.requirements: - requirements = hint.requirements.get("prerequisites", []) + if hint.prerequisites: + requirements = hint.prerequisites # Get the IDs of all hints that the user has unlocked all_unlocks = HintUnlocks.query.filter_by(account_id=user.account_id).all() diff --git a/CTFd/models/__init__.py b/CTFd/models/__init__.py index 713bfc3f..45f9d21b 100644 --- a/CTFd/models/__init__.py +++ b/CTFd/models/__init__.py @@ -181,6 +181,12 @@ class Hints(db.Model): return markup(build_markdown(self.content)) + @property + def prerequisites(self): + if self.requirements: + return self.requirements.get("prerequisites", []) + return [] + def __init__(self, *args, **kwargs): super(Hints, self).__init__(**kwargs)

CTFd/CTFd

7bae8360c83ad067c7f89d46bf57fd8e14f95d0d

diff --git a/tests/api/v1/user/test_hints.py b/tests/api/v1/user/test_hints.py index ad69882c..e7609135 100644 --- a/tests/api/v1/user/test_hints.py +++ b/tests/api/v1/user/test_hints.py @@ -3,6 +3,7 @@ from freezegun import freeze_time +from CTFd.models import Hints from CTFd.utils import set_config from tests.helpers import ( create_ctfd, @@ -180,3 +181,90 @@ def test_api_hint_admin_access(): r_admin = admin.delete("/api/v1/hints/1", json="") assert r_admin.status_code == 200 destroy_ctfd(app) + + +def test_api_hints_accessible_public(): + """Test that hints with no cost and no prerequsites can be viewed publicy""" + app = create_ctfd() + with app.app_context(): + # Set challenges to be visible publicly + set_config("challenge_visibility", "public") + + register_user(app) + chal = gen_challenge(app.db) + gen_hint( + app.db, chal.id, content="This is a free hint", cost=0, type="standard" + ) + gen_hint( + app.db, chal.id, content="This is a private hint", cost=1, type="standard" + ) + gen_hint( + app.db, chal.id, content="This is a private hint", cost=1, type="standard" + ) + hint = Hints.query.filter_by(id=3).first() + hint.requirements = {"prerequisites": [2]} + app.db.session.commit() + + with app.test_client() as non_logged_in_user: + r = non_logged_in_user.get("/api/v1/hints/1") + hint = r.get_json()["data"] + assert hint["content"] == "This is a free hint" + + r = non_logged_in_user.get("/api/v1/hints/2") + assert r.status_code == 403 + errors = r.get_json()["errors"] + assert errors == {"cost": ["You must login to unlock this hint"]} + + r = non_logged_in_user.get("/api/v1/hints/3") + assert r.status_code == 403 + errors = r.get_json()["errors"] + assert errors == {"cost": ["You must login to unlock this hint"]} + + r = non_logged_in_user.post( + "/api/v1/unlocks", json={"target": 2, "type": "hints"} + ) + assert r.status_code == 403 + + # Set challenges to be visible to only authed + set_config("challenge_visibility", "private") + + # Free hints no longer visible to unauthed + with app.test_client() as non_logged_in_user: + r = non_logged_in_user.get("/api/v1/hints/1", json="") + assert r.status_code == 403 + + # Verify existing hint behavior for authed users + with login_as_user(app) as client: + r = client.get("/api/v1/hints/1") + hint = r.get_json()["data"] + assert hint["content"] == "This is a free hint" + + r = client.get("/api/v1/hints/2") + assert r.status_code == 200 + assert "content" not in r.get_json()["data"] + + r = client.get("/api/v1/hints/3") + assert r.status_code == 403 + + gen_award(app.db, 2) + + # Haven't unlocked the prereq hint + r = client.get("/api/v1/hints/3") + assert r.status_code == 403 + + # Unlock the prereq + r = client.post("/api/v1/unlocks", json={"target": 2, "type": "hints"}) + assert r.status_code == 200 + r = client.get("/api/v1/hints/2") + assert r.status_code == 200 + + # Attempt to unlock again but dont have the points + r = client.get("/api/v1/hints/3") + assert r.status_code == 200 + assert "content" not in r.get_json()["data"] + + r = client.post("/api/v1/unlocks", json={"target": 3, "type": "hints"}) + assert r.status_code == 200 + r = client.get("/api/v1/hints/3") + assert r.status_code == 200 + assert "content" in r.get_json()["data"]

Hints nonfunctional unless logged in <!-- If this is a bug report please fill out the template below. If this is a feature request please describe the behavior that you'd like to see. --> **Environment**: - CTFd Version/Commit: 3.5.0 - Operating System: any - Web Browser and Version: any **What happened?** Clicking on a hint while being signed out does absolutely nothing. This makes it seem like the website is nonfunctional. **What did you expect to happen?** Hints with no cost should be viewable without being signed in. If the hint has a cost, an error/alert telling the user to sign in should be displayed. **How to reproduce your issue** Have a CTFd instance with the challenges page public, attempt to click on a challenge hint.

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CTFd__ctfcli-148

diff --git a/ctfcli/cli/challenges.py b/ctfcli/cli/challenges.py index b56525c..51755e6 100644 --- a/ctfcli/cli/challenges.py +++ b/ctfcli/cli/challenges.py @@ -1,3 +1,4 @@ +import contextlib import logging import os import subprocess @@ -203,167 +204,253 @@ class ChallengeCommand: click.secho(f"Could not process the challenge path: '{repo}'", fg="red") return 1 - def push(self, challenge: str = None) -> int: + def push(self, challenge: str = None, no_auto_pull: bool = False, quiet=False) -> int: log.debug(f"push: (challenge={challenge})") config = Config() - challenge_path = Path.cwd() if challenge: - challenge_path = config.project_path / Path(challenge) + challenge_instance = self._resolve_single_challenge(challenge) + if not challenge_instance: + return 1 - # Get a relative path from project root to the challenge - # As this is what git subtree push requires - challenge_path = challenge_path.relative_to(config.project_path) - challenge_repo = config.challenges.get(str(challenge_path), None) + challenges = [challenge_instance] + else: + challenges = self._resolve_all_challenges() - # if we don't find the challenge by the directory, - # check if it's saved with a direct path to challenge.yml - if not challenge_repo: - challenge_repo = config.challenges.get(str(challenge_path / "challenge.yml"), None) + failed_pushes = [] - if not challenge_repo: - click.secho( - f"Could not find added challenge '{challenge_path}' " - "Please check that the challenge is added to .ctf/config and that your path matches", - fg="red", - ) - return 1 + if quiet or len(challenges) <= 1: + context = contextlib.nullcontext(challenges) + else: + context = click.progressbar(challenges, label="Pushing challenges") - if not challenge_repo.endswith(".git"): - click.secho( - f"Cannot push challenge '{challenge_path}', as it's not a git-based challenge", - fg="yellow", - ) - return 1 + with context as context_challenges: + for challenge_instance in context_challenges: + click.echo() - head_branch = get_git_repo_head_branch(challenge_repo) + # Get a relative path from project root to the challenge + # As this is what git subtree push requires + challenge_path = challenge_instance.challenge_directory.resolve().relative_to(config.project_path) + challenge_repo = config.challenges.get(str(challenge_path), None) - log.debug(f"call(['git', 'add', '.'], cwd='{config.project_path / challenge_path}')") - git_add = subprocess.call(["git", "add", "."], cwd=config.project_path / challenge_path) + # if we don't find the challenge by the directory, + # check if it's saved with a direct path to challenge.yml + if not challenge_repo: + challenge_repo = config.challenges.get(str(challenge_path / "challenge.yml"), None) - log.debug( - f"call(['git', 'commit', '-m', 'Pushing changes to {challenge_path}'], " - f"cwd='{config.project_path / challenge_path}')" - ) - git_commit = subprocess.call( - ["git", "commit", "-m", f"Pushing changes to {challenge_path}"], - cwd=config.project_path / challenge_path, - ) + if not challenge_repo: + click.secho( + f"Could not find added challenge '{challenge_path}' " + "Please check that the challenge is added to .ctf/config and that your path matches", + fg="red", + ) + failed_pushes.append(challenge_instance) + continue - if any(r != 0 for r in [git_add, git_commit]): - click.secho( - "Could not commit the challenge changes. " "Please check git error messages above.", - fg="red", - ) - return 1 + if not challenge_repo.endswith(".git"): + click.secho( + f"Cannot push challenge '{challenge_path}', as it's not a git-based challenge", + fg="yellow", + ) + failed_pushes.append(challenge_instance) + continue - log.debug( - f"call(['git', 'subtree', 'push', '--prefix', '{challenge_path}', '{challenge_repo}', '{head_branch}'], " - f"cwd='{config.project_path / challenge_path}')" - ) - git_subtree_push = subprocess.call( - [ - "git", - "subtree", - "push", - "--prefix", - challenge_path, - challenge_repo, - head_branch, - ], - cwd=config.project_path, - ) + click.secho(f"Pushing '{challenge_path}' to '{challenge_repo}'", fg="blue") + head_branch = get_git_repo_head_branch(challenge_repo) - if git_subtree_push != 0: - click.secho( - "Could not push the challenge subtree. " "Please check git error messages above.", - fg="red", - ) - return 1 + log.debug( + f"call(['git', 'status', '--porcelain'], cwd='{config.project_path / challenge_path}'," + f" stdout=subprocess.PIPE, text=True)" + ) + git_status = subprocess.run( + ["git", "status", "--porcelain"], + cwd=config.project_path / challenge_path, + stdout=subprocess.PIPE, + text=True, + ) - return 0 + if git_status.stdout.strip() == "" and git_status.returncode == 0: + click.secho(f"No changes to be pushed for {challenge_path}", fg="green") + continue + + log.debug(f"call(['git', 'add', '.'], cwd='{config.project_path / challenge_path}')") + git_add = subprocess.call(["git", "add", "."], cwd=config.project_path / challenge_path) + + log.debug( + f"call(['git', 'commit', '-m', 'Pushing changes to {challenge_path}'], " + f"cwd='{config.project_path / challenge_path}')" + ) + git_commit = subprocess.call( + ["git", "commit", "-m", f"Pushing changes to {challenge_path}"], + cwd=config.project_path / challenge_path, + ) + + if any(r != 0 for r in [git_add, git_commit]): + click.secho( + "Could not commit the challenge changes. " "Please check git error messages above.", + fg="red", + ) + failed_pushes.append(challenge_instance) + continue + + log.debug( + f"call(['git', 'subtree', 'push', '--prefix', '{challenge_path}', '{challenge_repo}', " + f"'{head_branch}'], cwd='{config.project_path / challenge_path}')" + ) + git_subtree_push = subprocess.call( + [ + "git", + "subtree", + "push", + "--prefix", + challenge_path, + challenge_repo, + head_branch, + ], + cwd=config.project_path, + ) + + if git_subtree_push != 0: + click.secho( + "Could not push the challenge subtree. " "Please check git error messages above.", + fg="red", + ) + failed_pushes.append(challenge_instance) + continue + + # if auto pull is not disabled + if not no_auto_pull: + self.pull(str(challenge_path), quiet=True) - def pull(self, challenge: str = None) -> int: + if len(failed_pushes) == 0: + if not quiet: + click.secho("Success! All challenges pushed!", fg="green") + + return 0 + + if not quiet: + click.secho("Push failed for:", fg="red") + for challenge in failed_pushes: + click.echo(f" - {challenge}") + + return 1 + + def pull(self, challenge: str = None, quiet=False) -> int: log.debug(f"pull: (challenge={challenge})") config = Config() - challenge_path = Path.cwd() if challenge: - challenge_path = config.project_path / Path(challenge) + challenge_instance = self._resolve_single_challenge(challenge) + if not challenge_instance: + return 1 - # Get a relative path from project root to the challenge - # As this is what git subtree push requires - challenge_path = challenge_path.relative_to(config.project_path) - challenge_repo = config.challenges.get(str(challenge_path), None) + challenges = [challenge_instance] + else: + challenges = self._resolve_all_challenges() - # if we don't find the challenge by the directory, - # check if it's saved with a direct path to challenge.yml - if not challenge_repo: - challenge_repo = config.challenges.get(str(challenge_path / "challenge.yml"), None) + if quiet or len(challenges) <= 1: + context = contextlib.nullcontext(challenges) + else: + context = click.progressbar(challenges, label="Pulling challenges") - if not challenge_repo: - click.secho( - f"Could not find added challenge '{challenge_path}' " - "Please check that the challenge is added to .ctf/config and that your path matches", - fg="red", - ) - return 1 + failed_pulls = [] + with context as context_challenges: + for challenge_instance in context_challenges: + click.echo() - if not challenge_repo.endswith(".git"): - click.secho( - f"Cannot pull challenge '{challenge_path}', as it's not a git-based challenge", - fg="yellow", - ) - return 1 + # Get a relative path from project root to the challenge + # As this is what git subtree push requires + challenge_path = challenge_instance.challenge_directory.resolve().relative_to(config.project_path) + challenge_repo = config.challenges.get(str(challenge_path), None) - click.secho(f"Pulling latest '{challenge_repo}' to '{challenge_path}'", fg="blue") - head_branch = get_git_repo_head_branch(challenge_repo) + # if we don't find the challenge by the directory, + # check if it's saved with a direct path to challenge.yml + if not challenge_repo: + challenge_repo = config.challenges.get(str(challenge_path / "challenge.yml"), None) - log.debug( - f"call(['git', 'subtree', 'pull', '--prefix', '{challenge_path}', " - f"'{challenge_repo}', '{head_branch}', '--squash'], cwd='{config.project_path}')" - ) - git_subtree_pull = subprocess.call( - [ - "git", - "subtree", - "pull", - "--prefix", - challenge_path, - challenge_repo, - head_branch, - "--squash", - ], - cwd=config.project_path, - ) + if not challenge_repo: + click.secho( + f"Could not find added challenge '{challenge_path}' " + "Please check that the challenge is added to .ctf/config and that your path matches", + fg="red", + ) + failed_pulls.append(challenge_instance) + continue - if git_subtree_pull != 0: - click.secho( - f"Could not pull the subtree for challenge '{challenge_path}'. " - "Please check git error messages above.", - fg="red", - ) - return 1 + if not challenge_repo.endswith(".git"): + click.secho( + f"Cannot pull challenge '{challenge_path}', as it's not a git-based challenge", + fg="yellow", + ) + failed_pulls.append(challenge_instance) + continue - log.debug(f"call(['git', 'mergetool'], cwd='{config.project_path / challenge_path}')") - git_mergetool = subprocess.call(["git", "mergetool"], cwd=config.project_path / challenge_path) + click.secho(f"Pulling latest '{challenge_repo}' to '{challenge_path}'", fg="blue") + head_branch = get_git_repo_head_branch(challenge_repo) - log.debug(f"call(['git', 'clean', '-f'], cwd='{config.project_path / challenge_path}')") - git_clean = subprocess.call(["git", "clean", "-f"], cwd=config.project_path / challenge_path) + log.debug( + f"call(['git', 'subtree', 'pull', '--prefix', '{challenge_path}', " + f"'{challenge_repo}', '{head_branch}', '--squash'], cwd='{config.project_path}')" + ) - log.debug(f"call(['git', 'commit', '--no-edit'], cwd='{config.project_path / challenge_path}')") - subprocess.call(["git", "commit", "--no-edit"], cwd=config.project_path / challenge_path) + pull_env = os.environ.copy() + pull_env["GIT_MERGE_AUTOEDIT"] = "no" + + git_subtree_pull = subprocess.call( + [ + "git", + "subtree", + "pull", + "--prefix", + challenge_path, + challenge_repo, + head_branch, + "--squash", + ], + cwd=config.project_path, + env=pull_env, + ) - # git commit is allowed to return a non-zero code because it would also mean that there's nothing to commit - if any(r != 0 for r in [git_mergetool, git_clean]): - click.secho( - f"Could not commit the subtree for challenge '{challenge_path}'. " - "Please check git error messages above.", - fg="red", - ) - return 1 + if git_subtree_pull != 0: + click.secho( + f"Could not pull the subtree for challenge '{challenge_path}'. " + "Please check git error messages above.", + fg="red", + ) + failed_pulls.append(challenge_instance) + continue - return 0 + log.debug(f"call(['git', 'mergetool'], cwd='{config.project_path / challenge_path}')") + git_mergetool = subprocess.call(["git", "mergetool"], cwd=config.project_path / challenge_path) + + log.debug(f"call(['git', 'commit', '--no-edit'], cwd='{config.project_path / challenge_path}')") + subprocess.call(["git", "commit", "--no-edit"], cwd=config.project_path / challenge_path) + + log.debug(f"call(['git', 'clean', '-f'], cwd='{config.project_path / challenge_path}')") + git_clean = subprocess.call(["git", "clean", "-f"], cwd=config.project_path / challenge_path) + + # git commit is allowed to return a non-zero code + # because it would also mean that there's nothing to commit + if any(r != 0 for r in [git_mergetool, git_clean]): + click.secho( + f"Could not commit the subtree for challenge '{challenge_path}'. " + "Please check git error messages above.", + fg="red", + ) + failed_pulls.append(challenge_instance) + continue + + if len(failed_pulls) == 0: + if not quiet: + click.secho("Success! All challenges pulled!", fg="green") + return 0 + + if not quiet: + click.secho("Pull failed for:", fg="red") + for challenge in failed_pulls: + click.echo(f" - {challenge}") + + return 1 def restore(self, challenge: str = None) -> int: log.debug(f"restore: (challenge={challenge})") diff --git a/ctfcli/core/image.py b/ctfcli/core/image.py index e66e6e7..025187f 100644 --- a/ctfcli/core/image.py +++ b/ctfcli/core/image.py @@ -24,7 +24,9 @@ class Image: self.built = False def build(self) -> Optional[str]: - docker_build = subprocess.call(["docker", "build", "-t", self.name, "."], cwd=self.build_path.absolute()) + docker_build = subprocess.call( + ["docker", "build", "--load", "-t", self.name, "."], cwd=self.build_path.absolute() + ) if docker_build != 0: return

CTFd/ctfcli

26bcec897fcc1f5f23c8117e2a225a130a8b0dea

diff --git a/tests/core/test_image.py b/tests/core/test_image.py index 2e773f4..8e6ab37 100644 --- a/tests/core/test_image.py +++ b/tests/core/test_image.py @@ -56,7 +56,9 @@ class TestImage(unittest.TestCase): self.assertTrue(image.built) self.assertEqual(image_name, "test-challenge") - mock_call.assert_called_once_with(["docker", "build", "-t", "test-challenge", "."], cwd=build_path.absolute()) + mock_call.assert_called_once_with( + ["docker", "build", "--load", "-t", "test-challenge", "."], cwd=build_path.absolute() + ) @mock.patch("ctfcli.core.image.subprocess.call", return_value=1) def test_build_returns_none_if_failed(self, mock_call: MagicMock): @@ -68,7 +70,9 @@ class TestImage(unittest.TestCase): self.assertFalse(image.built) self.assertIsNone(image_name) - mock_call.assert_called_once_with(["docker", "build", "-t", "test-challenge", "."], cwd=build_path.absolute()) + mock_call.assert_called_once_with( + ["docker", "build", "--load", "-t", "test-challenge", "."], cwd=build_path.absolute() + ) @mock.patch("ctfcli.core.image.subprocess.call", return_value=0) def test_push_built_image(self, mock_call: MagicMock): @@ -150,7 +154,7 @@ class TestImage(unittest.TestCase): mock_call.assert_has_calls( [ call( - ["docker", "build", "-t", "test-challenge", "."], + ["docker", "build", "--load", "-t", "test-challenge", "."], cwd=build_path.absolute(), ), call( @@ -224,7 +228,7 @@ class TestImage(unittest.TestCase): mock_call.assert_has_calls( [ call( - ["docker", "build", "-t", "test-challenge", "."], + ["docker", "build", "--load", "-t", "test-challenge", "."], cwd=build_path.absolute(), ), call(

Support Buildkit drivers for image builds [Buildkit drivers](https://docs.docker.com/build/drivers/) offer a lot of additional features over the default `docker` driver, like multi-arch images and remote builders. They could be supported by moving tag/push to `docker build --push`, depending on docker buildx which became the default for docker engine in Feb 2023. Buildx/buildkit has other benefits too eg native caching for CI environments, that would be useful to support in a future PR. Happy to send a PR for this if you want.

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

Cadair__parfive-16

diff --git a/README.rst b/README.rst index 8c8c05e..7014682 100644 --- a/README.rst +++ b/README.rst @@ -24,6 +24,28 @@ A simple example is:: files = dl.download() +Parfive also bundles a CLI. The following example will download the two files concurrently.:: + + $ parfive 'http://212.183.159.230/5MB.zip' 'http://212.183.159.230/10MB.zip' + $ parfive --help + usage: parfive [-h] [--max-conn MAX_CONN] [--overwrite] [--no-file-progress] + [--directory DIRECTORY] [--print-filenames] + URLS [URLS ...] + + Parfive, the python asyncio based downloader + + positional arguments: + URLS URLs of files to be downloaded. + + optional arguments: + -h, --help show this help message and exit + --max-conn MAX_CONN Number of maximum connections. + --overwrite Overwrite if the file exists. + --no-file-progress Show progress bar for each file. + --directory DIRECTORY + Directory to which downloaded files are saved. + --print-filenames Print successfully downloaded files's names to stdout. + Results ^^^^^^^ diff --git a/docs/index.rst b/docs/index.rst index 64d40b0..afe33c5 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -12,12 +12,7 @@ to the user about the in progress downloads. It also aims to provide a clear interface for inspecting any failed downloads. The parfive package was motivated by the needs of -`SunPy's <https://sunpy.org>`__ ``net`` submodule, but should be generally -applicable to anyone who wants a user friendly way of downloading multiple -files in parallel. - -Parfive supports downloading files over either HTTP or FTP using -`aiohttp <http://aiohttp.readthedocs.io/>`__ and `aioftp <https://aioftp.readthedocs.io/>`__ +`SunPy's <https://sunpy.org>`__ ``net`` submodule, but should be generally applicable to anyone who wants a user friendly way of downloading multiple files in parallel. Parfive supports downloading files over either HTTP or FTP using `aiohttp <http://aiohttp.readthedocs.io/>`__ and `aioftp <https://aioftp.readthedocs.io/>`__ ``aioftp`` is an optional dependency, which does not need to be installed to download files over HTTP. @@ -60,6 +55,29 @@ A simple example is:: files = dl.download() +Parfive also bundles a CLI. The following example will download the two files concurrently.:: + + $ parfive 'http://212.183.159.230/5MB.zip' 'http://212.183.159.230/10MB.zip' + $ parfive --help + usage: parfive [-h] [--max-conn MAX_CONN] [--overwrite] [--no-file-progress] + [--directory DIRECTORY] [--print-filenames] + URLS [URLS ...] + + Parfive, the python asyncio based downloader + + positional arguments: + URLS URLs of files to be downloaded. + + optional arguments: + -h, --help show this help message and exit + --max-conn MAX_CONN Number of maximum connections. + --overwrite Overwrite if the file exists. + --no-file-progress Show progress bar for each file. + --directory DIRECTORY + Directory to which downloaded files are saved. + --print-filenames Print successfully downloaded files's names to stdout. + + .. automodapi:: parfive :no-heading: diff --git a/parfive/main.py b/parfive/main.py new file mode 100644 index 0000000..b49ab8c --- /dev/null +++ b/parfive/main.py @@ -0,0 +1,38 @@ +import argparse +import sys + +from parfive import Downloader + + +def main(): + args = parse_args(sys.argv[1:]) + downloader = Downloader(max_conn=args.max_conn, file_progress=not args.no_file_progress, overwrite=args.overwrite) + for url in args.urls: + downloader.enqueue_file(url, path=args.directory) + results = downloader.download() + for i in results: + print(i) + + err_str = '' + for err in results.errors: + err_str += f'{err.url} \t {err.exception}\n' + if err_str: + sys.exit(err_str) + +def parse_args(args): + parser = argparse.ArgumentParser(description='Parfive, the python asyncio based downloader') + parser.add_argument('urls', metavar='URLS', type=str, nargs='+', + help='URLs of files to be downloaded.') + parser.add_argument('--max-conn', type=int, default=5, + help='Number of maximum connections.') + parser.add_argument('--overwrite', action='store_const', const=True, default=False, + help='Overwrite if the file exists.') + parser.add_argument('--no-file-progress', action='store_const', const=True, default=False, dest='no_file_progress', + help='Show progress bar for each file.') + parser.add_argument('--directory', type=str, default='./', + help='Directory to which downloaded files are saved.') + parser.add_argument('--print-filenames', action='store_const', const=True, default=False, dest='print_filenames', + help='Print successfully downloaded files\'s names to stdout.') + + args = parser.parse_args(args) + return args diff --git a/setup.cfg b/setup.cfg index 5a57d97..d016fd0 100644 --- a/setup.cfg +++ b/setup.cfg @@ -20,6 +20,10 @@ setup_requires = setuptools_scm packages = find: +[options.entry_points] +console_scripts = + parfive = parfive.main:main + [options.extras_require] ftp = aioftp test =

Cadair/parfive

10fb4e49216c3cfd5a3c0dd0230e0917b3c0c27d

diff --git a/parfive/tests/test_main.py b/parfive/tests/test_main.py new file mode 100644 index 0000000..bfcaeab --- /dev/null +++ b/parfive/tests/test_main.py @@ -0,0 +1,38 @@ +from parfive.main import parse_args +import pytest + +REQUIRED_ARGUMENTS = ['test_url'] + +def test_no_url(): + with pytest.raises(SystemExit): + args = parse_args(['--overwrite']) + + +def helper(args, name, expected): + args = parse_args(REQUIRED_ARGUMENTS + args) + assert getattr(args, name) == expected + + +def test_overwrite(): + helper(['--overwrite'], 'overwrite', True) + helper([], 'overwrite', False) + + +def test_max_conn(): + helper(['--max-conn', '10'], 'max_conn', 10) + helper([], 'max_conn', 5) + + +def test_no_file_progress(): + helper(['--no-file-progress'], 'no_file_progress', True) + helper([], 'no_file_progress', False) + + +def test_print_filenames(): + helper(['--print-filenames'], 'print_filenames', True) + helper([], 'print_filenames', False) + +def test_directory(): + helper(['--directory', '/tmp'], 'directory', '/tmp') + helper([], 'directory', './') +

Command line interface? It might be useful to create a command line interface, so people can just fire off requests without having to write any code to use the library As a basic interface, just give it a file with one URL per line, or maybe a lot of URLs as arguments (although that could hit up against limits) If you wanted to be fancy, have it be able to read a tab delim or CSV file and specify what field it should look at for URLs. (yes, people could use the unix `cut` command to extract the URLs first, but not everyone's on a posix-type system)

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

CharJon__GeCO-126

diff --git a/geco/graphs/__init__.py b/geco/graphs/__init__.py index 8bea5ee..e9aad98 100644 --- a/geco/graphs/__init__.py +++ b/geco/graphs/__init__.py @@ -1,3 +1,4 @@ import geco.graphs.chimera as chimera import geco.graphs.pegasus as pegasus import geco.graphs.utilities as utilities +import geco.graphs.lavrov_graph as lavrov_graphs \ No newline at end of file diff --git a/geco/graphs/lavrov_graph.py b/geco/graphs/lavrov_graph.py new file mode 100644 index 0000000..b80882c --- /dev/null +++ b/geco/graphs/lavrov_graph.py @@ -0,0 +1,34 @@ +import networkx as nx + + +def lavrov_graph( + k +): + """ + Generate Lavrov graph as described in [1] using networkx. + + Parameters + ---------- + k: int + Number k for Lavrov graph, number of nodes is 2 * k + + Returns + ------- + graph: nx.Graph + The generated Lavrov graph + + References + ---------- + ..[1] https://math.stackexchange.com/questions/2811736/an-upper-bound-on-the-number-of-chordless-cycles-in-an-undirected-graph/2811761#2811761 + """ + + g = nx.Graph() + g.add_nodes_from([0,2 * k - 1]) + + for i in range(0, k): + g.add_edge(i, (i + 1) % k) + g.add_edge(i + k, (i + 1) % k + k) + g.add_edge(i, (i + 1) % k + k) + g.add_edge(i + k, (i + 1) % k) + + return g

CharJon/GeCO

6db1a549b3145b3bc5d3025a9bccc03be6575564

diff --git a/geco/graphs/tests/test_lavrov_graph.py b/geco/graphs/tests/test_lavrov_graph.py new file mode 100644 index 0000000..efdcbdb --- /dev/null +++ b/geco/graphs/tests/test_lavrov_graph.py @@ -0,0 +1,20 @@ +from geco.graphs.lavrov_graph import lavrov_graph + +import pytest + + +def test_lavrov_graph_properties(): + k = 200 + g = lavrov_graph(k) + assert g.number_of_nodes() == k * 2 + assert g.number_of_edges() == k * 4 + +def test_lavrov_graph_edges(): + g = lavrov_graph(5) + edges = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 0), # inner cycle + (5, 6), (6, 7), (7, 8), (8, 9), (9, 5), # outer cycle + (5, 1), (6, 2), (7, 3), (8, 4), (9, 0), # forward cross + (5, 4), (9, 3), (8, 2), (7, 1), (6, 0)] # backward cross + + for a,b in edges: + assert g.has_edge(a, b)

Add Lavrov graphs [This comment](https://math.stackexchange.com/a/2811761/1039279) describes an interesting graph type. Add a generator for this class of graphs. I do not know if they have a name yet, so let's call them after the author of the comment (Lavrov).

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

Clarifai__clarifai-python-228

diff --git a/clarifai/utils/logging.py b/clarifai/utils/logging.py index 9fbc6e9..44373af 100644 --- a/clarifai/utils/logging.py +++ b/clarifai/utils/logging.py @@ -1,6 +1,6 @@ import logging from collections import defaultdict -from typing import Dict, List, Optional +from typing import Dict, List, Optional, Union from rich import print as rprint from rich.logging import RichHandler @@ -73,18 +73,29 @@ def _get_library_name() -> str: return __name__.split(".")[0] -def _configure_logger(logger_level: str = "ERROR") -> None: - logging.basicConfig( - level=logger_level, - datefmt='%Y-%m-%d %H:%M:%S', - handlers=[RichHandler(rich_tracebacks=True)]) +def _configure_logger(name: str, logger_level: Union[int, str] = logging.NOTSET) -> None: + """Configure the logger with the specified name.""" + logger = logging.getLogger(name) + logger.setLevel(logger_level) -def get_logger(logger_level: str = "ERROR", name: Optional[str] = None) -> logging.Logger: + # Remove existing handlers + for handler in logger.handlers[:]: + logger.removeHandler(handler) + + # Add the new rich handler and formatter + handler = RichHandler(rich_tracebacks=True, log_time_format="%Y-%m-%d %H:%M:%S") + formatter = logging.Formatter('%(name)s: %(message)s') + handler.setFormatter(formatter) + logger.addHandler(handler) + + +def get_logger(logger_level: Union[int, str] = logging.NOTSET, + name: Optional[str] = None) -> logging.Logger: """Return a logger with the specified name.""" if name is None: name = _get_library_name() - _configure_logger(logger_level) + _configure_logger(name, logger_level) return logging.getLogger(name)

Clarifai/clarifai-python

445922866de2e88c75dbbae450568a311e7beaca

diff --git a/tests/test_misc.py b/tests/test_misc.py new file mode 100644 index 0000000..58f9658 --- /dev/null +++ b/tests/test_misc.py @@ -0,0 +1,19 @@ +import logging + +from rich.logging import RichHandler + +from clarifai.utils.logging import _get_library_name, get_logger + + +def test_get_logger(): + logger = get_logger("DEBUG", "test_logger") + assert logger.level == logging.DEBUG + assert logger.name == "test_logger" + assert isinstance(logger.handlers[0], RichHandler) + + +def test_get_logger_defaults(): + logger = get_logger() + assert logger.level == logging.NOTSET + assert logger.name == _get_library_name() + assert isinstance(logger.handlers[0], RichHandler)

Handler added to root logger This library adds a `RichHandler` to the root logger through `logging.basicConfig` every time `get_logger` is called (which seems to be every time any common class/object is initialized): https://github.com/Clarifai/clarifai-python/blob/dbdcb493bdb9255244276086bd193a305e2cbcc0/clarifai/utils/logging.py#L76-L90 There doesn't seem to be any option to configure this, and this can cause conflicts with a user's own logging setup and/or those of other libraries. (Especially since `RichHandler` seems to add a lot of formatting that a user's own logging setup might not support) Instead, this library should configure and add handlers to its own loggers instead of the root logger.

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

ClarkSource__k8t-40

diff --git a/k8t/cli.py b/k8t/cli.py index f60d58e..b4429f3 100644 --- a/k8t/cli.py +++ b/k8t/cli.py @@ -180,7 +180,7 @@ def new_environment(cname, name, directory): @click.option("--environment", "-e", "ename", help="Deployment environment to use.") @click.option("--name", "-n", help="Template filename.") @click.option("--prefix", "-p", help="Prefix for filename.") [email protected]("kind", type=click.Choice(list(scaffolding.list_available_templates()))) [email protected]("kind", type=click.Choice(sorted(list(scaffolding.list_available_templates())))) @click.argument("directory", type=click.Path(exists=True, file_okay=False), default=os.getcwd()) def new_template(cname, ename, name, prefix, kind, directory): if not project.check_directory(directory): diff --git a/k8t/secret_providers.py b/k8t/secret_providers.py index 5ce3012..ca07b08 100644 --- a/k8t/secret_providers.py +++ b/k8t/secret_providers.py @@ -8,9 +8,19 @@ # THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. import logging +import string import boto3 +try: + from secrets import choice +except ImportError: + from random import SystemRandom + + choice = SystemRandom().choice + + + LOGGER = logging.getLogger(__name__) @@ -25,3 +35,16 @@ def ssm(key: str) -> str: ] except client.exceptions.ParameterNotFound: raise RuntimeError("Could not find secret: {}".format(key)) + + +RANDOM_STORE = {} + +def random(key: str) -> str: + LOGGER.debug("Requesting secret from %s", key) + + if key not in RANDOM_STORE: + RANDOM_STORE[key] = "".join( + choice(string.ascii_lowercase + string.digits) for _ in range(24) + ) + + return RANDOM_STORE[key] diff --git a/k8t/secrets.py b/k8t/secrets.py index 33cf931..241f066 100644 --- a/k8t/secrets.py +++ b/k8t/secrets.py @@ -18,7 +18,10 @@ def get_secret(key: str, path: str, cluster: str, environment: str) -> str: raise RuntimeError( "No configuration for secrets found: {}".format(config)) - provider = getattr(secret_providers, config["secrets"]["provider"].lower()) + try: + provider = getattr(secret_providers, config["secrets"]["provider"].lower()) + except AttributeError: + raise NotImplementedError("secret provider {} does not exist.".format(config["secrets"]["provider"].lower())) return provider( "{0}/{1}".format(config['secrets']['prefix'],

ClarkSource/k8t

7d577b6a3e1a6de8f59025d806df83b05fe56852

diff --git a/tests/secret_providers.py b/tests/secret_providers.py new file mode 100644 index 0000000..6e2f75c --- /dev/null +++ b/tests/secret_providers.py @@ -0,0 +1,20 @@ +# -*- coding: utf-8 -*- +# ISC License +# +# Copyright 2019 FL Fintech E GmbH +# +# Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. +# +# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + +from k8t.secret_providers import random + + +def test_random(): + assert random('/foobar') == random('/foobar') != random('/foobaz') + + result = random('/foobam') + + assert result == random('/foobam') + +# vim: fenc=utf-8:ts=4:sw=4:expandtab

get_secret should offer a random provider to allow using the same templates for different environments we should add a random provider to the secrets function.

2401580b6f41fe72f1360493ee46e8a842bd04ba

isc

CleanCut__green-124

diff --git a/green/result.py b/green/result.py index f96019d..908bea4 100644 --- a/green/result.py +++ b/green/result.py @@ -417,7 +417,7 @@ class GreenTestResult(BaseTestResult): if obj_list: stats.append("{}={}".format(name, color_func(str(len(obj_list))))) if not stats: - self.stream.writeln(self.colors.passing("No Tests Found")) + self.stream.writeln(self.colors.failing("No Tests Found")) else: grade = self.colors.passing('OK') if self.errors or self.failures: @@ -616,4 +616,8 @@ class GreenTestResult(BaseTestResult): """ Tells whether or not the overall run was successful """ - return len(self.all_errors) == 0 + # fail if no tests are run. + if len(self.all_errors) == 0 and len(self.passing) == 0: + return False + else: + return len(self.all_errors) == 0

CleanCut/green

568e0240a41fe79af20bb520fef39062788aa09e

diff --git a/green/test/test_result.py b/green/test/test_result.py index 04f97f8..fdaa846 100644 --- a/green/test/test_result.py +++ b/green/test/test_result.py @@ -830,6 +830,8 @@ class TestGreenTestResultAdds(unittest.TestCase): """ self.args.verbose = 1 gtr = GreenTestResult(self.args, GreenStream(self.stream)) + self.assertEqual(gtr.wasSuccessful(), False) + gtr.passing.append('anything') self.assertEqual(gtr.wasSuccessful(), True) gtr.all_errors.append('anything') self.assertEqual(gtr.wasSuccessful(), False) diff --git a/green/test/test_runner.py b/green/test/test_runner.py index 5581bd8..86edcc4 100644 --- a/green/test/test_runner.py +++ b/green/test/test_runner.py @@ -194,8 +194,10 @@ class TestRun(unittest.TestCase): """ When we don't find any tests, we say so. """ - run(GreenTestSuite(), self.stream, self.args) + result = run(GreenTestSuite(), self.stream, self.args) self.assertIn('No Tests Found', self.stream.getvalue()) + self.assertEqual(result.testsRun, 0) + self.assertEqual(result.wasSuccessful(), False) def test_failedSaysSo(self): """

Return a fail if no tests are found. # Summary: Currently (v2.4.1) `green` creates an empty test suite if no tests are found and then runs that empty suite, returning passing code. This can cause false-positives for CI and should be changed. ## Example: ``` $ python -m green -vvv -s 1 -W -t --run-coverage emap-convert --debug 2016-05-24 15:32:20 DEBUG Attempting to load target 'emap-convert' with file_pattern 'test*.py' 2016-05-24 15:32:20 DEBUG IGNORED exception: No module named 'emap-convert' 2016-05-24 15:32:20 DEBUG Found 0 tests for target 'emap-convert' 2016-05-24 15:32:20 DEBUG No test loading attempts succeeded. Created an empty test suite. Coverage.py warning: No data was collected. Green 2.4.1, Coverage 4.1, Python 3.4.4 Name Stmts Miss Cover --------------------------- Ran 0 tests in 0.280s No Tests Found Build succeeded ``` As you can see, this technically failed because the package/module name was incorrect (it should have been `emap_convert` - note the underscore). However, Green reported a pass. ## Discussion: I would recommend changing the default action to fail if no tests are found, rather than pass. This might cause issues with some (albeit very odd) usage cases, so perhaps it's prudent to add a CLI option `--empty-suite-passes` or something like that.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

Clinical-Genomics__scout-593

diff --git a/scout/adapter/mongo/query.py b/scout/adapter/mongo/query.py index 3a07b82d8..055963b99 100644 --- a/scout/adapter/mongo/query.py +++ b/scout/adapter/mongo/query.py @@ -114,15 +114,16 @@ class QueryHandler(object): cadd_query = {'cadd_score': {'$gt': float(cadd)}} logger.debug("Adding cadd_score: %s to query" % cadd) - if query.get('cadd_inclusive') == 'yes': + if query.get('cadd_inclusive') == True: cadd_query = { '$or': [ cadd_query, {'cadd_score': {'$exists': False}} - ]} + ]} logger.debug("Adding cadd inclusive to query") mongo_query['$and'].append(cadd_query) + if query.get('genetic_models'): models = query['genetic_models']

Clinical-Genomics/scout

7b2419a20dd5dbae88f21b9a2afe2c2d4ad5277f

diff --git a/tests/adapter/test_query.py b/tests/adapter/test_query.py index e5aee3586..2d12aa555 100644 --- a/tests/adapter/test_query.py +++ b/tests/adapter/test_query.py @@ -57,7 +57,7 @@ def test_build_cadd_exclusive(adapter): def test_build_cadd_inclusive(adapter): case_id = 'cust000' cadd = 10.0 - cadd_inclusive = 'yes' + cadd_inclusive = True query = {'cadd_score': cadd, 'cadd_inclusive': cadd_inclusive} mongo_query = adapter.build_query(case_id, query=query)

CADD score filter monday-issue! Thank you kindly for the quick inclusion of CADD score filtering! Will make a couple of our doctors very happy. One major caveat though: the current version seems to filter out unknown CADD scores as well (similar to the unknown frequency bug)! Not intended usage..

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

Clinical-Genomics__scout-656

diff --git a/scout/build/panel.py b/scout/build/panel.py index 1a4dfa0fd..85b02bfef 100644 --- a/scout/build/panel.py +++ b/scout/build/panel.py @@ -44,7 +44,7 @@ def build_gene(gene_info, adapter): hgnc_gene = adapter.hgnc_gene(hgnc_id) if hgnc_gene is None: - raise IntegrityError + raise IntegrityError("hgnc_id {0} is not in the gene database!".format(hgnc_id)) gene_obj['symbol'] = hgnc_gene['hgnc_symbol'] diff --git a/scout/commands/load/panel.py b/scout/commands/load/panel.py index 1aa029868..0569e2e13 100644 --- a/scout/commands/load/panel.py +++ b/scout/commands/load/panel.py @@ -74,5 +74,5 @@ def panel(context, date, name, version, panel_type, panel_id, path, institute): try: adapter.load_panel(info) except IntegrityError as e: - logger.warning(e) + log.warning(e) context.abort() diff --git a/scout/parse/variant/coordinates.py b/scout/parse/variant/coordinates.py index fa24acf8c..5031d6b0a 100644 --- a/scout/parse/variant/coordinates.py +++ b/scout/parse/variant/coordinates.py @@ -19,7 +19,20 @@ def get_cytoband_coordinates(chrom, pos): return coordinate def get_sub_category(alt_len, ref_len, category, svtype=None): - """Get the subcategory""" + """Get the subcategory for a VCF variant + + The sub categories are: + 'snv', 'indel', 'del', 'ins', 'dup', 'bnd', 'inv' + + Args: + alt_len(int) + ref_len(int) + category(str) + svtype(str) + + Returns: + subcategory(str) + """ subcategory = '' if category in ('snv', 'indel', 'cancer'): @@ -32,99 +45,147 @@ def get_sub_category(alt_len, ref_len, category, svtype=None): return subcategory -def get_length(alt_len, ref_len, category, svtype=None, svlen=None): - """docstring for get_length""" +def get_length(alt_len, ref_len, category, pos, end, svtype=None, svlen=None): + """Return the length of a variant + + Args: + alt_len(int) + ref_len(int) + category(str) + svtype(str) + svlen(int) + """ + # -1 would indicate uncertain length + length = -1 if category in ('snv', 'indel', 'cancer'): if ref_len == alt_len: length = alt_len else: - length = abs(ref_len-alt_len) + length = abs(ref_len - alt_len) + elif category == 'sv': if svtype == 'bnd': length = int(10e10) else: if svlen: length = abs(int(svlen)) - else: - # -1 would indicate uncertain length - length = -1 + # Some software does not give a length but they give END + elif end: + if end != pos: + length = end - pos return length -def get_end(pos, length, alt, category, svtype=None): - """docstring for get_length""" - end = None +def get_end(pos, alt, category, snvend=None, svend=None, svlen=None): + """Return the end coordinate for a variant + + Args: + pos(int) + alt(str) + category(str) + snvend(str) + svend(int) + svlen(int) + + Returns: + end(int) + """ + # If nothing is known we set end to be same as start + end = pos + # If variant is snv or indel we know that cyvcf2 can handle end pos if category in ('snv', 'indel', 'cancer'): - end = pos + length + end = snvend + # With SVs we have to be a bit more careful elif category == 'sv': + # The END field from INFO usually works fine + end = svend + + # For some cases like insertions the callers set end to same as pos + # In those cases we can hope that there is a svlen... + if svend == pos: + if svlen: + end = pos + svlen + # If variant is 'BND' they have ':' in alt field + # Information about other end is in the alt field if ':' in alt: other_coordinates = alt.strip('ACGTN[]').split(':') # For BND end will represent the end position of the other end try: end = int(other_coordinates[1]) except ValueError as err: - end = pos + length - else: - end = pos + length - - return end + pass + return end -def parse_coordinates(chrom, ref, alt, position, category, svtype, svlen, end, mate_id=None): +def parse_coordinates(variant, category): """Find out the coordinates for a variant Args: - chrom(str) - ref(str) - alt(str) - position(int) - category(str) - svtype(str) - svlen(int) - end(int) - mate_id(str) + variant(cyvcf2.Variant) Returns: coordinates(dict): A dictionary on the form: { + 'position':<int>, 'end':<int>, + 'end_chrom':<str>, 'length':<int>, 'sub_category':<str>, 'mate_id':<str>, + 'cytoband_start':<str>, + 'cytoband_end':<str>, } """ - coordinates = { - 'end': end, - 'length': None, - 'sub_category': None, - 'mate_id':None, - 'cytoband_start':None, - 'cytoband_end':None, - 'end_chrom':None, - } + ref = variant.REF + alt = variant.ALT[0] + chrom = variant.CHROM + if (chrom.startswith('chr') or chrom.startswith('CHR')): + chrom = chrom[3:] + + svtype = variant.INFO.get('SVTYPE') if svtype: svtype = svtype.lower() + mate_id = variant.INFO.get('MATEID') + + svlen = variant.INFO.get('SVLEN') + + svend = variant.INFO.get('END') + snvend = int(variant.end) + + position = int(variant.POS) + ref_len = len(ref) alt_len = len(alt) - coordinates['mate_id'] = mate_id - coordinates['sub_category'] = get_sub_category(alt_len, ref_len, category, svtype) - coordinates['length'] = get_length(alt_len, ref_len, category, svtype, svlen) - coordinates['end'] = get_end(position, coordinates['length'], alt, category, svtype) - coordinates['end_chrom'] = chrom - - if coordinates['sub_category'] == 'bnd': - if ':' in alt: - other_coordinates = alt.strip('ACGTN[]').split(':') - # BND will often be translocations between different chromosomes - other_chrom = other_coordinates[0] - coordinates['end_chrom'] = other_coordinates[0].lstrip('chrCHR') - - coordinates['cytoband_start'] = get_cytoband_coordinates( - chrom, position - ) - coordinates['cytoband_end'] = get_cytoband_coordinates( - coordinates['end_chrom'], coordinates['end'] - ) + + sub_category = get_sub_category(alt_len, ref_len, category, svtype) + end = get_end(position, alt, category, snvend, svend) + + length = get_length(alt_len, ref_len, category, position, end, svtype, svlen) + end_chrom = chrom + + if sub_category == 'bnd': + if ':' in alt: + other_coordinates = alt.strip('ACGTN[]').split(':') + # BND will often be translocations between different chromosomes + other_chrom = other_coordinates[0] + if (other_chrom.startswith('chr') or other_chrom.startswith('CHR')): + other_chrom = other_chrom[3:] + end_chrom = other_chrom + + cytoband_start = get_cytoband_coordinates(chrom, position) + cytoband_end = get_cytoband_coordinates(end_chrom, end) + + coordinates = { + 'position': position, + 'end': end, + 'length': length, + 'sub_category': sub_category, + 'mate_id': mate_id, + 'cytoband_start': cytoband_start, + 'cytoband_end': cytoband_end, + 'end_chrom': end_chrom, + } + return coordinates diff --git a/scout/parse/variant/variant.py b/scout/parse/variant/variant.py index 625c8901d..de16616c1 100644 --- a/scout/parse/variant/variant.py +++ b/scout/parse/variant/variant.py @@ -81,20 +81,19 @@ def parse_variant(variant, case, variant_type='clinical', category = 'snv' parsed_variant['category'] = category - #sub category is 'snv', 'indel', 'del', 'ins', 'dup', 'inv', 'cnv' - # 'snv' and 'indel' are subcatogories of snv - parsed_variant['sub_category'] = None ################# General information ################# parsed_variant['reference'] = variant.REF - # We allways assume splitted and normalized vcfs + + ### We allways assume splitted and normalized vcfs!!! if len(variant.ALT) > 1: raise VcfError("Variants are only allowed to have one alternative") parsed_variant['alternative'] = variant.ALT[0] # cyvcf2 will set QUAL to None if '.' in vcf parsed_variant['quality'] = variant.QUAL + if variant.FILTER: parsed_variant['filters'] = variant.FILTER.split(';') else: @@ -109,33 +108,14 @@ def parse_variant(variant, case, variant_type='clinical', ################# Position specific ################# parsed_variant['chromosome'] = chrom - # position = start - parsed_variant['position'] = int(variant.POS) - svtype = variant.INFO.get('SVTYPE') - - svlen = variant.INFO.get('SVLEN') - - end = int(variant.end) - - mate_id = variant.INFO.get('MATEID') - - coordinates = parse_coordinates( - chrom=parsed_variant['chromosome'], - ref=parsed_variant['reference'], - alt=parsed_variant['alternative'], - position=parsed_variant['position'], - category=parsed_variant['category'], - svtype=svtype, - svlen=svlen, - end=end, - mate_id=mate_id, - ) + coordinates = parse_coordinates(variant, category) + parsed_variant['position'] = coordinates['position'] parsed_variant['sub_category'] = coordinates['sub_category'] parsed_variant['mate_id'] = coordinates['mate_id'] - parsed_variant['end'] = int(coordinates['end']) - parsed_variant['length'] = int(coordinates['length']) + parsed_variant['end'] = coordinates['end'] + parsed_variant['length'] = coordinates['length'] parsed_variant['end_chrom'] = coordinates['end_chrom'] parsed_variant['cytoband_start'] = coordinates['cytoband_start'] parsed_variant['cytoband_end'] = coordinates['cytoband_end']

Clinical-Genomics/scout

e41d7b94106581fa28da793e2ab19c466e2f2f5a

diff --git a/tests/parse/test_parse_coordinates.py b/tests/parse/test_parse_coordinates.py new file mode 100644 index 000000000..791148fb3 --- /dev/null +++ b/tests/parse/test_parse_coordinates.py @@ -0,0 +1,253 @@ +from scout.parse.variant.coordinates import (get_cytoband_coordinates, get_sub_category, + get_length, get_end, parse_coordinates) + + +class CyvcfVariant(object): + """Mock a cyvcf variant + + Default is to return a variant with three individuals high genotype + quality. + """ + def __init__(self, chrom='1', pos=80000, ref='A', alt='C', end=None, + gt_quals=[60, 60, 60], gt_types=[1, 1, 0], var_type='snv', + info_dict={}): + super(CyvcfVariant, self).__init__() + self.CHROM = chrom + self.POS = pos + self.REF = ref + self.ALT = [alt] + self.end = end or pos + self.gt_quals = gt_quals + self.gt_types = gt_types + self.var_type = var_type + self.INFO = info_dict + + +def test_parse_coordinates_snv(): + variant = CyvcfVariant() + + coordinates = parse_coordinates(variant, 'snv') + + assert coordinates['position'] == variant.POS + +def test_parse_coordinates_indel(): + variant = CyvcfVariant(alt='ACCC', end=80003) + + coordinates = parse_coordinates(variant, 'snv') + + assert coordinates['position'] == variant.POS + assert coordinates['end'] == variant.end + +def test_parse_coordinates_translocation(): + info_dict = { + 'SVTYPE': 'BND', + } + variant = CyvcfVariant( + ref='N', + alt='N[hs37d5:12060532[', + pos=724779, + end=724779, + var_type='sv', + info_dict=info_dict, + ) + + coordinates = parse_coordinates(variant, 'sv') + + assert coordinates['position'] == variant.POS + assert coordinates['end'] == 12060532 + assert coordinates['end_chrom'] == 'hs37d5' + assert coordinates['length'] == 10e10 + assert coordinates['sub_category'] == 'bnd' + + +###### parse subcategory ####### +def test_get_subcategory_snv(): + alt_len = 1 + ref_len = 1 + category = 'snv' + svtype = None + + sub_category = get_sub_category(alt_len, ref_len, category, svtype) + + assert sub_category == 'snv' + +def test_get_subcategory_indel(): + alt_len = 1 + ref_len = 3 + category = 'snv' + svtype = None + + sub_category = get_sub_category(alt_len, ref_len, category, svtype) + + assert sub_category == 'indel' + +###### parse length ####### + +# get_length(alt_len, ref_len, category, pos, end, svtype=None, svlen=None) +def test_get_length_snv(): + alt_len = 1 + ref_len = 1 + category = 'snv' + pos = end = 879537 + + length = get_length(alt_len, ref_len, category, pos, end) + + assert length == 1 + +def test_get_length_indel(): + alt_len = 3 + ref_len = 1 + category = 'snv' + pos = end = 879537 + + length = get_length(alt_len, ref_len, category, pos, end) + + assert length == 2 + +def test_get_sv_length_small_ins(): + ## GIVEN an insertion with whole sequence in alt field + alt_len = 296 + ref_len = 1 + category = 'sv' + # Pos and end is same for insertions + pos = end = 144343218 + svtype = 'ins' + svlen = 296 + + ## WHEN parsing the length + length = get_length(alt_len, ref_len, category, pos, end, svtype, svlen) + + ## THEN assert that the length is correct + assert length == 296 + +def test_get_sv_length_large_ins_no_length(): + ## GIVEN an imprecise insertion + alt_len = 5 + ref_len = 1 + category = 'sv' + # Pos and end is same for insertions + pos = end = 133920667 + svtype = 'ins' + svlen = None + + ## WHEN parsing the length + length = get_length(alt_len, ref_len, category, pos, end, svtype, svlen) + + ## THEN assert that the length is correct + assert length == -1 + +def test_get_sv_length_translocation(): + ## GIVEN an translocation + alt_len = 16 + ref_len = 1 + category = 'sv' + pos = 726044 + end = None + svtype = 'bnd' + svlen = None + + ## WHEN parsing the length + length = get_length(alt_len, ref_len, category, pos, end, svtype, svlen) + + ## THEN assert that the length is correct + assert length == 10e10 + +def test_get_sv_length_cnvnator_del(): + ## GIVEN an cnvnator type deletion + alt_len = 5 + ref_len = 1 + category = 'sv' + pos = 1 + end = 10000 + svtype = 'del' + svlen = -10000 + + ## WHEN parsing the length + length = get_length(alt_len, ref_len, category, pos, end, svtype, svlen) + + ## THEN assert that the length is correct + assert length == 10000 + +def test_get_sv_length_del_no_length(): + ## GIVEN an deletion without len + alt_len = 5 + ref_len = 1 + category = 'sv' + pos = 869314 + end = 870246 + svtype = 'del' + svlen = None + + ## WHEN parsing the length + length = get_length(alt_len, ref_len, category, pos, end, svtype, svlen) + + ## THEN assert that the length is correct + assert length == end - pos + +###### parse end ####### +# get_end(pos, alt, category, snvend, svend, svlen) + +# snv/indels are easy since cyvcf2 are parsing the end for us + +def test_get_end_snv(): + alt = 'T' + category = 'snv' + pos = snvend = 879537 + + end = get_end(pos, alt, category, snvend, svend=None, svlen=None) + + assert end == snvend + +def test_get_end_indel(): + alt = 'C' + category = 'indel' + pos = 302253 + snvend = 302265 + + end = get_end(pos, alt, category, snvend, svend=None, svlen=None) + + assert end == snvend + +# SVs are much harder since there are a lot of corner cases +# Most SVs (except translocations) have END annotated in INFO field +# The problem is that many times END==POS and then we have to do some magic on our own + +def test_get_end_tiddit_translocation(): + ## GIVEN a translocation + alt = 'N[hs37d5:12060532[' + category = 'sv' + pos = 724779 + + ## WHEN parsing the end coordinate + end = get_end(pos, alt, category, snvend=None, svend=None, svlen=None) + + ## THEN assert that the end is the same as en coordinate described in alt field + assert end == 12060532 + +def test_get_end_tiddit_translocation(): + ## GIVEN a translocation + alt = 'N[hs37d5:12060532[' + category = 'sv' + pos = 724779 + + ## WHEN parsing the end coordinate + end = get_end(pos, alt, category, snvend=None, svend=None, svlen=None) + + ## THEN assert that the end is the same as en coordinate described in alt field + assert end == 12060532 + +def test_get_end_deletion(): + ## GIVEN a translocation + alt = '<DEL>' + category = 'sv' + pos = 869314 + svend = 870246 + svlen = None + + ## WHEN parsing the end coordinate + end = get_end(pos, alt, category, snvend=None, svend=svend, svlen=svlen) + + ## THEN assert that the end is the same as en coordinate described in alt field + assert end == svend + +

CSV - length -1 for a deletion of 80 genes https://scout.scilifelab.se/cust003/17159/sv/variants?variant_type=clinical&gene_panels=EP&hgnc_symbols=&size=&chrom=&thousand_genomes_frequency= please have a look. Something doesn't fit here. A deletion of 1 bp can not contain 80 genes. thanks, Michela

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

CodeForPhilly__chime-190

diff --git a/src/penn_chime/charts.py b/src/penn_chime/charts.py index fb23935..c29bd5b 100644 --- a/src/penn_chime/charts.py +++ b/src/penn_chime/charts.py @@ -74,7 +74,7 @@ def admitted_patients_chart( return ( alt.Chart(census.head(plot_projection_days)) - .transform_fold(fold=["Hospitalized Census", "ICU Census", "Ventilated Census"]) + .transform_fold(fold=["Hospitalized", "ICU", "Ventilated"]) .mark_line(point=True) .encode( x=alt.X(**x_kwargs), diff --git a/src/penn_chime/models.py b/src/penn_chime/models.py index a578ad3..62219b1 100644 --- a/src/penn_chime/models.py +++ b/src/penn_chime/models.py @@ -70,11 +70,10 @@ def sim_sir_df(p) -> pd.DataFrame: def get_dispositions( - infected: np.ndarray, rates: Tuple[float, ...], market_share: float = 1.0 + patient_state: np.ndarray, rates: Tuple[float, ...], market_share: float = 1.0 ) -> Tuple[np.ndarray, ...]: """Get dispositions of infected adjusted by rate and market_share.""" - return (*(infected * rate * market_share for rate in rates),) - + return (*(patient_state * rate * market_share for rate in rates),) def build_admissions_df(p) -> pd.DataFrame: @@ -86,7 +85,6 @@ def build_admissions_df(p) -> pd.DataFrame: projection = pd.DataFrame.from_dict(data_dict) # New cases projection_admits = projection.iloc[:-1, :] - projection.shift(1) - projection_admits[projection_admits < 0] = 0 projection_admits["day"] = range(projection_admits.shape[0]) return projection_admits @@ -117,7 +115,7 @@ def build_census_df( census_df = census_df[["day", "Hospitalized", "ICU", "Ventilated"]] census_df = census_df.head(n_days) census_df = census_df.rename( - columns={disposition: f"{disposition} Census" + columns={disposition: f"{disposition}" for disposition in ("Hospitalized", "ICU", "Ventilated")} ) diff --git a/src/penn_chime/parameters.py b/src/penn_chime/parameters.py index 38438d7..37b3a4c 100644 --- a/src/penn_chime/parameters.py +++ b/src/penn_chime/parameters.py @@ -112,7 +112,13 @@ class Parameters: ) self.susceptible_v, self.infected_v, self.recovered_v = s_v, i_v, r_v - self.dispositions = hospitalized_v, icu_v, ventilated_v = \ + i_hospitalized_v, i_icu_v, i_ventilated_v = \ get_dispositions(i_v, self.rates, self.market_share) + r_hospitalized_v, r_icu_v, r_ventilated_v = \ + get_dispositions(r_v, self.rates, self.market_share) + + self.dispositions = (i_hospitalized_v+r_hospitalized_v, + i_icu_v+r_icu_v, i_ventilated_v+r_ventilated_v) + self.hospitalized_v, self.icu_v, self.ventilated_v = \ - hospitalized_v, icu_v, ventilated_v + i_hospitalized_v, i_icu_v, i_ventilated_v diff --git a/src/penn_chime/presentation.py b/src/penn_chime/presentation.py index 4d7c8aa..4b37660 100644 --- a/src/penn_chime/presentation.py +++ b/src/penn_chime/presentation.py @@ -44,6 +44,7 @@ def display_header(st, p): """, unsafe_allow_html=True, ) + st.markdown("""**IMPORTANT NOTICE**: Admissions and Census calculations were previously **undercounting**. Please update your reports. See more about this issue [here](https://github.com/CodeForPhilly/chime/pull/190).""") st.markdown( """*This tool was developed by the [Predictive Healthcare team](http://predictivehealthcare.pennmedicine.org/) at Penn Medicine. For questions on how to use this tool see the [User docs](https://code-for-philly.gitbook.io/chime/). For questions and comments please see our

CodeForPhilly/chime

7f7e33e2605ff280a100cd4eb4c69684ffba9725

diff --git a/tests/test_app.py b/tests/test_app.py index fc51e6a..73df291 100644 --- a/tests/test_app.py +++ b/tests/test_app.py @@ -6,7 +6,7 @@ import numpy as np # type: ignore import altair as alt # type: ignore from src.penn_chime.charts import new_admissions_chart, admitted_patients_chart -from src.penn_chime.models import sir, sim_sir +from src.penn_chime.models import sir, sim_sir, build_admissions_df from src.penn_chime.parameters import Parameters from src.penn_chime.presentation import display_header from src.penn_chime.settings import DEFAULTS @@ -228,8 +228,14 @@ def test_parameters(): assert round(param.infected_v[1], 0) == 43735 assert round(param.recovered_v[30], 0) == 224048 assert [d[0] for d in param.dispositions] == [100.0, 40.0, 20.0] - assert [round(d[-1], 0) for d in param.dispositions] == [115.0, 46.0, 23.0] + assert [round(d[-1], 0) for d in param.dispositions] == [1182.0, 473.0, 236.0] # change n_days, make sure it cascades param.n_days = 2 assert len(param.susceptible_v) == len(param.infected_v) == len(param.recovered_v) == param.n_days + 1 == 3 + + # test that admissions are being properly calculated (thanks @PhilMiller) + admissions = build_admissions_df(param) + cumulative_admissions = admissions.cumsum() + diff = cumulative_admissions["Hospitalized"][1:-1] - (0.05*0.05 * (param.infected_v[1:-1] + param.recovered_v[1:-1]) - 100) + assert (diff.abs() < 0.1).all()

Fix calculation of daily new infections Current daily new infections are being calculated as $I_{t+1} - I_{t}$, which doesn't account for the infected cases transitioning into recovered during that time step. The calculations should be $I_{new} = (I_{t+1} - I_{t}) + (R_{t+1} - R_{t})$

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

CodeForPhilly__chime-276

diff --git a/settings.cfg b/settings.cfg index 040d6e2..f8d1a3b 100644 --- a/settings.cfg +++ b/settings.cfg @@ -8,6 +8,6 @@ --icu-rate 0.0075 --market_share 0.15 --n-days 60 ---susceptible 4119405 +--population 4119405 --ventilated-los 10 --ventilated-rate 0.005 diff --git a/src/penn_chime/cli.py b/src/penn_chime/cli.py index 4fed0f7..a4ec533 100644 --- a/src/penn_chime/cli.py +++ b/src/penn_chime/cli.py @@ -91,7 +91,7 @@ def parse_args(): 1.0, "Social Distancing Reduction Rate: 0.0 - 1.0", ), - ("--susceptible", int, 1, None, "Regional Population >= 1"), + ("--population", int, 1, None, "Regional Population >= 1"), ("--ventilated-los", int, 0, None, "Ventilated Length of Stay (days)"), ("--ventilated-rate", float, 0.0, 1.0, "Ventilated Rate: 0.0 - 1.0"), ): @@ -110,7 +110,7 @@ def main(): market_share=a.market_share, n_days=a.n_days, relative_contact_rate=a.relative_contact_rate, - susceptible=a.susceptible, + population=a.population, hospitalized=RateLos(a.hospitalized_rate, a.hospitalized_los), icu=RateLos(a.icu_rate, a.icu_los), diff --git a/src/penn_chime/defaults.py b/src/penn_chime/defaults.py index dd28427..9b60cd0 100644 --- a/src/penn_chime/defaults.py +++ b/src/penn_chime/defaults.py @@ -7,15 +7,12 @@ class Regions: """Arbitrary number of counties.""" def __init__(self, **kwargs): - susceptible = 0 + population = 0 for key, value in kwargs.items(): setattr(self, key, value) - susceptible += value - self._susceptible = susceptible + population += value + self.population = population - @property - def susceptible(self): - return self._susceptible class Constants: @@ -55,4 +52,4 @@ class Constants: self.recovery_days = recovery_days def __repr__(self) -> str: - return f"Constants(susceptible_default: {self.region.susceptible}, known_infected: {self.known_infected})" + return f"Constants(population_default: {self.region.population}, known_infected: {self.known_infected})" diff --git a/src/penn_chime/models.py b/src/penn_chime/models.py index cc4858d..97fb33c 100644 --- a/src/penn_chime/models.py +++ b/src/penn_chime/models.py @@ -18,8 +18,7 @@ from .parameters import Parameters class SimSirModel: def __init__(self, p: Parameters) -> SimSirModel: - # TODO missing initial recovered value - susceptible = p.susceptible + # TODO missing initial non-zero 'recovered' value recovered = 0.0 recovery_days = p.recovery_days @@ -40,6 +39,8 @@ class SimSirModel: p.current_hospitalized / p.market_share / p.hospitalized.rate ) + susceptible = p.population - infected + detection_probability = ( p.known_infected / infected if infected > 1.0e-7 else None ) diff --git a/src/penn_chime/parameters.py b/src/penn_chime/parameters.py index 17b9722..7ea14da 100644 --- a/src/penn_chime/parameters.py +++ b/src/penn_chime/parameters.py @@ -17,7 +17,7 @@ class Parameters: doubling_time: float, known_infected: int, relative_contact_rate: float, - susceptible: int, + population: int, hospitalized: RateLos, icu: RateLos, @@ -33,7 +33,7 @@ class Parameters: self.doubling_time = doubling_time self.known_infected = known_infected self.relative_contact_rate = relative_contact_rate - self.susceptible = susceptible + self.population = population self.hospitalized = hospitalized self.icu = icu diff --git a/src/penn_chime/presentation.py b/src/penn_chime/presentation.py index 7523295..8925561 100644 --- a/src/penn_chime/presentation.py +++ b/src/penn_chime/presentation.py @@ -41,7 +41,7 @@ def display_header(st, m, p): infected_population_warning_str = ( """(Warning: The number of estimated infections is greater than the total regional population. Please verify the values entered in the sidebar.)""" - if m.infected > p.susceptible + if m.infected > p.population else "" ) @@ -92,7 +92,7 @@ and daily growth rate of **{daily_growth_t:.2f}%**. detection_prob_str=detection_prob_str, current_hosp=p.current_hospitalized, hosp_rate=p.hospitalized.rate, - S=p.susceptible, + S=p.population, market_share=p.market_share, recovery_days=p.recovery_days, r_naught=m.r_naught, @@ -238,11 +238,11 @@ def display_sidebar(st, d: Constants) -> Parameters: step=1.0, format="%f", ) - susceptible_input = NumberInputWrapper( + population_input = NumberInputWrapper( st_obj, "Regional Population", min_value=1, - value=d.region.susceptible, + value=d.region.population, step=100000, format="%i", ) @@ -261,7 +261,7 @@ def display_sidebar(st, d: Constants) -> Parameters: # Build in desired order st.sidebar.markdown("### Regional Parameters [ℹ]({docs_url}/what-is-chime/parameters)".format(docs_url=DOCS_URL)) - susceptible = susceptible_input() + population = population_input() market_share = market_share_input() known_infected = known_infected_input() current_hospitalized = current_hospitalized_input() @@ -298,7 +298,7 @@ def display_sidebar(st, d: Constants) -> Parameters: max_y_axis=max_y_axis, n_days=n_days, relative_contact_rate=relative_contact_rate / 100.0, - susceptible=susceptible, + population=population, hospitalized=RateLos(hospitalized_rate/ 100.0, hospitalized_los), icu=RateLos(icu_rate/ 100.0, icu_los),

CodeForPhilly/chime

0a0aece010073dd2facf67497efe649ff24a023a

diff --git a/tests/test_app.py b/tests/test_app.py index f5dc5dc..696663e 100644 --- a/tests/test_app.py +++ b/tests/test_app.py @@ -20,7 +20,7 @@ PARAM = Parameters( known_infected=5000, market_share=0.05, relative_contact_rate=0.15, - susceptible=500000, + population=500000, hospitalized=RateLos(0.05, 7), icu=RateLos(0.02, 9), ventilated=RateLos(0.01, 10), @@ -33,7 +33,7 @@ HALVING_PARAM = Parameters( known_infected=5000, market_share=0.05, relative_contact_rate=0.7, - susceptible=500000, + population=500000, hospitalized=RateLos(0.05, 7), icu=RateLos(0.02, 9), ventilated=RateLos(0.01, 10), @@ -238,7 +238,7 @@ def test_model(model=MODEL, param=PARAM): # test the class-calculated attributes assert model.detection_probability == 0.125 assert model.intrinsic_growth_rate == 0.12246204830937302 - assert model.beta == 3.2961405355450555e-07 + assert model.beta == 3.582761451679408e-07 assert model.r_t == 2.307298374881539 assert model.r_naught == 2.7144686763312222 assert model.doubling_time_t == 7.764405988534983 @@ -251,16 +251,19 @@ def test_model(model=MODEL, param=PARAM): second = raw_df.iloc[1, :] last = raw_df.iloc[-1, :] - assert first.susceptible == 500000.0 + assert first.susceptible + first.infected + first.recovered == param.population + assert last.susceptible + last.infected + last.recovered == param.population + + assert first.susceptible == 460000.0 assert round(second.infected, 0) == 43735 - assert round(last.susceptible, 0) == 67202 - assert round(raw_df.recovered[30], 0) == 224048 + assert round(last.susceptible, 0) == 59497 + assert round(raw_df.recovered[30], 0) == 216711 assert list(model.dispositions_df.iloc[0, :]) == [0, 100.0, 40.0, 20.0] - assert [round(i, 0) for i in model.dispositions_df.iloc[60, :]] == [60, 1182.0, 473.0, 236.0] + assert [round(i, 0) for i in model.dispositions_df.iloc[60, :]] == [60, 1101.0, 441.0, 220.0] - # test that admissions are being properly calculated (thanks @PhilMiller) + # test that admissions are being properly calculated cumulative_admits = model.admits_df.cumsum() diff = cumulative_admits.hospitalized[1:-1] - ( 0.05 * 0.05 * (raw_df.infected[1:-1] + raw_df.recovered[1:-1]) - 100

Conflation of regional population with susceptible population is wrong with large infection count The raw data shows a total of S+I+R that is larger than the user-provided regional population. This is because the number presumed initially infected based on hospitalization rate isn't subtracted from the population to compute the currently susceptible.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

CodeForPhilly__chime-418

diff --git a/src/penn_chime/models.py b/src/penn_chime/models.py index da7311f..6582b1c 100644 --- a/src/penn_chime/models.py +++ b/src/penn_chime/models.py @@ -9,7 +9,7 @@ from __future__ import annotations from datetime import date, datetime, timedelta from logging import INFO, basicConfig, getLogger from sys import stdout -from typing import Dict, Generator, Tuple, Sequence,Optional +from typing import Dict, Generator, Tuple, Sequence, Optional import numpy as np import pandas as pd @@ -66,14 +66,13 @@ class SimSirModel: intrinsic_growth_rate = get_growth_rate(p.doubling_time) self.beta = get_beta(intrinsic_growth_rate, gamma, self.susceptible, 0.0) + self.beta_t = get_beta(intrinsic_growth_rate, self.gamma, self.susceptible, p.relative_contact_rate) self.i_day = 0 # seed to the full length - self.beta_t = self.beta - self.run_projection(p) + self.run_projection(p, [(self.beta, p.n_days)]) self.i_day = i_day = int(get_argmin_ds(self.census_df, p.current_hospitalized)) - self.beta_t = get_beta(intrinsic_growth_rate, self.gamma, self.susceptible, p.relative_contact_rate) - self.run_projection(p) + self.run_projection(p, self.gen_policy(p)) logger.info('Set i_day = %s', i_day) p.date_first_hospitalized = p.current_date - timedelta(days=i_day) @@ -100,7 +99,7 @@ class SimSirModel: self.beta = get_beta(intrinsic_growth_rate, self.gamma, self.susceptible, 0.0) self.beta_t = get_beta(intrinsic_growth_rate, self.gamma, self.susceptible, p.relative_contact_rate) - self.run_projection(p) + self.run_projection(p, self.gen_policy(p)) loss = self.get_loss() losses[i] = loss @@ -109,7 +108,7 @@ class SimSirModel: intrinsic_growth_rate = get_growth_rate(p.doubling_time) self.beta = get_beta(intrinsic_growth_rate, self.gamma, self.susceptible, 0.0) self.beta_t = get_beta(intrinsic_growth_rate, self.gamma, self.susceptible, p.relative_contact_rate) - self.run_projection(p) + self.run_projection(p, self.gen_policy(p)) self.population = p.population else: @@ -146,18 +145,35 @@ class SimSirModel: self.daily_growth_rate = get_growth_rate(p.doubling_time) self.daily_growth_rate_t = get_growth_rate(self.doubling_time_t) - def run_projection(self, p): + def gen_policy(self, p: Parameters) -> Sequence[Tuple[float, int]]: + if p.mitigation_date is not None: + mitigation_day = -(p.current_date - p.mitigation_date).days + else: + mitigation_day = 0 + + total_days = self.i_day + p.n_days + + if mitigation_day < -self.i_day: + mitigation_day = -self.i_day + + pre_mitigation_days = self.i_day + mitigation_day + post_mitigation_days = total_days - pre_mitigation_days + + return [ + (self.beta, pre_mitigation_days), + (self.beta_t, post_mitigation_days), + ] + + def run_projection(self, p: Parameters, policy: Sequence[Tuple[float, int]]): self.raw_df = sim_sir_df( self.susceptible, self.infected, p.recovered, self.gamma, -self.i_day, - self.beta, - self.i_day, - self.beta_t, - p.n_days + policy ) + self.dispositions_df = build_dispositions_df(self.raw_df, self.rates, p.market_share, p.current_date) self.admits_df = build_admits_df(self.dispositions_df) self.census_df = build_census_df(self.admits_df, self.days) @@ -221,7 +237,7 @@ def sir( def gen_sir( - s: float, i: float, r: float, gamma: float, i_day: int, *args + s: float, i: float, r: float, gamma: float, i_day: int, policies: Sequence[Tuple[float, int]] ) -> Generator[Tuple[int, float, float, float], None, None]: """Simulate SIR model forward in time yielding tuples. Parameter order has changed to allow multiple (beta, n_days) @@ -230,8 +246,7 @@ def gen_sir( s, i, r = (float(v) for v in (s, i, r)) n = s + i + r d = i_day - while args: - beta, n_days, *args = args + for beta, n_days in policies: for _ in range(n_days): yield d, s, i, r s, i, r = sir(s, i, r, beta, gamma, n) @@ -241,11 +256,11 @@ def gen_sir( def sim_sir_df( s: float, i: float, r: float, - gamma: float, i_day: int, *args + gamma: float, i_day: int, policies: Sequence[Tuple[float, int]] ) -> pd.DataFrame: """Simulate the SIR model forward in time.""" return pd.DataFrame( - data=gen_sir(s, i, r, gamma, i_day, *args), + data=gen_sir(s, i, r, gamma, i_day, policies), columns=("day", "susceptible", "infected", "recovered"), ) diff --git a/src/penn_chime/parameters.py b/src/penn_chime/parameters.py index d9da047..d6c03a0 100644 --- a/src/penn_chime/parameters.py +++ b/src/penn_chime/parameters.py @@ -55,6 +55,7 @@ class Parameters: hospitalized: Disposition, icu: Disposition, relative_contact_rate: float, + mitigation_date: Optional[date] = None, ventilated: Disposition, current_date: date = date.today(), date_first_hospitalized: Optional[date] = None, @@ -68,7 +69,6 @@ class Parameters: region: Optional[Regions] = None, ): self.current_hospitalized = Positive(value=current_hospitalized) - self.relative_contact_rate = Rate(value=relative_contact_rate) Rate(value=hospitalized.rate), Rate(value=icu.rate), Rate(value=ventilated.rate) StrictlyPositive(value=hospitalized.days), StrictlyPositive(value=icu.days), @@ -92,6 +92,9 @@ class Parameters: self.date_first_hospitalized = OptionalDate(value=date_first_hospitalized) self.doubling_time = OptionalStrictlyPositive(value=doubling_time) + self.relative_contact_rate = Rate(value=relative_contact_rate) + self.mitigation_date = OptionalDate(value=mitigation_date) + self.infectious_days = StrictlyPositive(value=infectious_days) self.market_share = Rate(value=market_share) self.max_y_axis = OptionalStrictlyPositive(value=max_y_axis) diff --git a/src/penn_chime/presentation.py b/src/penn_chime/presentation.py index 6492e1b..0f50f42 100644 --- a/src/penn_chime/presentation.py +++ b/src/penn_chime/presentation.py @@ -11,6 +11,7 @@ from .constants import ( CHANGE_DATE, DATE_FORMAT, DOCS_URL, + EPSILON, FLOAT_INPUT_MIN, FLOAT_INPUT_STEP, ) @@ -207,6 +208,10 @@ def display_sidebar(st, d: Parameters) -> Parameters: st_obj, "Date of first hospitalized case - Enter this date to have chime estimate the initial doubling time", value=d.date_first_hospitalized, ) + mitigation_date_input = DateInput( + st_obj, "Date of social distancing measures effect (may be delayed from implementation)", + value=d.mitigation_date + ) relative_contact_pct_input = PercentInput( st_obj, "Social distancing (% reduction in social contact going forward)", @@ -312,7 +317,15 @@ def display_sidebar(st, d: Parameters) -> Parameters: doubling_time = doubling_time_input() date_first_hospitalized = None - relative_contact_rate = relative_contact_pct_input() + if st.sidebar.checkbox( + "Social distancing measures have been implemented", + value=(d.relative_contact_rate > EPSILON) + ): + mitigation_date = mitigation_date_input() + relative_contact_rate = relative_contact_pct_input() + else: + mitigation_date = None + relative_contact_rate = EPSILON st.sidebar.markdown( "### Severity Parameters [ℹ]({docs_url}/what-is-chime/parameters#severity-parameters)".format( @@ -346,6 +359,7 @@ def display_sidebar(st, d: Parameters) -> Parameters: hospitalized=Disposition(hospitalized_rate, hospitalized_days), icu=Disposition(icu_rate, icu_days), relative_contact_rate=relative_contact_rate, + mitigation_date=mitigation_date, ventilated=Disposition(ventilated_rate, ventilated_days), current_date=current_date, date_first_hospitalized=date_first_hospitalized, diff --git a/src/penn_chime/settings.py b/src/penn_chime/settings.py index 0bd1298..a9ccb34 100644 --- a/src/penn_chime/settings.py +++ b/src/penn_chime/settings.py @@ -16,6 +16,7 @@ def get_defaults(): infectious_days=14, market_share=0.15, n_days=100, + mitigation_date=date.today(), relative_contact_rate=0.3, ventilated=Disposition(0.005, 10), )

CodeForPhilly/chime

e6ff8aaa0be2be7c27ec9b98611147650d414270

diff --git a/tests/conftest.py b/tests/conftest.py index e822d91..b7cf01f 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -51,6 +51,7 @@ def DEFAULTS(): doubling_time=4.0, n_days=60, market_share=0.15, + mitigation_date=datetime(year=2020, month=3, day=28), relative_contact_rate=0.3, hospitalized=Disposition(0.025, 7), icu=Disposition(0.0075, 9), @@ -65,6 +66,7 @@ def param(): current_hospitalized=100, doubling_time=6.0, market_share=0.05, + mitigation_date=datetime(year=2020, month=3, day=28), relative_contact_rate=0.15, population=500000, hospitalized=Disposition(0.05, 7), @@ -81,6 +83,7 @@ def halving_param(): current_hospitalized=100, doubling_time=6.0, market_share=0.05, + mitigation_date=datetime(year=2020, month=3, day=28), relative_contact_rate=0.7, population=500000, hospitalized=Disposition(0.05, 7), diff --git a/tests/penn_chime/test_models.py b/tests/penn_chime/test_models.py index a8c4129..d5e6de2 100644 --- a/tests/penn_chime/test_models.py +++ b/tests/penn_chime/test_models.py @@ -3,11 +3,13 @@ from datetime import date import pytest import pandas as pd import numpy as np +from datetime import timedelta from src.penn_chime.models import ( sir, sim_sir_df, get_growth_rate, + SimSirModel, ) from src.penn_chime.constants import EPSILON @@ -64,7 +66,7 @@ def test_sim_sir(): Rounding to move fast past decimal place issues """ raw_df = sim_sir_df( - 5, 6, 7, 0.1, 0, 0.1, 40, # s # i # r # gamma # i_day # beta1 # n_days1 + 5, 6, 7, 0.1, 0, [(0.1, 40)], # s # i # r # gamma # i_day # beta1 # n_days1 ) first = raw_df.iloc[0, :] @@ -100,6 +102,20 @@ def test_model(model, param): assert model.r_t == 2.307298374881539 assert model.r_naught == 2.7144686763312222 assert model.doubling_time_t == 7.764405988534983 + assert model.i_day == 43 + + +def test_model_first_hosp_fit(param): + param.date_first_hospitalized = param.current_date - timedelta(days=43) + param.doubling_time = None + + my_model = SimSirModel(param) + + assert my_model.intrinsic_growth_rate == 0.12246204830937302 + assert abs(my_model.beta - 4.21501347256401e-07) < EPSILON + assert my_model.r_t == 2.307298374881539 + assert my_model.r_naught == 2.7144686763312222 + assert my_model.doubling_time_t == 7.764405988534983 def test_model_raw_start(model, param):

["model"] social isolation started earlier than model assumes <!-- Please note: Any changes to the model have a huge impact on rapidly evolving hospital system & public health decisions. The current model has been in use for a while now, and it has been validated against other similar models, so any changes to the model must meet a very high bar. However, these 2 types of issue reports are very welcome: - Bugs causing this model to produce invalid results. In this case, please include details and a suggested fix. - If this model is producing a significantly different result than another well-known epidemiological model. In this case, please include proof of this difference and a suggested fix to our approach. For questions or early discussion, please join us in [#chime-analysis](https://codeforphilly.org/chat?channel=chime-analysis) in Slack instead. --> ### Summary If I understand the model implementation correctly the model is run with beta prior to current date and beta_t after, where beta_t is the beta corrected for social isolation (suppression of contact rate). While this may be true in a new pandemic it is not true in this case: isolation started in many places ~2 weeks ago which is when the first cases started to appear ### Additional details I am pretty sure what I described is true when the model is run with a given doubling time - not so sure that this is also what happens in the optimized model (when given first hospitalization date) ### Suggested fix beta_t could be used as a default, or linked to a user input date

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

ContinualAI__avalanche-1216

diff --git a/avalanche/benchmarks/utils/data.py b/avalanche/benchmarks/utils/data.py index 533d79ee..9c11f60f 100644 --- a/avalanche/benchmarks/utils/data.py +++ b/avalanche/benchmarks/utils/data.py @@ -101,6 +101,10 @@ class AvalancheDataset(FlatData): DeprecationWarning, ) + if issubclass(type(datasets), TorchDataset) or \ + issubclass(type(datasets), AvalancheDataset): + datasets = [datasets] + # NOTES on implementation: # - raw datasets operations are implemented by _FlatData # - data attributes are implemented by DataAttribute diff --git a/avalanche/training/templates/base.py b/avalanche/training/templates/base.py index c0899806..532e8332 100644 --- a/avalanche/training/templates/base.py +++ b/avalanche/training/templates/base.py @@ -1,4 +1,5 @@ import warnings +from collections import defaultdict from typing import Iterable, Sequence, Optional, Union, List import torch @@ -90,6 +91,9 @@ class BaseTemplate: :param eval_streams: sequence of streams for evaluation. If None: use training experiences for evaluation. Use [] if you do not want to evaluate during training. + Experiences in `eval_streams` are grouped by stream name + when calling `eval`. If you use multiple streams, they must + have different names. """ self.is_training = True self._stop_training = False @@ -102,7 +106,7 @@ class BaseTemplate: experiences = [experiences] if eval_streams is None: eval_streams = [experiences] - self._eval_streams = eval_streams + self._eval_streams = _group_experiences_by_stream(eval_streams) self._before_training(**kwargs) @@ -244,3 +248,20 @@ class BaseTemplate: def _after_eval_exp(self, **kwargs): trigger_plugins(self, "after_eval_exp", **kwargs) + + +def _group_experiences_by_stream(eval_streams): + exps = [] + # First, we unpack the list of experiences. + for exp in eval_streams: + if isinstance(exp, Iterable): + exps.extend(exp) + else: + exps.append(exp) + # Then, we group them by stream. + exps_by_stream = defaultdict(list) + for exp in exps: + sname = exp.origin_stream.name + exps_by_stream[sname].append(exp) + # Finally, we return a list of lists. + return list(exps_by_stream.values())

ContinualAI/avalanche

f3abbc5500c928bb5fc5bcf4b31fcd0b504fdf26

diff --git a/tests/test_avalanche_dataset.py b/tests/test_avalanche_dataset.py index e7cf460b..67ccdecc 100644 --- a/tests/test_avalanche_dataset.py +++ b/tests/test_avalanche_dataset.py @@ -56,6 +56,17 @@ class FrozenTransformGroupsCenterCrop: class AvalancheDatasetTests(unittest.TestCase): + + def test_avalanche_dataset_creation_without_list(self): + dataset_mnist = load_image_benchmark() + dataset = AvalancheDataset(dataset_mnist) + self.assertIsInstance(dataset, AvalancheDataset) + self.assertEqual(len(dataset_mnist), len(dataset)) + + dataset = AvalancheDataset(dataset) + self.assertIsInstance(dataset, AvalancheDataset) + self.assertEqual(len(dataset_mnist), len(dataset)) + def test_disallowed_attribute_name(self): d_sz = 3 xdata = torch.rand(d_sz, 2) diff --git a/tests/training/test_strategies.py b/tests/training/test_strategies.py index 84fae146..a49b2d20 100644 --- a/tests/training/test_strategies.py +++ b/tests/training/test_strategies.py @@ -48,11 +48,37 @@ from avalanche.training.supervised.icarl import ICaRL from avalanche.training.supervised.joint_training import AlreadyTrainedError from avalanche.training.supervised.strategy_wrappers import PNNStrategy from avalanche.training.templates import SupervisedTemplate +from avalanche.training.templates.base import _group_experiences_by_stream from avalanche.training.utils import get_last_fc_layer from tests.unit_tests_utils import get_fast_benchmark, get_device class BaseStrategyTest(unittest.TestCase): + def test_eval_streams_normalization(self): + benchmark = get_fast_benchmark() + train_len = len(benchmark.train_stream) + test_len = len(benchmark.test_stream) + + res = _group_experiences_by_stream(benchmark.test_stream) + assert len(res) == 1 + assert len(res[0]) == test_len + + res = _group_experiences_by_stream([benchmark.test_stream]) + assert len(res) == 1 + assert len(res[0]) == test_len + + res = _group_experiences_by_stream( + [*benchmark.test_stream, *benchmark.train_stream]) + assert len(res) == 2 + assert len(res[0]) == test_len + assert len(res[1]) == train_len + + res = _group_experiences_by_stream( + [benchmark.test_stream, benchmark.train_stream]) + assert len(res) == 2 + assert len(res[0]) == test_len + assert len(res[1]) == train_len + def test_periodic_eval(self): model = SimpleMLP(input_size=6, hidden_size=10) model.classifier = IncrementalClassifier(model.classifier.in_features)

bug for stream-level metrics in periodic eval periodic eval is broken in some subtle cases. Instead of calling `eval` on the entire stream, it calls it multiple times for each experience, breaking stream-level metrics. Reproduce: ``` from avalanche.benchmarks import SplitMNIST from avalanche.training import Naive from avalanche.models import SimpleMLP if __name__ == '__main__': benchmark = SplitMNIST(5) model = SimpleMLP() strat = Naive(model, None, eval_mb_size=512, eval_every=1) stream = benchmark.test_stream strat.train(stream[0], eval_streams=list(stream[:2])) ``` outputs: ``` -- >> Start of training phase << -- -- >> Start of eval phase << -- -- Starting eval on experience 0 (Task 0) from test stream -- 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████| 5/5 [00:05<00:00, 1.08s/it] > Eval on experience 0 (Task 0) from test stream ended. Loss_Exp/eval_phase/test_stream/Task000/Exp000 = 2.3881 Top1_Acc_Exp/eval_phase/test_stream/Task000/Exp000 = 0.0033 -- >> End of eval phase << -- Loss_Stream/eval_phase/test_stream/Task000 = 2.3881 Top1_Acc_Stream/eval_phase/test_stream/Task000 = 0.0033 -- >> Start of eval phase << -- -- Starting eval on experience 1 (Task 0) from test stream -- 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████| 4/4 [00:01<00:00, 2.12it/s] > Eval on experience 1 (Task 0) from test stream ended. Loss_Exp/eval_phase/test_stream/Task000/Exp001 = 2.3041 Top1_Acc_Exp/eval_phase/test_stream/Task000/Exp001 = 0.2129 -- >> End of eval phase << -- Loss_Stream/eval_phase/test_stream/Task000 = 2.3041 Top1_Acc_Stream/eval_phase/test_stream/Task000 = 0.2129 ``` which means it's calling `eval` two times instead of a single one with the entire stream.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

ContinualAI__avalanche-1598

diff --git a/avalanche/benchmarks/scenarios/__init__.py b/avalanche/benchmarks/scenarios/__init__.py index f84a965c..83db8205 100644 --- a/avalanche/benchmarks/scenarios/__init__.py +++ b/avalanche/benchmarks/scenarios/__init__.py @@ -8,3 +8,4 @@ from .task_aware import * from .dataset_scenario import * from .exmodel_scenario import * from .online import * +from .validation_scenario import * diff --git a/avalanche/benchmarks/scenarios/dataset_scenario.py b/avalanche/benchmarks/scenarios/dataset_scenario.py index df0848ef..cf5f7afa 100644 --- a/avalanche/benchmarks/scenarios/dataset_scenario.py +++ b/avalanche/benchmarks/scenarios/dataset_scenario.py @@ -14,7 +14,6 @@ import random from avalanche.benchmarks.utils.data import AvalancheDataset import torch -from itertools import tee from typing import ( Callable, Generator, @@ -253,94 +252,9 @@ class LazyTrainValSplitter: yield self.split_strategy(new_experience.dataset) -def benchmark_with_validation_stream( - benchmark: CLScenario, - validation_size: Union[int, float] = 0.5, - shuffle: bool = False, - seed: Optional[int] = None, - split_strategy: Optional[ - Callable[[AvalancheDataset], Tuple[AvalancheDataset, AvalancheDataset]] - ] = None, -) -> CLScenario: - """Helper to obtain a benchmark with a validation stream. - - This generator accepts an existing benchmark instance and returns a version - of it in which the train stream has been split into training and validation - streams. - - Each train/validation experience will be by splitting the original training - experiences. Patterns selected for the validation experience will be removed - from the training experiences. - - The default splitting strategy is a random split as implemented by `split_validation_random`. - If you want to use class balancing you can use `split_validation_class_balanced`, or - use a custom `split_strategy`, as shown in the following example:: - - validation_size = 0.2 - foo = lambda exp: split_dataset_class_balanced(validation_size, exp) - bm = benchmark_with_validation_stream(bm, custom_split_strategy=foo) - - :param benchmark: The benchmark to split. - :param validation_size: The size of the validation experience, as an int - or a float between 0 and 1. Ignored if `custom_split_strategy` is used. - :param shuffle: If True, patterns will be allocated to the validation - stream randomly. This will use the default PyTorch random number - generator at its current state. Defaults to False. Ignored if - `custom_split_strategy` is used. If False, the first instances will be - allocated to the training dataset by leaving the last ones to the - validation dataset. - :param split_strategy: A function that implements a custom splitting - strategy. The function must accept an AvalancheDataset and return a tuple - containing the new train and validation dataset. By default, the splitting - strategy will split the data according to `validation_size` and `shuffle`). - A good starting to understand the mechanism is to look at the - implementation of the standard splitting function - :func:`random_validation_split_strategy`. - - :return: A benchmark instance in which the validation stream has been added. - """ - - if split_strategy is None: - if seed is None: - seed = random.randint(0, 1000000) - - # functools.partial is a more compact option - # However, MyPy does not understand what a partial is -_- - def random_validation_split_strategy_wrapper(data): - return split_validation_random(validation_size, shuffle, seed, data) - - split_strategy = random_validation_split_strategy_wrapper - else: - split_strategy = split_strategy - - stream = benchmark.streams["train"] - if isinstance(stream, EagerCLStream): # eager split - train_exps, valid_exps = [], [] - - exp: DatasetExperience - for exp in stream: - train_data, valid_data = split_strategy(exp.dataset) - train_exps.append(DatasetExperience(dataset=train_data)) - valid_exps.append(DatasetExperience(dataset=valid_data)) - else: # Lazy splitting (based on a generator) - split_generator = LazyTrainValSplitter(split_strategy, stream) - train_exps = (DatasetExperience(dataset=a) for a, _ in split_generator) - valid_exps = (DatasetExperience(dataset=b) for _, b in split_generator) - - train_stream = make_stream(name="train", exps=train_exps) - valid_stream = make_stream(name="valid", exps=valid_exps) - other_streams = benchmark.streams - - del other_streams["train"] - return CLScenario( - streams=[train_stream, valid_stream] + list(other_streams.values()) - ) - - __all__ = [ "_split_dataset_by_attribute", "benchmark_from_datasets", "DatasetExperience", "split_validation_random", - "benchmark_with_validation_stream", ] diff --git a/avalanche/benchmarks/scenarios/supervised.py b/avalanche/benchmarks/scenarios/supervised.py index 66c0ecc8..8e46446d 100644 --- a/avalanche/benchmarks/scenarios/supervised.py +++ b/avalanche/benchmarks/scenarios/supervised.py @@ -26,12 +26,11 @@ import torch from avalanche.benchmarks.utils.classification_dataset import ( ClassificationDataset, _as_taskaware_supervised_classification_dataset, - TaskAwareSupervisedClassificationDataset, ) from avalanche.benchmarks.utils.data import AvalancheDataset from avalanche.benchmarks.utils.data_attribute import DataAttribute from .dataset_scenario import _split_dataset_by_attribute, DatasetExperience -from .. import CLScenario, CLStream, EagerCLStream +from .generic_scenario import CLScenario, CLStream, EagerCLStream def class_incremental_benchmark( diff --git a/avalanche/benchmarks/scenarios/validation_scenario.py b/avalanche/benchmarks/scenarios/validation_scenario.py new file mode 100644 index 00000000..b3cb08eb --- /dev/null +++ b/avalanche/benchmarks/scenarios/validation_scenario.py @@ -0,0 +1,116 @@ +from typing import ( + Callable, + Generator, + Generic, + List, + Sequence, + TypeVar, + Union, + Tuple, + Optional, + Iterable, + Dict, +) + +import random +from avalanche.benchmarks.utils.data import AvalancheDataset +from .generic_scenario import EagerCLStream, CLScenario, CLExperience, make_stream +from .dataset_scenario import ( + LazyTrainValSplitter, + DatasetExperience, + split_validation_random, +) +from .supervised import with_classes_timeline + + +def benchmark_with_validation_stream( + benchmark: CLScenario, + validation_size: Union[int, float] = 0.5, + shuffle: bool = False, + seed: Optional[int] = None, + split_strategy: Optional[ + Callable[[AvalancheDataset], Tuple[AvalancheDataset, AvalancheDataset]] + ] = None, +) -> CLScenario: + """Helper to obtain a benchmark with a validation stream. + + This generator accepts an existing benchmark instance and returns a version + of it in which the train stream has been split into training and validation + streams. + + Each train/validation experience will be by splitting the original training + experiences. Patterns selected for the validation experience will be removed + from the training experiences. + + The default splitting strategy is a random split as implemented by `split_validation_random`. + If you want to use class balancing you can use `split_validation_class_balanced`, or + use a custom `split_strategy`, as shown in the following example:: + + validation_size = 0.2 + foo = lambda exp: split_dataset_class_balanced(validation_size, exp) + bm = benchmark_with_validation_stream(bm, custom_split_strategy=foo) + + :param benchmark: The benchmark to split. + :param validation_size: The size of the validation experience, as an int + or a float between 0 and 1. Ignored if `custom_split_strategy` is used. + :param shuffle: If True, patterns will be allocated to the validation + stream randomly. This will use the default PyTorch random number + generator at its current state. Defaults to False. Ignored if + `custom_split_strategy` is used. If False, the first instances will be + allocated to the training dataset by leaving the last ones to the + validation dataset. + :param split_strategy: A function that implements a custom splitting + strategy. The function must accept an AvalancheDataset and return a tuple + containing the new train and validation dataset. By default, the splitting + strategy will split the data according to `validation_size` and `shuffle`). + A good starting to understand the mechanism is to look at the + implementation of the standard splitting function + :func:`random_validation_split_strategy`. + + :return: A benchmark instance in which the validation stream has been added. + """ + + if split_strategy is None: + if seed is None: + seed = random.randint(0, 1000000) + + # functools.partial is a more compact option + # However, MyPy does not understand what a partial is -_- + def random_validation_split_strategy_wrapper(data): + return split_validation_random(validation_size, shuffle, seed, data) + + split_strategy = random_validation_split_strategy_wrapper + else: + split_strategy = split_strategy + + stream = benchmark.streams["train"] + if isinstance(stream, EagerCLStream): # eager split + train_exps, valid_exps = [], [] + + exp: DatasetExperience + for exp in stream: + train_data, valid_data = split_strategy(exp.dataset) + train_exps.append(DatasetExperience(dataset=train_data)) + valid_exps.append(DatasetExperience(dataset=valid_data)) + else: # Lazy splitting (based on a generator) + split_generator = LazyTrainValSplitter(split_strategy, stream) + train_exps = (DatasetExperience(dataset=a) for a, _ in split_generator) + valid_exps = (DatasetExperience(dataset=b) for _, b in split_generator) + + train_stream = make_stream(name="train", exps=train_exps) + valid_stream = make_stream(name="valid", exps=valid_exps) + other_streams = benchmark.streams + + # don't drop classes-timeline for compatibility with old API + e0 = next(iter(train_stream)) + if hasattr(e0, "dataset") and hasattr(e0.dataset, "targets"): + train_stream = with_classes_timeline(train_stream) + valid_stream = with_classes_timeline(valid_stream) + + del other_streams["train"] + return CLScenario( + streams=[train_stream, valid_stream] + list(other_streams.values()) + ) + + +__all__ = ["benchmark_with_validation_stream"] diff --git a/avalanche/models/dynamic_modules.py b/avalanche/models/dynamic_modules.py index 1cf58098..3086681f 100644 --- a/avalanche/models/dynamic_modules.py +++ b/avalanche/models/dynamic_modules.py @@ -246,7 +246,7 @@ class IncrementalClassifier(DynamicModule): self.active_units[: old_act_units.shape[0]] = old_act_units # update with new active classes if self.training: - self.active_units[curr_classes] = 1 + self.active_units[list(curr_classes)] = 1 # update classifier weights if old_nclasses == new_nclasses:

ContinualAI/avalanche

524f70c50cb7090ac05aef87326300514e2d4d6f

diff --git a/tests/benchmarks/scenarios/test_dataset_scenario.py b/tests/benchmarks/scenarios/test_dataset_scenario.py index d5c11eab..dbb86ab7 100644 --- a/tests/benchmarks/scenarios/test_dataset_scenario.py +++ b/tests/benchmarks/scenarios/test_dataset_scenario.py @@ -6,12 +6,14 @@ from torch.utils.data import TensorDataset, DataLoader from avalanche.benchmarks import ( benchmark_from_datasets, - benchmark_with_validation_stream, CLScenario, CLStream, split_validation_random, task_incremental_benchmark, ) +from avalanche.benchmarks.scenarios.validation_scenario import ( + benchmark_with_validation_stream, +) from avalanche.benchmarks.scenarios.dataset_scenario import ( DatasetExperience, split_validation_class_balanced, @@ -383,3 +385,9 @@ class DatasetWithValidationStreamTests(unittest.TestCase): mb = get_mbatch(dd, len(dd)) self.assertTrue(torch.equal(test_x, mb[0])) self.assertTrue(torch.equal(test_y, mb[1])) + + def test_regressioni1597(args): + # regression test for issue #1597 + bm = get_fast_benchmark() + for exp in bm.train_stream: + assert hasattr(exp, "classes_in_this_experience") diff --git a/tests/training/test_plugins.py b/tests/training/test_plugins.py index 6c223c73..9ba6dda9 100644 --- a/tests/training/test_plugins.py +++ b/tests/training/test_plugins.py @@ -16,6 +16,8 @@ from torch.utils.data.dataloader import DataLoader from avalanche.benchmarks import ( nc_benchmark, GenericCLScenario, +) +from avalanche.benchmarks.scenarios.validation_scenario import ( benchmark_with_validation_stream, ) from avalanche.benchmarks.utils.data_loader import TaskBalancedDataLoader

benchmark_with_validation stream removes or hides classes_in_experience attribute 🐛 **Describe the bug** When using benchmark_with_validation_stream, the classes_in_experience attribute is removed or hidden and cannot be caught during model adaptation. 🐜 **To Reproduce** ```{python} import torch import argparse from torch.nn import CrossEntropyLoss from torch.optim import SGD from avalanche.benchmarks.classic import SplitCIFAR100 from avalanche.benchmarks import benchmark_with_validation_stream from avalanche.models import SlimResNet18 from avalanche.models.dynamic_modules import IncrementalClassifier from avalanche.training.supervised import Naive def main(args): # Device config device = torch.device( f"cuda:{args.cuda}" if torch.cuda.is_available() and args.cuda >= 0 else "cpu" ) # model model = SlimResNet18(1) model.linear = IncrementalClassifier(model.linear.in_features, model.linear.out_features) benchmark = SplitCIFAR100(n_experiences=5, seed=1, dataset_root="/DATA/data") benchmark = benchmark_with_validation_stream(benchmark, validation_size=0.05) # Than we can extract the parallel train and test streams train_stream = benchmark.train_stream test_stream = benchmark.test_stream # Prepare for training & testing optimizer = SGD(model.parameters(), lr=0.001, momentum=0.9) criterion = CrossEntropyLoss() # Continual learning strategy with default logger cl_strategy = Naive( model, optimizer, criterion, train_mb_size=32, train_epochs=0, eval_mb_size=32, device=device, ) # train and test loop results = [] for train_task in train_stream: print("Current Classes: ", train_task.classes_in_this_experience) cl_strategy.train(train_task) results.append(cl_strategy.eval(test_stream)) if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument( "--cuda", type=int, default=0, help="Select zero-indexed cuda device. -1 to use CPU.", ) args = parser.parse_args() main(args) ``` 🐝 **Expected behavior** Should work with and without calling benchmark_with_validation_stream, but here gives an error ``` print("Current Classes: ", train_task.classes_in_this_experience) File "/home/albin/Documents/Projects/avalanche_dev/avalanche/benchmarks/scenarios/generic_scenario.py", line 170, in __getattribute__ v = super().__getattribute__(item) AttributeError: 'DatasetExperience' object has no attribute 'classes_in_this_experience' ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

CybOXProject__mixbox-35

diff --git a/mixbox/dates.py b/mixbox/dates.py index be279e1..794e0b0 100644 --- a/mixbox/dates.py +++ b/mixbox/dates.py @@ -73,10 +73,10 @@ def serialize_date(value): """ if not value: return None - elif isinstance(value, datetime.date): - return value.isoformat() elif isinstance(value, datetime.datetime): return value.date().isoformat() + elif isinstance(value, datetime.date): + return value.isoformat() else: return parse_date(value).isoformat() diff --git a/mixbox/fields.py b/mixbox/fields.py index f623c6b..cad106a 100644 --- a/mixbox/fields.py +++ b/mixbox/fields.py @@ -373,7 +373,7 @@ class DateField(TypedField): return serialize_date(value) def binding_value(self, value): - return serialize_datetime(value) + return serialize_date(value) class CDATAField(TypedField):

CybOXProject/mixbox

bab51cfd20757f9a64a61571631203dbbc3644f8

diff --git a/tests/dates_tests.py b/tests/dates_tests.py index f139939..d3be86b 100644 --- a/tests/dates_tests.py +++ b/tests/dates_tests.py @@ -15,6 +15,12 @@ class DatesTests(unittest.TestCase): dstr = "2015-04-01" parsed = dates.parse_date(dstr) self.assertEqual(dstr, parsed.isoformat()) + + def test_serialize_datetime_as_date(self): + now = dates.now() + self.assertTrue(isinstance(now, datetime.datetime)) + nowstr = dates.serialize_date(now) + self.assertEquals(nowstr, now.date().isoformat()) def test_parse_datetime(self): dtstr = '2015-04-02T16:44:30.423149+00:00'

DateField does not properly serialize datetime objects When storing a Python `datetime` object in a property specified by a `DateField`, the value incorrectly serializes to an ISO timestamp (`YYYY-MM-DDThh:mm:ss`) instead of to a `xs:date` format (`YYYY-MM-DD`). class Foo(Entity): my_date = DateField("my_date"); obj = Foo() obj.my_date = datetime.datetime.now() There are two issues: * the `DateField::binding_value` function uses `serialize_datetime` instead of `serialize_date` * the `serialize_date` function erroneously includes time information in its output when processing datetimes

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

CycloneDX__cyclonedx-python-332

diff --git a/cyclonedx_py/utils/conda.py b/cyclonedx_py/utils/conda.py index 3cf2fc5..b5c26a0 100644 --- a/cyclonedx_py/utils/conda.py +++ b/cyclonedx_py/utils/conda.py @@ -20,15 +20,14 @@ import json import sys from json import JSONDecodeError -from typing import Optional +from typing import Optional, Tuple +from urllib.parse import urlparse if sys.version_info >= (3, 8): from typing import TypedDict else: from typing_extensions import TypedDict -from urllib.parse import urlparse - class CondaPackage(TypedDict): """ @@ -72,56 +71,72 @@ def parse_conda_list_str_to_conda_package(conda_list_str: str) -> Optional[Conda line = conda_list_str.strip() - if line[0:1] == '#' or line[0:1] == '@' or len(line) == 0: + if '' == line or line[0] in ['#', '@']: # Skip comments, @EXPLICT or empty lines return None # Remove any hash package_hash = None if '#' in line: - hash_parts = line.split('#') - if len(hash_parts) > 1: - package_hash = hash_parts.pop() - line = ''.join(hash_parts) + *_line_parts, package_hash = line.split('#') + line = ''.join(*_line_parts) package_parts = line.split('/') - package_name_version_build_string = package_parts.pop() - package_arch = package_parts.pop() - package_url = urlparse('/'.join(package_parts)) + if len(package_parts) < 2: + raise ValueError(f'Unexpected format in {package_parts}') + *_package_url_parts, package_arch, package_name_version_build_string = package_parts + package_url = urlparse('/'.join(_package_url_parts)) - try: - package_nvbs_parts = package_name_version_build_string.split('-') - build_number_with_opt_string = package_nvbs_parts.pop() - if '.' in build_number_with_opt_string: - # Remove any .conda at the end if present or other package type eg .tar.gz - pos = build_number_with_opt_string.find('.') - build_number_with_opt_string = build_number_with_opt_string[0:pos] - - build_string: str - build_number: Optional[int] - - if '_' in build_number_with_opt_string: - bnbs_parts = build_number_with_opt_string.split('_') - # Build number will be the last part - check if it's an integer - # Updated logic given https://github.com/CycloneDX/cyclonedx-python-lib/issues/65 - candidate_build_number: str = bnbs_parts.pop() - if candidate_build_number.isdigit(): - build_number = int(candidate_build_number) - build_string = build_number_with_opt_string - else: - build_number = None - build_string = build_number_with_opt_string - else: - build_string = '' - build_number = int(build_number_with_opt_string) - - build_version = package_nvbs_parts.pop() - package_name = '-'.join(package_nvbs_parts) - except IndexError as e: - raise ValueError(f'Error parsing {package_nvbs_parts} from {conda_list_str}') from e + package_name, build_version, build_string = split_package_string(package_name_version_build_string) + build_string, build_number = split_package_build_string(build_string) return CondaPackage( base_url=package_url.geturl(), build_number=build_number, build_string=build_string, channel=package_url.path[1:], dist_name=f'{package_name}-{build_version}-{build_string}', name=package_name, platform=package_arch, version=build_version, md5_hash=package_hash ) + + +def split_package_string(package_name_version_build_string: str) -> Tuple[str, str, str]: + """Helper method for parsing package_name_version_build_string. + + Returns: + Tuple (package_name, build_version, build_string) + """ + package_nvbs_parts = package_name_version_build_string.split('-') + if len(package_nvbs_parts) < 3: + raise ValueError(f'Unexpected format in {package_nvbs_parts}') + + *_package_name_parts, build_version, build_string = package_nvbs_parts + package_name = '-'.join(_package_name_parts) + + _pos = build_string.find('.') + if _pos >= 0: + # Remove any .conda at the end if present or other package type eg .tar.gz + build_string = build_string[0:_pos] + + return package_name, build_version, build_string + + +def split_package_build_string(build_string: str) -> Tuple[str, Optional[int]]: + """Helper method for parsing build_string. + + Returns: + Tuple (build_string, build_number) + """ + + if '' == build_string: + return '', None + + if build_string.isdigit(): + return '', int(build_string) + + _pos = build_string.rindex('_') if '_' in build_string else -1 + if _pos >= 1: + # Build number will be the last part - check if it's an integer + # Updated logic given https://github.com/CycloneDX/cyclonedx-python-lib/issues/65 + build_number = build_string[_pos + 1:] + if build_number.isdigit(): + return build_string, int(build_number) + + return build_string, None diff --git a/poetry.lock b/poetry.lock index db46888..d333b19 100644 --- a/poetry.lock +++ b/poetry.lock @@ -107,7 +107,7 @@ typed-ast = {version = ">=1.4,<2.0", markers = "python_version < \"3.8\""} [[package]] name = "flake8-bugbear" -version = "22.1.11" +version = "22.3.20" description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle." category = "dev" optional = false @@ -442,7 +442,7 @@ testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytes [metadata] lock-version = "1.1" python-versions = "^3.6" -content-hash = "817a5868658e3804313ae035125ee83b7f78cc32260ef64fe4b8551bde68acc5" +content-hash = "ef3ff89f1dd8de6e1433cbfa1c112cd8f5666dcab77f82781fc6ea9d8bb0d377" [metadata.files] attrs = [ @@ -527,8 +527,8 @@ flake8-annotations = [ {file = "flake8_annotations-2.7.0-py3-none-any.whl", hash = "sha256:3edfbbfb58e404868834fe6ec3eaf49c139f64f0701259f707d043185545151e"}, ] flake8-bugbear = [ - {file = "flake8-bugbear-22.1.11.tar.gz", hash = "sha256:4c2a4136bd4ecb8bf02d5159af302ffc067642784c9d0488b33ce4610da825ee"}, - {file = "flake8_bugbear-22.1.11-py3-none-any.whl", hash = "sha256:ce7ae44aaaf67ef192b8a6de94a5ac617144e1675ad0654fdea556f48dc18d9b"}, + {file = "flake8-bugbear-22.3.20.tar.gz", hash = "sha256:152e64a86f6bff6e295d630ccc993f62434c1fd2b20d2fae47547cb1c1b868e0"}, + {file = "flake8_bugbear-22.3.20-py3-none-any.whl", hash = "sha256:19fe179ee3286e16198603c438788e2949e79f31d653f0bdb56d53fb69217bd0"}, ] flake8-isort = [ {file = "flake8-isort-4.1.1.tar.gz", hash = "sha256:d814304ab70e6e58859bc5c3e221e2e6e71c958e7005239202fee19c24f82717"}, diff --git a/pyproject.toml b/pyproject.toml index cb76bc6..50cd349 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,7 +46,7 @@ coverage = "^6.2" mypy = "^0.941" flake8 = "^4.0.1" flake8-annotations = {version = "^2.7.0", python = ">= 3.6.2"} -flake8-bugbear = "^22.1.11" +flake8-bugbear = "^22.3.20" flake8-isort = { version = "^4.1.0", python = ">= 3.6.1" } [tool.poetry.scripts]

CycloneDX/cyclonedx-python

c02d770cf18a57e118347a0a57db29ae65919c35

diff --git a/tests/fixtures/conda-list-broken.txt b/tests/fixtures/conda-list-broken.txt new file mode 100644 index 0000000..ed67b21 --- /dev/null +++ b/tests/fixtures/conda-list-broken.txt @@ -0,0 +1,2 @@ +# This package list id malformed. +https://repo.anaconda.com/pkgs/main/linux-64/malformed_source.conda diff --git a/tests/fixtures/conda-list-build-number-text.txt b/tests/fixtures/conda-list-build-number-text.txt new file mode 100644 index 0000000..ab3e4c2 --- /dev/null +++ b/tests/fixtures/conda-list-build-number-text.txt @@ -0,0 +1,45 @@ +# This file is part of https://github.com/CycloneDX/cyclonedx-python/issues/331 + +# This file may be used to create an environment using: +# $ conda create --name <env> --file <this file> +# platform: linux-64 +@EXPLICIT +https://repo.anaconda.com/pkgs/main/linux-64/_libgcc_mutex-0.1-main.conda +https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2022.2.1-h06a4308_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.35.1-h7274673_9.conda +https://repo.anaconda.com/pkgs/main/linux-64/libstdcxx-ng-9.3.0-hd4cf53a_17.conda +https://repo.anaconda.com/pkgs/main/noarch/tzdata-2021e-hda174b7_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/libgomp-9.3.0-h5101ec6_17.conda +https://repo.anaconda.com/pkgs/main/linux-64/_openmp_mutex-4.5-1_gnu.tar.bz2 +https://repo.anaconda.com/pkgs/main/linux-64/libgcc-ng-9.3.0-h5101ec6_17.conda +https://repo.anaconda.com/pkgs/main/linux-64/libffi-3.3-he6710b0_2.conda +https://repo.anaconda.com/pkgs/main/linux-64/ncurses-6.3-h7f8727e_2.conda +https://repo.anaconda.com/pkgs/main/linux-64/openssl-1.1.1m-h7f8727e_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/xz-5.2.5-h7b6447c_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/yaml-0.2.5-h7b6447c_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/zlib-1.2.11-h7f8727e_4.conda +https://repo.anaconda.com/pkgs/main/linux-64/readline-8.1.2-h7f8727e_1.conda +https://repo.anaconda.com/pkgs/main/linux-64/tk-8.6.11-h1ccaba5_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/sqlite-3.38.0-hc218d9a_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/python-3.9.7-h12debd9_1.conda +https://repo.anaconda.com/pkgs/main/linux-64/certifi-2021.10.8-py39h06a4308_2.conda +https://repo.anaconda.com/pkgs/main/noarch/charset-normalizer-2.0.4-pyhd3eb1b0_0.conda +https://repo.anaconda.com/pkgs/main/noarch/colorama-0.4.4-pyhd3eb1b0_0.conda +https://repo.anaconda.com/pkgs/main/noarch/idna-3.3-pyhd3eb1b0_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/pycosat-0.6.3-py39h27cfd23_0.conda +https://repo.anaconda.com/pkgs/main/noarch/pycparser-2.21-pyhd3eb1b0_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/pysocks-1.7.1-py39h06a4308_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/ruamel_yaml-0.15.100-py39h27cfd23_0.conda +https://repo.anaconda.com/pkgs/main/noarch/six-1.16.0-pyhd3eb1b0_1.conda +https://repo.anaconda.com/pkgs/main/noarch/wheel-0.37.1-pyhd3eb1b0_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/cffi-1.15.0-py39hd667e15_1.conda +https://repo.anaconda.com/pkgs/main/linux-64/setuptools-58.0.4-py39h06a4308_0.conda +https://repo.anaconda.com/pkgs/main/noarch/tqdm-4.63.0-pyhd3eb1b0_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/brotlipy-0.7.0-py39h27cfd23_1003.conda +https://repo.anaconda.com/pkgs/main/linux-64/conda-package-handling-1.7.3-py39h27cfd23_1.conda +https://repo.anaconda.com/pkgs/main/linux-64/cryptography-36.0.0-py39h9ce1e76_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/pip-21.2.4-py39h06a4308_0.conda +https://repo.anaconda.com/pkgs/main/noarch/pyopenssl-22.0.0-pyhd3eb1b0_0.conda +https://repo.anaconda.com/pkgs/main/noarch/urllib3-1.26.8-pyhd3eb1b0_0.conda +https://repo.anaconda.com/pkgs/main/noarch/requests-2.27.1-pyhd3eb1b0_0.conda +https://repo.anaconda.com/pkgs/main/linux-64/conda-4.12.0-py39h06a4308_0.conda diff --git a/tests/test_parser_conda.py b/tests/test_parser_conda.py index 7f3810a..287341e 100644 --- a/tests/test_parser_conda.py +++ b/tests/test_parser_conda.py @@ -18,6 +18,7 @@ # Copyright (c) OWASP Foundation. All Rights Reserved. import os +import re from unittest import TestCase from cyclonedx_py.parser.conda import CondaListExplicitParser, CondaListJsonParser @@ -54,3 +55,32 @@ class TestCondaParser(TestCase): self.assertEqual('2.10', c_noarch.version) self.assertEqual(1, len(c_noarch.external_references)) self.assertEqual(0, len(c_noarch.external_references.pop().hashes)) + + def test_conda_list_build_number_text(self) -> None: + conda_list_output_file = os.path.join(os.path.dirname(__file__), 'fixtures/conda-list-build-number-text.txt') + + with (open(conda_list_output_file, 'r')) as conda_list_ouptut_fh: + parser = CondaListExplicitParser(conda_data=conda_list_ouptut_fh.read()) + + self.assertEqual(39, parser.component_count()) + components = parser.get_components() + + c_libgcc_mutex = next(filter(lambda c: c.name == '_libgcc_mutex', components), None) + self.assertIsNotNone(c_libgcc_mutex) + self.assertEqual('_libgcc_mutex', c_libgcc_mutex.name) + self.assertEqual('0.1', c_libgcc_mutex.version) + c_pycparser = next(filter(lambda c: c.name == 'pycparser', components), None) + self.assertIsNotNone(c_pycparser) + self.assertEqual('pycparser', c_pycparser.name) + self.assertEqual('2.21', c_pycparser.version) + c_openmp_mutex = next(filter(lambda c: c.name == '_openmp_mutex', components), None) + self.assertIsNotNone(c_openmp_mutex) + self.assertEqual('_openmp_mutex', c_openmp_mutex.name) + self.assertEqual('4.5', c_openmp_mutex.version) + + def test_conda_list_malformed(self) -> None: + conda_list_output_file = os.path.join(os.path.dirname(__file__), 'fixtures/conda-list-broken.txt') + + with (open(conda_list_output_file, 'r')) as conda_list_ouptut_fh: + with self.assertRaisesRegex(ValueError, re.compile(r'^unexpected format', re.IGNORECASE)): + CondaListExplicitParser(conda_data=conda_list_ouptut_fh.read()) diff --git a/tests/test_utils_conda.py b/tests/test_utils_conda.py index 0bed7f8..584dc38 100644 --- a/tests/test_utils_conda.py +++ b/tests/test_utils_conda.py @@ -129,3 +129,51 @@ class TestUtilsConda(TestCase): self.assertEqual(cp['platform'], 'linux-64') self.assertEqual(cp['version'], '0.1') self.assertEqual(cp['md5_hash'], 'd7c89558ba9fa0495403155b64376d81') + + def test_parse_conda_list_build_number(self) -> None: + cp: CondaPackage = parse_conda_list_str_to_conda_package( + conda_list_str='https://repo.anaconda.com/pkgs/main/osx-64/chardet-4.0.0-py39hecd8cb5_1003.conda' + ) + + self.assertIsInstance(cp, dict) + self.assertEqual('https://repo.anaconda.com/pkgs/main', cp['base_url']) + self.assertEqual(1003, cp['build_number']) + self.assertEqual('py39hecd8cb5_1003', cp['build_string']) + self.assertEqual('pkgs/main', cp['channel']) + self.assertEqual('chardet-4.0.0-py39hecd8cb5_1003', cp['dist_name']) + self.assertEqual('chardet', cp['name']) + self.assertEqual('osx-64', cp['platform']) + self.assertEqual('4.0.0', cp['version']) + self.assertIsNone(cp['md5_hash']) + + def test_parse_conda_list_no_build_number(self) -> None: + cp: CondaPackage = parse_conda_list_str_to_conda_package( + conda_list_str='https://repo.anaconda.com/pkgs/main/linux-64/_libgcc_mutex-0.1-main.conda' + ) + + self.assertIsInstance(cp, dict) + self.assertEqual('https://repo.anaconda.com/pkgs/main', cp['base_url']) + self.assertEqual(None, cp['build_number']) + self.assertEqual('main', cp['build_string']) + self.assertEqual('pkgs/main', cp['channel']) + self.assertEqual('_libgcc_mutex-0.1-main', cp['dist_name']) + self.assertEqual('_libgcc_mutex', cp['name']) + self.assertEqual('linux-64', cp['platform']) + self.assertEqual('0.1', cp['version']) + self.assertIsNone(cp['md5_hash']) + + def test_parse_conda_list_no_build_number2(self) -> None: + cp: CondaPackage = parse_conda_list_str_to_conda_package( + conda_list_str='https://repo.anaconda.com/pkgs/main/linux-64/_openmp_mutex-4.5-1_gnu.tar.bz2' + ) + + self.assertIsInstance(cp, dict) + self.assertEqual('https://repo.anaconda.com/pkgs/main', cp['base_url']) + self.assertEqual(None, cp['build_number']) + self.assertEqual('1_gnu', cp['build_string']) + self.assertEqual('pkgs/main', cp['channel']) + self.assertEqual('_openmp_mutex-4.5-1_gnu', cp['dist_name']) + self.assertEqual('_openmp_mutex', cp['name']) + self.assertEqual('linux-64', cp['platform']) + self.assertEqual('4.5', cp['version']) + self.assertIsNone(cp['md5_hash'])

bug: conda-parser raises error when unexpected build-number is detected ## Environment XUbuntu 20.04 Python 3.8.10 conda 4.12.0 #miniconda Name: cyclonedx-bom Version: 3.1.0 ## What I did * update conda base ``` ->$ conda update -n base -c defaults conda -y Collecting package metadata (current_repodata.json): done Solving environment: done # All requested packages already installed. >$ conda env list # conda environments: # base * /home/fis/miniconda3 ``` * Create explicit list * [base_spec.txt](https://github.com/CycloneDX/cyclonedx-python/files/8289398/base_spec.txt) ``` >$ conda list -n base --explicit > ./base_spec.txt ``` * Create sbom from explicit list - Error ``` ->$ cyclonedx-py -c -i ./base_spec.txt --format json --schema-version 1.3 -o ./conda_base_cyclonedx_1.3_sbom.json Traceback (most recent call last): File "/home/fis/.local/bin/cyclonedx-py", line 8, in <module> sys.exit(main()) File "/home/fis/.local/lib/python3.8/site-packages/cyclonedx_py/client.py", line 260, in main CycloneDxCmd(args).execute() File "/home/fis/.local/lib/python3.8/site-packages/cyclonedx_py/client.py", line 113, in execute output = self.get_output() File "/home/fis/.local/lib/python3.8/site-packages/cyclonedx_py/client.py", line 63, in get_output parser = self._get_input_parser() File "/home/fis/.local/lib/python3.8/site-packages/cyclonedx_py/client.py", line 244, in _get_input_parser return CondaListExplicitParser(conda_data=input_data) File "/home/fis/.local/lib/python3.8/site-packages/cyclonedx_py/parser/conda.py", line 41, in __init__ self._parse_to_conda_packages(data_str=conda_data) File "/home/fis/.local/lib/python3.8/site-packages/cyclonedx_py/parser/conda.py", line 101, in _parse_to_conda_packages conda_package = parse_conda_list_str_to_conda_package(conda_list_str=line) File "/home/fis/.local/lib/python3.8/site-packages/cyclonedx_py/utils/conda.py", line 116, in parse_conda_list_str_to_conda_package build_number = int(build_number_with_opt_string) ValueError: invalid literal for int() with base 10: 'main' ->$ cat base_spec.txt | grep "main\." https://repo.anaconda.com/pkgs/main/linux-64/_libgcc_mutex-0.1-main.conda ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CycloneDX__cyclonedx-python-348

diff --git a/cyclonedx_py/parser/pipenv.py b/cyclonedx_py/parser/pipenv.py index 8e1676f..9339201 100644 --- a/cyclonedx_py/parser/pipenv.py +++ b/cyclonedx_py/parser/pipenv.py @@ -44,7 +44,7 @@ class PipEnvParser(BaseParser): type='pypi', name=package_name, version=str(package_data.get('version') or 'unknown').lstrip('=') ) ) - if package_data.get('index') == 'pypi' and isinstance(package_data.get('hashes'), list): + if isinstance(package_data.get('hashes'), list): # Add download location with hashes stored in Pipfile.lock for pip_hash in package_data['hashes']: ext_ref = ExternalReference(

CycloneDX/cyclonedx-python

194d2878fe088f8f1a680cc4eb95504c046d34a2

diff --git a/tests/test_parser_pipenv.py b/tests/test_parser_pipenv.py index 9d19f1d..751d282 100644 --- a/tests/test_parser_pipenv.py +++ b/tests/test_parser_pipenv.py @@ -50,7 +50,8 @@ class TestPipEnvParser(TestCase): self.assertEqual('anyio', c_anyio.name) self.assertEqual('3.3.3', c_anyio.version) - self.assertEqual(0, len(c_anyio.external_references), f'{c_anyio.external_references}') + self.assertEqual(2, len(c_anyio.external_references), f'{c_anyio.external_references}') + self.assertEqual(1, len(c_anyio.external_references.pop().hashes)) self.assertEqual('toml', c_toml.name) self.assertEqual('0.10.2', c_toml.version)

bug: hashes not always included in BOM when present in Pipfile.lock Hashes appear to only be included in BOM output if they were originally called in the Pipfile as direct dependencies. According to the usage document (docs/usage.rst) hashes should be included if they are present. Given the following Pipfile, only boto3 and pydantic will have their hashes included in the BOM. ``` [[source]] url = "https://pypi.org/simple" verify_ssl = true name = "pypi" [packages] boto3 = "*" pydantic = "*" [dev-packages] bandit = "*" ``` snippet of the Pipfile.lock ``` { "_meta": { "hash": { "sha256": "4cd7bf004b61eda536feaa2f04368e49b2197105af5c61c19d74adda5b73294b" }, "pipfile-spec": 6, "requires": { "python_version": "3.9" }, "sources": [ { "name": "pypi", "url": "https://pypi.org/simple", "verify_ssl": true } ] }, "default": { "boto3": { "hashes": [ "sha256:1a272a1dd36414b1626a47bb580425203be0b5a34caa117f38a5e18adf21f918", "sha256:8129ad42cc0120d1c63daa18512d6f0b1439e385b2b6e0fe987f116bdf795546" ], "index": "pypi", "version": "==1.20.54" }, "botocore": { "hashes": [ "sha256:06ae8076c4dcf3d72bec4d37e5f2dce4a92a18a8cdaa3bfaa6e3b7b5e30a8d7e", "sha256:4bb9ba16cccee5f5a2602049bc3e2db6865346b2550667f3013bdf33b0a01ceb" ], "markers": "python_version >= '3.6'", "version": "==1.23.54" }, ``` And the relevant BOM snippet is: ``` "components": [ { "type": "library", "bom-ref": "b019649c-e545-40a9-b934-6c7214d0964d", "name": "boto3", "version": "1.20.54", "purl": "pkg:pypi/[email protected]", "externalReferences": [ { "type": "distribution", "url": "https://pypi.org/project/boto3/1.20.54", "comment": "Distribution available from pypi.org", "hashes": [ { "alg": "SHA-256", "content": "1a272a1dd36414b1626a47bb580425203be0b5a34caa117f38a5e18adf21f918" } ] }, { "type": "distribution", "url": "https://pypi.org/project/boto3/1.20.54", "comment": "Distribution available from pypi.org", "hashes": [ { "alg": "SHA-256", "content": "8129ad42cc0120d1c63daa18512d6f0b1439e385b2b6e0fe987f116bdf795546" } ] } ] }, { "type": "library", "bom-ref": "5934293e-4285-4c3e-8176-91352e77c789", "name": "botocore", "version": "1.23.54", "purl": "pkg:pypi/[email protected]" }, ``` Potential fixes: * Upstream repository change & update documentation to specify constraint * Remove cyclonedx-python requirement for the index attribute to be present

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CycloneDX__cyclonedx-python-366

diff --git a/cyclonedx_py/parser/conda.py b/cyclonedx_py/parser/conda.py index 1c9197b..487ad08 100644 --- a/cyclonedx_py/parser/conda.py +++ b/cyclonedx_py/parser/conda.py @@ -25,10 +25,12 @@ from cyclonedx.model import ExternalReference, ExternalReferenceType, HashAlgori from cyclonedx.model.component import Component from cyclonedx.parser import BaseParser -# See https://github.com/package-url/packageurl-python/issues/65 -from packageurl import PackageURL # type: ignore - -from ..utils.conda import CondaPackage, parse_conda_json_to_conda_package, parse_conda_list_str_to_conda_package +from ..utils.conda import ( + CondaPackage, + conda_package_to_purl, + parse_conda_json_to_conda_package, + parse_conda_list_str_to_conda_package, +) class _BaseCondaParser(BaseParser, metaclass=ABCMeta): @@ -60,11 +62,10 @@ class _BaseCondaParser(BaseParser, metaclass=ABCMeta): """ for conda_package in self._conda_packages: + purl = conda_package_to_purl(conda_package) c = Component( - name=conda_package['name'], version=str(conda_package['version']), - purl=PackageURL( - type='pypi', name=conda_package['name'], version=str(conda_package['version']) - ) + name=conda_package['name'], version=conda_package['version'], + purl=purl ) c.external_references.add(ExternalReference( reference_type=ExternalReferenceType.DISTRIBUTION, diff --git a/cyclonedx_py/utils/conda.py b/cyclonedx_py/utils/conda.py index b5c26a0..a8c1ae0 100644 --- a/cyclonedx_py/utils/conda.py +++ b/cyclonedx_py/utils/conda.py @@ -23,6 +23,9 @@ from json import JSONDecodeError from typing import Optional, Tuple from urllib.parse import urlparse +# See https://github.com/package-url/packageurl-python/issues/65 +from packageurl import PackageURL # type: ignore + if sys.version_info >= (3, 8): from typing import TypedDict else: @@ -41,9 +44,29 @@ class CondaPackage(TypedDict): name: str platform: str version: str + package_format: Optional[str] md5_hash: Optional[str] +def conda_package_to_purl(pkg: CondaPackage) -> PackageURL: + """ + Return the purl for the specified package. + See https://github.com/package-url/purl-spec/blob/master/PURL-TYPES.rst#conda + """ + qualifiers = { + 'build': pkg['build_string'], + 'channel': pkg['channel'], + 'subdir': pkg['platform'], + } + if pkg['package_format'] is not None: + qualifiers['type'] = str(pkg['package_format']) + + purl = PackageURL( + type='conda', name=pkg['name'], version=pkg['version'], qualifiers=qualifiers + ) + return purl + + def parse_conda_json_to_conda_package(conda_json_str: str) -> Optional[CondaPackage]: try: package_data = json.loads(conda_json_str) @@ -53,6 +76,7 @@ def parse_conda_json_to_conda_package(conda_json_str: str) -> Optional[CondaPack if not isinstance(package_data, dict): return None + package_data.setdefault('package_format', None) package_data.setdefault('md5_hash', None) return CondaPackage(package_data) # type: ignore # @FIXME write proper type safe dict at this point @@ -87,17 +111,18 @@ def parse_conda_list_str_to_conda_package(conda_list_str: str) -> Optional[Conda *_package_url_parts, package_arch, package_name_version_build_string = package_parts package_url = urlparse('/'.join(_package_url_parts)) - package_name, build_version, build_string = split_package_string(package_name_version_build_string) + package_name, build_version, build_string, package_format = split_package_string(package_name_version_build_string) build_string, build_number = split_package_build_string(build_string) return CondaPackage( base_url=package_url.geturl(), build_number=build_number, build_string=build_string, channel=package_url.path[1:], dist_name=f'{package_name}-{build_version}-{build_string}', - name=package_name, platform=package_arch, version=build_version, md5_hash=package_hash + name=package_name, platform=package_arch, version=build_version, package_format=package_format, + md5_hash=package_hash ) -def split_package_string(package_name_version_build_string: str) -> Tuple[str, str, str]: +def split_package_string(package_name_version_build_string: str) -> Tuple[str, str, str, str]: """Helper method for parsing package_name_version_build_string. Returns: @@ -110,12 +135,12 @@ def split_package_string(package_name_version_build_string: str) -> Tuple[str, s *_package_name_parts, build_version, build_string = package_nvbs_parts package_name = '-'.join(_package_name_parts) + # Split package_format (.conda or .tar.gz) at the end _pos = build_string.find('.') - if _pos >= 0: - # Remove any .conda at the end if present or other package type eg .tar.gz - build_string = build_string[0:_pos] + package_format = build_string[_pos + 1:] + build_string = build_string[0:_pos] - return package_name, build_version, build_string + return package_name, build_version, build_string, package_format def split_package_build_string(build_string: str) -> Tuple[str, Optional[int]]:

CycloneDX/cyclonedx-python

b028c2b96fb2caea2d7f084b6ef88cba1bcade2b

diff --git a/tests/test_parser_conda.py b/tests/test_parser_conda.py index ece9aec..fcbd711 100644 --- a/tests/test_parser_conda.py +++ b/tests/test_parser_conda.py @@ -29,10 +29,10 @@ from cyclonedx_py.parser.conda import CondaListExplicitParser, CondaListJsonPars class TestCondaParser(TestCase): def test_conda_list_json(self) -> None: - conda_list_ouptut_file = os.path.join(os.path.dirname(__file__), + conda_list_output_file = os.path.join(os.path.dirname(__file__), 'fixtures/conda-list-output.json') - with (open(conda_list_ouptut_file, 'r')) as conda_list_output_fh: + with (open(conda_list_output_file, 'r')) as conda_list_output_fh: parser = CondaListJsonParser(conda_data=conda_list_output_fh.read()) self.assertEqual(34, parser.component_count()) @@ -42,15 +42,17 @@ class TestCondaParser(TestCase): self.assertIsNotNone(c_idna) self.assertEqual('idna', c_idna.name) self.assertEqual('2.10', c_idna.version) + self.assertEqual('pkg:conda/[email protected]?build=pyhd3eb1b0_0&channel=pkgs/main&subdir=noarch', + c_idna.purl.to_string()) self.assertEqual(1, len(c_idna.external_references), f'{c_idna.external_references}') self.assertEqual(0, len(c_idna.external_references.pop().hashes)) self.assertEqual(0, len(c_idna.hashes), f'{c_idna.hashes}') def test_conda_list_explicit_md5(self) -> None: - conda_list_ouptut_file = os.path.join(os.path.dirname(__file__), + conda_list_output_file = os.path.join(os.path.dirname(__file__), 'fixtures/conda-list-explicit-md5.txt') - with (open(conda_list_ouptut_file, 'r')) as conda_list_output_fh: + with (open(conda_list_output_file, 'r')) as conda_list_output_fh: parser = CondaListExplicitParser(conda_data=conda_list_output_fh.read()) self.assertEqual(34, parser.component_count()) @@ -60,6 +62,8 @@ class TestCondaParser(TestCase): self.assertIsNotNone(c_idna) self.assertEqual('idna', c_idna.name) self.assertEqual('2.10', c_idna.version) + self.assertEqual('pkg:conda/[email protected]?build=pyhd3eb1b0_0&channel=pkgs/main&subdir=noarch&type=tar.bz2', + c_idna.purl.to_string()) self.assertEqual(1, len(c_idna.external_references), f'{c_idna.external_references}') self.assertEqual(0, len(c_idna.external_references.pop().hashes)) self.assertEqual(1, len(c_idna.hashes), f'{c_idna.hashes}') @@ -70,8 +74,8 @@ class TestCondaParser(TestCase): def test_conda_list_build_number_text(self) -> None: conda_list_output_file = os.path.join(os.path.dirname(__file__), 'fixtures/conda-list-build-number-text.txt') - with (open(conda_list_output_file, 'r')) as conda_list_ouptut_fh: - parser = CondaListExplicitParser(conda_data=conda_list_ouptut_fh.read()) + with (open(conda_list_output_file, 'r')) as conda_list_output_fh: + parser = CondaListExplicitParser(conda_data=conda_list_output_fh.read()) self.assertEqual(39, parser.component_count()) components = parser.get_components() @@ -80,21 +84,29 @@ class TestCondaParser(TestCase): self.assertIsNotNone(c_libgcc_mutex) self.assertEqual('_libgcc_mutex', c_libgcc_mutex.name) self.assertEqual('0.1', c_libgcc_mutex.version) + self.assertEqual('pkg:conda/[email protected]?build=main&channel=pkgs/main&subdir=linux-64&type=conda', + c_libgcc_mutex.purl.to_string()) self.assertEqual(0, len(c_libgcc_mutex.hashes), f'{c_libgcc_mutex.hashes}') + c_pycparser = next(filter(lambda c: c.name == 'pycparser', components), None) self.assertIsNotNone(c_pycparser) self.assertEqual('pycparser', c_pycparser.name) self.assertEqual('2.21', c_pycparser.version) + self.assertEqual('pkg:conda/[email protected]?build=pyhd3eb1b0_0&channel=pkgs/main&subdir=noarch&type=conda', + c_pycparser.purl.to_string()) self.assertEqual(0, len(c_pycparser.hashes), f'{c_pycparser.hashes}') + c_openmp_mutex = next(filter(lambda c: c.name == '_openmp_mutex', components), None) self.assertIsNotNone(c_openmp_mutex) self.assertEqual('_openmp_mutex', c_openmp_mutex.name) self.assertEqual('4.5', c_openmp_mutex.version) + self.assertEqual('pkg:conda/[email protected]?build=1_gnu&channel=pkgs/main&subdir=linux-64&type=tar.bz2', + c_openmp_mutex.purl.to_string()) self.assertEqual(0, len(c_openmp_mutex.hashes), f'{c_openmp_mutex.hashes}') def test_conda_list_malformed(self) -> None: conda_list_output_file = os.path.join(os.path.dirname(__file__), 'fixtures/conda-list-broken.txt') - with (open(conda_list_output_file, 'r')) as conda_list_ouptut_fh: + with (open(conda_list_output_file, 'r')) as conda_list_output_fh: with self.assertRaisesRegex(ValueError, re.compile(r'^unexpected format', re.IGNORECASE)): - CondaListExplicitParser(conda_data=conda_list_ouptut_fh.read()) + CondaListExplicitParser(conda_data=conda_list_output_fh.read()) diff --git a/tests/test_utils_conda.py b/tests/test_utils_conda.py index 796b196..87a37b1 100644 --- a/tests/test_utils_conda.py +++ b/tests/test_utils_conda.py @@ -60,6 +60,7 @@ class TestUtilsConda(TestCase): self.assertEqual('chardet', cp['name']) self.assertEqual('osx-64', cp['platform']) self.assertEqual('4.0.0', cp['version']) + self.assertEqual('conda', cp['package_format']) self.assertIsNone(cp['md5_hash']) def test_parse_conda_list_str_with_hash_1(self) -> None: @@ -77,6 +78,7 @@ class TestUtilsConda(TestCase): self.assertEqual('tzdata', cp['name']) self.assertEqual('noarch', cp['platform']) self.assertEqual('2021a', cp['version'], ) + self.assertEqual('conda', cp['package_format']) self.assertEqual('d42e4db918af84a470286e4c300604a3', cp['md5_hash']) def test_parse_conda_list_str_with_hash_2(self) -> None: @@ -94,6 +96,7 @@ class TestUtilsConda(TestCase): self.assertEqual('ca-certificates', cp['name']) self.assertEqual('osx-64', cp['platform']) self.assertEqual('2021.7.5', cp['version'], ) + self.assertEqual('conda', cp['package_format']) self.assertEqual('c2d0ae65c08dacdcf86770b7b5bbb187', cp['md5_hash']) def test_parse_conda_list_str_with_hash_3(self) -> None: @@ -111,6 +114,7 @@ class TestUtilsConda(TestCase): self.assertEqual('idna', cp['name']) self.assertEqual('noarch', cp['platform']) self.assertEqual('2.10', cp['version'], ) + self.assertEqual('tar.bz2', cp['package_format']) self.assertEqual('153ff132f593ea80aae2eea61a629c92', cp['md5_hash']) def test_parse_conda_list_str_with_hash_4(self) -> None: @@ -128,6 +132,7 @@ class TestUtilsConda(TestCase): self.assertEqual('_libgcc_mutex', cp['name']) self.assertEqual('linux-64', cp['platform']) self.assertEqual('0.1', cp['version']) + self.assertEqual('tar.bz2', cp['package_format']) self.assertEqual('d7c89558ba9fa0495403155b64376d81', cp['md5_hash']) def test_parse_conda_list_build_number(self) -> None: @@ -144,6 +149,7 @@ class TestUtilsConda(TestCase): self.assertEqual('chardet', cp['name']) self.assertEqual('osx-64', cp['platform']) self.assertEqual('4.0.0', cp['version']) + self.assertEqual('conda', cp['package_format']) self.assertIsNone(cp['md5_hash']) def test_parse_conda_list_no_build_number(self) -> None: @@ -160,6 +166,7 @@ class TestUtilsConda(TestCase): self.assertEqual('_libgcc_mutex', cp['name']) self.assertEqual('linux-64', cp['platform']) self.assertEqual('0.1', cp['version']) + self.assertEqual('conda', cp['package_format']) self.assertIsNone(cp['md5_hash']) def test_parse_conda_list_no_build_number2(self) -> None: @@ -176,4 +183,5 @@ class TestUtilsConda(TestCase): self.assertEqual('_openmp_mutex', cp['name']) self.assertEqual('linux-64', cp['platform']) self.assertEqual('4.5', cp['version']) + self.assertEqual('tar.bz2', cp['package_format']) self.assertIsNone(cp['md5_hash'])

[CONDA] Incorrect purl type in SBoM from Conda Explicit MD5 list * What I did ``` # Create Conda environment with openssl included $ conda create -y --name openssl openssl=1.1.1o # Create an explicit MD5 list $ conda list -n openssl --explicit --md5 > openssl-1.1.1_explict_md5_spec.txt # Create a SBoM from the explicit MD5 list $ cyclonedx-py -c -i ./openssl-1.1.1_explict_md5_spec.txt --format json --schema-version 1.3 -o ./openssl-1.1.1_conda_explicit_md5_cyclonedx_1.3_sbom.json ``` * Resulting explicit MD5 list ``` $ cat openssl-3.0.3_explict_md5_spec.txt # This file may be used to create an environment using: # $ conda create --name <env> --file <this file> # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2021.10.8-ha878542_0.tar.bz2#575611b8a84f45960e87722eeb51fa26 https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.1.0-h8d9b700_16.tar.bz2#f013cf7749536ce43d82afbffdf499ab https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.1.0-h8d9b700_16.tar.bz2#4f05bc9844f7c101e6e147dab3c88d5c https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.3-h166bdaf_0.tar.bz2#f4c4e71d7cf611b513170eaa0852bf1d ``` * Resulting SBoM's purls' type depict components are from pypi, expected purl type to be conda ``` $ cat openssl_openssl_3.0.3_cyclonedx_1.3_sbom.json | grep purl "purl": "pkg:pypi/[email protected]", "purl": "pkg:pypi/[email protected]", "purl": "pkg:pypi/[email protected]", "purl": "pkg:pypi/[email protected]", "purl": "pkg:pypi/[email protected]", "purl": "pkg:pypi/[email protected]", ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

CycloneDX__cyclonedx-python-367

diff --git a/cyclonedx_py/parser/conda.py b/cyclonedx_py/parser/conda.py index 59fc527..1c9197b 100644 --- a/cyclonedx_py/parser/conda.py +++ b/cyclonedx_py/parser/conda.py @@ -21,7 +21,7 @@ import json from abc import ABCMeta, abstractmethod from typing import List -from cyclonedx.model import ExternalReference, ExternalReferenceType, XsUri +from cyclonedx.model import ExternalReference, ExternalReferenceType, HashAlgorithm, HashType, XsUri from cyclonedx.model.component import Component from cyclonedx.parser import BaseParser @@ -71,6 +71,11 @@ class _BaseCondaParser(BaseParser, metaclass=ABCMeta): url=XsUri(conda_package['base_url']), comment=f"Distribution name {conda_package['dist_name']}" )) + if conda_package['md5_hash'] is not None: + c.hashes.add(HashType( + algorithm=HashAlgorithm.MD5, + hash_value=str(conda_package['md5_hash']) + )) self._components.append(c)

CycloneDX/cyclonedx-python

e2be444b8db7dd12031f3e9b481dfdae23f3e59e

diff --git a/tests/test_parser_conda.py b/tests/test_parser_conda.py index cf6c6a5..ece9aec 100644 --- a/tests/test_parser_conda.py +++ b/tests/test_parser_conda.py @@ -21,6 +21,8 @@ import os import re from unittest import TestCase +from cyclonedx.model import HashAlgorithm, HashType + from cyclonedx_py.parser.conda import CondaListExplicitParser, CondaListJsonParser @@ -42,6 +44,7 @@ class TestCondaParser(TestCase): self.assertEqual('2.10', c_idna.version) self.assertEqual(1, len(c_idna.external_references), f'{c_idna.external_references}') self.assertEqual(0, len(c_idna.external_references.pop().hashes)) + self.assertEqual(0, len(c_idna.hashes), f'{c_idna.hashes}') def test_conda_list_explicit_md5(self) -> None: conda_list_ouptut_file = os.path.join(os.path.dirname(__file__), @@ -59,6 +62,10 @@ class TestCondaParser(TestCase): self.assertEqual('2.10', c_idna.version) self.assertEqual(1, len(c_idna.external_references), f'{c_idna.external_references}') self.assertEqual(0, len(c_idna.external_references.pop().hashes)) + self.assertEqual(1, len(c_idna.hashes), f'{c_idna.hashes}') + hash: HashType = c_idna.hashes.pop() + self.assertEqual(HashAlgorithm.MD5, hash.alg) + self.assertEqual('153ff132f593ea80aae2eea61a629c92', hash.content) def test_conda_list_build_number_text(self) -> None: conda_list_output_file = os.path.join(os.path.dirname(__file__), 'fixtures/conda-list-build-number-text.txt') @@ -73,14 +80,17 @@ class TestCondaParser(TestCase): self.assertIsNotNone(c_libgcc_mutex) self.assertEqual('_libgcc_mutex', c_libgcc_mutex.name) self.assertEqual('0.1', c_libgcc_mutex.version) + self.assertEqual(0, len(c_libgcc_mutex.hashes), f'{c_libgcc_mutex.hashes}') c_pycparser = next(filter(lambda c: c.name == 'pycparser', components), None) self.assertIsNotNone(c_pycparser) self.assertEqual('pycparser', c_pycparser.name) self.assertEqual('2.21', c_pycparser.version) + self.assertEqual(0, len(c_pycparser.hashes), f'{c_pycparser.hashes}') c_openmp_mutex = next(filter(lambda c: c.name == '_openmp_mutex', components), None) self.assertIsNotNone(c_openmp_mutex) self.assertEqual('_openmp_mutex', c_openmp_mutex.name) self.assertEqual('4.5', c_openmp_mutex.version) + self.assertEqual(0, len(c_openmp_mutex.hashes), f'{c_openmp_mutex.hashes}') def test_conda_list_malformed(self) -> None: conda_list_output_file = os.path.join(os.path.dirname(__file__), 'fixtures/conda-list-broken.txt')

[CONDA] Include component hashes when generating SBoM from Conda Explicit MD5 List * What I did ``` # Create Conda environment with openssl included conda create -y --name openssl openssl=1.1.1o # Create an explicit MD5 list conda list -n openssl --explicit --md5 > openssl-1.1.1_explict_md5_spec.txt # Create a SBoM from the environment cyclonedx-py -c -i ./openssl-1.1.1_explict_md5_spec.txt --format json --schema-version 1.3 -o ./openssl-1.1.1_conda_explicit_md5_cyclonedx_1.3_sbom.json ``` * Resulting explicit MD5 list ``` $ cat openssl-3.0.3_explict_md5_spec.txt # This file may be used to create an environment using: # $ conda create --name <env> --file <this file> # platform: linux-64 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2021.10.8-ha878542_0.tar.bz2#575611b8a84f45960e87722eeb51fa26 https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.1.0-h8d9b700_16.tar.bz2#f013cf7749536ce43d82afbffdf499ab https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.1.0-h8d9b700_16.tar.bz2#4f05bc9844f7c101e6e147dab3c88d5c https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.3-h166bdaf_0.tar.bz2#f4c4e71d7cf611b513170eaa0852bf1d ``` * Resulting SBoM's first component in components, all other components include similar information ``` "components": [ { "type": "library", "bom-ref": "999ea8df-ef27-47db-a8fd-a305112a051d", "name": "_libgcc_mutex", "version": "0.1", "purl": "pkg:pypi/[email protected]", "externalReferences": [ { "url": "https://repo.anaconda.com/pkgs/main", "comment": "Distribution name _libgcc_mutex-0.1-main", "type": "distribution" } ] }, ``` * Requesting the package MD5 be added to the component.hashes entry in components * ref https://cyclonedx.org/docs/1.3/json/#metadata_component_hashes_items_content * You can get the package MD5 from the explicit MD5 list, it is after the hashtag

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DCC-Lab__RayTracing-133

diff --git a/raytracing/rays.py b/raytracing/rays.py index 7787434..11de6ad 100644 --- a/raytracing/rays.py +++ b/raytracing/rays.py @@ -29,6 +29,12 @@ class Rays: self._thetaHistogram = None self._directionBinEdges = None + self._countHistogramParameters = None + self._xValuesCountHistogram = None + + self._anglesHistogramParameters = None + self._xValuesAnglesHistogram = None + def __len__(self) -> int: if self.rays is None: return 0 @@ -53,15 +59,17 @@ class Rays: return self._thetaValues def rayCountHistogram(self, binCount=None, minValue=None, maxValue=None): - if self._yHistogram is None: - if binCount is None: - binCount = 40 - if minValue is None: - minValue = min(self.yValues) + if binCount is None: + binCount = 40 + + if minValue is None: + minValue = min(self.yValues) + + if maxValue is None: + maxValue = max(self.yValues) - if maxValue is None: - maxValue = max(self.yValues) + if self._countHistogramParameters != (binCount, minValue, maxValue): (self._yHistogram, binEdges) = histogram(self.yValues, bins=binCount, @@ -70,27 +78,30 @@ class Rays: xValues = [] for i in range(len(binEdges) - 1): xValues.append((binEdges[i] + binEdges[i + 1]) / 2) + self._xValuesCountHistogram = xValues - return (xValues, self._yHistogram) + return (self._xValuesCountHistogram, self._yHistogram) def rayAnglesHistogram(self, binCount=None, minValue=None, maxValue=None): - if self._thetaHistogram is None: - if binCount is None: - binCount = 40 + if binCount is None: + binCount = 40 - if minValue is None: - minValue = min(self.thetaValues) + if minValue is None: + minValue = min(self.thetaValues) - if maxValue is None: - maxValue = max(self.thetaValues) + if maxValue is None: + maxValue = max(self.thetaValues) + + if self._anglesHistogramParameters != (binCount, minValue, maxValue): (self._thetaHistogram, binEdges) = histogram(self.thetaValues, bins=binCount, range=(minValue, maxValue)) self._thetaHistogram = list(self._thetaHistogram) xValues = [] for i in range(len(binEdges) - 1): xValues.append((binEdges[i] + binEdges[i + 1]) / 2) + self._xValuesAnglesHistogram = xValues - return (xValues, self._thetaHistogram) + return (self._xValuesAnglesHistogram, self._thetaHistogram) def display(self, title="Intensity profile", showTheta=True): plt.ioff() @@ -159,6 +170,12 @@ class Rays: self._thetaHistogram = None self._directionBinEdges = None + self._countHistogramParameters = None + self._xValuesCountHistogram = None + + self._anglesHistogramParameters = None + self._xValuesAnglesHistogram = None + def load(self, filePath, append=False): with open(filePath, 'rb') as infile: loadedRays = pickle.Unpickler(infile).load()

DCC-Lab/RayTracing

25d5ffdd500afc561b8ce7d25dded3b532fd44a1

diff --git a/raytracing/tests/testsRays.py b/raytracing/tests/testsRays.py new file mode 100644 index 0000000..9bb4c7c --- /dev/null +++ b/raytracing/tests/testsRays.py @@ -0,0 +1,34 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class TestRays(unittest.TestCase): + + def testRayCountHist(self): + r = Rays([Ray()]) + init = r.rayCountHistogram() + self.assertIsNotNone(init) # First time compute + final = r.rayCountHistogram() + self.assertIsNotNone(final) # Second time compute, now works + + self.assertTupleEqual(init, final) + final = r.rayCountHistogram(10) + self.assertNotEqual(init, final) + + def testRayAnglesHist(self): + r = Rays([Ray()]) + init = r.rayAnglesHistogram() + self.assertIsNotNone(init) # First time compute + final = r.rayAnglesHistogram() + self.assertIsNotNone(final) # Second time compute, now works + + self.assertTupleEqual(init, final) + final = r.rayAnglesHistogram(10) + self.assertNotEqual(init, final) + + +if __name__ == '__main__': + unittest.main()

rayCountHistogram() and rayAnglesHistogram() of Rays raise exception when already computed When we compute `rayCountHistogram()` for a first time, it works perfectly. But when we run it a second time, it throws an exception because a variable is referenced before asignment.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-135

diff --git a/raytracing/rays.py b/raytracing/rays.py index 11de6ad..283eb00 100644 --- a/raytracing/rays.py +++ b/raytracing/rays.py @@ -4,20 +4,36 @@ import matplotlib.pyplot as plt import pickle import time import os - -""" A group of rays kept as a list, to be used as a starting -point (i.e. an object) or as a cumulative detector (i.e. at an image -or output plane) for ImagingPath, MatrixGroup or any tracing function. -Subclasses can provide a computed ray for Monte Carlo simulation. +import collections.abc as collections + +""" A source or a detector of rays + +We can obtain intensity distributions at from given plane by propagating +many rays and collecting them at another plane. `Rays` is the base class +that provides the essential mechanisms to obtain histograms on a list +of rays (created or collected). This list of rays is a property of the base +class. Subclasses are specific to a given ray distribution (Lambertian for +instance) and will create each ray on demand, then store them as they go +in the rays list. + +It is an iterable object, which means it can be used in an expression +like `for ray in rays:` which is convenient both when propagating rays +or when analysing the resulting rays that reached a plane in ImagingPath, +MatrixGroup or any tracing function. """ - class Rays: def __init__(self, rays=None): if rays is None: self.rays = [] else: - self.rays = rays + if isinstance(rays, collections.Iterable): + if all([isinstance(ray, Ray) for ray in rays]): + self.rays = list(rays) + else: + raise TypeError("'rays' elements must be of type Ray.") + else: + raise TypeError("'rays' must be iterable (i.e. a list or a tuple of Ray).") self.iteration = 0 self.progressLog = 10000 @@ -160,6 +176,8 @@ class Rays: return self.rays[item] def append(self, ray): + if not isinstance(ray, Ray): + raise TypeError("'ray' must be a 'Ray' object.") if self.rays is not None: self.rays.append(ray) @@ -214,21 +232,6 @@ class Rays: # https://en.wikipedia.org/wiki/Xiaolin_Wu's_line_algorithm # and https://stackoverflow.com/questions/3122049/drawing-an-anti-aliased-line-with-thepython-imaging-library - # @property - # def intensityError(self): - # return list(map(lambda x : sqrt(x), self.distribution)) - - # @property - # def normalizedIntensity(self): - # maxValue = max(self.values) - # return list(map(lambda x : x/maxValue, self.distribution)) - - # @property - # def normalizedIntensityError(self): - # maxValue = max(self.distribution) - # return list(map(lambda x : x/maxValue, self.error)) - - class UniformRays(Rays): def __init__(self, yMax=1.0, yMin=None, thetaMax=pi / 2, thetaMin=None, M=100, N=100): self.yMax = yMax @@ -256,8 +259,8 @@ class LambertianRays(Rays): if yMin is None: self.yMin = -yMax - self.thetaMax = -pi / 2 - self.thetaMin = pi / 2 + self.thetaMin = -pi / 2 + self.thetaMax = pi / 2 self.M = M self.N = N self.I = I @@ -288,9 +291,9 @@ class RandomRays(Rays): def __getitem__(self, item): if self.rays is None: - raise NotImplemented("You cannot access RandomRays") + raise NotImplementedError("You cannot access RandomRays") elif len(self.rays) < item: - raise NotImplemented("You cannot access RandomRays") + raise NotImplementedError("You cannot access RandomRays") else: return self.rays[item] @@ -301,7 +304,7 @@ class RandomRays(Rays): return self.randomRay() def randomRay(self) -> Ray: - raise NotImplemented("You must implement randomRay() in your subclass") + raise NotImplementedError("You must implement randomRay() in your subclass") class RandomUniformRays(RandomRays):

DCC-Lab/RayTracing

203b3739d0804718664037706e2d43068fcd6ac5

diff --git a/raytracing/tests/testsComponents.py b/raytracing/tests/testsComponents.py new file mode 100644 index 0000000..a4aba5b --- /dev/null +++ b/raytracing/tests/testsComponents.py @@ -0,0 +1,60 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class Test4fSystem(unittest.TestCase): + + def test4fSystem(self): + elements = [Space(10), Lens(10), Space(15), Lens(5), Space(5)] + mg = MatrixGroup(elements, label="4f system") + system = System4f(10, 5, label="4f system") + self.assertEqual(system.A, -0.5) + self.assertEqual(system.B, 0) + self.assertEqual(system.C, 0) + self.assertEqual(system.D, -2) + self.assertEqual(system.L, 30) + self.assertEqual(mg.backIndex, system.backIndex) + self.assertEqual(mg.frontIndex, system.frontIndex) + self.assertEqual(mg.backVertex, system.backVertex) + self.assertEqual(mg.frontVertex, system.frontVertex) + self.assertEqual(mg.label, system.label) + self.assertTrue(system.isImaging) + + def test2fSystem(self): + elements = [Space(10), Lens(10), Space(10)] + mg = MatrixGroup(elements, label="2f system") + system = System2f(10, label="2f system") + self.assertEqual(system.A, 0) + self.assertEqual(system.B, 10) + self.assertEqual(system.C, -1 / 10) + self.assertEqual(system.D, 0) + self.assertEqual(system.L, 20) + self.assertEqual(mg.backIndex, system.backIndex) + self.assertEqual(mg.frontIndex, system.frontIndex) + self.assertEqual(mg.backVertex, system.backVertex) + self.assertEqual(mg.frontVertex, system.frontVertex) + self.assertEqual(mg.label, system.label) + self.assertFalse(system.isImaging) + + def test4fIsTwo2f(self): + f1, f2 = 10, 12 + system4f = System4f(f1=10, f2=12) + system2f_1 = System2f(f1) + system2f_2 = System2f(f2) + composed4fSystem = MatrixGroup(system2f_1.elements + system2f_2.elements) + self.assertEqual(composed4fSystem.A, system4f.A) + self.assertEqual(composed4fSystem.B, system4f.B) + self.assertEqual(composed4fSystem.C, system4f.C) + self.assertEqual(composed4fSystem.D, system4f.D) + self.assertEqual(composed4fSystem.L, system4f.L) + self.assertEqual(composed4fSystem.backIndex, system4f.backIndex) + self.assertEqual(composed4fSystem.frontIndex, system4f.frontIndex) + self.assertEqual(composed4fSystem.backVertex, system4f.backVertex) + self.assertEqual(composed4fSystem.frontVertex, system4f.frontVertex) + + +if __name__ == '__main__': + unittest.main() diff --git a/raytracing/tests/testsRays.py b/raytracing/tests/testsRays.py index 9bb4c7c..1638b29 100644 --- a/raytracing/tests/testsRays.py +++ b/raytracing/tests/testsRays.py @@ -7,6 +7,31 @@ inf = float("+inf") class TestRays(unittest.TestCase): + def testRaysInitDifferentInputs(self): + listOfRays = [Ray(), Ray(1, 1), Ray(1, -2), Ray(0, -1)] + tupleOfRays = tuple(listOfRays) + npArrayOfRays = array(listOfRays) + raysFromList = Rays(listOfRays) + raysFromTuple = Rays(tupleOfRays) + raysFromArray = Rays(npArrayOfRays) + rays = Rays(listOfRays) + self.assertListEqual(raysFromList.rays, listOfRays) + self.assertListEqual(raysFromTuple.rays, listOfRays) + self.assertListEqual(raysFromArray.rays, listOfRays) + self.assertListEqual(Rays(rays).rays, listOfRays) + + with self.assertRaises(TypeError) as error: + # This should raise an TypeError exception + Rays("Ray(), Ray(1), Ray(1,1)") + + with self.assertRaises(TypeError) as error: + # This should raise an TypeError exception + Rays([Ray(), [1, 2], Ray()]) + + with self.assertRaises(TypeError) as error: + # This should raise an TypeError exception + Rays(Matrix()) + def testRayCountHist(self): r = Rays([Ray()]) init = r.rayCountHistogram() diff --git a/raytracing/tests/testsRaysSubclasses.py b/raytracing/tests/testsRaysSubclasses.py new file mode 100644 index 0000000..0b3710d --- /dev/null +++ b/raytracing/tests/testsRaysSubclasses.py @@ -0,0 +1,14 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class TestRandomRays(unittest.TestCase): + + def testRandomRay(self): + rays = RandomRays() # We keep default value, we are not intersted in the construction of a specific object + with self.assertRaises(NotImplementedError): + # This works + rays.randomRay()

Rays() accepts objects from every type This can cause further problems. In `__init__` itself it is not a big deal (except for coherence and logic) if `Rays` receive a string of nonsense or a list of numbers, but other methods will inevitably fail with exceptions of different types.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-141

diff --git a/raytracing/rays.py b/raytracing/rays.py index aaf1971..83ffaf1 100644 --- a/raytracing/rays.py +++ b/raytracing/rays.py @@ -288,9 +288,9 @@ class RandomRays(Rays): def __getitem__(self, item): if self.rays is None: - raise NotImplemented("You cannot access RandomRays") + raise NotImplementedError("You cannot access RandomRays") elif len(self.rays) < item: - raise NotImplemented("You cannot access RandomRays") + raise NotImplementedError("You cannot access RandomRays") else: return self.rays[item] @@ -301,7 +301,7 @@ class RandomRays(Rays): return self.randomRay() def randomRay(self) -> Ray: - raise NotImplemented("You must implement randomRay() in your subclass") + raise NotImplementedError("You must implement randomRay() in your subclass") class RandomUniformRays(RandomRays):

DCC-Lab/RayTracing

3a1d740763e8a3138f7c2c025f0dce707249acd9

diff --git a/raytracing/tests/testsComponents.py b/raytracing/tests/testsComponents.py new file mode 100644 index 0000000..a4aba5b --- /dev/null +++ b/raytracing/tests/testsComponents.py @@ -0,0 +1,60 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class Test4fSystem(unittest.TestCase): + + def test4fSystem(self): + elements = [Space(10), Lens(10), Space(15), Lens(5), Space(5)] + mg = MatrixGroup(elements, label="4f system") + system = System4f(10, 5, label="4f system") + self.assertEqual(system.A, -0.5) + self.assertEqual(system.B, 0) + self.assertEqual(system.C, 0) + self.assertEqual(system.D, -2) + self.assertEqual(system.L, 30) + self.assertEqual(mg.backIndex, system.backIndex) + self.assertEqual(mg.frontIndex, system.frontIndex) + self.assertEqual(mg.backVertex, system.backVertex) + self.assertEqual(mg.frontVertex, system.frontVertex) + self.assertEqual(mg.label, system.label) + self.assertTrue(system.isImaging) + + def test2fSystem(self): + elements = [Space(10), Lens(10), Space(10)] + mg = MatrixGroup(elements, label="2f system") + system = System2f(10, label="2f system") + self.assertEqual(system.A, 0) + self.assertEqual(system.B, 10) + self.assertEqual(system.C, -1 / 10) + self.assertEqual(system.D, 0) + self.assertEqual(system.L, 20) + self.assertEqual(mg.backIndex, system.backIndex) + self.assertEqual(mg.frontIndex, system.frontIndex) + self.assertEqual(mg.backVertex, system.backVertex) + self.assertEqual(mg.frontVertex, system.frontVertex) + self.assertEqual(mg.label, system.label) + self.assertFalse(system.isImaging) + + def test4fIsTwo2f(self): + f1, f2 = 10, 12 + system4f = System4f(f1=10, f2=12) + system2f_1 = System2f(f1) + system2f_2 = System2f(f2) + composed4fSystem = MatrixGroup(system2f_1.elements + system2f_2.elements) + self.assertEqual(composed4fSystem.A, system4f.A) + self.assertEqual(composed4fSystem.B, system4f.B) + self.assertEqual(composed4fSystem.C, system4f.C) + self.assertEqual(composed4fSystem.D, system4f.D) + self.assertEqual(composed4fSystem.L, system4f.L) + self.assertEqual(composed4fSystem.backIndex, system4f.backIndex) + self.assertEqual(composed4fSystem.frontIndex, system4f.frontIndex) + self.assertEqual(composed4fSystem.backVertex, system4f.backVertex) + self.assertEqual(composed4fSystem.frontVertex, system4f.frontVertex) + + +if __name__ == '__main__': + unittest.main() diff --git a/raytracing/tests/testsRaysSubclasses.py b/raytracing/tests/testsRaysSubclasses.py new file mode 100644 index 0000000..0b3710d --- /dev/null +++ b/raytracing/tests/testsRaysSubclasses.py @@ -0,0 +1,14 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class TestRandomRays(unittest.TestCase): + + def testRandomRay(self): + rays = RandomRays() # We keep default value, we are not intersted in the construction of a specific object + with self.assertRaises(NotImplementedError): + # This works + rays.randomRay()

RandomRays raises a constant, not an exception In `RandomRays`, some methods have `raise NotImplemented("...")`, but `NotImplemented` is a constant used in some binary methods (see https://docs.python.org/3/library/constants.html). I suspect what we want is `raise NotImplementedError("...")`.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-176

diff --git a/raytracing/rays.py b/raytracing/rays.py index 9129491..a424fad 100644 --- a/raytracing/rays.py +++ b/raytracing/rays.py @@ -207,6 +207,10 @@ class Rays: def load(self, filePath, append=False): with open(filePath, 'rb') as infile: loadedRays = pickle.Unpickler(infile).load() + if not isinstance(loadedRays, collections.Iterable): + raise IOError(f"{filePath} does not contain an iterable of Ray objects.") + if not all([isinstance(ray, Ray) for ray in loadedRays]): + raise IOError(f"{filePath} must contain only Ray objects.") if append and self._rays is not None: self._rays.extend(loadedRays) else:

DCC-Lab/RayTracing

ce69bb2fc28ba9864f2631abd5e87819aad1de74

diff --git a/raytracing/tests/testsRays.py b/raytracing/tests/testsRays.py index 33ac2e3..833ade3 100644 --- a/raytracing/tests/testsRays.py +++ b/raytracing/tests/testsRays.py @@ -69,7 +69,6 @@ class TestRays(unittest.TestCase): r = Rays(listOfRays) self.assertEqual(len(r), len(listOfRays)) - def testRaysGetRay(self): raysList = [Ray(), Ray(1), Ray(-1)] rays = Rays(raysList) @@ -244,7 +243,6 @@ class TestRays(unittest.TestCase): self.assertIsNone(r._anglesHistogramParameters) self.assertIsNone(r._xValuesAnglesHistogram) - def testAppendInvalidInput(self): rays = Rays() with self.assertRaises(TypeError): @@ -258,7 +256,7 @@ class TestRaysSaveAndLoad(unittest.TestCase): self.fileName = 'testFile.pkl' with open(self.fileName, 'wb') as file: pickle.Pickler(file).dump(self.testRays.rays) - time.sleep(1) # Make sure everything is ok + time.sleep(0.5) # Make sure everything is ok def tearDown(self) -> None: if os.path.exists(self.fileName): @@ -294,6 +292,33 @@ class TestRaysSaveAndLoad(unittest.TestCase): self.assertLoadNotFailed(rays) # We don't append, we override self.assertListEqual(rays.rays, self.testRays.rays) + def testLoadWrongFileContent(self): + wrongObj = 7734 + fileName = 'wrongObj.pkl' + with open(fileName, 'wb') as file: + pickle.Pickler(file).dump(wrongObj) + time.sleep(0.5) # Make sure everything is ok + + try: + with self.assertRaises(IOError): + Rays().load(fileName) + except AssertionError as exception: + self.fail(str(exception)) + finally: + os.remove(fileName) + + wrongIterType = [Ray(), Ray(1), [1, 1]] + with open(fileName, 'wb') as file: + pickle.Pickler(file).dump(wrongIterType) + time.sleep(0.5) + try: + with self.assertRaises(IOError): + Rays().load(fileName) + except AssertionError as exception: + self.fail(str(exception)) + finally: + os.remove(fileName) + def assertSaveNotFailed(self, rays: Rays, name: str, deleteNow: bool = True): try: rays.save(name)

Rays can load any "pickled" file This can lead to unwanted behaviors. We should check if the content of the file is an iterable of `Ray` objects. `load` directly extends (or override) the inner list or rays in `Rays`. This can cause unexpected problems without proper guidance to what caused the issue.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-180

diff --git a/raytracing/laserpath.py b/raytracing/laserpath.py index 4f74727..edcf1b2 100644 --- a/raytracing/laserpath.py +++ b/raytracing/laserpath.py @@ -1,6 +1,7 @@ from .matrixgroup import * from .imagingpath import * + class LaserPath(MatrixGroup): """LaserPath: the main class of the module for coherent laser beams: it is the combination of Matrix() or MatrixGroup() @@ -17,6 +18,7 @@ class LaserPath(MatrixGroup): is set to indicate it, but it will propagate nevertheless and without diffraction due to that aperture. """ + def __init__(self, elements=None, label=""): self.inputBeam = None self.isResonator = False @@ -33,11 +35,14 @@ class LaserPath(MatrixGroup): round trip: you will need to duplicate elements in reverse and append them manually. """ + if not self.hasPower: + return None, None + b = self.D - self.A - sqrtDelta = cmath.sqrt(b*b + 4.0 *self.B *self.C) - - q1 = (- b + sqrtDelta)/(2.0*self.C) - q2 = (- b - sqrtDelta)/(2.0*self.C) + sqrtDelta = cmath.sqrt(b * b + 4.0 * self.B * self.C) + + q1 = (- b + sqrtDelta) / (2.0 * self.C) + q2 = (- b - sqrtDelta) / (2.0 * self.C) return (GaussianBeam(q=q1), GaussianBeam(q=q2)) @@ -49,10 +54,10 @@ class LaserPath(MatrixGroup): (q1, q2) = self.eigenModes() q = [] - if q1.isFinite: + if q1 is not None and q1.isFinite: q.append(q1) - if q2.isFinite: + if q2 is not None and q2.isFinite: q.append(q2) return q @@ -133,12 +138,11 @@ class LaserPath(MatrixGroup): for element in self.elements: if isinstance(element, Space): for i in range(N): - highResolution.append(Space(d=element.L/N, + highResolution.append(Space(d=element.L / N, n=element.frontIndex)) else: highResolution.append(element) - beamTrace = highResolution.trace(beam) (x, y) = self.rearrangeBeamTraceForPlotting(beamTrace) axes.plot(x, y, 'r', linewidth=1) @@ -166,11 +170,11 @@ class LaserPath(MatrixGroup): position = beam.z + relativePosition size = beam.waist - axes.arrow(position, size+arrowSize, 0, -arrowSize, - width=0.1, fc='g', ec='g', - head_length=arrowHeight, head_width=arrowWidth, - length_includes_head=True) - axes.arrow(position, -size-arrowSize, 0, arrowSize, - width=0.1, fc='g', ec='g', - head_length=arrowHeight, head_width=arrowWidth, - length_includes_head=True) + axes.arrow(position, size + arrowSize, 0, -arrowSize, + width=0.1, fc='g', ec='g', + head_length=arrowHeight, head_width=arrowWidth, + length_includes_head=True) + axes.arrow(position, -size - arrowSize, 0, arrowSize, + width=0.1, fc='g', ec='g', + head_length=arrowHeight, head_width=arrowWidth, + length_includes_head=True)

DCC-Lab/RayTracing

03535abea0f84ad4eeb61c8da671579d95d6217e

diff --git a/raytracing/tests/testsLaserPath.py b/raytracing/tests/testsLaserPath.py new file mode 100644 index 0000000..6b90b03 --- /dev/null +++ b/raytracing/tests/testsLaserPath.py @@ -0,0 +1,26 @@ +import unittest +import envtest # modifies path +from raytracing import * + +inf = float("+inf") + + +class TestLaserPath(unittest.TestCase): + + def testEigenModes(self): + lp = LaserPath([Space(10)]) + self.assertTupleEqual(lp.eigenModes(), (None, None)) + + lp = LaserPath() + self.assertTupleEqual(lp.eigenModes(), (None, None)) + + lp = LaserPath([CurvedMirror(-10)]) + self.assertNotEqual(lp.eigenModes(), (None, None)) + + def testLaserModes(self): + lp = LaserPath() + self.assertListEqual(lp.laserModes(), []) + + +if __name__ == '__main__': + unittest.main()

EigenModes of LaserPath fails with exception when C = 0 When we create a `LaserPath` and its C component is 0, we have a division by 0, which raises an exception. We should check if the laser path has power (`self.hasPower`) before and return `(None, None)` (maybe?) if not. We then need to change other methods, like `laserModes` and `display`.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-187

diff --git a/raytracing/laserpath.py b/raytracing/laserpath.py index edcf1b2..ec4fd0c 100644 --- a/raytracing/laserpath.py +++ b/raytracing/laserpath.py @@ -62,7 +62,7 @@ class LaserPath(MatrixGroup): return q - def display(self, inputBeam=None, inputBeams=None, comments=None): + def display(self, inputBeam=None, inputBeams=None, comments=None): # pragma: no cover """ Display the optical system and trace the laser beam. If comments are included they will be displayed on a graph in the bottom half of the plot. @@ -71,7 +71,7 @@ class LaserPath(MatrixGroup): if self.isResonator: beams = self.laserModes() - if len(self.label) == "": + if self.label == "": self.label = "Laser modes as calculated" elif inputBeam is not None: beams = [inputBeam] @@ -80,7 +80,7 @@ class LaserPath(MatrixGroup): else: beams = [self.inputBeam] - if len(self.label) == "": + if self.label == "": self.label = "User-specified gaussian beams" if comments is not None: @@ -95,7 +95,7 @@ class LaserPath(MatrixGroup): self._showPlot() - def createBeamTracePlot(self, axes, beams): + def createBeamTracePlot(self, axes, beams): # pragma: no cover """ Create a matplotlib plot to draw the laser beam and the elements. """ @@ -122,7 +122,7 @@ class LaserPath(MatrixGroup): y.append(ray.w) return (x, y) - def drawBeamTrace(self, axes, beam): + def drawBeamTrace(self, axes, beam): # pragma: no cover """ Draw beam trace corresponding to input beam Because the laser beam diffracts through space, we cannot simply propagate the beam over large distances and trace it @@ -148,7 +148,7 @@ class LaserPath(MatrixGroup): axes.plot(x, y, 'r', linewidth=1) axes.plot(x, [-v for v in y], 'r', linewidth=1) - def drawWaists(self, axes, beam): + def drawWaists(self, axes, beam): # pragma: no cover """ Draws the expected waist (i.e. the focal spot or the spot where the size is minimum) for all positions of the beam. This will show "waists" that are virtual if there is an additional lens between the beam and the expceted diff --git a/raytracing/matrixgroup.py b/raytracing/matrixgroup.py index fe54cb8..b34038c 100644 --- a/raytracing/matrixgroup.py +++ b/raytracing/matrixgroup.py @@ -10,6 +10,7 @@ class MatrixGroup(Matrix): """ def __init__(self, elements=None, label=""): + self.iteration = 0 super(MatrixGroup, self).__init__(1, 0, 0, 1, label=label) self.elements = [] @@ -36,7 +37,7 @@ class MatrixGroup(Matrix): if len(self.elements) != 0: lastElement = self.elements[-1] if lastElement.backIndex != matrix.frontIndex: - if isinstance(matrix, Space): # For Space(), we fix it + if isinstance(matrix, Space): # For Space(), we fix it msg = "Fixing mismatched indices between last element and appended Space(). Use Space(d=someDistance, n=someIndex)." warnings.warn(msg, UserWarning) matrix.frontIndex = lastElement.backIndex @@ -55,12 +56,6 @@ class MatrixGroup(Matrix): self.frontVertex = transferMatrix.frontVertex self.backVertex = transferMatrix.backVertex - def ImagingPath(self): - return ImagingPath(elements=self.elements, label=self.label) - - def LaserPath(self): - return LaserPath(elements=self.elements, label=self.label) - def transferMatrix(self, upTo=float('+Inf')): """ The transfer matrix between front edge and distance=upTo @@ -227,3 +222,16 @@ class MatrixGroup(Matrix): axes.annotate(label, xy=(z, 0.0), xytext=(z, -halfHeight * 0.5), xycoords='data', fontsize=12, ha='center', va='bottom') + + def __iter__(self): + self.iteration = 0 + return self + + def __next__(self): + if self.elements is None: + raise StopIteration + if self.iteration < len(self.elements): + element = self.elements[self.iteration] + self.iteration += 1 + return element + raise StopIteration

DCC-Lab/RayTracing

fe768d07b48df2be9428da6dc3d7f738c652915e

diff --git a/raytracing/tests/testsLaserPath.py b/raytracing/tests/testsLaserPath.py index 6b90b03..38134af 100644 --- a/raytracing/tests/testsLaserPath.py +++ b/raytracing/tests/testsLaserPath.py @@ -7,20 +7,75 @@ inf = float("+inf") class TestLaserPath(unittest.TestCase): - def testEigenModes(self): + def testLaserPathNoElements(self): + lasPath = LaserPath() + self.assertIsNone(lasPath.inputBeam) + self.assertFalse(lasPath.isResonator) + self.assertTrue(lasPath.showElementLabels) + self.assertTrue(lasPath.showPointsOfInterest) + self.assertTrue(lasPath.showPointsOfInterestLabels) + self.assertTrue(lasPath.showPlanesAcrossPointsOfInterest) + self.assertListEqual(lasPath.elements, []) + + def testLaserPath(self): + elements = [Space(5), Lens(5), Space(20), Lens(15), Space(15)] + lp = LaserPath(elements, "Laser Path") + self.assertListEqual(lp.elements, elements) + self.assertEqual(lp.label, "Laser Path") + + def testLaserPathIncorrectElements(self): + elements = [Ray(), Lens(10)] + with self.assertRaises(TypeError): + LaserPath(elements) + + def testEigenModesNoPower(self): lp = LaserPath([Space(10)]) self.assertTupleEqual(lp.eigenModes(), (None, None)) - lp = LaserPath() - self.assertTupleEqual(lp.eigenModes(), (None, None)) + def testEigenModes(self): + lp = LaserPath([Space(10), Lens(10)]) + beam1, beam2 = lp.eigenModes() + self.assertEqual(beam1.q.real, -5) + self.assertEqual(beam2.q.real, -5) + self.assertAlmostEqual(beam1.q.imag, -5 * 3 ** 0.5) + self.assertAlmostEqual(beam2.q.imag, 5 * 3 ** 0.5) - lp = LaserPath([CurvedMirror(-10)]) - self.assertNotEqual(lp.eigenModes(), (None, None)) + lp = LaserPath([Lens(10)]) + beam1, beam2 = lp.eigenModes() + self.assertEqual(beam1.q, beam2.q) + self.assertEqual(beam1.q, 0) + + def testLaserModesNoPower(self): + lp = LaserPath([Space(10)]) + self.assertListEqual(lp.laserModes(), []) def testLaserModes(self): + lp = LaserPath([Space(10), Lens(10)]) + laserModes = lp.laserModes() + self.assertEqual(len(laserModes), 1) + beam = laserModes[0] + self.assertEqual(beam.q.real, -5) + self.assertAlmostEqual(beam.q.imag, 5 * 3 ** 0.5) + + elements = [Space(1, 1.33), DielectricInterface(1.33, 1, 1), ThickLens(1.33, -10, -5, -20)] + lp = LaserPath(elements) + laserModes = lp.laserModes() + self.assertEqual(len(laserModes), 1) + beam = laserModes[0] + self.assertAlmostEqual(beam.q.real, -5.90770102) + self.assertAlmostEqual(beam.q.imag, 1.52036515) + + lp = LaserPath([Space(10), CurvedMirror(5)]) + self.assertListEqual(lp.laserModes(), []) lp = LaserPath() self.assertListEqual(lp.laserModes(), []) + def testRearrangeBeamTraceForPlotting(self): + x = [x for x in range(1, 6)] + y = [y for y in range(1, 6)] + rayList = [GaussianBeam(w=x_, z=y_) for (x_, y_) in zip(x, y)] + lp = LaserPath() + self.assertTupleEqual(lp.rearrangeBeamTraceForPlotting(rayList), (x, y)) if __name__ == '__main__': unittest.main() diff --git a/raytracing/tests/testsMatrixGroup.py b/raytracing/tests/testsMatrixGroup.py index 6d587cb..d473aa7 100644 --- a/raytracing/tests/testsMatrixGroup.py +++ b/raytracing/tests/testsMatrixGroup.py @@ -319,6 +319,11 @@ class TestMatrixGroup(unittest.TestCase): self.assertEqual(mg.D, supposedMatrix.D) self.assertEqual(mg.L, supposedMatrix.L) + def testInitWithAnotherMatrixGroup(self): + mg = MatrixGroup([Lens(5)]) + mg2 = MatrixGroup(mg) + self.assertListEqual(mg.elements, mg2.elements) + if __name__ == '__main__': unittest.main()

ImagingPath and LaserPath methods in MatrixGroup raise exception. They respectively return a ImagingPath instance and a LaserPath instance, but those classes are in other files not imported. It is also worth mentioning that they both inherit from MatrixGroup, so it is kind of incoherent to use them in MatrixGroup. Question: Are those methods really necessary in MatrixGroup? - Yes: We have to find a way to import them without having a circular import problem. - No: We should remove them.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-192

diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index 82765ea..6a7e46b 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -151,8 +151,12 @@ class ImagingPath(MatrixGroup): If the element B in the transfer matrix for the imaging path is zero, there is no value for the height and angle that makes a proper chief ray. So the function will return None. + If there is no aperture stop, there is no chief ray either. None is also returned. """ (stopPosition, stopDiameter) = self.apertureStop() + if stopPosition is None: + return None + transferMatrixToApertureStop = self.transferMatrix(upTo=stopPosition) A = transferMatrixToApertureStop.A B = transferMatrixToApertureStop.B

DCC-Lab/RayTracing

8b8d8f660c634a5cee6b0e3f926e298824ffa4d7

diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index 4e9ed76..b543b8b 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -56,6 +56,10 @@ class TestImagingPath(unittest.TestCase): path = ImagingPath(elements) self.assertIsNotNone(path.entrancePupil()) + def testChiefRayNoApertureStop(self): + path = ImagingPath(System2f(10)) + chiefRay = path.chiefRay() + self.assertIsNone(chiefRay) if __name__ == '__main__': unittest.main()

ImagingPath: chiefRay not working with no aperture stop When we create an `ImagingPath` without any aperture stop, `chiefRay` raises a `TypeError`, because there is no aperture stop. For example: ```python path = ImagingPath(System2f(10)) # A 2f system with f = 10 and infinite diameter path.chiefRay() # Fails with TypeError, even with a specified y ``` I think we should return `None`, because no aperture stop means no specific chief ray.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-196

diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index 9960d83..6c89bff 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -585,6 +585,9 @@ class ImagingPath(MatrixGroup): """ fieldOfView = self.fieldOfView() (distance, conjugateMatrix) = self.forwardConjugate() + if conjugateMatrix is None: + return float("+inf") + magnification = conjugateMatrix.A return abs(fieldOfView * magnification)

DCC-Lab/RayTracing

adc82c7e2d87b0d90f2a9790fe6f36c67a7d94d2

diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index b543b8b..2e24ab7 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,5 +61,10 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.assertIsNone(chiefRay) + def testImageSizeDIs0(self): + path = ImagingPath(System2f(f=10, diameter=10)) + path.append(Aperture(20)) + self.assertEqual(path.imageSize(), inf) + if __name__ == '__main__': unittest.main()

ImagingPath: imageSize fails when D is 0 When `D == 0`, there is no forward conjugate (nor backward), so we return `conjugateMatrix` as `None`. Because of that, `imageSize` raises an `AttributeError`. We should check if `conjugateMatrix` is `None`, but what should we return? Since there is no image, return `None`?

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-199

diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index aa348eb..5c3b21d 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -161,7 +161,7 @@ class ImagingPath(MatrixGroup): A = transferMatrixToApertureStop.A B = transferMatrixToApertureStop.B - if B == 0: + if transferMatrixToApertureStop.isImaging: return None if y is None:

DCC-Lab/RayTracing

84522313da81dcea8cf30d398e63b5223c102976

diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index a6b39da..4239a06 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,6 +61,12 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.assertIsNone(chiefRay) + def testChiefRayBIs0(self): + path = ImagingPath(System4f(pi*2, pi*1.25)) + path.append(System4f(pi, pi/1.2)) + path.append(Aperture(10)) + self.assertIsNone(path.chiefRay()) + def testChiefRayInfiniteFieldOfViewNoY(self): path = ImagingPath() path.append(System2f(10, path.maxHeight + 1)) @@ -81,5 +87,6 @@ class TestImagingPath(unittest.TestCase): path.append(Aperture(20)) self.assertEqual(path.imageSize(), inf) + if __name__ == '__main__': unittest.main()

ImagingPath: chiefRay doesn't return None when B is very close but not 0 When `B == 0` in an `ImagingPath` instance, there is no chief ray. But because we use a computer, some calculations can lead to something close to 0 but not quite 0. For example: ```python path = ImagingPath(System4f(pi * 2, pi * 1.25)) # This is an imaging system with B = 0 path.append(System4f(pi, pi / 1.2)) # This is another imaging system with B = 0 path.append(Aperture(10)) self.assertIsNone(path.chiefRay()) # This fails because B is close to but not 0 (approx. -7e-16) ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-200

diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index eaea927..aa348eb 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -166,6 +166,8 @@ class ImagingPath(MatrixGroup): if y is None: y = self.fieldOfView() + if abs(y) == float("+inf"): + raise ValueError("Must provide y when the filed of view is infinite") return Ray(y=y, theta=-A * y / B)

DCC-Lab/RayTracing

427fbe9fdcb21c452788b180ba683dff6a0c7321

diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index 6590fe8..a6b39da 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,6 +61,12 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.assertIsNone(chiefRay) + def testChiefRayInfiniteFieldOfViewNoY(self): + path = ImagingPath() + path.append(System2f(10, path.maxHeight + 1)) + with self.assertRaises(ValueError): + path.chiefRay() + def testMarginalRaysNoApertureStop(self): path = ImagingPath(System4f(10, 10)) self.assertIsNone(path.marginalRays())

ImagingPath: chiefRay returns y=inf and theta=-inf with really big (but not infinite) aperture and no specific y given When we create an `ImagingPath` with a really big aperture stop (but not infinite), the chief ray obtained has y = -theta = inf. This doesn't really make sense. This happens because the aperture is bigger than the max height and at one point (in `fieldOfView`), if `abs(y) < self.maxHeight`, we return `float("+inf")`. If the aperture is bigger than the max height accepted, then we should consider it like an infite aperture? Example: ```python path = ImagingPath(System2f(10, 100_000)) # 2f system with f = 10 and 100_000 units aperture print(path.chiefRay()) ``` The output is: ```python / \ | inf | | | | -inf | \ / z = 0.000 ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-202

diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index b9ee7de..eaea927 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -188,7 +188,6 @@ class ImagingPath(MatrixGroup): """ return self.chiefRay(y=None) - def marginalRays(self, y=0): """This function calculates the marginal rays for a height y at object. The marginal rays for height y are the rays that hit the upper and lower @@ -256,6 +255,9 @@ class ImagingPath(MatrixGroup): """ (stopPosition, stopDiameter) = self.apertureStop() + if stopPosition is None: + return None # No aperture stop -> no marginal rays + transferMatrixToApertureStop = self.transferMatrix(upTo=stopPosition) A = transferMatrixToApertureStop.A B = transferMatrixToApertureStop.B @@ -687,10 +689,10 @@ class ImagingPath(MatrixGroup): display range : 7 """ - + displayRange = self.largestDiameter - if displayRange == float('+Inf') or displayRange <= 2*self.objectHeight: - displayRange = 2*self.objectHeight + if displayRange == float('+Inf') or displayRange <= 2 * self.objectHeight: + displayRange = 2 * self.objectHeight conjugates = self.intermediateConjugates() if len(conjugates) != 0: @@ -982,7 +984,7 @@ class ImagingPath(MatrixGroup): arrowHeadHeight = self.objectHeight * 0.1 heightFactor = self.objectHeight / yScaling - arrowHeadWidth = xScaling * 0.01 * (heightFactor/0.2) ** (3/4) + arrowHeadWidth = xScaling * 0.01 * (heightFactor / 0.2) ** (3 / 4) axes.arrow( self.objectPosition, @@ -1015,7 +1017,7 @@ class ImagingPath(MatrixGroup): arrowHeadHeight = arrowHeight * 0.1 heightFactor = arrowHeight / yScaling - arrowHeadWidth = xScaling * 0.01 * (heightFactor/0.2) ** (3/4) + arrowHeadWidth = xScaling * 0.01 * (heightFactor / 0.2) ** (3 / 4) axes.arrow( imagePosition, @@ -1086,7 +1088,7 @@ class ImagingPath(MatrixGroup): center = z + pupilPosition (xScaling, yScaling) = self.axesToDataScale(axes) heightFactor = halfHeight * 2 / yScaling - width = xScaling * 0.01 / 2 * (heightFactor/0.2) ** (3/4) + width = xScaling * 0.01 / 2 * (heightFactor / 0.2) ** (3 / 4) axes.add_patch(patches.Polygon( [[center - width, halfHeight],

DCC-Lab/RayTracing

2c3d3f64b5aa09fc0a45a2422fe8bef834972b0b

diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index be8f0e1..6590fe8 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,6 +61,10 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.assertIsNone(chiefRay) + def testMarginalRaysNoApertureStop(self): + path = ImagingPath(System4f(10, 10)) + self.assertIsNone(path.marginalRays()) + def testMarginalRaysIsImaging(self): path = ImagingPath(System4f(10, 10)) path.append(Aperture(10))

ImagingPath: marginalRays raises exception when no apertureStop When we want the marginal rays of an `ImagingPath` that has no aperture stop, a `TypeError` is raised. Example: ```python path = ImagingPath(System4f(10, 10)) path.marginalRays() # Raises TypeError, no field stop ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-204

diff --git a/raytracing/imagingpath.py b/raytracing/imagingpath.py index 6c89bff..b9ee7de 100644 --- a/raytracing/imagingpath.py +++ b/raytracing/imagingpath.py @@ -260,6 +260,9 @@ class ImagingPath(MatrixGroup): A = transferMatrixToApertureStop.A B = transferMatrixToApertureStop.B + if transferMatrixToApertureStop.isImaging: + return None + thetaUp = (stopDiameter / 2.0 - A * y) / B thetaDown = (-stopDiameter / 2.0 - A * y) / B

DCC-Lab/RayTracing

4e999c92bde9e68c018859054193bf4a00d560a3

diff --git a/raytracing/tests/testsImagingPath.py b/raytracing/tests/testsImagingPath.py index 2e24ab7..be8f0e1 100644 --- a/raytracing/tests/testsImagingPath.py +++ b/raytracing/tests/testsImagingPath.py @@ -61,6 +61,11 @@ class TestImagingPath(unittest.TestCase): chiefRay = path.chiefRay() self.assertIsNone(chiefRay) + def testMarginalRaysIsImaging(self): + path = ImagingPath(System4f(10, 10)) + path.append(Aperture(10)) + self.assertIsNone(path.marginalRays()) + def testImageSizeDIs0(self): path = ImagingPath(System2f(f=10, diameter=10)) path.append(Aperture(20))

ImagingPath: division by 0 in marginalRays When we have an `ImagingPath` that has a transfer matrix to the aperture stop with `B == 0`, there is a division by 0 in the calculations of theta + and -. We should check when it's the case and return `None`.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-220

diff --git a/raytracing/gaussianbeam.py b/raytracing/gaussianbeam.py index 77dbfab..03bd73b 100644 --- a/raytracing/gaussianbeam.py +++ b/raytracing/gaussianbeam.py @@ -4,20 +4,46 @@ import cmath class GaussianBeam(object): """A gaussian laser beam using the ABCD formalism for propagation of complex radius of curvature q. - w is the 1/e beam size in electric field extracted from q - R is the radius of curvature (positive means diverging) extracted from q - n is index in which the beam is. Necessary to compute beam size. - wavelength must be in the same units as z. + Parameters + ---------- + q : complex + The complex beam parameter (default=None) + w : float + The 1/e beam size in electric field extracted from q. (default=None) + R : float + The radius of curvature (positive means diverging) extracted from q. (default=+Inf) + n : float + The index of refraction in which the beam is. (default=1.0) + wavelength : float + The wave length of the laser beam. This parameter is necessary to compute the beam size (default=632.8e-6) + z : float + The axial distance from the waist (default=0) + + Attributes + ---------- + isClipped : bool + The formalism of gaussian beams does not consider any apertures: the beam + remains gaussian no matter what. This variable will indicate if the beam + diameter was too close to the apertures in the system. + + Notes + ----- + wavelength and z must be in the same units. """ def __init__(self, q:complex=None, w:float=None, R:float=float("+Inf"), n:float=1.0, wavelength=632.8e-6, z=0): # Gaussian beam matrix formalism + if q is not None: self.q = q - elif w is not None: + if w is not None: self.q = 1/( 1.0/R - complex(0,1)*wavelength/n/(math.pi*w*w)) - else: - self.q = None + if q is None and w is None: + raise ValueError("Please specify 'q' or 'w'.") + + if q is not None and w is not None: + if not cmath.isclose(a=self.q, b=q, abs_tol=0.1): + raise ValueError("Mismatch between the given q and the computed q (10% tolerance).") self.wavelength = wavelength @@ -28,6 +54,9 @@ class GaussianBeam(object): @property def R(self): + """ + The radius of curvature (positive means diverging) extracted from q. + """ invQReal = (1/self.q).real if invQReal == 0: return float("+Inf") @@ -36,10 +65,20 @@ class GaussianBeam(object): @property def isFinite(self): + """ + Using the complex radius, the imaginary part of -1/q is the beam size. + If this value is negative, the calculation will yield a exp(x**2/w**2) + which grows exponentially instead of being a gaussian. Hence, this + is not a finite and reasonable complex radius. This is used for + resonator and cavity calculations to discard unphysical solutions. + """ return (-1/self.q).imag > 0 @property def w(self): + """ + The 1/e beam size in electric field extracted from q. + """ qInv = (-1/self.q).imag if qInv > 0: return math.sqrt( self.wavelength/self.n/(math.pi * qInv)) @@ -48,6 +87,9 @@ class GaussianBeam(object): @property def wo(self): + """ + The 1/e beam size in electric field extracted from q at the waist of the beam. + """ if self.zo > 0: return math.sqrt( self.zo * self.wavelength/math.pi ) else: @@ -55,22 +97,35 @@ class GaussianBeam(object): @property def waist(self): + """ + The same as the wo. + """ return self.wo @property def waistPosition(self): + """The position of the waist of the beam.""" return -self.q.real @property def zo(self): + """ + The same as rayleighRange. + """ return float(self.q.imag) @property def confocalParameter(self): + """ + The same as rayleighRange. + """ return self.zo @property def rayleighRange(self): + """ + Returns the rayleigh range of the beam. + """ return self.zo def __str__(self):

DCC-Lab/RayTracing

52e850c6260b476c4925eb543702195f73cc779b

diff --git a/raytracing/tests/testsGaussian.py b/raytracing/tests/testsGaussian.py index 8c26cff..be32f22 100644 --- a/raytracing/tests/testsGaussian.py +++ b/raytracing/tests/testsGaussian.py @@ -6,7 +6,6 @@ inf = float("+inf") class TestBeam(unittest.TestCase): def testBeam(self): - beam = GaussianBeam() beam = GaussianBeam(w=1) self.assertEqual(beam.w, 1) self.assertEqual(beam.R, float("+Inf")) @@ -19,10 +18,13 @@ class TestBeam(unittest.TestCase): def testInvalidParameters(self): with self.assertRaises(Exception) as context: - beam = GaussianBeam(w=1,R=0) + beam = GaussianBeam() + + with self.assertRaises(Exception) as context: + beam = GaussianBeam(w=1,R=0) def testMultiplicationBeam(self): - # No default parameters + # No default parameters beamIn = GaussianBeam(w=0.01, R=1, n=1.5, wavelength=0.400e-3) beamOut = Space(d=0,n=1.5)*beamIn self.assertEqual(beamOut.q, beamIn.q)

GaussianBeam: q or w should be specified (not both None) This can lead to some incoherence: we should check (if q and w are given) that q computed with w is relatively close to q given. Also, we should not be able to set both as `None`. Having w and q has `None` does nothing good, only lead to issues with methods, because we take for granted that q is a complex number. It doesn't make sense to have a `GaussianBeam` where q and w are `None`.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-223

diff --git a/raytracing/matrix.py b/raytracing/matrix.py index 43f9790..c84cede 100644 --- a/raytracing/matrix.py +++ b/raytracing/matrix.py @@ -846,7 +846,8 @@ class Matrix(object): @property def hasPower(self): - """ If True, then there is a non-null focal length because C!=0 + """ If True, then there is a non-null focal length because C!=0. We compare to an epsilon value, because + computational errors can occur and lead to C being very small, but not 0. Examples -------- @@ -861,7 +862,7 @@ class Matrix(object): >>> print('hasPower:' , M2.hasPower) hasPower: False """ - return self.C != 0 + return abs(self.C) > Matrix.__epsilon__ def pointsOfInterest(self, z): """ Any points of interest for this matrix (focal points,

DCC-Lab/RayTracing

ba11e628ea9be0cf8f45efc2013c49529bd2d801

diff --git a/raytracing/tests/testsMatrix.py b/raytracing/tests/testsMatrix.py index 9c75340..886a9b4 100644 --- a/raytracing/tests/testsMatrix.py +++ b/raytracing/tests/testsMatrix.py @@ -344,6 +344,15 @@ class TestMatrix(unittest.TestCase): m2 = Matrix(A=1, B=1, C=3, D=4) self.assertFalse(m2.isImaging) + def testHasNoPower(self): + f1 = 1.0000000000000017 + f2 = 2.05 * f1 + + # This simulates a 4f system (since we test Matrix, we should only use basic matrices) + m = Matrix(1, f1, 0, 1) * Matrix(1, 0, -1 / f1, 1) * Matrix(1, f1, 0, 1) * Matrix(1, f2, 0, 1) + m = m * Matrix(1, 0, -1 / f2, 1) * Matrix(1, f1, 0, 1) + self.assertFalse(m.hasPower) + def testEffectiveFocalLengthsHasPower(self): m = Matrix(1, 2, 3, 4) focalLengths = (-1 / 3, -1 / 3)

Matrix: hasPower returns True when it should be False When we want to know if a `Matrix` has power, we check if `self.C != 0`. In some cases, computational errors occurs due to the fact that we are handling floats and `self.C` is really close to 0. Example: ```python d1 = 1.0000000000000017 # Some computation errors tend to add digits at the end of the number d2 = 1.0000000000000017 * 2.05 matrixGroup = System4f(d1, d2) # We use a 4f system because it is a real physical system # Any matrix with C close but not 0 will do print(matrixGroup.C) # We check what is the value of the C component of the ewuivalent matrix ``` The output is: ```python 1.1102230246251565e-16 ``` Which is **VERY** small, but still not 0. Obviously, a 4f system has no power, but with computational errors, the code considers it has power.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-258

diff --git a/raytracing/figure.py b/raytracing/figure.py index a0b9014..dee5eb4 100644 --- a/raytracing/figure.py +++ b/raytracing/figure.py @@ -180,6 +180,8 @@ class Figure: conjugates = self.path.intermediateConjugates() if len(conjugates) != 0: for (planePosition, magnification) in conjugates: + if not 0 <= planePosition <= self.path.L: + continue magnification = abs(magnification) if displayRange < self.path._objectHeight * magnification: displayRange = self.path._objectHeight * magnification diff --git a/raytracing/matrixgroup.py b/raytracing/matrixgroup.py index e6d9e57..0270ed3 100644 --- a/raytracing/matrixgroup.py +++ b/raytracing/matrixgroup.py @@ -262,7 +262,10 @@ class MatrixGroup(Matrix): planePosition = transferMatrix.L + distance if planePosition != 0 and conjugate is not None: magnification = conjugate.A - planes.append([planePosition, magnification]) + if any([isclose(pos, planePosition) and isclose(mag, magnification) for pos, mag in planes]): + continue + else: + planes.append([planePosition, magnification]) return planes def trace(self, inputRay):

DCC-Lab/RayTracing

12e2e1fe89e74637d25304b4e101c71103de480c

diff --git a/raytracing/tests/envtest.py b/raytracing/tests/envtest.py index c20889c..5a57a3b 100644 --- a/raytracing/tests/envtest.py +++ b/raytracing/tests/envtest.py @@ -5,7 +5,6 @@ import tempfile class RaytracingTestCase(unittest.TestCase): tempDir = os.path.join(tempfile.gettempdir(), "tempDir") - removeAlreadyExists = False def __init__(self, tests=()): super(RaytracingTestCase, self).__init__(tests) @@ -13,13 +12,7 @@ class RaytracingTestCase(unittest.TestCase): @classmethod def createTempDirectory(cls): if os.path.exists(cls.tempDir): - if cls.removeAlreadyExists: - cls.deleteTempDirectory() - else: - fulltempDir = os.path.join(os.getcwd(), cls.tempDir) - msg = f"'{fulltempDir}' directory already exists. " \ - f"Please set RaytracingTestCase.removeAlreadyExists to True if you want to delete this directory." - raise FileExistsError(msg) + cls.deleteTempDirectory() os.mkdir(cls.tempDir) @classmethod diff --git a/raytracing/tests/testsEnvtest.py b/raytracing/tests/testsEnvtest.py index dc54551..cb0ae26 100644 --- a/raytracing/tests/testsEnvtest.py +++ b/raytracing/tests/testsEnvtest.py @@ -55,27 +55,8 @@ class TestEnvtestClass(unittest.TestCase): def testTemptempDir(self): self.assertTrue(self.tempDir.endswith("tempDir")) - def testRemoveAlreadyExistsFalse(self): - envtest.RaytracingTestCase.removeAlreadyExists = False - self.assertFalse(envtest.RaytracingTestCase.removeAlreadyExists) - - def testRemoveAlreadyExistsTrue(self): - envtest.RaytracingTestCase.removeAlreadyExists = True - self.assertTrue(envtest.RaytracingTestCase.removeAlreadyExists) - - def testCreateTempDirectoryAlreadyExistsDoNotDelete(self): - msg = f"'{self.tempDir}' directory already exists. Please set RaytracingTestCase.removeAlreadyExists to True if" - msg += f" you want to delete this directory." - envtest.RaytracingTestCase.removeAlreadyExists = False - os.mkdir(self.tempDir) - with self.assertRaises(FileExistsError) as context: - envtest.RaytracingTestCase.createTempDirectory() - self.assertEqual(str(context.exception), msg) - os.rmdir(self.tempDir) # Delete the directory! - def testCreateTempDirectoryAlreadyExistsAndDelete(self): tempDir = envtest.RaytracingTestCase.tempDir - envtest.RaytracingTestCase.removeAlreadyExists = True os.mkdir(tempDir) try: envtest.RaytracingTestCase.createTempDirectory() diff --git a/raytracing/tests/testsFigure.py b/raytracing/tests/testsFigure.py index daf1098..0c29ffd 100644 --- a/raytracing/tests/testsFigure.py +++ b/raytracing/tests/testsFigure.py @@ -14,12 +14,12 @@ class TestFigure(unittest.TestCase): self.assertEqual(path.figure.displayRange(), largestDiameter) - def testDisplayRange(self): + def testDisplayRangeImageOutOfView(self): path = ImagingPath() path.append(Space(2)) path.append(CurvedMirror(-5, 10)) - self.assertAlmostEqual(path.figure.displayRange(), 5 * 10) + self.assertAlmostEqual(path.figure.displayRange(), 20) path.objectHeight = 1 self.assertEqual(path.figure.displayRange(), 10) diff --git a/raytracing/tests/testsMatrixGroup.py b/raytracing/tests/testsMatrixGroup.py index d6554e5..3f20888 100644 --- a/raytracing/tests/testsMatrixGroup.py +++ b/raytracing/tests/testsMatrixGroup.py @@ -275,6 +275,12 @@ class TestMatrixGroup(envtest.RaytracingTestCase): self.assertAlmostEqual(intermediateConjugates[0][0], results[0][0]) self.assertAlmostEqual(intermediateConjugates[0][1], results[0][1]) + def testIntermediateConjugatesDuplicates(self): + elements = [Space(10), Lens(10), Space(15), Lens(5), Space(5)] + mg = MatrixGroup(elements) + intermediateConj = mg.intermediateConjugates() + self.assertListEqual(intermediateConj, [[30.0, -0.5]]) + def testHasFiniteApertutreDiameter(self): space = Space(10, 1.2541255) mg = MatrixGroup([space])

MatrixGroup: intermediateConjugates gives duplicates When we want the intermediate conjugates of some matrix groups, we have a list with duplicates. Is it normal? Example: ```python path = ImagingPath(System4f(10, 5)) print(path.intermediateConjugates()) ``` the output is: ```python [[30.0, -0.5], [30.0, -0.5]] ``` @dccote I feel like it is redundant information.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-259

diff --git a/raytracing/figure.py b/raytracing/figure.py index a0b9014..dee5eb4 100644 --- a/raytracing/figure.py +++ b/raytracing/figure.py @@ -180,6 +180,8 @@ class Figure: conjugates = self.path.intermediateConjugates() if len(conjugates) != 0: for (planePosition, magnification) in conjugates: + if not 0 <= planePosition <= self.path.L: + continue magnification = abs(magnification) if displayRange < self.path._objectHeight * magnification: displayRange = self.path._objectHeight * magnification

DCC-Lab/RayTracing

12e2e1fe89e74637d25304b4e101c71103de480c

diff --git a/raytracing/tests/envtest.py b/raytracing/tests/envtest.py index c20889c..5a57a3b 100644 --- a/raytracing/tests/envtest.py +++ b/raytracing/tests/envtest.py @@ -5,7 +5,6 @@ import tempfile class RaytracingTestCase(unittest.TestCase): tempDir = os.path.join(tempfile.gettempdir(), "tempDir") - removeAlreadyExists = False def __init__(self, tests=()): super(RaytracingTestCase, self).__init__(tests) @@ -13,13 +12,7 @@ class RaytracingTestCase(unittest.TestCase): @classmethod def createTempDirectory(cls): if os.path.exists(cls.tempDir): - if cls.removeAlreadyExists: - cls.deleteTempDirectory() - else: - fulltempDir = os.path.join(os.getcwd(), cls.tempDir) - msg = f"'{fulltempDir}' directory already exists. " \ - f"Please set RaytracingTestCase.removeAlreadyExists to True if you want to delete this directory." - raise FileExistsError(msg) + cls.deleteTempDirectory() os.mkdir(cls.tempDir) @classmethod diff --git a/raytracing/tests/testsEnvtest.py b/raytracing/tests/testsEnvtest.py index dc54551..cb0ae26 100644 --- a/raytracing/tests/testsEnvtest.py +++ b/raytracing/tests/testsEnvtest.py @@ -55,27 +55,8 @@ class TestEnvtestClass(unittest.TestCase): def testTemptempDir(self): self.assertTrue(self.tempDir.endswith("tempDir")) - def testRemoveAlreadyExistsFalse(self): - envtest.RaytracingTestCase.removeAlreadyExists = False - self.assertFalse(envtest.RaytracingTestCase.removeAlreadyExists) - - def testRemoveAlreadyExistsTrue(self): - envtest.RaytracingTestCase.removeAlreadyExists = True - self.assertTrue(envtest.RaytracingTestCase.removeAlreadyExists) - - def testCreateTempDirectoryAlreadyExistsDoNotDelete(self): - msg = f"'{self.tempDir}' directory already exists. Please set RaytracingTestCase.removeAlreadyExists to True if" - msg += f" you want to delete this directory." - envtest.RaytracingTestCase.removeAlreadyExists = False - os.mkdir(self.tempDir) - with self.assertRaises(FileExistsError) as context: - envtest.RaytracingTestCase.createTempDirectory() - self.assertEqual(str(context.exception), msg) - os.rmdir(self.tempDir) # Delete the directory! - def testCreateTempDirectoryAlreadyExistsAndDelete(self): tempDir = envtest.RaytracingTestCase.tempDir - envtest.RaytracingTestCase.removeAlreadyExists = True os.mkdir(tempDir) try: envtest.RaytracingTestCase.createTempDirectory() diff --git a/raytracing/tests/testsFigure.py b/raytracing/tests/testsFigure.py index daf1098..0c29ffd 100644 --- a/raytracing/tests/testsFigure.py +++ b/raytracing/tests/testsFigure.py @@ -14,12 +14,12 @@ class TestFigure(unittest.TestCase): self.assertEqual(path.figure.displayRange(), largestDiameter) - def testDisplayRange(self): + def testDisplayRangeImageOutOfView(self): path = ImagingPath() path.append(Space(2)) path.append(CurvedMirror(-5, 10)) - self.assertAlmostEqual(path.figure.displayRange(), 5 * 10) + self.assertAlmostEqual(path.figure.displayRange(), 20) path.objectHeight = 1 self.assertEqual(path.figure.displayRange(), 10)

Generating unnecessary images illumination = ImagingPath() illumination.append(Space(d=10)) illumination.append(Lens(f=10, diameter=100, label="Collector")) illumination.append(Space(d=10+30)) illumination.append(Lens(f=30, diameter=100, label="Condenser")) illumination.append(Space(d=30+7)) illumination.append(Lens(f=7, diameter=100, label="Objective")) illumination.append(Space(d=7+30)) illumination.append(Lens(f=30, diameter=100, label="Tube")) illumination.append(Space(d=30+10)) illumination.append(Lens(f=10, diameter=100, label="Eyepiece")) illumination.append(Space(d=10)) illumination.append(Aperture(diameter=20, label="Eye entrance")) illumination.append(Space(d=10)) illumination.display(limitObjectToFieldOfView=True, onlyChiefAndMarginalRays=True) Gives this :  Because of this : 

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-273

diff --git a/raytracing/matrix.py b/raytracing/matrix.py index ff6293f..5878f23 100644 --- a/raytracing/matrix.py +++ b/raytracing/matrix.py @@ -136,6 +136,10 @@ class Matrix(object): self.isFlipped = False super(Matrix, self).__init__() + @property + def isIdentity(self): + return self.A == 1 and self.D == 1 and self.B == 0 and self.C == 0 + @property def determinant(self): """The determinant of the ABCD matrix is always frontIndex/backIndex, @@ -181,7 +185,7 @@ class Matrix(object): "Unrecognized right side element in multiply: '{0}'\ cannot be multiplied by a Matrix".format(rightSide)) - def mul_matrix(self, rightSideMatrix): + def mul_matrix(self, rightSideMatrix: 'Matrix'): r""" This function is used to combine two elements into a single matrix. The multiplication of two ABCD matrices calculates the total ABCD matrix of the system. Total length of the elements is calculated (z) but apertures are lost. We compute @@ -269,7 +273,17 @@ class Matrix(object): else: bv = rightSideMatrix.backVertex - return Matrix(a, b, c, d, frontVertex=fv, backVertex=bv, physicalLength=L) + if self.isIdentity: # If LHS is identity, take the other's indices + fIndex = rightSideMatrix.frontIndex + bIndex = rightSideMatrix.backIndex + elif rightSideMatrix.isIdentity: # If RHS is identity, take other's indices + fIndex = self.frontIndex + bIndex = self.backIndex + else: # Else, take the "first one" front index and the "last one" back index (physical first and last) + fIndex = rightSideMatrix.frontIndex + bIndex = self.backIndex + + return Matrix(a, b, c, d, frontVertex=fv, backVertex=bv, physicalLength=L, frontIndex=fIndex, backIndex=bIndex) def mul_ray(self, rightSideRay): r"""This function does the multiplication of a ray by a matrix. @@ -332,16 +346,19 @@ class Matrix(object): """ outputRay = Ray() - outputRay.y = self.A * rightSideRay.y + self.B * rightSideRay.theta - outputRay.theta = self.C * rightSideRay.y + self.D * rightSideRay.theta - outputRay.z = self.L + rightSideRay.z - outputRay.apertureDiameter = self.apertureDiameter + if rightSideRay.isNotBlocked: + outputRay.y = self.A * rightSideRay.y + self.B * rightSideRay.theta + outputRay.theta = self.C * rightSideRay.y + self.D * rightSideRay.theta + outputRay.z = self.L + rightSideRay.z + outputRay.apertureDiameter = self.apertureDiameter - if abs(rightSideRay.y) > abs(self.apertureDiameter / 2.0): - outputRay.isBlocked = True + if abs(rightSideRay.y) > abs(self.apertureDiameter / 2.0): + outputRay.isBlocked = True + else: + outputRay.isBlocked = rightSideRay.isBlocked else: - outputRay.isBlocked = rightSideRay.isBlocked + outputRay = rightSideRay return outputRay @@ -576,8 +593,8 @@ class Matrix(object): other elements there may be more. For groups of elements, there can be any number of rays in the list. - If you only care about the final ray that has propagated through, use - `traceThrough()` + If you only care about the final ray that has propagated through, use + `traceThrough()` """ rayTrace = [] @@ -1547,7 +1564,7 @@ class Space(Matrix): """ distance = upTo if distance < self.L: - return Space(distance) + return Space(distance, self.frontIndex) else: return self

DCC-Lab/RayTracing

92c62c400ca31119d4896422f4fba2bd030d3739

diff --git a/raytracing/tests/testsMatrix.py b/raytracing/tests/testsMatrix.py index 58e8738..267ae0a 100644 --- a/raytracing/tests/testsMatrix.py +++ b/raytracing/tests/testsMatrix.py @@ -36,6 +36,42 @@ class TestMatrix(envtest.RaytracingTestCase): self.assertEqual(m3.C, 1 * 7 + 3 * 8) self.assertEqual(m3.D, 2 * 7 + 4 * 8) + def testIsIdentity(self): + m = Matrix() + self.assertTrue(m.isIdentity) + + def testIsNotIdentity(self): + m = Matrix(1, 2, 0, 1) + self.assertFalse(m.isIdentity) + + def testMatrixProductIndicesBoth1(self): + m1 = Matrix() + m2 = Matrix() + m3 = m1 * m2 + self.assertEqual(m3.frontIndex, 1) + self.assertEqual(m3.backIndex, 1) + + def testMatrixProductIndicesLHSIsIdentity(self): + m1 = Matrix(backIndex=1.33) + m2 = Matrix(1, 10, 0, 1, frontIndex=1.5, backIndex=1.5) + m3 = m1 * m2 + self.assertEqual(m3.frontIndex, 1.5) + self.assertEqual(m3.backIndex, 1.5) + + def testMatrixProductIndicesRHSIsIdentity(self): + m1 = Matrix(backIndex=1.33) + m2 = Matrix(1, 10, 0, 1, frontIndex=1.5, backIndex=1.5) + m3 = m2 * m1 + self.assertEqual(m3.frontIndex, 1.5) + self.assertEqual(m3.backIndex, 1.5) + + def testMatrixProductIndicesNoIdentity(self): + m1 = Matrix(1, 10, 0, 1, backIndex=1.33, frontIndex=1) + m2 = Matrix(1, 10, 0, 1, backIndex=1, frontIndex=1.33) + m3 = m2 * m1 + self.assertEqual(m3.frontIndex, 1) + self.assertEqual(m3.backIndex, 1) + def testMatrixProductWithRayMath(self): m1 = Matrix(A=1, B=2, C=3, D=4) rayIn = Ray(y=1, theta=0.1) @@ -323,7 +359,8 @@ class TestMatrix(envtest.RaytracingTestCase): # One less ray, because last is blocked self.assertEqual(len(traceManyThrough), len(rays) - 1) - @envtest.skipIf(sys.platform == 'darwin' and sys.version_info.major == 3 and sys.version_info.minor <= 7,"Endless loop on macOS") + @envtest.skipIf(sys.platform == 'darwin' and sys.version_info.major == 3 and sys.version_info.minor <= 7, + "Endless loop on macOS") # Some information here: https://github.com/gammapy/gammapy/issues/2453 def testTraceManyThroughInParallel(self): rays = [Ray(y, y) for y in range(5)] @@ -336,7 +373,8 @@ class TestMatrix(envtest.RaytracingTestCase): except: pass - @envtest.skipIf(sys.platform == 'darwin' and sys.version_info.major == 3 and sys.version_info.minor <= 7,"Endless loop on macOS") + @envtest.skipIf(sys.platform == 'darwin' and sys.version_info.major == 3 and sys.version_info.minor <= 7, + "Endless loop on macOS") # Some information here: https://github.com/gammapy/gammapy/issues/2453 def testTraceManyThroughInParallel(self): rays = [Ray(y, y) for y in range(5)]

Matrix multiplication returns a matrix with n1 = n2 = 1 I don't really know what we should do: in some cases, both matrices have the same n1 and n2, then the result should have n1 and n2. But sometimes they differ. I saw it happen in `MatrixGroup` when we append and build a transfer matrix: we create an identity matrix, but it has n1 = n2 = 1, and when we multiply with an element of the group (which can have n1 != n2 and both != 1), the product returns a matrix with the right ABCD components, back and front vertex, but don't have the right indices of refraction. Since `MatrixGroup` already checks if there is a mismatch between indices, we could apply the indices of the right-hand side (or left-hand side, or the one that is not 1, I don't know) of the product. But at the same time we assume something, hence `__mul__` becomes less general. @dccote what do you think we should do? Here is an example: ````python elements = [] elements.append(DielectricInterface(n1=1, n2=n1, R=R1, diameter=diameter)) elements.append(Space(d=tc1, n=n1)) elements.append(DielectricInterface(n1=n1, n2=n2, R=R2, diameter=diameter)) elements.append(Space(d=tc2, n=n2)) elements.append(DielectricInterface(n1=n2, n2=1, R=R3, diameter=diameter)) group = MatrixGroup(elements) # This fails because of the transfer matrix in append ```` `append` code: ````python def append(self, matrix): transferMatrix = Matrix(A=1, B=0, C=0, D=1) distance = upTo for element in self.elements: if element.L <= distance: transferMatrix = element * transferMatrix # This is the problem, * keeps default indices value distance -= element.L else: transferMatrix = element.transferMatrix(upTo=distance) * transferMatrix break return transferMatrix ```` `mul_matrix` code ````python def mul_matrix(self, rightSideMatrix): a = self.A * rightSideMatrix.A + self.B * rightSideMatrix.C b = self.A * rightSideMatrix.B + self.B * rightSideMatrix.D c = self.C * rightSideMatrix.A + self.D * rightSideMatrix.C d = self.C * rightSideMatrix.B + self.D * rightSideMatrix.D L = self.L + rightSideMatrix.L fv = rightSideMatrix.frontVertex if fv is None and self.frontVertex is not None: fv = rightSideMatrix.L + self.frontVertex if self.backVertex is not None: bv = rightSideMatrix.L + self.backVertex else: bv = rightSideMatrix.backVertex return Matrix(a, b, c, d, frontVertex=fv, backVertex=bv, physicalLength=L) # We should not keep n1 = n2 = 1 ````

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-282

diff --git a/raytracing/matrix.py b/raytracing/matrix.py index 2f8ff11..7f32c1b 100644 --- a/raytracing/matrix.py +++ b/raytracing/matrix.py @@ -122,6 +122,8 @@ class Matrix(object): # Length of this element self.L = float(physicalLength) # Aperture + if apertureDiameter <= 0: + raise ValueError("The aperture diameter must be strictly positive.") self.apertureDiameter = apertureDiameter # First and last interfaces. Used for BFL and FFL @@ -163,7 +165,7 @@ class Matrix(object): if self.C == 0: return self.A * self.D - + return self.A * self.D - self.B * self.C def __mul__(self, rightSide):

DCC-Lab/RayTracing

0da4c11f47ae13a1db8272b8edc52387ad1863dd

diff --git a/raytracing/tests/testsMatrix.py b/raytracing/tests/testsMatrix.py index f36fe01..c160580 100644 --- a/raytracing/tests/testsMatrix.py +++ b/raytracing/tests/testsMatrix.py @@ -20,9 +20,17 @@ class TestMatrix(envtest.RaytracingTestCase): m = Matrix() self.assertIsNotNone(m) + def testNullApertureDiameter(self): + with self.assertRaises(ValueError): + Matrix(apertureDiameter=0) + + def testNegativeApertureDiameter(self): + with self.assertRaises(ValueError): + Matrix(apertureDiameter=-0.1) + def testMatrixExplicit(self): m = Matrix(A=1, B=0, C=0, D=1, physicalLength=1, - frontVertex=0, backVertex=0, apertureDiameter=1.0) + frontVertex=0, backVertex=0, apertureDiameter=0.5) self.assertIsNotNone(m) self.assertEqual(m.A, 1) self.assertEqual(m.B, 0) @@ -31,7 +39,7 @@ class TestMatrix(envtest.RaytracingTestCase): self.assertEqual(m.L, 1) self.assertEqual(m.backVertex, 0) self.assertEqual(m.frontVertex, 0) - self.assertEqual(m.apertureDiameter, 1) + self.assertEqual(m.apertureDiameter, 0.5) def testMatrixProductMath(self): m1 = Matrix(A=4, B=3, C=1, D=1) @@ -586,16 +594,16 @@ class TestMatrix(envtest.RaytracingTestCase): self.assertNotEqual(m, "Trust me, this is a Matrix. This is equal to Matrix()") def testEqualityMatricesNotEqualSameABCD(self): - m = Matrix(1,0,0,1) - m2 = Matrix(1,0,0,1, frontVertex=1) + m = Matrix(1, 0, 0, 1) + m2 = Matrix(1, 0, 0, 1, frontVertex=1) self.assertNotEqual(m, m2) - m2 = Matrix(1,0,0,1, backVertex=1) + m2 = Matrix(1, 0, 0, 1, backVertex=1) self.assertNotEqual(m, m2) - m2 = Matrix(1,0,0,1, frontIndex=10, backIndex=10) + m2 = Matrix(1, 0, 0, 1, frontIndex=10, backIndex=10) self.assertNotEqual(m, m2) def testEqualityMatricesNotEqualDifferentABCD(self): - m = Matrix(1,0,0,1) + m = Matrix(1, 0, 0, 1) m2 = Matrix(A=1 / 2, D=2) self.assertNotEqual(m, m2)

Matrix accepts a negative aperture diameter This doesn't make any sense. Even the doc specifies that it must be positive.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DCC-Lab__RayTracing-293

diff --git a/raytracing/axicon.py b/raytracing/axicon.py index 4bf6013..680a686 100644 --- a/raytracing/axicon.py +++ b/raytracing/axicon.py @@ -2,130 +2,170 @@ from .matrix import * import matplotlib.pyplot as plt - class Axicon(Matrix): - """ - This class is an advanced module that describes an axicon lens, not part of the basic formalism. - Using this class an axicon conical lens can be presented. - Axicon lenses are used to obtain a line focus instead of a point. - - Parameters - ---------- - alpha : float - alpha is the small angle in radians of the axicon - (typically 2.5 or 5 degrees) corresponding to 90-apex angle - n : float - index of refraction. - This value cannot be less than 1.0. - diameter : float - Aperture of the element. (default = +Inf) - The diameter of the aperture must be a positive value. - label : string - The label of the axicon lens. - - """ - - def __init__(self, alpha, n, diameter=float('+Inf'), label=''): - - self.n = n - self.alpha = alpha - super(Axicon, self).__init__(A=1, B=0, C=0,D=1, physicalLength=0, apertureDiameter=diameter, label=label) - - def deviationAngle(self): - """ This function provides deviation angle delta - - Returns - ------- - delta : float - the deviation angle - - See ALso - -------- - https://ru.b-ok2.org/book/2482970/9062b7, p.48 - - """ - - return (self.n-1.0)*self.alpha - - - def focalLineLength(self, yMax=None): - """ Provides the line length, assuming a ray at height yMax - - Parameters - ---------- - yMax : float - the height of the ray (default=None) - If no height is defined for the ray, then yMax would be set to the height of the axicon (apertureDiameter/2) - - Returns - ------- - focalLineLength : float - the length of the focal line - - See ALso - -------- - https://ru.b-ok2.org/book/2482970/9062b7, p.48 - - """ + """ + This class is an advanced module that describes an axicon lens, + not part of the basic formalism. Using this class an axicon + conical lens can be presented. + Axicon lenses are used to obtain a line focus instead of a point. + The formalism is described in Kloos, sec. 2.2.3 - if yMax == None: - yMax = self.apertureDiameter/2 + Parameters + ---------- + alpha : float + alpha is the small angle in radians of the axicon + (typically 2.5 or 5 degrees) corresponding to 90-apex angle + n : float + index of refraction. + This value cannot be less than 1.0. It is assumed the axicon + is in air. + diameter : float + Aperture of the element. (default = +Inf) + The diameter of the aperture must be a positive value. + label : string + The label of the axicon lens. - return yMax/(self.n-1.0)/self.alpha + """ - def mul_ray(self, rightSideRay): - """ This function is used to calculate the output ray through an axicon. + def __init__(self, alpha, n, diameter=float('+Inf'), label=''): - Parameters - ---------- - rightSideRay : object of ray class - A ray with a defined height and angle. + self.n = n + self.alpha = alpha + super(Axicon, self).__init__(A=1, B=0, C=0, D=1, physicalLength=0, apertureDiameter=diameter, label=label, + frontIndex=1.0, backIndex=1.0) - Returns - ------- - outputRay : object of ray class - the height and angle of the output ray. + def deviationAngle(self): + """ This function provides deviation angle delta assuming that + the axicon is in air and that the incidence is near normal, + which is the usual way of using an axicon. - See Also - -------- - raytracing.Matrix.mul_ray + Returns + ------- + delta : float + the deviation angle + See ALso + -------- + https://ru.b-ok2.org/book/2482970/9062b7, p.48 + + """ + + return (self.n - 1.0) * self.alpha + + def focalLineLength(self, yMax=None): + """ Provides the line length, assuming a ray at height yMax + + Parameters + ---------- + yMax : float + the height of the ray (default=None) + If no height is defined for the ray, then yMax would be set to the height of the axicon (apertureDiameter/2) + + Returns + ------- + focalLineLength : float + the length of the focal line + + See ALso + -------- + https://ru.b-ok2.org/book/2482970/9062b7, p.48 + + """ + + if yMax == None: + yMax = self.apertureDiameter / 2 + + return abs(yMax) / (self.n - 1.0) / self.alpha + + def mul_ray(self, rightSideRay): + """ This function is used to calculate the output ray through an axicon. + + Parameters + ---------- + rightSideRay : object of ray class + A ray with a defined height and angle. + + Returns + ------- + outputRay : object of ray class + the height and angle of the output ray. + + See Also + -------- + raytracing.Matrix.mul_ray + + + """ + + outputRay = super(Axicon, self).mul_ray(rightSideRay) + + if rightSideRay.y > 0: + outputRay.theta += -self.deviationAngle() + elif rightSideRay.y < 0: + outputRay.theta += self.deviationAngle() + # theta == 0 is not deviated + + return outputRay + + def mul_matrix(self, rightSideMatrix): + """ The final matrix of an optical path with an axicon can be calculated using this function. + + Parameters + ---------- + rightSideMatrix : object of matrix class + The ABCD matrix of an element or an optical path. - """ + Notes + ----- + For now the final matrix with an axicon in the path cannot be calculated. - outputRay = super(Axicon, self).mul_ray(rightSideRay) + """ - if rightSideRay.y > 0: - outputRay.theta += -self.deviationAngle() - elif rightSideRay.y < 0: - outputRay.theta += self.deviationAngle() - # theta == 0 is not deviated - - return outputRay + raise TypeError("Cannot calculate final matrix with axicon in path. \ + You can only propagate rays all the way through") - def mul_mat(self, rightSideMatrix): - """ The final matrix of an optical path with an axicon can be calculated using this function. + def mul_beam(self, rightSideBeam): + """This function calculates the multiplication of a coherent beam with complex radius + of curvature q by an ABCD matrix. - Parameters - ---------- - rightSideMatrix : object of matrix class - The ABCD matrix of an element or an optical path. + Parameters + ---------- + rightSideBeam : object from GaussianBeam class + including the beam properties - Notes - ----- - For now the final matrix with an axicon in the path cannot be calculated. - """ + Returns + ------- + outputBeam : object from GaussianBeam class + The properties of the beam at the output of the system with the defined ABCD matrix - raise TypeError("Cannot calculate final matrix with axicon in path. \ - You can only propagate rays all rhe way through") + Examples + -------- + >>> from raytracing import * + >>> # M1 is an ABCD matrix of a lens (f=10) + >>> M1= Matrix(A=1,B=0,C=-1/10,D=1,physicalLength=5,label='Lens') + >>> # B is a Gaussian Beam + >>> B=GaussianBeam(q=complex(1,1),w=1,R=5,n=1) + >>> print('The output properties of are:' , M1.mul_beam(B)) + The output ray of Lens M1 : Complex radius: (0.976+1.22j) + w(z): 0.020, R(z): 2.500, z: 5.000, λ: 632.8 nm + zo: 1.220, wo: 0.016, wo position: -0.976 - def drawAt(self, z, axes): - halfHeight = 4 - if self.apertureDiameter != float('Inf'): - halfHeight = self.apertureDiameter/2 + See Also + -------- + raytracing.Matrix.mul_matrix + raytracing.Matrix.mul_ray + raytracing.GaussianBeam + """ - plt.arrow(z, 0, 0, halfHeight, width=0.1, fc='k', ec='k',head_length=0.25, head_width=0.25,length_includes_head=True) - plt.arrow(z, 0, 0, -halfHeight, width=0.1, fc='k', ec='k',head_length=0.25, head_width=0.25, length_includes_head=True) + raise TypeError("Cannot use Axicon with GaussianBeam, only with Ray") + def drawAt(self, z, axes): # pragma: no cover + halfHeight = 4 + if self.apertureDiameter != float('Inf'): + halfHeight = self.apertureDiameter / 2 + plt.arrow(z, 0, 0, halfHeight, width=0.1, fc='k', ec='k', head_length=0.25, head_width=0.25, + length_includes_head=True) + plt.arrow(z, 0, 0, -halfHeight, width=0.1, fc='k', ec='k', head_length=0.25, head_width=0.25, + length_includes_head=True) diff --git a/raytracing/ray.py b/raytracing/ray.py index ca4e0b7..b044e1d 100644 --- a/raytracing/ray.py +++ b/raytracing/ray.py @@ -1,3 +1,6 @@ +import warnings + + class Ray: """A vector and a light ray as transformed by ABCD matrices. @@ -32,7 +35,7 @@ class Ray: """ - def __init__(self, y: float = 0, theta: float = 0, z: float = 0, isBlocked:bool = False): + def __init__(self, y: float = 0, theta: float = 0, z: float = 0, isBlocked: bool = False): self.y = y self.theta = theta @@ -81,12 +84,18 @@ class Ray: rays : list of ray The created list of rays that define this fan. + Notes + ----- + This method is deprecated. The class Rays and its subclasses should be used to generate multiple Ray objects. + See Also -------- raytracing.Matrix.trace() raytracing.Matrix.traceMany(). """ + warnings.warn("The creation of a group of rays with this method is deprecated. Usage of the class Rays and its" + "subclasses is recommended.", DeprecationWarning) if N >= 2: deltaRadian = float(radianMax - radianMin) / (N - 1) @@ -129,13 +138,19 @@ class Ray: rays : list of ray The created list of rays that define these fan groups. + Notes + ----- + This method is deprecated. The class Rays and its subclasses should be used to generate multiple Ray objects. + See Also -------- raytracing.Matrix.trace() raytracing.Matrix.traceMany(). """ - + warnings.warn("The creation of a group of rays with this method is deprecated. Usage of the class Rays and its" + "subclasses is recommended.", DeprecationWarning) + if N >= 2: deltaRadian = float(radianMax - radianMin) / (N - 1) elif N == 1:

DCC-Lab/RayTracing

0574559c65ccce3efb17d36176d0985c9c20a781

diff --git a/raytracing/tests/testsAxicon.py b/raytracing/tests/testsAxicon.py new file mode 100644 index 0000000..483cafa --- /dev/null +++ b/raytracing/tests/testsAxicon.py @@ -0,0 +1,108 @@ +import envtest + +from raytracing import * +from numpy import random +from numpy import * + +inf = float("+inf") +degrees = math.pi/180 + +class TestAxicon(envtest.RaytracingTestCase): + + def testAxicon(self): + n = 1.5 + alpha = 2.6*degrees + diameter = 100 + label = "Axicon" + axicon = Axicon(alpha, n, diameter, label) + self.assertEqual(axicon.n, n) + self.assertEqual(axicon.alpha, alpha) + self.assertEqual(axicon.apertureDiameter, diameter) + self.assertEqual(axicon.label, label) + self.assertEqual(axicon.frontIndex, 1.0) + self.assertEqual(axicon.backIndex, 1.0) + + def testDeviationAngleIs0(self): + n = 1 + alpha = random.randint(2000, 5000, 1).item() / 1000*degrees + axicon = Axicon(alpha, n) + self.assertEqual(axicon.deviationAngle(), 0) + + def testDeviationAngleIs0Too(self): + n = random.randint(1000, 3000, 1).item() / 1000 + alpha = 0*degrees + axicon = Axicon(alpha, n) + self.assertEqual(axicon.deviationAngle(), 0) + + def testDeviationAngle(self): + n = 1.33 + alpha = 4*degrees + axicon = Axicon(alpha, n) + self.assertAlmostEqual(axicon.deviationAngle(), 1.32*degrees, places=15) + + def testFocalLineLengthYIsNoneAndInfiniteDiameter(self): + n = random.randint(1000, 3000, 1).item() / 1000 + alpha = random.randint(2000, 5000, 1).item() / 1000*degrees + axicon = Axicon(alpha, n) + self.assertEqual(axicon.focalLineLength(), inf) + + def testFocalLineLengthYIsNone(self): + n = 1.5 + alpha = 2.6*degrees + axicon = Axicon(alpha, n, 100) + y = 50 + L = y/tan(axicon.deviationAngle()) + self.assertAlmostEqual(axicon.focalLineLength(), L,0) + + def testFocalLineLengthSignOfY(self): + n = 1.43 + alpha = 1.95*degrees + axicon = Axicon(alpha=alpha, n=n, diameter=100) + self.assertAlmostEqual(axicon.focalLineLength(-2), axicon.focalLineLength(2)) + + def testFocalLineLengthPositiveY(self): + n = 1.43 + alpha = 1.95*degrees + axicon = Axicon(alpha, n, 100) + y = 2 + L = y/tan(axicon.deviationAngle()) + self.assertAlmostEqual(axicon.focalLineLength(y), L, 1) + + def testHighRayIsDeviatedDown(self): + ray = Ray(10, 0) + n = 1.1 + alpha = 2.56*degrees + axicon = Axicon(alpha, n, 50) + outputRay = axicon*ray + self.assertEqual(outputRay.theta, -axicon.deviationAngle()) + self.assertTrue(outputRay.theta < 0) + + def testLowRayIsDeviatedUp(self): + ray = Ray(-10, 0) + n = 1.1 + alpha = 2.56*degrees + axicon = Axicon(alpha, n, 50) + outputRay = axicon*ray + self.assertEqual(outputRay.theta, axicon.deviationAngle()) + self.assertTrue(outputRay.theta > 0) + + def testMulMatrix(self): + matrix = Matrix() + axicon = Axicon(2.6543, 1.2*degrees) + with self.assertRaises(TypeError): + axicon.mul_matrix(matrix) + + def testDifferentMultiplications(self): + ray = Ray() + beam = GaussianBeam(w=1, R=10, n=1.67) + matrix = Matrix() + axicon = Axicon(4.3, 1.67*degrees) + self.assertIsNotNone(axicon * ray) + with self.assertRaises(TypeError): + axicon * beam + + with self.assertRaises(TypeError): + axicon * matrix + +if __name__ == '__main__': + envtest.main() diff --git a/raytracing/tests/testsMatrixGroup.py b/raytracing/tests/testsMatrixGroup.py index 95fa3ac..f0e835f 100644 --- a/raytracing/tests/testsMatrixGroup.py +++ b/raytracing/tests/testsMatrixGroup.py @@ -4,7 +4,7 @@ from raytracing import * inf = float("+inf") -testSaveHugeFile = True +testSaveHugeFiles = True class TestMatrixGroup(envtest.RaytracingTestCase): @@ -591,11 +591,11 @@ class TestSaveAndLoadMatrixGroup(envtest.RaytracingTestCase): mg = MatrixGroup([Space(20), ThickLens(1.22, 10, 10, 10)]) self.assertSaveNotFailed(mg, self.fileName) - @envtest.skipIf(not testSaveHugeFile, "Don't test saving a lot of matrices") + @envtest.skipIf(not testSaveHugeFiles, "Don't test saving a lot of matrices") def testSaveHugeFile(self): fname = self.tempFilePath("hugeFile.pkl") - spaces = [Space(10) for _ in range(500)] - lenses = [Lens(10) for _ in range(500)] + spaces = [Space(10) for _ in range(200)] + lenses = [Lens(10) for _ in range(200)] elements = spaces + lenses mg = MatrixGroup(elements) self.assertSaveNotFailed(mg, fname) @@ -655,11 +655,11 @@ class TestSaveAndLoadMatrixGroup(envtest.RaytracingTestCase): self.assertLoadNotFailed(mg2, fname) self.assertLoadEqualsMatrixGroup(mg2, mg1) - @envtest.skipIf(not testSaveHugeFile, "Don't test saving a lot of matrices") + @envtest.skipIf(not testSaveHugeFiles, "Don't test saving a lot of matrices") def testSaveThenLoadHugeFile(self): fname = self.tempFilePath("hugeFile.pkl") - spaces = [Space(10) for _ in range(500)] - lenses = [Lens(10) for _ in range(500)] + spaces = [Space(10) for _ in range(125)] + lenses = [Lens(10) for _ in range(125)] elements = spaces + lenses mg1 = MatrixGroup(elements) mg2 = MatrixGroup()

Axicon does not change the values of backIndex and frontIndex The `Axicon` class does not change the default values of `backIndex` and `frontIndex` with the input value `n`.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DHI__mikeio-238

diff --git a/mikeio/dataset.py b/mikeio/dataset.py index b447f1c7..39255424 100644 --- a/mikeio/dataset.py +++ b/mikeio/dataset.py @@ -162,31 +162,44 @@ class Dataset(TimeSeries): def __len__(self): return len(self.items) - def __getitem__(self, x): + def __setitem__(self, key, value): - if isinstance(x, slice): - s = self.time.slice_indexer(x.start, x.stop) + if isinstance(key, int): + self.data[key] = value + + elif isinstance(key, str): + item_lookup = {item.name: i for i, item in enumerate(self.items)} + key = item_lookup[key] + self.data[key] = value + else: + + raise ValueError(f"indexing with a {type(key)} is not (yet) supported") + + def __getitem__(self, key): + + if isinstance(key, slice): + s = self.time.slice_indexer(key.start, key.stop) time_steps = list(range(s.start, s.stop)) return self.isel(time_steps, axis=0) - if isinstance(x, int): - return self.data[x] + if isinstance(key, int): + return self.data[key] - if isinstance(x, str): + if isinstance(key, str): item_lookup = {item.name: i for i, item in enumerate(self.items)} - x = item_lookup[x] - return self.data[x] + key = item_lookup[key] + return self.data[key] - if isinstance(x, ItemInfo): - return self.__getitem__(x.name) + if isinstance(key, ItemInfo): + return self.__getitem__(key.name) - if isinstance(x, list): + if isinstance(key, list): data = [] items = [] item_lookup = {item.name: i for i, item in enumerate(self.items)} - for v in x: + for v in key: data_item = self.__getitem__(v) if isinstance(v, str): i = item_lookup[v] @@ -199,7 +212,7 @@ class Dataset(TimeSeries): return Dataset(data, self.time, items) - raise ValueError(f"indexing with a {type(x)} is not (yet) supported") + raise ValueError(f"indexing with a {type(key)} is not (yet) supported") def __radd__(self, other): return self.__add__(other) @@ -229,51 +242,61 @@ class Dataset(TimeSeries): else: return self._multiply_value(other) - def _add_dataset(self, other, sign=1.0): + def _add_dataset(self, other, sign=1.0): self._check_datasets_match(other) try: - data = [self[x] + sign*other[y] for x, y in zip(self.items, other.items)] + data = [self[x] + sign * other[y] for x, y in zip(self.items, other.items)] except: raise ValueError("Could not add data in Dataset") time = self.time.copy() items = deepcopy(self.items) - return Dataset(data, time, items) + return Dataset(data, time, items) def _check_datasets_match(self, other): if self.n_items != other.n_items: - raise ValueError(f"Number of items must match ({self.n_items} and {other.n_items})") + raise ValueError( + f"Number of items must match ({self.n_items} and {other.n_items})" + ) for j in range(self.n_items): if self.items[j].type != other.items[j].type: - raise ValueError(f"Item types must match. Item {j}: {self.items[j].type} != {other.items[j].type}") + raise ValueError( + f"Item types must match. Item {j}: {self.items[j].type} != {other.items[j].type}" + ) if self.items[j].unit != other.items[j].unit: - raise ValueError(f"Item units must match. Item {j}: {self.items[j].unit} != {other.items[j].unit}") + raise ValueError( + f"Item units must match. Item {j}: {self.items[j].unit} != {other.items[j].unit}" + ) if not np.all(self.time == other.time): raise ValueError("All timesteps must match") if self.shape != other.shape: - raise ValueError("shape must match") + raise ValueError("shape must match") def _add_value(self, value): try: data = [value + self[x] for x in self.items] except: - raise ValueError(f"{value} could not be added to Dataset") + raise ValueError(f"{value} could not be added to Dataset") items = deepcopy(self.items) time = self.time.copy() return Dataset(data, time, items) - def _multiply_value(self, value): try: data = [value * self[x] for x in self.items] except: - raise ValueError(f"{value} could not be multiplied to Dataset") + raise ValueError(f"{value} could not be multiplied to Dataset") items = deepcopy(self.items) time = self.time.copy() return Dataset(data, time, items) def describe(self, **kwargs): """Generate descriptive statistics by wrapping pandas describe()""" - all_df = [pd.DataFrame(self.data[j].flatten(), columns=[self.items[j].name]).describe(**kwargs) for j in range(self.n_items)] + all_df = [ + pd.DataFrame(self.data[j].flatten(), columns=[self.items[j].name]).describe( + **kwargs + ) + for j in range(self.n_items) + ] return pd.concat(all_df, axis=1) def copy(self): diff --git a/mikeio/eum.py b/mikeio/eum.py index 88f16571..0dfe3360 100644 --- a/mikeio/eum.py +++ b/mikeio/eum.py @@ -347,7 +347,7 @@ class EUMType(IntEnum): Ground_Water_Abstraction_Flux = 100238 Fraction = 100239 Yield_Factor = 100240 - Specific_Solute_Flux_Per_Area = 100241 + Specific_Solute_Flux_per_Area = 100241 Current_Speed = 100242 Current_Direction = 100243 Current_Magnitude = 100244 @@ -621,6 +621,7 @@ class EUMType(IntEnum): Heat_Flux_Resistance = 110200 Absolute_Humidity = 110210 Length = 110220 + Area = 110225 Volume = 110230 Element_Volume = 110231 Wave_Power = 110232 @@ -694,6 +695,13 @@ class EUMType(IntEnum): Molal_Concentration = 110300 Suspended_sediment_load_per_area = 110301 Bollard_Force = 110302 + Discharge_per_Pressure = 110303 + RotationalSpeed = 110304 + Infiltration_per_Area = 110305 + Mass_per_Length_per_Time = 110306 + NearBedLoad_per_Length = 110307 + Substance_per_UnitArea = 110308 + AccNearBedLoad_per_Length = 110309 def __init__(self, code): self.code = code @@ -832,6 +840,17 @@ class EUMUnit(IntEnum): pound = 1207 kiloton = 1205 megaton = 1206 + ounce = 1209 + per_kg = 1250 + per_gram = 1251 + per_mg = 1252 + per_mu_g = 1253 + per_ton = 1254 + per_kiloton = 1255 + per_megaton = 1256 + per_pound = 1257 + per_ton_US = 1258 + per_ounce = 1259 kg_per_sec = 4200 gram_per_sec = 4203 mg_per_sec = 4202 @@ -915,6 +934,8 @@ class EUMUnit(IntEnum): pound_per_feet_per_sec_pow_2 = 5402 newton_per_meter_pow_3 = 5500 kN_per_meter_pow_3 = 5501 + kilogram_M2 = 5550 + poundSqrFeet = 5551 gram_per_meter_pow_3_per_day = 4601 _mg_per_l__pow__1_per_2__per_day = 5300 _mg_per_l__pow__1_per_2__per_hour = 5301 @@ -1062,11 +1083,15 @@ class EUMUnit(IntEnum): meter_pow_3_per_hour_per_meter = 7503 meter_pow_3_per_day_per_meter = 7504 feet_pow_3_per_hour_per_feet = 4719 + m3_per_hour_per_M = 4730 + m3_per_day_per_M = 4731 feet_pow_3_per_day_per_feet = 4732 galUK_per_day_per_feet = 4712 gallon_per_day_per_feet = 4713 gallon_per_min_per_feet = 4714 liter_per_day_per_meter = 4715 + liter_per_minute_per_meter = 4716 + liter_per_second_per_meter = 4717 liter_per_min_per_meter = 7501 liter_per_sec_per_meter = 7500 gram_per_min = 4208 @@ -1087,15 +1112,6 @@ class EUMUnit(IntEnum): meter_pow_3_per_mu_g = 6903 ton_per_day = 4219 millimeterD50 = 1012 - per_kg = 1250 - per_gram = 1251 - per_mg = 1252 - per_mu_g = 1253 - per_ton = 1254 - per_kiloton = 1255 - per_megaton = 1256 - per_pound = 1257 - per_ton_US = 1258 millisecond = 1406 feet_US_pow_2 = 3208 yard_US_pow_2 = 3209 @@ -1112,6 +1128,7 @@ class EUMUnit(IntEnum): galUK_per_sec = 1826 galUK_per_year = 1827 galUK_per_PE_per_day = 1828 + ydUS3_per_sec = 1829 acre_feet_per_day_per_acre = 2022 Mgal_per_day_per_acre = 2032 MgalUK_per_day_per_acre = 2033 @@ -1121,8 +1138,25 @@ class EUMUnit(IntEnum): meter_per_sec_pow_2 = 2100 feet_per_sec_pow_2 = 2101 pound_per_feet_US_pow_2 = 2215 + ounce_per_cubic_feet = 2216 + ounce_per_cubic_feet_US = 2217 + ounce_per_Yard3 = 2218 + ounce_per_yard_US3 = 2219 + ounce_per_square_feet = 2220 + ounce_per_square_feet_US = 2221 kg_per_meter_per_sec = 2300 Pascal_second = 2301 + kilogram_per_meter_per_day = 2302 + gram_per_Meter_per_Day = 2303 + gram_per_Km_per_Day = 2304 + pound_per_Feet_per_Day = 2305 + pound_per_FeetUS_per_Day = 2306 + ounce_per_Feet_per_Day = 2307 + ounce_per_FeetUS_per_Day = 2308 + kilogram_per_Yard_per_Second = 2309 + kilogram_per_Feet_per_Second = 2310 + pound_per_Yard_per_Second = 2311 + pound_per_Feet_per_Second = 2312 degree50 = 2402 degree_pow_2 = 2403 degree_per_meter = 2500 @@ -1134,6 +1168,8 @@ class EUMUnit(IntEnum): rev_per_min = 2610 percent_per_hour = 2611 percent_per_sec = 2613 + revolution_per_second = 2614 + revolution_per_hour = 2615 _per_degree_C = 2850 _per_degree_F = 2851 per_meter_pow_3 = 3003 @@ -1161,6 +1197,16 @@ class EUMUnit(IntEnum): mg_per_mile_pow_2 = 4428 pound_per_meter = 4429 ton_per_meter = 4430 + pound_per_Feet = 4431 + pound_per_Yard = 4432 + pound_per_FeetUS = 4433 + pound_per_YardUS = 4434 + ounce_per_Feet = 4435 + ounce_per_Yard = 4436 + ounce_per_FeetUS = 4437 + ounce_per_YardUS = 4438 + kilogram_per_Yard = 4439 + kilogram_per_Feet = 4440 mg_per_liter_per_day = 4603 yard_pow_3_per_year_per_yard = 4728 yard_US_pow_3_per_year_per_yard_US = 4729 @@ -1222,6 +1268,7 @@ class EUMUnit(IntEnum): Mgal_per_day_per_psi = 7507 MgalUK_per_day_per_psi = 7508 acre_feet_per_day_per_psi = 7509 + m3_per_hour_per_bar = 7510 _per_meter_per_sec = 9200 meter_per_sec_per_ha = 9201 feet_per_sec_per_acre = 9202 @@ -1229,6 +1276,7 @@ class EUMUnit(IntEnum): per_acre = 9301 per_hectare = 9302 per_km_pow_2 = 9303 + per_cubic_meter = 9350 currency_per_meter_pow_3 = 9351 currency_per_feet_pow_3 = 9352 per_watt = 9600 @@ -1253,6 +1301,10 @@ class EUMUnit(IntEnum): mmol_per_kg = 12041 mu_mol_per_kg = 12042 nmol_per_kg = 12043 + mole_per_m2 = 12060 + millimole_per_m2 = 12061 + micromole_per_m2 = 12062 + nanomole_per_m2 = 12063 meter_per_meter = 99014 per_minute = 99015 percent_per_min = 2612

DHI/mikeio

1805f86b1e3e2f6c9946759f99e9bdf957be9347

diff --git a/tests/test_dataset.py b/tests/test_dataset.py index 1191c867..36b453b9 100644 --- a/tests/test_dataset.py +++ b/tests/test_dataset.py @@ -11,6 +11,7 @@ from mikeio.eum import EUMType, ItemInfo, EUMUnit def _get_time(nt): return list(rrule(freq=SECONDLY, count=nt, dtstart=datetime(2000, 1, 1))) + @pytest.fixture def ds1(): nt = 10 @@ -24,6 +25,7 @@ def ds1(): items = [ItemInfo("Foo"), ItemInfo("Bar")] return Dataset(data, time, items) + @pytest.fixture def ds2(): nt = 10 @@ -37,6 +39,7 @@ def ds2(): items = [ItemInfo("Foo"), ItemInfo("Bar")] return Dataset(data, time, items) + def test_get_names(): data = [] @@ -241,8 +244,9 @@ def test_select_subset_isel_multiple_idxs(): def test_decribe(ds1): df = ds1.describe() assert df.columns[0] == "Foo" - assert df.loc['mean'][1] == pytest.approx(0.2) - assert df.loc['max'][0] == pytest.approx(0.1) + assert df.loc["mean"][1] == pytest.approx(0.2) + assert df.loc["max"][0] == pytest.approx(0.1) + def test_create_undefined(): @@ -468,6 +472,21 @@ def test_get_data_name(): assert ds["Foo"].shape == (100, 100, 30) +def test_set_data_name(): + + nt = 100 + + time = _get_time(nt) + items = [ItemInfo("Foo")] + ds = Dataset([np.zeros((nt, 10))], time, items) + + assert ds["Foo"][0, 0] == 0.0 + + ds["Foo"] = np.zeros((nt, 10)) + 1.0 + + assert ds["Foo"][0, 0] == 1.0 + + def test_get_bad_name(): nt = 100 data = [] @@ -909,29 +928,32 @@ def test_init(): assert ds.n_elements == n_elements assert ds.items[0].name == "Foo" + def test_add_scalar(ds1): ds2 = ds1 + 10.0 assert np.all(ds2[0] - ds1[0] == 10.0) ds3 = 10.0 + ds1 assert np.all(ds3[0] == ds2[0]) - assert np.all(ds3[1] == ds2[1]) - + assert np.all(ds3[1] == ds2[1]) + + def test_sub_scalar(ds1): ds2 = ds1 - 10.0 assert np.all(ds1[0] - ds2[0] == 10.0) ds3 = 10.0 - ds1 assert np.all(ds3[0] == 9.9) - assert np.all(ds3[1] == 9.8) + assert np.all(ds3[1] == 9.8) + def test_mul_scalar(ds1): ds2 = ds1 * 2.0 - assert np.all(ds2[0]*0.5 == ds1[0]) + assert np.all(ds2[0] * 0.5 == ds1[0]) ds3 = 2.0 * ds1 assert np.all(ds3[0] == ds2[0]) - assert np.all(ds3[1] == ds2[1]) + assert np.all(ds3[1] == ds2[1]) def test_add_dataset(ds1, ds2): @@ -941,7 +963,7 @@ def test_add_dataset(ds1, ds2): ds4 = ds2 + ds1 assert np.all(ds3[0] == ds4[0]) - assert np.all(ds3[1] == ds4[1]) + assert np.all(ds3[1] == ds4[1]) ds2b = ds2.copy() ds2b.items[0] = ItemInfo(EUMType.Wind_Velocity) @@ -951,17 +973,19 @@ def test_add_dataset(ds1, ds2): ds2c = ds2.copy() tt = ds2c.time.to_numpy() - tt[-1] = tt[-1] + np.timedelta64(1, 's') + tt[-1] = tt[-1] + np.timedelta64(1, "s") ds2c.time = pd.DatetimeIndex(tt) with pytest.raises(ValueError): # time does not match ds1 + ds2c + def test_sub_dataset(ds1, ds2): ds3 = ds2 - ds1 assert np.all(ds3[0] == 0.9) assert np.all(ds3[1] == 1.8) + def test_non_equidistant(): nt = 4 d = np.random.uniform(size=nt) diff --git a/tests/test_eum.py b/tests/test_eum.py index 74b7c6b2..43628b7f 100644 --- a/tests/test_eum.py +++ b/tests/test_eum.py @@ -1,4 +1,6 @@ -from mikeio.eum import EUMType, ItemInfo +from mikeio.eum import EUMType, EUMUnit, ItemInfo + +from mikecore.eum import eumItem, eumUnit def test_item_is_equivalent_to_int(): @@ -53,3 +55,15 @@ def test_eum_type_search(): types = EUMType.search("velocity") assert len(types) > 0 + + +def test_eum_conversion(): + """Verify that all EUM types and units in mikecore have equivalents in MIKE IO""" + + for code in eumItem: + EUMType(code) + + for code in eumUnit: + EUMUnit(code) + + assert True

Dataset item assignment 

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

DHI__mikeio-442

diff --git a/mikeio/pfs.py b/mikeio/pfs.py index 10d80fce..e8812520 100644 --- a/mikeio/pfs.py +++ b/mikeio/pfs.py @@ -203,8 +203,11 @@ def parse_yaml_preserving_duplicates(src, unique_keywords=True): data[key] = [] data[key].append(val) else: - warnings.warn(f"Keyword {key} defined multiple times. Value: {val}") - data[key] = val + warnings.warn( + f"Keyword {key} defined multiple times (first will be used). Value: {val}" + ) + if key not in data: + data[key] = val else: data[key] = val return data @@ -243,7 +246,7 @@ class Pfs: """ def __init__(self, input, encoding="cp1252", names=None, unique_keywords=True): - if isinstance(input, (str, Path)): + if isinstance(input, (str, Path)) or hasattr(input, "read"): if names is not None: raise ValueError("names cannot be given as argument if input is a file") sections, names = self._read_pfs_file(input, encoding, unique_keywords) @@ -404,8 +407,11 @@ class Pfs: def _pfs2yaml(self, filename, encoding=None) -> str: - with (open(filename, encoding=encoding)) as f: - pfsstring = f.read() + if hasattr(filename, "read"): # To read in memory strings StringIO + pfsstring = filename.read() + else: + with (open(filename, encoding=encoding)) as f: + pfsstring = f.read() lines = pfsstring.split("\n") @@ -453,7 +459,9 @@ class Pfs: key = key.strip() value = s[(idx + 1) :] - if s.count("'") == 2: # This is a quoted string and not a list + if ( + s[0] == "'" and s[-1] == "'" + ): # This is a quoted string and not a list s = s else: if "," in value:

DHI/mikeio

3f8bb643a6d4e0fefae07356fcf6a16ac2972035

diff --git a/tests/test_pfs.py b/tests/test_pfs.py index 1bf1e42e..6355799d 100644 --- a/tests/test_pfs.py +++ b/tests/test_pfs.py @@ -1,3 +1,4 @@ +from io import StringIO import sys import os import pytest @@ -375,8 +376,8 @@ def test_non_unique_keywords(): assert len(pfs.BoundaryExtractor.POINT_1) == 2 assert isinstance(pfs.BoundaryExtractor.POINT_1[1], mikeio.PfsSection) - # last value will be kept - assert pfs.BoundaryExtractor.z_min == 19 + # first value will be kept (like MIKE FM) + assert pfs.BoundaryExtractor.z_min == -3000 def test_non_unique_keywords_allowed(): @@ -419,3 +420,97 @@ def test_mdf(): pfs.data[2].POLYGONS.Data == "8 8 Untitled 359236.79224376212 6168403.076453222 1 0 -1 -1 16711680 65535 3 0 1 0 1 1000 1000 0 0 0 0 0 1 1000 2 2 0 10 3 38 32 25 8 Untitled 367530.58488032949 6174892.7846391136 0 0 -1 -1 16711680 65535 3 1 700000 0 1 1000 1000 0 0 0 0 0 1 1000 2 2 0 10 14 34 25 32 39 1 37 35 31 23 26 17 30 22 24 8 Untitled 358191.86702583247 6164004.5695307152 1 0 -1 -1 16711680 65535 3 0 1 0 1 1000 1000 0 0 0 0 0 1 1000 2 2 0 10 2 1 36 8 Untitled 356300.2080261847 6198016.2887355704 1 0 -1 -1 16711680 65535 3 0 1 0 1 1000 1000 0 0 0 0 0 1 1000 2 2 0 10 2 9 0 9 Ndr Roese 355957.23455536627 6165986.6140259188 0 0 -1 -1 16711680 65535 3 1 180000 0 1 1000 1000 0 0 0 0 0 1 1000 2 2 0 10 6 33 37 36 39 38 34 16 Area of interest 355794.66401566722 6167799.1149176853 0 0 -1 -1 16711680 65535 3 1 50000 0 1 1000 1000 0 0 0 0 0 1 1000 2 2 0 10 1 40 8 Untitled 353529.91916129418 6214840.5979535272 0 0 -1 -1 16711680 65535 3 1 700000 0 1 1000 1000 0 0 0 0 0 1 1000 2 2 0 10 8 41 8 7 27 4 6 11 12 8 Untitled 351165.00127937191 6173083.0605236143 1 0 -1 -1 16711680 65535 3 0 1 0 1 1000 1000 0 0 0 0 0 1 1000 2 2 0 10 1 2 " ) + + +def test_read_in_memory_string(): + + text = """ +[ENGINE] + option = foo,bar +EndSect // ENGINE +""" + pfs = mikeio.Pfs(StringIO(text)) + + assert pfs.ENGINE.option == ["foo", "bar"] + + +def test_read_mixed_array(): + + text = """ +[ENGINE] + advanced= false + fill_list = false, 'TEST' +EndSect // ENGINE +""" + pfs = mikeio.Pfs(StringIO(text)) + + assert pfs.ENGINE.advanced == False + assert isinstance(pfs.ENGINE.fill_list, (list, tuple)) + assert len(pfs.ENGINE.fill_list) == 2 + assert pfs.ENGINE.fill_list[0] == False + assert pfs.ENGINE.fill_list[1] == "TEST" + + +def test_read_mixed_array2(): + + text = """ +[ENGINE] + fill_list = 'dsd', 0, 0.0, false +EndSect // ENGINE +""" + pfs = mikeio.Pfs(StringIO(text)) + assert isinstance(pfs.ENGINE.fill_list, (list, tuple)) + assert len(pfs.ENGINE.fill_list) == 4 + assert pfs.ENGINE.fill_list[0] == "dsd" + assert pfs.ENGINE.fill_list[1] == 0 + assert pfs.ENGINE.fill_list[2] == 0.0 + assert pfs.ENGINE.fill_list[3] == False + + +def test_read_mixed_array3(): + + text = """ +[ENGINE] + fill_list = 'dsd', 0, 0.0, "str2", false, 'str3' +EndSect // ENGINE +""" + pfs = mikeio.Pfs(StringIO(text)) + assert isinstance(pfs.ENGINE.fill_list, (list, tuple)) + assert len(pfs.ENGINE.fill_list) == 6 + assert pfs.ENGINE.fill_list[0] == "dsd" + assert pfs.ENGINE.fill_list[1] == 0 + assert pfs.ENGINE.fill_list[2] == 0.0 + assert pfs.ENGINE.fill_list[3] == "str2" + assert pfs.ENGINE.fill_list[4] == False + assert pfs.ENGINE.fill_list[5] == "str3" + + +def test_read_array(): + + text = """ +[ENGINE] + fill_list = 1, 2 +EndSect // ENGINE +""" + pfs = mikeio.Pfs(StringIO(text)) + + assert isinstance(pfs.ENGINE.fill_list, (list, tuple)) + assert len(pfs.ENGINE.fill_list) == 2 + assert pfs.ENGINE.fill_list[0] == 1 + assert pfs.ENGINE.fill_list[1] == 2 + + +def test_read_string_array(): + + text = """ +[ENGINE] + fill_list = 'foo', 'bar', 'baz' +EndSect // ENGINE +""" + pfs = mikeio.Pfs(StringIO(text)) + + assert isinstance(pfs.ENGINE.fill_list, (list, tuple)) + assert len(pfs.ENGINE.fill_list) == 3 + assert pfs.ENGINE.fill_list[0] == "foo" + assert pfs.ENGINE.fill_list[1] == "bar" + assert pfs.ENGINE.fill_list[2] == "baz"

PFS. read write of parameter list, which contains both boolean and string MIKE IO version 1.2.dev0 This is probably a rare case, but it seems that this line will fail: fill_list = false, 'TEST' if you read it from a pfs file and try to write it again you will get this: fill_list = 'false, 'TEST'' Which is different. This only occurs if the line contains both boolean and string. Here is another example: fill_list = 0,'TEST',false which gives fill_list = '0,'TEST',false' Some other combined cases can be even worse(!) - the below line cannot be parsed: fill_list = 'dsd', 0, 0.0, false Gives this error: E expected <block end>, but found ',' E in "<unicode string>", line 16, column 22: E fill_list: 'dsd', 0.0, false Probably because the string is first on the line.

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

DKISTDC__dkist-288

diff --git a/.readthedocs.yml b/.readthedocs.yml index a3619c6..13f5cf2 100644 --- a/.readthedocs.yml +++ b/.readthedocs.yml @@ -7,6 +7,7 @@ sphinx: # Optionally build your docs in additional formats such as PDF formats: - pdf + - htmlzip build: os: ubuntu-22.04 diff --git a/changelog/288.bugfix.rst b/changelog/288.bugfix.rst new file mode 100644 index 0000000..e669795 --- /dev/null +++ b/changelog/288.bugfix.rst @@ -0,0 +1,1 @@ +Fix a bug preventing the transfer of a single dataset with ``transfer_complete_datasets``. diff --git a/dkist/net/client.py b/dkist/net/client.py index ea1a888..c4f6963 100644 --- a/dkist/net/client.py +++ b/dkist/net/client.py @@ -89,12 +89,12 @@ class DKISTQueryResponseTable(QueryResponseTable): for colname, unit in units.items(): if colname not in results.colnames: continue # pragma: no cover - none_values = results[colname] == None - if any(none_values): + none_values = np.array(results[colname] == None) + if none_values.any(): results[colname][none_values] = np.nan results[colname] = u.Quantity(results[colname], unit=unit) - if results: + if results and "Wavelength" not in results.colnames: results["Wavelength"] = u.Quantity([results["Wavelength Min"], results["Wavelength Max"]]).T results.remove_columns(("Wavelength Min", "Wavelength Max"))

DKISTDC/dkist

185c2490bd914ad3b12d9df2b845a3ffdbedd642

diff --git a/dkist/data/test/AGLKO-inv.ecsv b/dkist/data/test/AGLKO-inv.ecsv new file mode 100644 index 0000000..916821d --- /dev/null +++ b/dkist/data/test/AGLKO-inv.ecsv @@ -0,0 +1,114 @@ +# %ECSV 1.0 +# --- +# datatype: +# - {name: Start Time, datatype: string} +# - {name: End Time, datatype: string} +# - {name: Instrument, datatype: string} +# - {name: Wavelength, unit: nm, datatype: string, subtype: 'float64[2]'} +# - {name: Bounding Box, datatype: string} +# - {name: Movie Filename, datatype: string} +# - {name: Storage Bucket, datatype: string} +# - {name: Dataset ID, datatype: string} +# - {name: Dataset Size, unit: Gibyte, datatype: float64} +# - {name: Experiment IDs, datatype: string, subtype: 'string[1]'} +# - {name: Exposure Time, unit: s, datatype: float64} +# - {name: Level 0 Frame count, datatype: int64} +# - {name: Primary Experiment ID, datatype: string} +# - {name: Primary Proposal ID, datatype: string} +# - {name: Proposal IDs, datatype: string, subtype: 'string[1]'} +# - {name: Recipe Instance ID, datatype: int64} +# - {name: Recipe Run ID, datatype: int64} +# - {name: Recipe ID, datatype: int64} +# - {name: Full Stokes, datatype: bool} +# - {name: Stokes Parameters, datatype: string} +# - {name: Target Types, datatype: string, subtype: 'string[1]'} +# - {name: Creation Date, datatype: string} +# - {name: Number of Frames, datatype: int64} +# - {name: Average Fried Parameter, datatype: float64} +# - {name: asdf Filename, datatype: string} +# - {name: Experiment Description, datatype: string} +# - {name: Embargoed, datatype: bool} +# - {name: Last Updated, datatype: string} +# - {name: Preview URL, datatype: string} +# - {name: Downloadable, datatype: bool} +# - {name: Has Spectral Axis, datatype: bool} +# - {name: Has Temporal Axis, datatype: bool} +# - {name: Average Spectral Sampling, unit: nm, datatype: float64} +# - {name: Average Spatial Sampling, unit: arcsec, datatype: float64} +# - {name: Average Temporal Sampling, unit: s, datatype: float64} +# - {name: Quality Report Filename, datatype: string} +# - {name: Input Dataset Parameters Part ID, datatype: int64} +# - {name: Input Dataset Observe Frames Part ID, datatype: int64} +# - {name: Input Dataset Calibration Frames Part ID, datatype: int64} +# - {name: Summit Software Version, datatype: string} +# - {name: Calibration Workflow Name, datatype: string} +# - {name: Calibration Workflow Version, datatype: string} +# - {name: HDU Creation Date, datatype: string} +# - {name: Observing Program Execution ID, datatype: string} +# - {name: Instrument Program Execution ID, datatype: string} +# - {name: Header Specification Version, datatype: string} +# - {name: Header Documentation URL, datatype: string} +# - {name: Info URL, datatype: string} +# - {name: Calibration Documentation URL, datatype: string} +# meta: !!omap +# - __attributes__: {total_available_results: 1} +# - __serialized_columns__: +# Average Spatial Sampling: +# __class__: astropy.units.quantity.Quantity +# unit: !astropy.units.Unit {unit: arcsec} +# value: !astropy.table.SerializedColumn {name: Average Spatial Sampling} +# Average Spectral Sampling: +# __class__: astropy.units.quantity.Quantity +# unit: &id002 !astropy.units.Unit {unit: nm} +# value: !astropy.table.SerializedColumn {name: Average Spectral Sampling} +# Average Temporal Sampling: +# __class__: astropy.units.quantity.Quantity +# unit: &id001 !astropy.units.Unit {unit: s} +# value: !astropy.table.SerializedColumn {name: Average Temporal Sampling} +# Creation Date: +# __class__: astropy.time.core.Time +# format: isot +# in_subfmt: '*' +# out_subfmt: '*' +# precision: 3 +# scale: utc +# value: !astropy.table.SerializedColumn {name: Creation Date} +# Dataset Size: +# __class__: astropy.units.quantity.Quantity +# unit: !astropy.units.Unit {unit: Gibyte} +# value: !astropy.table.SerializedColumn {name: Dataset Size} +# End Time: +# __class__: astropy.time.core.Time +# format: isot +# in_subfmt: '*' +# out_subfmt: '*' +# precision: 3 +# scale: utc +# value: !astropy.table.SerializedColumn {name: End Time} +# Exposure Time: +# __class__: astropy.units.quantity.Quantity +# unit: *id001 +# value: !astropy.table.SerializedColumn {name: Exposure Time} +# Last Updated: +# __class__: astropy.time.core.Time +# format: isot +# in_subfmt: '*' +# out_subfmt: '*' +# precision: 3 +# scale: utc +# value: !astropy.table.SerializedColumn {name: Last Updated} +# Start Time: +# __class__: astropy.time.core.Time +# format: isot +# in_subfmt: '*' +# out_subfmt: '*' +# precision: 3 +# scale: utc +# value: !astropy.table.SerializedColumn {name: Start Time} +# Wavelength: +# __class__: astropy.units.quantity.Quantity +# unit: *id002 +# value: !astropy.table.SerializedColumn {name: Wavelength} +# schema: astropy-2.0 +"Start Time" "End Time" Instrument Wavelength "Bounding Box" "Movie Filename" "Storage Bucket" "Dataset ID" "Dataset Size" "Experiment IDs" "Exposure Time" "Level 0 Frame count" "Primary Experiment ID" "Primary Proposal ID" "Proposal IDs" "Recipe Instance ID" "Recipe Run ID" "Recipe ID" "Full Stokes" "Stokes Parameters" "Target Types" "Creation Date" "Number of Frames" "Average Fried Parameter" "asdf Filename" "Experiment Description" Embargoed "Last Updated" "Preview URL" Downloadable "Has Spectral Axis" "Has Temporal Axis" "Average Spectral Sampling" "Average Spatial Sampling" "Average Temporal Sampling" "Quality Report Filename" "Input Dataset Parameters Part ID" "Input Dataset Observe Frames Part ID" "Input Dataset Calibration Frames Part ID" "Summit Software Version" "Calibration Workflow Name" "Calibration Workflow Version" "HDU Creation Date" "Observing Program Execution ID" "Instrument Program Execution ID" "Header Specification Version" "Header Documentation URL" "Info URL" "Calibration Documentation URL" +2022-10-24T21:28:07.635 2022-10-24T22:20:01.304 VISP [630.2424776472172,631.826964866207] (219.9,-350.33),(189.44,-485.39) pid_1_123/AGLKO/AGLKO.mp4 data AGLKO 8.0 "[""eid_1_123""]" 48.00811267605634 4000 eid_1_123 pid_1_123 "[""pid_1_123""]" 359 587 1 True IQUV "[""unknown""]" 2023-04-21T22:18:17.759 4000 0.0532291613649084 pid_1_123/AGLKO/VISP_L1_20221024T212807_AGLKO.asdf "Solar Orbiter is an ESA/NASA's Sun orbiting mission that was launched in February 2020. The nominal science phase of the mission started in November 2021. The six remote sensing and four in situ instruments on board Solar Orbiter provide high-resolution observation of the solar atmosphere and measure the plasma properties at the satellite. The Solar Orbiter observations allow for the study of the connection between the Sun and the heliosphere. On 13 October 2022, the Solar Orbiter will reach its perihelion 0.32 AU, and on 16 October, it will be in quadrature with Earth with respect to the Sun. As Solar Orbiter moves closer to the Sun-Earth line, we propose to co-observe a single active region with DKIST over multiple days. This will allow us to simultaneously collect some of the highest spatial resolution photospheric, chromospheric (both with the VBI at DKIST), and coronal (with the EUI onboard Solar Orbiter) imaging ever sampled. On top of this, high-resolution spectropolarimetric data sampled by the ViSP and the SPICE instruments will provide context about the local magnetic field and line-of-sight velocities in exquisite detail. Such co-observations will return open-source datasets that will allow researchers to understand better the evolution of active regions (which are, of course, extremely important as the predominant locations where space weather events are driven from) and to probe the flows of mass and energy between different atmospheric layers in unprecedented detail. We propose that these datasets be sampled over 2-3 days, between the 22nd and 27th October 2022." False 2023-05-19T22:14:07.195 https://api.dkistdc.nso.edu/download/movie?datasetId=AGLKO&download=false True True True 0.00162511509639976 0.04160701928854328 1556.834391000005 pid_1_123/AGLKO/AGLKO.pdf 409 456 454 Alakai_8-0 l0_to_l1_visp 2.0.1 2023-04-21T20:11:06.741000 eid_1_123_opcDZ50l_R001.95962.19588221 id.100944.338872 3.5.0 https://docs.dkist.nso.edu/projects/data-products/en/v3.5.0 https://docs.dkist.nso.edu https://docs.dkist.nso.edu/projects/visp/en/v2.0.1/l0_to_l1_visp.html diff --git a/dkist/utils/tests/test_inventory.py b/dkist/utils/tests/test_inventory.py index de6e1a5..f2629ad 100644 --- a/dkist/utils/tests/test_inventory.py +++ b/dkist/utils/tests/test_inventory.py @@ -1,4 +1,7 @@ -from dkist.utils.inventory import _path_format_table, dehumanize_inventory, humanize_inventory +from dkist.data.test import rootdir +from dkist.net.client import DKISTQueryResponseTable +from dkist.utils.inventory import (_path_format_table, dehumanize_inventory, + humanize_inventory, path_format_inventory) def test_humanize_loop(): @@ -114,3 +117,8 @@ def test_path_format_table(): table = table[table.find('\n')+1:] assert table == output + + +def test_cycle_single_row(): + tt = DKISTQueryResponseTable.read(rootdir / "AGLKO-inv.ecsv") + path_format_inventory(dict(tt[0]))

`transfer_complete_datasets` is being weird `transfer_complete_datasets("BKEWK", path="~/dkist_data")`

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

DMTF__python-redfish-library-79

diff --git a/requirements.txt b/requirements.txt index 060d85f..fba487f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -jsonpatch +jsonpatch<=1.24 ; python_version == '3.4' +jsonpatch ; python_version >= '3.5' or python_version == '2.7' jsonpath_rw jsonpointer -urlparse2 \ No newline at end of file diff --git a/setup.py b/setup.py index 344e597..c5ea3b7 100644 --- a/setup.py +++ b/setup.py @@ -24,8 +24,14 @@ setup(name='redfish', packages=find_packages('src'), package_dir={'': 'src'}, install_requires=[ - 'jsonpatch', 'jsonpath_rw', 'jsonpointer', - 'urlparse2', - ]) + ], + extras_require={ + ':python_version == "3.4"': [ + 'jsonpatch<=1.24' + ], + ':python_version >= "3.5" or python_version == "2.7"': [ + 'jsonpatch' + ] + }) diff --git a/src/redfish/ris/rmc_helper.py b/src/redfish/ris/rmc_helper.py index e633a49..da402ab 100644 --- a/src/redfish/ris/rmc_helper.py +++ b/src/redfish/ris/rmc_helper.py @@ -1,5 +1,5 @@ # Copyright Notice: -# Copyright 2016-2019 DMTF. All rights reserved. +# Copyright 2016-2020 DMTF. All rights reserved. # License: BSD 3-Clause License. For full text see link: https://github.com/DMTF/python-redfish-library/blob/master/LICENSE.md # -*- coding: utf-8 -*- @@ -12,9 +12,10 @@ import json import errno import logging import hashlib -import urlparse2 import redfish.rest +from six.moves.urllib.parse import urlparse + from .ris import (RisMonolith) from .sharedtypes import (JSONEncoder) from .config import (AutoConfigParser) @@ -146,7 +147,7 @@ class RmcClient(object): def get_cache_dirname(self): """The rest client's current base URL converted to path""" - parts = urlparse2.urlparse(self.get_base_url()) + parts = urlparse(self.get_base_url()) pathstr = '%s/%s' % (parts.netloc, parts.path) return pathstr.replace('//', '/') diff --git a/tox.ini b/tox.ini index 986f141..b1b8a84 100644 --- a/tox.ini +++ b/tox.ini @@ -14,6 +14,14 @@ commands = --with-timer \ --with-coverage --cover-erase --cover-package=src +[testenv:py27] +deps = + coverage + fixtures + mock + nose + nose-timer + [testenv:pep8] basepython = python3.6 deps = flake8

DMTF/python-redfish-library

58e4a2dfa58cbe51f4a8bef1fa20371d5197c8ed

diff --git a/tests/ris/test_rmc_helper.py b/tests/ris/test_rmc_helper.py new file mode 100644 index 0000000..dbf4a29 --- /dev/null +++ b/tests/ris/test_rmc_helper.py @@ -0,0 +1,29 @@ +# Copyright Notice: +# Copyright 2020 DMTF. All rights reserved. +# License: BSD 3-Clause License. For full text see link: +# https://github.com/DMTF/Redfish-Protocol-Validator/blob/master/LICENSE.md + +import unittest +try: + from unittest import mock +except ImportError: + import mock + +from redfish.ris import rmc_helper + + +class RmcHelper(unittest.TestCase): + def setUp(self): + super(RmcHelper, self).setUp() + + @mock.patch('redfish.rest.v1.HttpClient') + def test_get_cache_dirname(self, mock_http_client): + url = 'http://example.com' + helper = rmc_helper.RmcClient(url=url, username='oper', password='xyz') + mock_http_client.return_value.get_base_url.return_value = url + dir_name = helper.get_cache_dirname() + self.assertEqual(dir_name, 'example.com/') + + +if __name__ == '__main__': + unittest.main()

Remove old library dependency - urlparse2 urlparse2 is an unmaintained library - last commit is 6 years old. The library is not python3 compatible (at least it's dependecy - recordtype library). HP's fork of python-redfish-library dropped urlparse2 last year... https://github.com/HewlettPackard/python-ilorest-library/issues/28 Please, remove this dependency and use built-in functions to parse URL. Thanks.

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

DOV-Vlaanderen__pydov-388

diff --git a/pydov/util/location.py b/pydov/util/location.py index d28fa33..f2b01aa 100644 --- a/pydov/util/location.py +++ b/pydov/util/location.py @@ -29,7 +29,16 @@ class AbstractLocation(object): """ + def _get_id_seed(self): + """Get the seed for generating a random but stable GML ID for this + location. + + Should return the same value for locations considered equal. + """ + raise NotImplementedError('This should be implemented in a subclass.') + def _get_id(self): + random.seed(self._get_id_seed()) random_id = ''.join(random.choice( string.ascii_letters + string.digits) for x in range(8)) return f'pydov.{random_id}' @@ -184,6 +193,7 @@ class Box(AbstractLocation): self.miny = miny self.maxx = maxx self.maxy = maxy + self.epsg = epsg self.element = etree.Element( '{http://www.opengis.net/gml/3.2}Envelope') @@ -203,6 +213,11 @@ class Box(AbstractLocation): upper_corner.text = '{:.06f} {:.06f}'.format(self.maxx, self.maxy) self.element.append(upper_corner) + def _get_id_seed(self): + return ','.join(str(i) for i in [ + self.minx, self.miny, self.maxx, self.miny, self.epsg + ]) + def get_element(self): return self.element @@ -230,6 +245,7 @@ class Point(AbstractLocation): """ self.x = x self.y = y + self.epsg = epsg self.element = etree.Element('{http://www.opengis.net/gml/3.2}Point') self.element.set('srsDimension', '2') @@ -242,6 +258,11 @@ class Point(AbstractLocation): coordinates.text = '{:.06f} {:.06f}'.format(self.x, self.y) self.element.append(coordinates) + def _get_id_seed(self): + return ','.join(str(i) for i in [ + self.x, self.y, self.epsg + ]) + def get_element(self): return self.element diff --git a/pydov/util/owsutil.py b/pydov/util/owsutil.py index 113a85e..fdd5b37 100644 --- a/pydov/util/owsutil.py +++ b/pydov/util/owsutil.py @@ -333,6 +333,28 @@ def set_geometry_column(location, geometry_column): return location.toXML() +def unique_gml_ids(location): + """Make sure the location query has unique GML id's for all features. + Parameters + ---------- + location : etree.ElementTree + XML tree of the location filter. + Returns + ------- + etree.ElementTree + XML tree of the location filter with unique GML ids. + """ + gml_items = location.findall('.//*[@{http://www.opengis.net/gml/3.2}id]') + gml_ids = [i.get('{http://www.opengis.net/gml/3.2}id') for i in gml_items] + + if len(gml_ids) == len(set(gml_ids)): + return location + else: + for ix, item in enumerate(gml_items): + item.set('{http://www.opengis.net/gml/3.2}id', f'pydov.{ix}') + return location + + def wfs_build_getfeature_request(typename, geometry_column=None, location=None, filter=None, sort_by=None, propertyname=None, max_features=None, start_index=0, @@ -439,6 +461,7 @@ def wfs_build_getfeature_request(typename, geometry_column=None, location=None, if location is not None: location = set_geometry_column(location, geometry_column) + location = unique_gml_ids(location) filter_parent.append(location) if filter is not None or location is not None:

DOV-Vlaanderen/pydov

33c8b897494baba50aeea24b4421a407e40a057f

diff --git a/tests/test_util_location.py b/tests/test_util_location.py index bed8407..292dcc2 100644 --- a/tests/test_util_location.py +++ b/tests/test_util_location.py @@ -25,7 +25,8 @@ from tests.abstract import clean_xml class TestLocation(object): """Class grouping tests for the AbstractLocation subtypes.""" - def test_gml_id(self): + def test_gml_id_unique(self): + """Test whether GML id's for two different locations are unique.""" box1 = Box(94720, 186910, 112220, 202870) id1 = box1.get_element().get('{http://www.opengis.net/gml/3.2}id') @@ -36,6 +37,18 @@ class TestLocation(object): assert id2.startswith('pydov') assert id1 != id2 + def test_gml_id_stable(self): + """Test whether GML id's for two equal locations are the same.""" + box1 = Box(94720, 186910, 112220, 202870) + id1 = box1.get_element().get('{http://www.opengis.net/gml/3.2}id') + + box2 = Box(94720, 186910, 112220, 202870) + id2 = box2.get_element().get('{http://www.opengis.net/gml/3.2}id') + + assert id1.startswith('pydov') + assert id2.startswith('pydov') + assert id1 == id2 + def test_box(self, mp_gml_id): """Test the default Box type. diff --git a/tests/test_util_owsutil.py b/tests/test_util_owsutil.py index 8d15c3d..801f347 100644 --- a/tests/test_util_owsutil.py +++ b/tests/test_util_owsutil.py @@ -3,13 +3,13 @@ import copy import pytest from owslib.etree import etree -from owslib.fes2 import FilterRequest, PropertyIsEqualTo, SortBy, SortProperty +from owslib.fes2 import FilterRequest, PropertyIsEqualTo, SortBy, SortProperty, Or from owslib.iso import MD_Metadata from owslib.util import nspath_eval from pydov.util import owsutil from pydov.util.dovutil import build_dov_url -from pydov.util.location import Box, Within +from pydov.util.location import Box, Within, WithinDistance from tests.abstract import clean_xml location_md_metadata = 'tests/data/types/boring/md_metadata.xml' @@ -406,6 +406,41 @@ class TestWfsGetFeatureRequest(object): '214775.000000</gml:upperCorner></gml:Envelope></fes:Within></fes' ':Filter></wfs:Query></wfs:GetFeature>') + def test_wfs_build_getfeature_request_gml_id_stable(self): + """Test the owsutil.wfs_build_getfeature_request method with a + typename, box and geometry_column. + Test whether the XML of the WFS GetFeature call is stable. + """ + xml1 = owsutil.wfs_build_getfeature_request( + 'dov-pub:Boringen', + location=Within(Box(151650, 214675, 151750, 214775)), + geometry_column='geom') + + xml2 = owsutil.wfs_build_getfeature_request( + 'dov-pub:Boringen', + location=Within(Box(151650, 214675, 151750, 214775)), + geometry_column='geom') + + assert etree.tostring(xml1) == etree.tostring(xml2) + + def test_wfs_build_getfeature_request_gml_id_unique(self): + """Test the owsutil.wfs_build_getfeature_request method with a + typename, two boxes and geometry_column. + Test whether the GML ids in the XML of the WFS GetFeature are unique. + """ + xml = owsutil.wfs_build_getfeature_request( + 'dov-pub:Boringen', + location=Or([ + Within(Box(100000, 120000, 200000, 220000)), + WithinDistance(Box(100000, 120000, 200000, 220000), 10) + ]), + geometry_column='geom') + + gml_items = xml.findall('.//*[@{http://www.opengis.net/gml/3.2}id]') + gml_ids = [i.get('{http://www.opengis.net/gml/3.2}id') for i in gml_items] + + assert len(gml_ids) == len(set(gml_ids)) + def test_wfs_build_getfeature_request_propertyname(self): """Test the owsutil.wfs_build_getfeature_request method with a list of propertynames.

Box and Point locations do not serialize into stable XML <!-- You can ask questions about the DOV webservices or about the `pydov` package. If you have a question about the `pydov` Python package, please use following template. --> * PyDOV version: master * Python version: 3.10.6 * Operating System: ubuntu ### Description The pydov.util.location.Box and pydov.util.location.Point classes use a random gml:id since pydov 3.0.0 and GML 3.2. This has as a consequence that they do not serialize into stable XML anymore, causing issues in the RepeatableLog(Recorder|Replayer). ### What I Did ```python from pydov.util.location import Point from owslib.etree import etree p1 = Point(10, 10) p1_xml = etree.tostring(p1.get_element()) print(p1_xml) p2 = Point(10, 10) p2_xml = etree.tostring(p2.get_element()) print(p2_xml) print('XML is equal:', p1_xml == p2_xml) ``` ``` b'<gml32:Point xmlns:gml32="http://www.opengis.net/gml/3.2" srsDimension="2" srsName="http://www.opengis.net/gml/srs/epsg.xml#31370" gml32:id="pydov.1D2pYSHo"><gml32:pos>10.000000 10.000000</gml32:pos></gml32:Point>' b'<gml32:Point xmlns:gml32="http://www.opengis.net/gml/3.2" srsDimension="2" srsName="http://www.opengis.net/gml/srs/epsg.xml#31370" gml32:id="pydov.tlRGFRLY"><gml32:pos>10.000000 10.000000</gml32:pos></gml32:Point>' XML is equal: False ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DarkEnergySurvey__mkauthlist-16

diff --git a/.gitignore b/.gitignore index 5b6ffac..086cdcc 100644 --- a/.gitignore +++ b/.gitignore @@ -10,4 +10,5 @@ dist *.out *.aux *.log -*.spl \ No newline at end of file +*.spl +*.cls \ No newline at end of file diff --git a/data/author_order.csv b/data/author_order.csv index 3749293..de4b8f3 100644 --- a/data/author_order.csv +++ b/data/author_order.csv @@ -1,5 +1,6 @@ Melchior Sheldon, Erin +#Commented, Name Drlica-Wagner Rykoff Plazas Malagón \ No newline at end of file diff --git a/data/example_author_list.csv b/data/example_author_list.csv index 4efafbb..ccbc4ed 100644 --- a/data/example_author_list.csv +++ b/data/example_author_list.csv @@ -4,7 +4,7 @@ Drlica-Wagner,Alex,A.~Drlica-Wagner,False,"Fermi National Accelerator Laboratory Rykoff,Eli,E.~S.~Rykoff,False,"Kavli Institute for Particle Astrophysics \& Cosmology, P. O. Box 2450, Stanford University, Stanford, CA 94305, USA","Data quality expert", Rykoff,Eli,E.~S.~Rykoff,False,"SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA","Data quality expert", Sheldon,Erin,E.~Sheldon,False,"Brookhaven National Laboratory, Bldg 510, Upton, NY 11973, USA","Data backend", -Abbott,Tim,T. M. C.~Abbott,True,"Cerro Tololo Inter-American Observatory, National Optical Astronomy Observatory, Casilla 603, La Serena, Chile",, +Zhang,Yuanyuan,Y.~Zhang,True,"Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, IL 60510, USA",, Abdalla,Filipe,F.~B.~Abdalla,True,"Department of Physics \& Astronomy, University College London, Gower Street, London, WC1E 6BT, UK",, Abdalla,Filipe,F.~B.~Abdalla,True,"Department of Physics and Electronics, Rhodes University, PO Box 94, Grahamstown, 6140, South Africa",, Allam,Sahar,S.~Allam,True,"Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, IL 60510, USA",, @@ -66,4 +66,4 @@ Tarle,Gregory,G.~Tarle,True,"Department of Physics, University of Michigan, Ann Vikram,Vinu,V.~Vikram,True,"Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA",, Walker,Alistair,A.~R.~Walker,True,"Cerro Tololo Inter-American Observatory, National Optical Astronomy Observatory, Casilla 603, La Serena, Chile",, Wester,William,W.~Wester,True,"Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, IL 60510, USA",, -Zhang,Yuanyuan,Y.~Zhang,True,"Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, IL 60510, USA",, \ No newline at end of file +Abbott,Tim,T.~M.~C.~Abbott,True,"Cerro Tololo Inter-American Observatory, National Optical Astronomy Observatory, Casilla 603, La Serena, Chile",, diff --git a/mkauthlist/mkauthlist.py b/mkauthlist/mkauthlist.py index 1393e93..4745d3a 100755 --- a/mkauthlist/mkauthlist.py +++ b/mkauthlist/mkauthlist.py @@ -134,7 +134,7 @@ def write_contributions(filename,data): logging.info('Writing contribution file: %s'%filename) - out = open(filename,'wb') + out = open(filename,'w') out.write(output) out.close() @@ -374,7 +374,7 @@ if __name__ == "__main__": affidict = odict() authdict = odict() - # Hack for Munich affiliation... + # Hack for umlauts in affiliations... for k,v in HACK.items(): logging.warn("Hacking '%s' ..."%k) select = (np.char.count(data['Affiliation'],k) > 0) @@ -382,13 +382,18 @@ if __name__ == "__main__": # Pre-sort the csv file by the auxiliary file if args.aux is not None: - aux = [r for r in csv.DictReader(open(args.aux),['Lastname','Firstname'])] + auxcols = ['Lastname','Firstname'] + aux = [[r[c] for c in auxcols] for r in + csv.DictReader(open(args.aux),fieldnames=auxcols) + if not r[auxcols[0]].startswith('#')] + aux = np.rec.fromrecords(aux,names=auxcols) if len(np.unique(aux)) != len(aux): logging.error('Non-unique names in aux file.') print(open(args.aux).read()) raise Exception() - - raw = np.array(zip(data['Lastname'],range(len(data)))) + + # Ugh, python2/3 compatibility + raw = np.array(list(zip(data['Lastname'],list(range(len(data)))))) order = np.empty((0,2),dtype=raw.dtype) for r in aux: lastname = r['Lastname']

DarkEnergySurvey/mkauthlist

15365e9ab90a623e3109739dd3f9c7d1fbb91fb7

diff --git a/tests/test_authlist.py b/tests/test_authlist.py index 958472e..cb57ba3 100644 --- a/tests/test_authlist.py +++ b/tests/test_authlist.py @@ -9,7 +9,7 @@ import logging import subprocess import unittest -class TestAuthlistFunc(unittest.TestCase): +class TestAuthlist(unittest.TestCase): def setUp(self): self.csv = 'example_author_list.csv' @@ -32,12 +32,13 @@ class TestAuthlistFunc(unittest.TestCase): # shutil.copy(os.path.join('data',filename),'.') def tearDown(self): - self.clean = [self.csv,self.tex,self.aux,self.out,self.log,self.bib,self.pdf,self.order] + self.clean = [self.csv,self.tex,self.aux,self.out,self.log,self.bib, + self.pdf,self.order,self.cntrb] self.clean += self.cls cmd = "rm -f "+' '.join(self.clean) print(cmd) - subprocess.check_output(cmd,shell=True) + #subprocess.check_output(cmd,shell=True) def latex(self, tex=None, pdf=None): if tex is None: tex = self.tex @@ -49,35 +50,76 @@ class TestAuthlistFunc(unittest.TestCase): shutil.copy(tex.replace('.tex','.pdf'),pdf) def test_mkauthlist(self): + """Run 'vanilla' mkauthlist.""" cmd = "mkauthlist -f --doc %(csv)s %(tex)s"%self.files print(cmd) subprocess.check_output(cmd,shell=True) self.latex(pdf='test_mkauthlist.pdf') - def test_author_order(self): + def test_order(self): + """Explicitly order some authors.""" cmd = "mkauthlist -f --doc %(csv)s %(tex)s -a %(order)s"%self.files print(cmd) subprocess.check_output(cmd,shell=True) - self.latex(pdf='test_order.pdf') + + # Shouldn't be any need to build the file + #self.latex(pdf='test_order.pdf') + + with open(self.tex,'r') as f: + authors = [l for l in f.readlines() if l.startswith('\\author')] + self.assertEqual(authors[1],'\\author{E.~Sheldon}\n') + self.assertEqual(authors[4],'\\author{A.~A.~Plazas}\n') + self.assertEqual(authors[5],'\\author{Y.~Zhang}\n') + self.assertEqual(authors[-1],'\\author{T.~M.~C.~Abbott}\n') def test_contribution(self): + """Write author contributions.""" cmd = "mkauthlist -f --doc %(csv)s %(tex)s --cntrb %(cntrb)s"%self.files print(cmd) subprocess.check_output(cmd,shell=True) - self.latex(pdf='test_contrib.pdf') - if not os.path.exists(self.cntrb): - msg = "No contributions found" - raise Exception(msg) - - with open(self.cntrb) as cntrb: - lines = cntrb.readlines() - msg = "Unexpected author contributions: " - if not lines[0].split()[0] == 'Author': - raise Exception(msg+'\n'+lines[0]) - msg = "Unexpected author contributions" - if not lines[1].split()[0] == 'P.~Melchior:': - raise Exception(msg+'\n'+lines[1]) + # Shouldn't be any need to build the file + #self.latex(pdf='test_contrib.pdf') + + with open(self.cntrb,'r') as f: + lines = f.readlines() + self.assertEqual(lines[0],'Author contributions are listed below. \\\\\n') + self.assertEqual(lines[1],'P.~Melchior: Lead designer and author \\\\\n') + self.assertEqual(lines[-1],'T.~M.~C.~Abbott: \\\\\n') + + def test_sort(self): + """Sort all authors alphabetically.""" + cmd = "mkauthlist -f --doc %(csv)s %(tex)s --sort"%self.files + print(cmd) + subprocess.check_output(cmd,shell=True) + + with open(self.tex,'r') as f: + authors = [l for l in f.readlines() if l.startswith('\\author')] + self.assertEqual(authors[0],'\\author{T.~M.~C.~Abbott}\n') + self.assertEqual(authors[-1],'\\author{Y.~Zhang}\n') + + def test_sort_order(self): + """Order some authors, sort the rest.""" + cmd = "mkauthlist -f --doc %(csv)s %(tex)s --sort -a %(order)s"%self.files + print(cmd) + subprocess.check_output(cmd,shell=True) + + with open(self.tex,'r') as f: + authors = [l for l in f.readlines() if l.startswith('\\author')] + self.assertEqual(authors[1],'\\author{E.~Sheldon}\n') + self.assertEqual(authors[-1],'\\author{Y.~Zhang}\n') + + def test_sort_builder(self): + """Sort builders, but leave other authors unchanged.""" + cmd = "mkauthlist -f --doc %(csv)s %(tex)s -sb"%self.files + print(cmd) + subprocess.check_output(cmd,shell=True) + + with open(self.tex,'r') as f: + authors = [l for l in f.readlines() if l.startswith('\\author')] + self.assertEqual(authors[3],'\\author{E.~Sheldon}\n') + self.assertEqual(authors[4],'\\author{T.~M.~C.~Abbott}\n') + self.assertEqual(authors[-1],'\\author{Y.~Zhang}\n') if __name__ == "__main__": unittest.main() diff --git a/tests/test_journals.py b/tests/test_journals.py index 09c7f86..4833263 100755 --- a/tests/test_journals.py +++ b/tests/test_journals.py @@ -9,7 +9,7 @@ import logging import subprocess import unittest -class TestJournalFunc(unittest.TestCase): +class TestJournal(unittest.TestCase): def setUp(self): self.csv = 'example_author_list.csv'

Python 3 byte strings The Python 3 `str` object is based on Unicode, which means that `file.write(..., 'wb')` doesn't work anymore. We need to change this, but we should probably also understand why we were specifying `'wb'` in the first place. Some documentation on the Python 3 change: https://www.python.org/dev/peps/pep-0404/#strings-and-bytes https://stackoverflow.com/a/33054552/4075339 And the specific place that needs to be changed: [L137](https://github.com/DarkEnergySurvey/mkauthlist/blob/1fb62affeaa73c5192cce84323f77f66d466306a/mkauthlist/mkauthlist.py#L137)

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DarkEnergySurvey__mkauthlist-29

diff --git a/data/author_order.csv b/data/author_order.csv index de4b8f3..e3bd9af 100644 --- a/data/author_order.csv +++ b/data/author_order.csv @@ -3,4 +3,5 @@ Sheldon, Erin #Commented, Name Drlica-Wagner Rykoff -Plazas Malagón \ No newline at end of file +Plazas Malagón +Sanchez, Carles diff --git a/data/example_author_list.csv b/data/example_author_list.csv index b298675..b765fd0 100644 --- a/data/example_author_list.csv +++ b/data/example_author_list.csv @@ -56,6 +56,7 @@ Ogando,Ricardo,R.~Ogando,True,"Laborat\'orio Interinstitucional de e-Astronomia Ogando,Ricardo,R.~Ogando,True,"Observat\'orio Nacional, Rua Gal. Jos\'e Cristino 77, Rio de Janeiro, RJ - 20921-400, Brazil",, Plazas Malagón,Andrés,A.~A.~Plazas,True,"Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., Pasadena, CA 91109, USA",, Romer,Kathy,A.~K.~Romer,True,"Department of Physics and Astronomy, Pevensey Building, University of Sussex, Brighton, BN1 9QH, UK",, +Sanchez,Carles,C.~S{\'a}nchez,True,"Institut de F\'{\i}sica d'Altes Energies (IFAE), The Barcelona Institute of Science and Technology, Campus UAB, 08193 Bellaterra (Barcelona) Spain",, Sanchez,Eusebio,E.~Sanchez,True,"Centro de Investigaciones Energ\'eticas, Medioambientales y Tecnol\'ogicas (CIEMAT), Madrid, Spain",, Scarpine,Vic,V.~Scarpine,True,"Fermi National Accelerator Laboratory, P. O. Box 500, Batavia, IL 60510, USA",, Sevilla,Ignacio,I.~Sevilla-Noarbe,True,"Centro de Investigaciones Energ\'eticas, Medioambientales y Tecnol\'ogicas (CIEMAT), Madrid, Spain",, diff --git a/mkauthlist/mkauthlist.py b/mkauthlist/mkauthlist.py index ca31101..4992446 100755 --- a/mkauthlist/mkauthlist.py +++ b/mkauthlist/mkauthlist.py @@ -358,27 +358,36 @@ if __name__ == "__main__": print(open(args.aux).read()) raise Exception() - # Ugh, python2/3 compatibility - raw = np.array(list(zip(data['Lastname'],list(range(len(data)))))) - order = np.empty((0,2),dtype=raw.dtype) + # This is probably not the cleanest way to do this... + raw = np.vstack([data['Lastname'],data['Firstname'],np.arange(len(data))]).T + order = np.empty((0,raw.shape[-1]),dtype=raw.dtype) for r in aux: - lastname = r['Lastname'] + lastname = r['Lastname'].strip() + firstname = r['Firstname'] match = (raw[:,0] == lastname) - if not np.any(match): - logging.warn("Auxiliary name %s not found"%lastname) + + if firstname: + firstname = r['Firstname'].strip() + match &= (raw[:,1] == firstname) + + # Check that match found + if np.sum(match) < 1: + msg = "Auxiliary name not found: %s"%(lastname) + if firstname: msg += ', %s'%firstname + logging.warn(msg) continue - # Eventually deal with duplicate names... but for now throw an error. - firstnames = np.unique(data['Firstname'][data['Lastname']==lastname]) - if not len(firstnames) == 1: - logging.error('Non-unique last name; order by hand.') - for f in firstnames: - print(f) - raise Exception() + # Check unique firstname + if not len(np.unique(raw[match][:,1])) == 1: + msg = "Non-unique name: %s"%(lastname) + if firstname: msg += ', %s'%firstname + logging.error(msg) + raise ValueError(msg) + order = np.vstack([order,raw[match]]) raw = raw[~match] order = np.vstack([order,raw]) - data = data[order[:,1].astype(int)] + data = data[order[:,-1].astype(int)] ### REVTEX ### if cls in ['revtex','aastex61']:

DarkEnergySurvey/mkauthlist

2644d26323e073616ccad45dea426bb9c485ee3a

diff --git a/tests/test_authlist.py b/tests/test_authlist.py index e879ff7..15ffb44 100644 --- a/tests/test_authlist.py +++ b/tests/test_authlist.py @@ -70,7 +70,7 @@ class TestAuthlist(unittest.TestCase): authors = [l for l in f.readlines() if l.startswith('\\author')] self.assertEqual(authors[1],'\\author{E.~Sheldon}\n') self.assertEqual(authors[4],'\\author{A.~A.~Plazas}\n') - self.assertEqual(authors[5],'\\author{Y.~Zhang}\n') + self.assertEqual(authors[6],'\\author{Y.~Zhang}\n') self.assertEqual(authors[-1],'\\author{T.~M.~C.~Abbott}\n') def test_contribution(self):

Ordering with duplicate lastnames We currently throw an error when ordering on non-unique last names. We should be able to explicitly use author first names in ordering, but we currently don't require first names be included in the ordering file. This was causing issues for @joezuntz.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DataBiosphere__newt-transformer-24

diff --git a/newt/transform/gen3old.py b/newt/transform/gen3old.py index 2c1ac2f..6c0c940 100644 --- a/newt/transform/gen3old.py +++ b/newt/transform/gen3old.py @@ -34,13 +34,17 @@ class Gen3Transformer(AbstractTransformer): @staticmethod def _build_metadata_dict(input_metadata): - def build_metadata_field(metadata, field_name: str): + def build_metadata_field(metadata, field_name: str, key: str): """ Builds dict from metadata where key is node_id, value is the corresponding metadata """ - return {entry['node_id']: entry for entry in metadata[field_name]} + return {entry[key]: entry for entry in metadata[field_name]} for field in input_metadata: - input_metadata[field] = build_metadata_field(input_metadata, field) + if field == 'project' or field == 'program': + key = 'id' + else: + key = 'node_id' + input_metadata[field] = build_metadata_field(input_metadata, field, key) return input_metadata def __init__(self, input_dict: dict) -> None: diff --git a/newt/transform/gen3standard.py b/newt/transform/gen3standard.py index 5970385..c68389d 100644 --- a/newt/transform/gen3standard.py +++ b/newt/transform/gen3standard.py @@ -38,7 +38,8 @@ class Bundle(dict): self['data_bundle'] = self.data_bundle self['data_objects'] = self.data_objects - def add_metadata_field(self, metadata_source: dict, + def add_metadata_field(self, + metadata_source: dict, source_field_name: str, linked_field_name: str, link_name: str): @@ -57,7 +58,6 @@ class Bundle(dict): linked_field_dict = metadata_source[linked_field_name][linked_field_key] # Add it to this bundle's metadata self.metadata[linked_field_name] = linked_field_dict - else: # When the item is a child of an existing field # Get the ID from the item we already have @@ -104,13 +104,18 @@ class Gen3Transformer(AbstractTransformer): @staticmethod def _build_metadata_dict(input_metadata): - def build_metadata_field(metadata, field_name: str): + def build_metadata_field(metadata, field_name: str, key: str): """ Builds dict from metadata where key is node_id, value is the corresponding metadata """ - return {entry['node_id']: entry for entry in metadata[field_name]} + return {entry[key]: entry for entry in metadata[field_name]} for field in input_metadata: - input_metadata[field] = build_metadata_field(input_metadata, field) + # Working around details of gen3 data model + if field == 'project' or field == 'program': + key = 'id' + else: + key = 'node_id' + input_metadata[field] = build_metadata_field(input_metadata, field, key) return input_metadata def __init__(self, input_dict: dict) -> None: @@ -124,7 +129,8 @@ class Gen3Transformer(AbstractTransformer): MetadataLink('aliquot', 'sample', 'samples.id#1'), MetadataLink('sample', 'case', 'cases.id'), MetadataLink('case', 'study', 'studies.id#1'), - MetadataLink('demographic', 'case', 'cases.id') + MetadataLink('demographic', 'case', 'cases.id'), + MetadataLink('study', 'project', 'projects.id') ] def _build_bundle(self, metadata_dict: dict): diff --git a/scripts/data_bleach.py b/scripts/data_bleach.py index c14fc27..fe3ec49 100644 --- a/scripts/data_bleach.py +++ b/scripts/data_bleach.py @@ -13,6 +13,7 @@ PUBLIC_FIELDS = [x.split('.') for x in [ "sample.biospecimen_type", "sample.composition", "sample.node_id", + "sample.submitter_id", "demographic.bmi", "demographic.weight", "demographic.height", @@ -24,7 +25,9 @@ PUBLIC_FIELDS = [x.split('.') for x in [ "aliquot.experimental_strategy", "aliquot.analyte_isolation_method", "sample.biospecimen_anatomic_site_detail", - "sample.biospecimen_anatomic_site"]] + "sample.biospecimen_anatomic_site", + "project.code", + "project.name"]] def error(*args, **kwargs):

DataBiosphere/newt-transformer

619bca38de35f68d12168d198892f1de3cfd40c3

diff --git a/tests/test_data/topmed-public.json b/tests/test_data/topmed-public.json index d2f5b41..61fce82 100644 --- a/tests/test_data/topmed-public.json +++ b/tests/test_data/topmed-public.json @@ -1,21833 +1,1 @@ -{ - "data_objects": [ - { - "checksums": [ - { - "checksum": "7af0014daca79bcc4bbed32fc128c066", - "type": "md5" - } - ], - "created": "2018-05-26T13:37:25.618273", - "id": "dg.4503/887388d7-a974-4259-86af-f5305172363d", - "name": "", - "size": "20699570093", - "updated": "2018-05-26T13:37:25.618283", - "urls": [ - { - "url": "s3://cgp-commons-public/topmed_open_access/3d9dd79c-e4e8-5d59-ac44-65c907c22a2e/NWD905240.recab.cram" - }, - { - "url": "gs://cgp-commons-multi-region-public/topmed_open_access/3d9dd79c-e4e8-5d59-ac44-65c907c22a2e/NWD905240.recab.cram" - } - ], - "version": "aa94f120" - }, - { - "checksums": [ - { - "checksum": "f9e72bdf25bf4b4f0e581d9218fec2eb", - "type": "md5" - } - ], - "created": "2018-05-26T13:37:19.491772", - "id": 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Change data_bleach.py to retain sample.submitter_id The field `sample.submitter_id` is a useful value that should not be sanitized (cleared) by `data_bleach.py`

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataBiosphere__newt-transformer-28

diff --git a/newt/main.py b/newt/main.py index f44243e..3910850 100644 --- a/newt/main.py +++ b/newt/main.py @@ -16,9 +16,9 @@ def open_json_file(json_path): return json.load(fp) -def write_output(bundles: typing.Iterator[Bundle], out_file): +def write_output(bundles: typing.Iterator[Bundle], out_file, pretty_print): with open(out_file, 'w') as fp: - json.dump(list(bundles), fp) + json.dump(list(bundles), fp, indent=2 if pretty_print else None) def add_parser_to_subparser(sub_parser, parse_name, parse_help): @@ -29,6 +29,8 @@ def add_parser_to_subparser(sub_parser, parse_name, parse_help): parser.add_argument('--output-json', dest='output_json', help='where to write transformed output.', required=False, default='out.json') + parser.add_argument('--pp', action='store_true', default=False, + help='pretty print output json.') def main(argv=None): @@ -61,4 +63,4 @@ def main(argv=None): raise ValueError(f'Invalid metadata source format {options.transform_source}') bundle_iterator = transformer.transform() - write_output(bundle_iterator, options.output_json) + write_output(bundle_iterator, options.output_json, options.pp) diff --git a/newt/transform/gen3standard.py b/newt/transform/gen3standard.py index c68389d..4c48f91 100644 --- a/newt/transform/gen3standard.py +++ b/newt/transform/gen3standard.py @@ -51,7 +51,10 @@ class Bundle(dict): :param linked_field_name: the metadata field that is linked to :param link_name: the actual name of the link in the source_field. Usually there is some subtle variation """ - if source_field_name in self.metadata.keys(): + if linked_field_name == 'program': + # Since gen3 export exports a single program, we just grab the only value + self.metadata[linked_field_name] = list(metadata_source[linked_field_name].values())[0] + elif source_field_name in self.metadata.keys(): # Get the id of the specific item we want to add linked_field_key = self.metadata[source_field_name]['link_fields'][link_name] # Get the dictionary that goes with that specific item @@ -130,7 +133,8 @@ class Gen3Transformer(AbstractTransformer): MetadataLink('sample', 'case', 'cases.id'), MetadataLink('case', 'study', 'studies.id#1'), MetadataLink('demographic', 'case', 'cases.id'), - MetadataLink('study', 'project', 'projects.id') + MetadataLink('study', 'project', 'projects.id'), + MetadataLink('project', 'program', 'id') ] def _build_bundle(self, metadata_dict: dict): diff --git a/scripts/data_bleach.py b/scripts/data_bleach.py index 8a9be24..c2f17e2 100644 --- a/scripts/data_bleach.py +++ b/scripts/data_bleach.py @@ -26,8 +26,9 @@ PUBLIC_FIELDS = [x.split('.') for x in [ "aliquot.analyte_isolation_method", "sample.biospecimen_anatomic_site_detail", "sample.biospecimen_anatomic_site", - "project.code", - "project.name"]] + "project.name", + "program.code", + "project.dbgap_accession_number"]] def error(*args, **kwargs):

DataBiosphere/newt-transformer

9ca346cb3dcdb18535e06c95fee10470f72d60cd

diff --git a/tests/schemas.py b/tests/schemas.py index 1acc954..8ac2944 100644 --- a/tests/schemas.py +++ b/tests/schemas.py @@ -124,7 +124,7 @@ data_object_schema = { data_bundle = { "type": "object", # TODO: required, but we don't have checksums for bundles - 'required': ['data_object_ids', 'created', 'updated', 'version'], # , 'checksums'], + 'required': ['data_object_ids', 'created', 'updated', 'version', 'user_metadata'], # , 'checksums'], "properties": { "id": { "type": "string", @@ -211,8 +211,14 @@ data_bundle = { "user_metadata": { "type": "object", "additionalProperties": True, - "description": "OPTIONAL\n" - "A set of key-value pairs that represent metadata provided by the uploader." + "description": "REQUIRED\n" + "A set of key-value pairs that represent metadata provided by the uploader.", + 'required': ['project', 'program'], + "properties": { + "project": {"type": "object"}, + "program": {"type": "object"} + + } } } } diff --git a/tests/test_all.py b/tests/test_all.py index 03f3f9b..501d145 100644 --- a/tests/test_all.py +++ b/tests/test_all.py @@ -83,7 +83,7 @@ class TestSheepdogGen3TransformingStandard(AbstractTransformerTest, unittest.Tes def test_sheepdog_gen3_transforming(self): message('Run the transformer on sheepdog\'s output') - argv = ['new', str(self.test_file), '--output-json', str(self.out_file)] + argv = ['new', str(self.test_file), '--output-json', str(self.out_file), '--pp'] message(f'Passing args: {" ".join(argv)}') main(argv) diff --git a/tests/test_data/topmed-public.json b/tests/test_data/topmed-public.json index 61fce82..d0a64e6 100644 --- a/tests/test_data/topmed-public.json +++ b/tests/test_data/topmed-public.json @@ -1,1 +1,1 @@ -{"metadata": {"medication": [], "electrocardiogram_test": [], "aggregated_snp_array": [], "medical_history": [], "sample": [{"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "HG01110_sample", "hours_to_collection": "", "prosector_notes": "", 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"biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": "31f6dc4c-a8e7-402e-a292-f6de85287a58", "cases.submitter_id": "NA19238"}, "method_of_sample_procurement": "", "node_id": "e450679d-0c17-467c-8fd5-dba1510f041b", "collection_site": "", "freezing_method": "", "biospecimen_physical_site": "", "biospecimen_type": "Normal - other", "preservation_method": "", "tissue_type": "", "biospecimen_anatomic_site_uberon_id": "", "hours_to_sample_procurement": ""}, {"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "HG01111_sample", "hours_to_collection": "", "prosector_notes": "", "autolysis_score": "", "collection_kit": "", "biospecimen_anatomic_site_detail": "", "biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": "6d13d82a-aa6c-4a3c-8f3d-528899391043", "cases.submitter_id": "HG01111"}, "method_of_sample_procurement": "", "node_id": "f2555751-d329-4b81-a0e9-7989562c860d", "collection_site": "", "freezing_method": "", "biospecimen_physical_site": "", "biospecimen_type": "Normal - blood", "preservation_method": "", "tissue_type": "", "biospecimen_anatomic_site_uberon_id": "", "hours_to_sample_procurement": ""}, {"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "HG01249_sample", "hours_to_collection": "", "prosector_notes": "", "autolysis_score": "", "collection_kit": "", "biospecimen_anatomic_site_detail": "", "biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": 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Add `program` metadata The Gen3 data model provides a `program` object, in addition to `project` and `study`. Currently the `newt` output includes `project` and `study` yet not `program`. The `program` object should be included in the `newt` output for indexing/display purposes. ┆Issue is synchronized with this [JIRA Task](https://ucsc-cgl.atlassian.net/browse/NEWT-23) ┆Project Name: CGP-Newt ┆Issue Number: NEWT-23

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataBiosphere__newt-transformer-32

diff --git a/newt/main.py b/newt/main.py index f44243e..3910850 100644 --- a/newt/main.py +++ b/newt/main.py @@ -16,9 +16,9 @@ def open_json_file(json_path): return json.load(fp) -def write_output(bundles: typing.Iterator[Bundle], out_file): +def write_output(bundles: typing.Iterator[Bundle], out_file, pretty_print): with open(out_file, 'w') as fp: - json.dump(list(bundles), fp) + json.dump(list(bundles), fp, indent=2 if pretty_print else None) def add_parser_to_subparser(sub_parser, parse_name, parse_help): @@ -29,6 +29,8 @@ def add_parser_to_subparser(sub_parser, parse_name, parse_help): parser.add_argument('--output-json', dest='output_json', help='where to write transformed output.', required=False, default='out.json') + parser.add_argument('--pp', action='store_true', default=False, + help='pretty print output json.') def main(argv=None): @@ -61,4 +63,4 @@ def main(argv=None): raise ValueError(f'Invalid metadata source format {options.transform_source}') bundle_iterator = transformer.transform() - write_output(bundle_iterator, options.output_json) + write_output(bundle_iterator, options.output_json, options.pp) diff --git a/newt/transform/gen3standard.py b/newt/transform/gen3standard.py index c68389d..4c48f91 100644 --- a/newt/transform/gen3standard.py +++ b/newt/transform/gen3standard.py @@ -51,7 +51,10 @@ class Bundle(dict): :param linked_field_name: the metadata field that is linked to :param link_name: the actual name of the link in the source_field. Usually there is some subtle variation """ - if source_field_name in self.metadata.keys(): + if linked_field_name == 'program': + # Since gen3 export exports a single program, we just grab the only value + self.metadata[linked_field_name] = list(metadata_source[linked_field_name].values())[0] + elif source_field_name in self.metadata.keys(): # Get the id of the specific item we want to add linked_field_key = self.metadata[source_field_name]['link_fields'][link_name] # Get the dictionary that goes with that specific item @@ -130,7 +133,8 @@ class Gen3Transformer(AbstractTransformer): MetadataLink('sample', 'case', 'cases.id'), MetadataLink('case', 'study', 'studies.id#1'), MetadataLink('demographic', 'case', 'cases.id'), - MetadataLink('study', 'project', 'projects.id') + MetadataLink('study', 'project', 'projects.id'), + MetadataLink('project', 'program', 'id') ] def _build_bundle(self, metadata_dict: dict): diff --git a/scripts/data_bleach.py b/scripts/data_bleach.py index 8a9be24..6f51f70 100644 --- a/scripts/data_bleach.py +++ b/scripts/data_bleach.py @@ -26,8 +26,9 @@ PUBLIC_FIELDS = [x.split('.') for x in [ "aliquot.analyte_isolation_method", "sample.biospecimen_anatomic_site_detail", "sample.biospecimen_anatomic_site", - "project.code", - "project.name"]] + "project.name", + "program.code", + "project.dbgap_accession_number"]] def error(*args, **kwargs): @@ -39,6 +40,23 @@ def is_protected_field(key, context): return not any([context + [key] == field for field in PUBLIC_FIELDS]) +def get_sanitized_value(value): + result = None + if value is None: + result = None + elif isinstance(value, str): + result = "--------" if len(value) > 0 else "" + elif isinstance(value, bool): + result = False + elif isinstance(value, float): + result = 0.0 + elif isinstance(value, int): + result = 0 + elif isinstance(value, list): + result = [] + return result + + def recursive_clear(d, context=None): """ clear the values of a dictionary unless the value is another dictionary @@ -53,7 +71,7 @@ def recursive_clear(d, context=None): recursive_clear(val, context=context + [key]) else: if is_protected_field(key, context): - d[key] = '' + d[key] = get_sanitized_value(d[key]) def sanitize_bundle(bundle):

DataBiosphere/newt-transformer

9ca346cb3dcdb18535e06c95fee10470f72d60cd

diff --git a/tests/schemas.py b/tests/schemas.py index 1acc954..8ac2944 100644 --- a/tests/schemas.py +++ b/tests/schemas.py @@ -124,7 +124,7 @@ data_object_schema = { data_bundle = { "type": "object", # TODO: required, but we don't have checksums for bundles - 'required': ['data_object_ids', 'created', 'updated', 'version'], # , 'checksums'], + 'required': ['data_object_ids', 'created', 'updated', 'version', 'user_metadata'], # , 'checksums'], "properties": { "id": { "type": "string", @@ -211,8 +211,14 @@ data_bundle = { "user_metadata": { "type": "object", "additionalProperties": True, - "description": "OPTIONAL\n" - "A set of key-value pairs that represent metadata provided by the uploader." + "description": "REQUIRED\n" + "A set of key-value pairs that represent metadata provided by the uploader.", + 'required': ['project', 'program'], + "properties": { + "project": {"type": "object"}, + "program": {"type": "object"} + + } } } } diff --git a/tests/test_all.py b/tests/test_all.py index 03f3f9b..501d145 100644 --- a/tests/test_all.py +++ b/tests/test_all.py @@ -83,7 +83,7 @@ class TestSheepdogGen3TransformingStandard(AbstractTransformerTest, unittest.Tes def test_sheepdog_gen3_transforming(self): message('Run the transformer on sheepdog\'s output') - argv = ['new', str(self.test_file), '--output-json', str(self.out_file)] + argv = ['new', str(self.test_file), '--output-json', str(self.out_file), '--pp'] message(f'Passing args: {" ".join(argv)}') main(argv) diff --git a/tests/test_data/topmed-public.json b/tests/test_data/topmed-public.json index 61fce82..d0a64e6 100644 --- a/tests/test_data/topmed-public.json +++ b/tests/test_data/topmed-public.json @@ -1,1 +1,1 @@ -{"metadata": {"medication": [], "electrocardiogram_test": [], "aggregated_snp_array": [], "medical_history": [], "sample": [{"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "HG01110_sample", "hours_to_collection": "", "prosector_notes": "", 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"biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": "31f6dc4c-a8e7-402e-a292-f6de85287a58", "cases.submitter_id": "NA19238"}, "method_of_sample_procurement": "", "node_id": "e450679d-0c17-467c-8fd5-dba1510f041b", "collection_site": "", "freezing_method": "", "biospecimen_physical_site": "", "biospecimen_type": "Normal - other", "preservation_method": "", "tissue_type": "", "biospecimen_anatomic_site_uberon_id": "", "hours_to_sample_procurement": ""}, {"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "HG01111_sample", "hours_to_collection": "", "prosector_notes": "", "autolysis_score": "", "collection_kit": "", "biospecimen_anatomic_site_detail": "", "biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": "6d13d82a-aa6c-4a3c-8f3d-528899391043", "cases.submitter_id": "HG01111"}, "method_of_sample_procurement": "", "node_id": "f2555751-d329-4b81-a0e9-7989562c860d", "collection_site": "", "freezing_method": "", "biospecimen_physical_site": "", "biospecimen_type": "Normal - blood", "preservation_method": "", "tissue_type": "", "biospecimen_anatomic_site_uberon_id": "", "hours_to_sample_procurement": ""}, {"pathology_notes": "", "biospecimen_anatomic_site": "", "internal_notes": "", "submitter_id": "HG01249_sample", "hours_to_collection": "", "prosector_notes": "", "autolysis_score": "", "collection_kit": "", "biospecimen_anatomic_site_detail": "", "biospecimen_anatomic_site_uberon_term": "", "sample_type": "", "label": "sample", "project_id": "topmed-public", "current_weight": "", "composition": "B-lymphocyte", "oct_embedded": "", "is_ffpe": "", "link_fields": {"cases.id": 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Sanitize data using values of the same type Elasticsearch is very particular about the type of each JSON value. When sanitizing data with `data_bleach.py` the sanitized value must be of the same type as the original value. Currently, `data_bleach.py` sanitizes all values using an empty string value. ┆Issue is synchronized with this [JIRA Task](https://ucsc-cgl.atlassian.net/browse/NEWT-27) ┆Project Name: CGP-Newt ┆Issue Number: NEWT-27

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataBiosphere__newt-transformer-36

diff --git a/newt/main.py b/newt/main.py index 3910850..aafa6f9 100644 --- a/newt/main.py +++ b/newt/main.py @@ -16,6 +16,39 @@ def open_json_file(json_path): return json.load(fp) +def _recursive_traversal(d, f): + """ + recursively apply function f to each value in a dictionary + + f takes in the dictionary, the key, and the value + """ + for k, v in d.items(): + if type(v) == dict: + _recursive_traversal(v, f) + else: + f(d, k, v) + + +def fix_empty_strings(bundle_iterator): + """ + As bundles come through, the metadata is cleaned to replace + "" with None + + :param bundle_iterator: An iterator of :class:`Bundle` + :return: a bundle iterator + """ + def replace_empty_strings(d, k, v): + if v == '': + d[k] = None + for bundle in bundle_iterator: + try: + metadata = bundle.metadata + except AttributeError: + metadata = bundle['metadata'] + _recursive_traversal(metadata, replace_empty_strings) + yield bundle + + def write_output(bundles: typing.Iterator[Bundle], out_file, pretty_print): with open(out_file, 'w') as fp: json.dump(list(bundles), fp, indent=2 if pretty_print else None) @@ -63,4 +96,4 @@ def main(argv=None): raise ValueError(f'Invalid metadata source format {options.transform_source}') bundle_iterator = transformer.transform() - write_output(bundle_iterator, options.output_json, options.pp) + write_output(fix_empty_strings(bundle_iterator), options.output_json, options.pp)

DataBiosphere/newt-transformer

88473e29facefb7d8362e9956b5696091fe1c60f

diff --git a/tests/test_transform.py b/tests/test_transform.py index 6a46ee0..efe8bb1 100644 --- a/tests/test_transform.py +++ b/tests/test_transform.py @@ -7,7 +7,8 @@ import uuid import jsonschema from pathlib import Path -from newt.main import main +from newt.main import main, fix_empty_strings +from newt.transform.gen3standard import Bundle from tests.schemas import schema as output_schema @@ -60,7 +61,8 @@ class TestSheepdogGen3Transforming(AbstractTransformerTest, unittest.TestCase): # since bundle did is changed each time the transformer runs, just normalize it for comparison for bundle in test_output: bundle['bundle_did'] = valid_bundle_did - self.assertTrue(valid_output in test_output) + # TODO: delete all of this code + # self.assertTrue(valid_output in test_output) def test_sheepdog_gen3_transforming(self): message('Run the transformer on sheepdog\'s output') @@ -88,3 +90,15 @@ class TestSheepdogGen3TransformingStandard(AbstractTransformerTest, unittest.Tes main(argv) self._validate_output() + + def test_clearing_empty_strings(self): + test_d = {'foo': {'a': {'1': ''}, + 'b': '', + 'c': True}, + 'bar': '', + 'baz': ''} + b = Bundle(test_d) + list(fix_empty_strings([b])) + assert test_d['bar'] is None + assert test_d['foo']['b'] is None + assert test_d['foo']['a']['1'] is None

Gen3 export/transform produces inconsistent JSON value types This is a duplication of a TLP ticket ┆Issue is synchronized with this [JIRA Task](https://ucsc-cgl.atlassian.net/browse/NEWT-28) ┆Project Name: CGP-Newt ┆Issue Number: NEWT-28

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataBiosphere__toil-4077

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 89ac5dfe..901f7a19 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -97,9 +97,7 @@ py37_main: - virtualenv -p python3.7 venv && . venv/bin/activate && pip install -U pip wheel && make prepare && make develop extras=[all] packages='htcondor awscli' - make test tests=src/toil/test/src - make test tests=src/toil/test/utils - - make test tests=src/toil/test/lib/test_ec2.py - - make test tests=src/toil/test/lib/aws - - make test tests=src/toil/test/lib/test_conversions.py + - TOIL_SKIP_DOCKER=true make test tests=src/toil/test/lib py37_appliance_build: stage: basic_tests @@ -118,9 +116,7 @@ py38_main: - virtualenv -p python3.8 venv && . venv/bin/activate && pip install -U pip wheel && make prepare && make develop extras=[all] packages='htcondor awscli' - make test tests=src/toil/test/src - make test tests=src/toil/test/utils - - make test tests=src/toil/test/lib/test_ec2.py - - make test tests=src/toil/test/lib/aws - - make test tests=src/toil/test/lib/test_conversions.py + - TOIL_SKIP_DOCKER=true make test tests=src/toil/test/lib py38_appliance_build: stage: basic_tests @@ -139,6 +135,7 @@ py39_main: - virtualenv -p python3.9 venv && . venv/bin/activate && pip install -U pip wheel && make prepare && make develop extras=[all] packages=htcondor - make test tests=src/toil/test/src - make test tests=src/toil/test/utils + - TOIL_SKIP_DOCKER=true make test tests=src/toil/test/lib py39_appliance_build: stage: basic_tests diff --git a/docker/Dockerfile.py b/docker/Dockerfile.py index dbb20af4..454ab9b5 100644 --- a/docker/Dockerfile.py +++ b/docker/Dockerfile.py @@ -32,7 +32,6 @@ dependencies = ' '.join(['libffi-dev', # For client side encryption for extras 'python3.9-distutils' if python == 'python3.9' else '', # 'python3.9-venv' if python == 'python3.9' else '', 'python3-pip', - 'libcurl4-openssl-dev', 'libssl-dev', 'wget', 'curl', @@ -40,7 +39,6 @@ dependencies = ' '.join(['libffi-dev', # For client side encryption for extras "nodejs", # CWL support for javascript expressions 'rsync', 'screen', - 'build-essential', # We need a build environment to build Singularity 3. 'libarchive13', 'libc6', 'libseccomp2', @@ -53,7 +51,13 @@ dependencies = ' '.join(['libffi-dev', # For client side encryption for extras 'cryptsetup', 'less', 'vim', - 'git']) + 'git', + # Dependencies for Mesos which the deb doesn't actually list + 'libsvn1', + 'libcurl4-nss-dev', + 'libapr1', + # Dependencies for singularity + 'containernetworking-plugins']) def heredoc(s): @@ -67,7 +71,7 @@ motd = heredoc(''' Run toil <workflow>.py --help to see all options for running your workflow. For more information see http://toil.readthedocs.io/en/latest/ - Copyright (C) 2015-2020 Regents of the University of California + Copyright (C) 2015-2022 Regents of the University of California Version: {applianceSelf} @@ -77,8 +81,7 @@ motd = heredoc(''' motd = ''.join(l + '\\n\\\n' for l in motd.splitlines()) print(heredoc(''' - # We can't use a newer Ubuntu until we no longer need Mesos - FROM ubuntu:16.04 + FROM ubuntu:20.04 ARG TARGETARCH @@ -87,30 +90,27 @@ print(heredoc(''' RUN apt-get -y update --fix-missing && apt-get -y upgrade && apt-get -y install apt-transport-https ca-certificates software-properties-common && apt-get clean && rm -rf /var/lib/apt/lists/* - RUN echo "deb http://repos.mesosphere.io/ubuntu/ xenial main" \ - > /etc/apt/sources.list.d/mesosphere.list \ - && apt-key adv --keyserver keyserver.ubuntu.com --recv E56151BF \ - && echo "deb http://deb.nodesource.com/node_6.x xenial main" \ - > /etc/apt/sources.list.d/nodesource.list \ - && apt-key adv --keyserver keyserver.ubuntu.com --recv 68576280 - RUN add-apt-repository -y ppa:deadsnakes/ppa RUN apt-get -y update --fix-missing && \ DEBIAN_FRONTEND=noninteractive apt-get -y upgrade && \ DEBIAN_FRONTEND=noninteractive apt-get -y install {dependencies} && \ - if [ $TARGETARCH = amd64 ] ; then DEBIAN_FRONTEND=noninteractive apt-get -y install mesos=1.0.1-2.0.94.ubuntu1604 ; fi && \ apt-get clean && \ rm -rf /var/lib/apt/lists/* - + + # Install a Mesos build from somewhere and test it. + # This is /ipfs/QmRCNmVVrWPPQiEw2PrFLmb8ps6oETQvtKv8dLVN8ZRwFz/mesos-1.11.x.deb + RUN if [ $TARGETARCH = amd64 ] ; then \ + wget -q https://rpm.aventer.biz/Ubuntu/dists/focal/binary-amd64/mesos-1.11.x.deb && \ + dpkg -i mesos-1.11.x.deb && \ + rm mesos-1.11.x.deb && \ + mesos-agent --help >/dev/null ; \ + fi + # Install a particular old Debian Sid Singularity from somewhere. - # The dependencies it thinks it needs aren't really needed and aren't - # available here. ADD singularity-sources.tsv /etc/singularity/singularity-sources.tsv - RUN wget "$(cat /etc/singularity/singularity-sources.tsv | grep "^$TARGETARCH" | cut -f3)" && \ - (dpkg -i singularity-container_3*.deb || true) && \ - dpkg --force-depends --configure -a && \ - sed -i 's/containernetworking-plugins, //' /var/lib/dpkg/status && \ + RUN wget -q "$(cat /etc/singularity/singularity-sources.tsv | grep "^$TARGETARCH" | cut -f3)" && \ + dpkg -i singularity-container_3*.deb && \ sed -i 's!bind path = /etc/localtime!#bind path = /etc/localtime!g' /etc/singularity/singularity.conf && \ mkdir -p /usr/local/libexec/toil && \ mv /usr/bin/singularity /usr/local/libexec/toil/singularity-real \ @@ -127,9 +127,6 @@ print(heredoc(''' RUN chmod 777 /usr/bin/waitForKey.sh && chmod 777 /usr/bin/customDockerInit.sh && chmod 777 /usr/local/bin/singularity - # fixes an incompatibility updating pip on Ubuntu 16 w/ python3.8 - RUN sed -i "s/platform.linux_distribution()/('Ubuntu', '16.04', 'xenial')/g" /usr/lib/python3/dist-packages/pip/download.py - # The stock pip is too old and can't install from sdist with extras RUN {pip} install --upgrade pip==21.3.1 @@ -150,9 +147,6 @@ print(heredoc(''' && chmod u+x /usr/local/bin/docker \ && /usr/local/bin/docker -v - # Fix for Mesos interface dependency missing on ubuntu - RUN {pip} install protobuf==3.0.0 - # Fix for https://issues.apache.org/jira/browse/MESOS-3793 ENV MESOS_LAUNCHER=posix @@ -174,7 +168,7 @@ print(heredoc(''' env PATH /opt/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin # We want to pick the right Python when the user runs it - RUN rm /usr/bin/python3 && rm /usr/bin/python && \ + RUN rm -f /usr/bin/python3 && rm -f /usr/bin/python && \ ln -s /usr/bin/{python} /usr/bin/python3 && \ ln -s /usr/bin/python3 /usr/bin/python diff --git a/src/toil/batchSystems/kubernetes.py b/src/toil/batchSystems/kubernetes.py index 0e00e3c5..9be3d4ba 100644 --- a/src/toil/batchSystems/kubernetes.py +++ b/src/toil/batchSystems/kubernetes.py @@ -21,7 +21,6 @@ cannot yet be launched. That functionality will need to wait for user-mode Docker """ import datetime -import getpass import logging import os import string @@ -47,7 +46,7 @@ from toil.batchSystems.contained_executor import pack_job from toil.common import Toil from toil.job import JobDescription from toil.lib.conversions import human2bytes -from toil.lib.misc import slow_down, utc_now +from toil.lib.misc import slow_down, utc_now, get_user_name from toil.lib.retry import ErrorCondition, retry from toil.resource import Resource from toil.statsAndLogging import configure_root_logger, set_log_level @@ -1246,7 +1245,7 @@ class KubernetesBatchSystem(BatchSystemCleanupSupport): # and all lowercase letters, numbers, or - or . acceptable_chars = set(string.ascii_lowercase + string.digits + '-.') - return ''.join([c for c in getpass.getuser().lower() if c in acceptable_chars])[:100] + return ''.join([c for c in get_user_name().lower() if c in acceptable_chars])[:100] @classmethod def add_options(cls, parser: Union[ArgumentParser, _ArgumentGroup]) -> None: diff --git a/src/toil/batchSystems/mesos/batchSystem.py b/src/toil/batchSystems/mesos/batchSystem.py index bca66b2e..aed82c27 100644 --- a/src/toil/batchSystems/mesos/batchSystem.py +++ b/src/toil/batchSystems/mesos/batchSystem.py @@ -12,7 +12,6 @@ # See the License for the specific language governing permissions and # limitations under the License. import ast -import getpass import json import logging import os @@ -43,7 +42,7 @@ from toil.batchSystems.mesos import JobQueue, MesosShape, TaskData, ToilJob from toil.job import JobDescription from toil.lib.conversions import b_to_mib, mib_to_b from toil.lib.memoize import strict_bool -from toil.lib.misc import get_public_ip +from toil.lib.misc import get_public_ip, get_user_name log = logging.getLogger(__name__) @@ -319,7 +318,7 @@ class MesosBatchSystem(BatchSystemLocalSupport, The Mesos driver thread which handles the scheduler's communication with the Mesos master """ framework = addict.Dict() - framework.user = getpass.getuser() # We must determine the user name ourselves with pymesos + framework.user = get_user_name() # We must determine the user name ourselves with pymesos framework.name = "toil" framework.principal = framework.name # Make the driver which implements most of the scheduler logic and calls back to us for the user-defined parts. diff --git a/src/toil/lib/misc.py b/src/toil/lib/misc.py index d62133b0..879606f9 100644 --- a/src/toil/lib/misc.py +++ b/src/toil/lib/misc.py @@ -1,4 +1,5 @@ import datetime +import getpass import logging import os import random @@ -36,6 +37,23 @@ def get_public_ip() -> str: # to provide a default argument return '127.0.0.1' +def get_user_name() -> str: + """ + Get the current user name, or a suitable substitute string if the user name + is not available. + """ + try: + try: + return getpass.getuser() + except KeyError: + # This is expected if the user isn't in /etc/passwd, such as in a + # Docker container when running as a weird UID. Make something up. + return 'UnknownUser' + str(os.getuid()) + except Exception as e: + # We can't get the UID, or something weird has gone wrong. + logger.error('Unexpected error getting user name: %s', e) + return 'UnknownUser' + def utc_now() -> datetime.datetime: """Return a datetime in the UTC timezone corresponding to right now.""" return datetime.datetime.utcnow().replace(tzinfo=pytz.UTC) diff --git a/src/toil/provisioners/abstractProvisioner.py b/src/toil/provisioners/abstractProvisioner.py index 7712cb31..c039c8b9 100644 --- a/src/toil/provisioners/abstractProvisioner.py +++ b/src/toil/provisioners/abstractProvisioner.py @@ -731,10 +731,10 @@ class AbstractProvisioner(ABC): # mesos-agent. If there are multiple keys to be transferred, then the last one to be transferred must be # set to keyPath. MESOS_LOG_DIR = '--log_dir=/var/lib/mesos ' - LEADER_DOCKER_ARGS = '--registry=in_memory --cluster={name}' + LEADER_DOCKER_ARGS = '--webui_dir=/share/mesos/webui --registry=in_memory --cluster={name}' # --no-systemd_enable_support is necessary in Ubuntu 16.04 (otherwise, # Mesos attempts to contact systemd but can't find its run file) - WORKER_DOCKER_ARGS = '--work_dir=/var/lib/mesos --master={ip}:5050 --attributes=preemptable:{preemptable} --no-hostname_lookup --no-systemd_enable_support' + WORKER_DOCKER_ARGS = '--launcher_dir=/libexec/mesos --work_dir=/var/lib/mesos --master={ip}:5050 --attributes=preemptable:{preemptable} --no-hostname_lookup --no-systemd_enable_support' if self.clusterType == 'mesos': if role == 'leader':

DataBiosphere/toil

b6b33030b165ac03a823f08b00f8fd8fa7590520

diff --git a/src/toil/test/lib/test_misc.py b/src/toil/test/lib/test_misc.py new file mode 100644 index 00000000..1924f7ae --- /dev/null +++ b/src/toil/test/lib/test_misc.py @@ -0,0 +1,83 @@ +# Copyright (C) 2015-2022 Regents of the University of California +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import logging + +import getpass + +from toil.lib.misc import get_user_name +from toil.test import ToilTest + +logger = logging.getLogger(__name__) +logging.basicConfig(level=logging.DEBUG) + + +class UserNameAvailableTest(ToilTest): + """ + Make sure we can get user names when they are available. + """ + + def test_get_user_name(self): + # We assume we have the user in /etc/passwd when running the tests. + real_user_name = getpass.getuser() + apparent_user_name = get_user_name() + self.assertEqual(apparent_user_name, real_user_name) + +class UserNameUnvailableTest(ToilTest): + """ + Make sure we can get something for a user name when user names are not + available. + """ + + def setUp(self): + super().setUp() + # Monkey patch getpass.getuser to fail + self.original_getuser = getpass.getuser + def fake_getuser(): + raise KeyError('Fake key error') + getpass.getuser = fake_getuser + def tearDown(self): + # Fix the module we hacked up + getpass.getuser = self.original_getuser + super().tearDown() + + def test_get_user_name(self): + apparent_user_name = get_user_name() + # Make sure we got something + self.assertTrue(isinstance(apparent_user_name, str)) + self.assertNotEqual(apparent_user_name, '') + +class UserNameVeryBrokenTest(ToilTest): + """ + Make sure we can get something for a user name when user name fetching is + broken in ways we did not expect. + """ + + def setUp(self): + super().setUp() + # Monkey patch getpass.getuser to fail + self.original_getuser = getpass.getuser + def fake_getuser(): + raise RuntimeError('Fake error that we did not anticipate') + getpass.getuser = fake_getuser + def tearDown(self): + # Fix the module we hacked up + getpass.getuser = self.original_getuser + super().tearDown() + + def test_get_user_name(self): + apparent_user_name = get_user_name() + # Make sure we got something + self.assertTrue(isinstance(apparent_user_name, str)) + self.assertNotEqual(apparent_user_name, '') +

Toil can't start when the current user has no username As reported in https://github.com/ComparativeGenomicsToolkit/cactus/issues/677, the Kubernetes batch system calls `getpass.getuser()` when composing command line options, as Toil is starting up, but doesn't handle the `KeyError` it raises if you're running as a UID with no `/etc/passwd` entry and no username. We should probably wrap that call, and any other requests for the current username, in a wrapper that always returns something even if no username is set at the system level. ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1150) ┆friendlyId: TOIL-1150

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataBiosphere__toil-4445

diff --git a/src/toil/common.py b/src/toil/common.py index d0eb1bc8..d4a8c73c 100644 --- a/src/toil/common.py +++ b/src/toil/common.py @@ -198,7 +198,7 @@ class Config: self.writeLogs = None self.writeLogsGzip = None self.writeLogsFromAllJobs: bool = False - self.write_messages: str = "" + self.write_messages: Optional[str] = None # Misc self.environment: Dict[str, str] = {} @@ -222,6 +222,24 @@ class Config: # CWL self.cwl: bool = False + def prepare_start(self) -> None: + """ + After options are set, prepare for initial start of workflow. + """ + self.workflowAttemptNumber = 0 + + def prepare_restart(self) -> None: + """ + Before restart options are set, prepare for a restart of a workflow. + Set up any execution-specific parameters and clear out any stale ones. + """ + self.workflowAttemptNumber += 1 + # We should clear the stored message bus path, because it may have been + # auto-generated and point to a temp directory that could no longer + # exist and that can't safely be re-made. + self.write_messages = None + + def setOptions(self, options: Namespace) -> None: """Creates a config object from the options object.""" OptionType = TypeVar("OptionType") @@ -407,6 +425,8 @@ class Config: set_option("write_messages", os.path.abspath) if not self.write_messages: + # The user hasn't specified a place for the message bus so we + # should make one. self.write_messages = gen_message_bus_path() assert not (self.writeLogs and self.writeLogsGzip), \ @@ -947,14 +967,14 @@ class Toil(ContextManager["Toil"]): self.options.caching = config.caching if not config.restart: - config.workflowAttemptNumber = 0 + config.prepare_start() jobStore.initialize(config) else: jobStore.resume() # Merge configuration from job store with command line options config = jobStore.config + config.prepare_restart() config.setOptions(self.options) - config.workflowAttemptNumber += 1 jobStore.write_config() self.config = config self._jobStore = jobStore diff --git a/src/toil/lib/aws/session.py b/src/toil/lib/aws/session.py index 4ef36f16..cbc2b686 100644 --- a/src/toil/lib/aws/session.py +++ b/src/toil/lib/aws/session.py @@ -18,7 +18,6 @@ import os import re import socket import threading -from functools import lru_cache from typing import (Any, Callable, Dict, @@ -37,16 +36,33 @@ import boto3.resources.base import boto.connection import botocore from boto3 import Session +from botocore.client import Config from botocore.credentials import JSONFileCache from botocore.session import get_session logger = logging.getLogger(__name__) -@lru_cache(maxsize=None) -def establish_boto3_session(region_name: Optional[str] = None) -> Session: +# A note on thread safety: +# +# Boto3 Session: Not thread safe, 1 per thread is required. +# +# Boto3 Resources: Not thread safe, one per thread is required. +# +# Boto3 Client: Thread safe after initialization, but initialization is *not* +# thread safe and only one can be being made at a time. They also are +# restricted to a single Python *process*. +# +# See: <https://stackoverflow.com/questions/52820971/is-boto3-client-thread-safe> + +# We use this lock to control initialization so only one thread can be +# initializing Boto3 (or Boto2) things at a time. +_init_lock = threading.RLock() + +def _new_boto3_session(region_name: Optional[str] = None) -> Session: """ - This is the One True Place where Boto3 sessions should be established, and - prepares them with the necessary credential caching. + This is the One True Place where new Boto3 sessions should be made, and + prepares them with the necessary credential caching. Does *not* cache + sessions, because each thread needs its own caching. :param region_name: If given, the session will be associated with the given AWS region. """ @@ -55,35 +71,12 @@ def establish_boto3_session(region_name: Optional[str] = None) -> Session: # See https://github.com/boto/botocore/pull/1338/ # And https://github.com/boto/botocore/commit/2dae76f52ae63db3304b5933730ea5efaaaf2bfc - botocore_session = get_session() - botocore_session.get_component('credential_provider').get_provider( - 'assume-role').cache = JSONFileCache() - - return Session(botocore_session=botocore_session, region_name=region_name, profile_name=os.environ.get("TOIL_AWS_PROFILE", None)) - -@lru_cache(maxsize=None) -def client(service_name: str, *args: List[Any], region_name: Optional[str] = None, **kwargs: Dict[str, Any]) -> botocore.client.BaseClient: - """ - Get a Boto 3 client for a particular AWS service. - - Global alternative to AWSConnectionManager. - """ - session = establish_boto3_session(region_name=region_name) - # MyPy can't understand our argument unpacking. See <https://github.com/vemel/mypy_boto3_builder/issues/121> - client: botocore.client.BaseClient = session.client(service_name, *args, **kwargs) # type: ignore - return client - -@lru_cache(maxsize=None) -def resource(service_name: str, *args: List[Any], region_name: Optional[str] = None, **kwargs: Dict[str, Any]) -> boto3.resources.base.ServiceResource: - """ - Get a Boto 3 resource for a particular AWS service. + with _init_lock: + botocore_session = get_session() + botocore_session.get_component('credential_provider').get_provider( + 'assume-role').cache = JSONFileCache() - Global alternative to AWSConnectionManager. - """ - session = establish_boto3_session(region_name=region_name) - # MyPy can't understand our argument unpacking. See <https://github.com/vemel/mypy_boto3_builder/issues/121> - resource: boto3.resources.base.ServiceResource = session.resource(service_name, *args, **kwargs) # type: ignore - return resource + return Session(botocore_session=botocore_session, region_name=region_name, profile_name=os.environ.get("TOIL_AWS_PROFILE", None)) class AWSConnectionManager: """ @@ -98,6 +91,10 @@ class AWSConnectionManager: connections to multiple regions may need to be managed in the same provisioner. + We also support None for a region, in which case no region will be + passed to Boto/Boto3. The caller is responsible for implementing e.g. + TOIL_AWS_REGION support. + Since connection objects may not be thread safe (see <https://boto3.amazonaws.com/v1/documentation/api/1.14.31/guide/session.html#multithreading-or-multiprocessing-with-sessions>), one is created for each thread that calls the relevant lookup method. @@ -115,18 +112,18 @@ class AWSConnectionManager: """ # This stores Boto3 sessions in .item of a thread-local storage, by # region. - self.sessions_by_region: Dict[str, threading.local] = collections.defaultdict(threading.local) + self.sessions_by_region: Dict[Optional[str], threading.local] = collections.defaultdict(threading.local) # This stores Boto3 resources in .item of a thread-local storage, by - # (region, service name) tuples - self.resource_cache: Dict[Tuple[str, str], threading.local] = collections.defaultdict(threading.local) + # (region, service name, endpoint URL) tuples + self.resource_cache: Dict[Tuple[Optional[str], str, Optional[str]], threading.local] = collections.defaultdict(threading.local) # This stores Boto3 clients in .item of a thread-local storage, by - # (region, service name) tuples - self.client_cache: Dict[Tuple[str, str], threading.local] = collections.defaultdict(threading.local) + # (region, service name, endpoint URL) tuples + self.client_cache: Dict[Tuple[Optional[str], str, Optional[str]], threading.local] = collections.defaultdict(threading.local) # This stores Boto 2 connections in .item of a thread-local storage, by # (region, service name) tuples. - self.boto2_cache: Dict[Tuple[str, str], threading.local] = collections.defaultdict(threading.local) + self.boto2_cache: Dict[Tuple[Optional[str], str], threading.local] = collections.defaultdict(threading.local) - def session(self, region: str) -> boto3.session.Session: + def session(self, region: Optional[str]) -> boto3.session.Session: """ Get the Boto3 Session to use for the given region. """ @@ -134,35 +131,68 @@ class AWSConnectionManager: if not hasattr(storage, 'item'): # This is the first time this thread wants to talk to this region # through this manager - storage.item = establish_boto3_session(region_name=region) + storage.item = _new_boto3_session(region_name=region) return cast(boto3.session.Session, storage.item) - def resource(self, region: str, service_name: str) -> boto3.resources.base.ServiceResource: + def resource(self, region: Optional[str], service_name: str, endpoint_url: Optional[str] = None) -> boto3.resources.base.ServiceResource: """ Get the Boto3 Resource to use with the given service (like 'ec2') in the given region. + + :param endpoint_url: AWS endpoint URL to use for the client. If not + specified, a default is used. """ - key = (region, service_name) + key = (region, service_name, endpoint_url) storage = self.resource_cache[key] if not hasattr(storage, 'item'): - # The Boto3 stubs are missing an overload for `resource` that takes - # a non-literal string. See - # <https://github.com/vemel/mypy_boto3_builder/issues/121#issuecomment-1011322636> - storage.item = self.session(region).resource(service_name) # type: ignore + with _init_lock: + # We lock inside the if check; we don't care if the memoization + # sometimes results in multiple different copies leaking out. + # We lock because we call .resource() + + if endpoint_url is not None: + # The Boto3 stubs are missing an overload for `resource` that takes + # a non-literal string. See + # <https://github.com/vemel/mypy_boto3_builder/issues/121#issuecomment-1011322636> + storage.item = self.session(region).resource(service_name, endpoint_url=endpoint_url) # type: ignore + else: + # We might not be able to pass None to Boto3 and have it be the same as no argument. + storage.item = self.session(region).resource(service_name) # type: ignore + return cast(boto3.resources.base.ServiceResource, storage.item) - def client(self, region: str, service_name: str) -> botocore.client.BaseClient: + def client(self, region: Optional[str], service_name: str, endpoint_url: Optional[str] = None, config: Optional[Config] = None) -> botocore.client.BaseClient: """ Get the Boto3 Client to use with the given service (like 'ec2') in the given region. + + :param endpoint_url: AWS endpoint URL to use for the client. If not + specified, a default is used. + :param config: Custom configuration to use for the client. """ - key = (region, service_name) + + if config is not None: + # Don't try and memoize if a custom config is used + with _init_lock: + if endpoint_url is not None: + return self.session(region).client(service_name, endpoint_url=endpoint_url, config=config) # type: ignore + else: + return self.session(region).client(service_name, config=config) # type: ignore + + key = (region, service_name, endpoint_url) storage = self.client_cache[key] if not hasattr(storage, 'item'): - # The Boto3 stubs are probably missing an overload here too. See: - # <https://github.com/vemel/mypy_boto3_builder/issues/121#issuecomment-1011322636> - storage.item = self.session(region).client(service_name) # type: ignore + with _init_lock: + # We lock because we call .client() + + if endpoint_url is not None: + # The Boto3 stubs are probably missing an overload here too. See: + # <https://github.com/vemel/mypy_boto3_builder/issues/121#issuecomment-1011322636> + storage.item = self.session(region).client(service_name, endpoint_url=endpoint_url) # type: ignore + else: + # We might not be able to pass None to Boto3 and have it be the same as no argument. + storage.item = self.session(region).client(service_name) # type: ignore return cast(botocore.client.BaseClient , storage.item) - def boto2(self, region: str, service_name: str) -> boto.connection.AWSAuthConnection: + def boto2(self, region: Optional[str], service_name: str) -> boto.connection.AWSAuthConnection: """ Get the connected boto2 connection for the given region and service. """ @@ -172,5 +202,39 @@ class AWSConnectionManager: key = (region, service_name) storage = self.boto2_cache[key] if not hasattr(storage, 'item'): - storage.item = getattr(boto, service_name).connect_to_region(region, profile_name=os.environ.get("TOIL_AWS_PROFILE", None)) + with _init_lock: + storage.item = getattr(boto, service_name).connect_to_region(region, profile_name=os.environ.get("TOIL_AWS_PROFILE", None)) return cast(boto.connection.AWSAuthConnection, storage.item) + +# If you don't want your own AWSConnectionManager, we have a global one and some global functions +_global_manager = AWSConnectionManager() + +def establish_boto3_session(region_name: Optional[str] = None) -> Session: + """ + Get a Boto 3 session usable by the current thread. + + This function may not always establish a *new* session; it can be memoized. + """ + + # Just use a global version of the manager. Note that we change the argument order! + return _global_manager.session(region_name) + +def client(service_name: str, region_name: Optional[str] = None, endpoint_url: Optional[str] = None, config: Optional[Config] = None) -> botocore.client.BaseClient: + """ + Get a Boto 3 client for a particular AWS service, usable by the current thread. + + Global alternative to AWSConnectionManager. + """ + + # Just use a global version of the manager. Note that we change the argument order! + return _global_manager.client(region_name, service_name, endpoint_url=endpoint_url, config=config) + +def resource(service_name: str, region_name: Optional[str] = None, endpoint_url: Optional[str] = None) -> boto3.resources.base.ServiceResource: + """ + Get a Boto 3 resource for a particular AWS service, usable by the current thread. + + Global alternative to AWSConnectionManager. + """ + + # Just use a global version of the manager. Note that we change the argument order! + return _global_manager.resource(region_name, service_name, endpoint_url=endpoint_url) diff --git a/src/toil/utils/toilStatus.py b/src/toil/utils/toilStatus.py index a25aa648..45617555 100644 --- a/src/toil/utils/toilStatus.py +++ b/src/toil/utils/toilStatus.py @@ -232,11 +232,14 @@ class ToilStatus: """ print("\nMessage bus path: ", self.message_bus_path) - - replayed_messages = replay_message_bus(self.message_bus_path) - for key in replayed_messages: - if replayed_messages[key].exit_code != 0: - print(replayed_messages[key]) + if self.message_bus_path is not None: + if os.path.exists(self.message_bus_path): + replayed_messages = replay_message_bus(self.message_bus_path) + for key in replayed_messages: + if replayed_messages[key].exit_code != 0: + print(replayed_messages[key]) + else: + print("Message bus file is missing!") return None

DataBiosphere/toil

2804edfc6128c2c9e66ff348696eda95cb63b400

diff --git a/src/toil/test/src/busTest.py b/src/toil/test/src/busTest.py index 6be0ab45..da6edb54 100644 --- a/src/toil/test/src/busTest.py +++ b/src/toil/test/src/busTest.py @@ -13,12 +13,19 @@ # limitations under the License. import logging +import os from threading import Thread, current_thread +from typing import Optional from toil.batchSystems.abstractBatchSystem import BatchJobExitReason from toil.bus import JobCompletedMessage, JobIssuedMessage, MessageBus, replay_message_bus +from toil.common import Toil +from toil.job import Job +from toil.exceptions import FailedJobsException from toil.test import ToilTest, get_temp_file + + logger = logging.getLogger(__name__) class MessageBusTest(ToilTest): @@ -95,5 +102,62 @@ class MessageBusTest(ToilTest): # And having polled for those, our handler should have run self.assertEqual(message_count, 11) + def test_restart_without_bus_path(self) -> None: + """ + Test the ability to restart a workflow when the message bus path used + by the previous attempt is gone. + """ + temp_dir = self._createTempDir(purpose='tempDir') + job_store = self._getTestJobStorePath() + + bus_holder_dir = os.path.join(temp_dir, 'bus_holder') + os.mkdir(bus_holder_dir) + + start_options = Job.Runner.getDefaultOptions(job_store) + start_options.logLevel = 'DEBUG' + start_options.retryCount = 0 + start_options.clean = "never" + start_options.write_messages = os.path.abspath(os.path.join(bus_holder_dir, 'messagebus.txt')) + + root = Job.wrapJobFn(failing_job_fn) + + try: + with Toil(start_options) as toil: + # Run once and observe a failed job + toil.start(root) + except FailedJobsException: + pass + + logger.info('First attempt successfully failed, removing message bus log') + + # Get rid of the bus + os.unlink(start_options.write_messages) + os.rmdir(bus_holder_dir) + + logger.info('Making second attempt') + + # Set up options without a specific bus path + restart_options = Job.Runner.getDefaultOptions(job_store) + restart_options.logLevel = 'DEBUG' + restart_options.retryCount = 0 + restart_options.clean = "never" + restart_options.restart = True + + try: + with Toil(restart_options) as toil: + # Run again and observe a failed job (and not a failure to start) + toil.restart() + except FailedJobsException: + pass + + logger.info('Second attempt successfully failed') + + +def failing_job_fn(job: Job) -> None: + """ + This function is guaranteed to fail. + """ + raise RuntimeError('Job attempted to run but failed') +

Toil relying on tmpfile directory structure during --restart This came up here: https://github.com/ComparativeGenomicsToolkit/cactus/issues/987 and, from the stack trace, doesn't look like it's coming from Cactus (?). The user reruns with `--restart` and Toil tries to write a temporary file into a temporary directory that doesn't exist. I'm guessing it was made on the initial run then cleaned since. But this seems like something that shouldn't happen (ie Toil should only require that the jobstore is preserved not the tempdir). I'm not sure if their use of `--stats` which is probably less well tested (at least in Cactus) could be a factor.

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataBiosphere__toil-4802

diff --git a/src/toil/batchSystems/abstractBatchSystem.py b/src/toil/batchSystems/abstractBatchSystem.py index 9da541de..fd0b30f9 100644 --- a/src/toil/batchSystems/abstractBatchSystem.py +++ b/src/toil/batchSystems/abstractBatchSystem.py @@ -59,13 +59,28 @@ class BatchJobExitReason(enum.IntEnum): MEMLIMIT: int = 6 """Job hit batch system imposed memory limit.""" + @classmethod + def to_string(cls, value: int) -> str: + """ + Convert to human-readable string. + + Given an int that may be or may be equal to a value from the enum, + produce the string value of its matching enum entry, or a stringified + int. + """ + try: + return cls(value).name + except ValueError: + return str(value) + class UpdatedBatchJobInfo(NamedTuple): jobID: int exitStatus: int """ The exit status (integer value) of the job. 0 implies successful. - EXIT_STATUS_UNAVAILABLE_VALUE is used when the exit status is not available (e.g. job is lost). + EXIT_STATUS_UNAVAILABLE_VALUE is used when the exit status is not available + (e.g. job is lost, or otherwise died but actual exit code was not reported). """ exitReason: Optional[BatchJobExitReason] @@ -437,7 +452,7 @@ class BatchSystemSupport(AbstractBatchSystem): file_name: str = f'toil_{self.config.workflowID}.{toil_job_id}.{cluster_job_id}.{std}.log' logs_dir: str = self.get_batch_logs_dir() return os.path.join(logs_dir, file_name) - + def format_std_out_err_glob(self, toil_job_id: int) -> str: """ Get a glob string that will match all file paths generated by format_std_out_err_path for a job. @@ -445,7 +460,7 @@ class BatchSystemSupport(AbstractBatchSystem): file_glob: str = f'toil_{self.config.workflowID}.{toil_job_id}.*.log' logs_dir: str = self.get_batch_logs_dir() return os.path.join(logs_dir, file_glob) - + @staticmethod def workerCleanup(info: WorkerCleanupInfo) -> None: """ @@ -509,7 +524,7 @@ class AbstractScalableBatchSystem(AbstractBatchSystem): """ A batch system that supports a variable number of worker nodes. - Used by :class:`toil.provisioners.clusterScaler.ClusterScaler` + Used by :class:`toil.provisioners.clusterScaler.ClusterScaler` to scale the number of worker nodes in the cluster up or down depending on overall load. """ diff --git a/src/toil/batchSystems/abstractGridEngineBatchSystem.py b/src/toil/batchSystems/abstractGridEngineBatchSystem.py index 16dd563a..93986381 100644 --- a/src/toil/batchSystems/abstractGridEngineBatchSystem.py +++ b/src/toil/batchSystems/abstractGridEngineBatchSystem.py @@ -225,23 +225,20 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): return activity def _handle_job_status( - self, job_id: int, status: Union[int, None], activity: bool + self, job_id: int, status: Union[int, Tuple[int, Optional[BatchJobExitReason]], None], activity: bool ) -> bool: """ Helper method for checkOnJobs to handle job statuses """ if status is not None: + if isinstance(status, int): + code = status + reason = None + else: + code, reason = status self.updatedJobsQueue.put( UpdatedBatchJobInfo( - jobID=job_id, exitStatus=status, exitReason=None, wallTime=None - ) - ) - self.forgetJob(job_id) - return True - if status is not None and isinstance(status, BatchJobExitReason): - self.updatedJobsQueue.put( - UpdatedBatchJobInfo( - jobID=job_id, exitStatus=1, exitReason=status, wallTime=None + jobID=job_id, exitStatus=code, exitReason=reason, wallTime=None ) ) self.forgetJob(job_id) @@ -279,9 +276,9 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): logger.error("GridEngine like batch system failure", exc_info=ex) raise - def coalesce_job_exit_codes(self, batch_job_id_list: list) -> list: + def coalesce_job_exit_codes(self, batch_job_id_list: list) -> List[Union[int, Tuple[int, Optional[BatchJobExitReason]], None]]: """ - Returns exit codes for a list of jobs. + Returns exit codes and possibly exit reasons for a list of jobs, or None if they are running. Called by AbstractGridEngineWorker.checkOnJobs(). @@ -351,16 +348,19 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): raise NotImplementedError() @abstractmethod - def getJobExitCode(self, batchJobID): + def getJobExitCode(self, batchJobID) -> Union[int, Tuple[int, Optional[BatchJobExitReason]], None]: """ - Returns job exit code or an instance of abstractBatchSystem.BatchJobExitReason. - if something else happened other than the job exiting. - Implementation-specific; called by AbstractGridEngineWorker.checkOnJobs() + Returns job exit code and possibly an instance of abstractBatchSystem.BatchJobExitReason. - :param string batchjobID: batch system job ID + Returns None if the job is still running. + + If the job is not running but the exit code is not available, it + will be EXIT_STATUS_UNAVAILABLE_VALUE. Implementation-specific; + called by AbstractGridEngineWorker.checkOnJobs(). - :rtype: int|toil.batchSystems.abstractBatchSystem.BatchJobExitReason: exit code int - or BatchJobExitReason if something else happened other than job exiting. + The exit code will only be 0 if the job affirmatively succeeded. + + :param string batchjobID: batch system job ID """ raise NotImplementedError() diff --git a/src/toil/batchSystems/lsf.py b/src/toil/batchSystems/lsf.py index 645e54db..68dcef7a 100644 --- a/src/toil/batchSystems/lsf.py +++ b/src/toil/batchSystems/lsf.py @@ -25,12 +25,12 @@ import re import subprocess from datetime import datetime from random import randint -from typing import Dict, List, Optional, Union +from typing import Dict, List, Optional, Tuple, Union from dateutil.parser import parse from dateutil.tz import tzlocal -from toil.batchSystems.abstractBatchSystem import BatchJobExitReason +from toil.batchSystems.abstractBatchSystem import BatchJobExitReason, EXIT_STATUS_UNAVAILABLE_VALUE from toil.batchSystems.abstractGridEngineBatchSystem import \ AbstractGridEngineBatchSystem from toil.batchSystems.lsfHelper import (check_lsf_json_output_supported, @@ -161,7 +161,7 @@ class LSFBatchSystem(AbstractGridEngineBatchSystem): status_resonse.append(None) return status_resonse - def getJobExitCode(self, lsfJobID): + def getJobExitCode(self, lsfJobID) -> Union[int, Tuple[int, Optional[BatchJobExitReason]], None]: # the task is set as part of the job ID if using getBatchSystemID() if "NOT_SUBMITTED" in lsfJobID: logger.error("bjobs detected job failed to submit") @@ -186,7 +186,7 @@ class LSFBatchSystem(AbstractGridEngineBatchSystem): return self.fallbackGetJobExitCode(job) - def parse_bjobs_record(self, bjobs_record: dict, job: int) -> Union[int, None]: + def parse_bjobs_record(self, bjobs_record: dict, job: int) -> Union[int, Tuple[int, Optional[BatchJobExitReason]], None]: """ Helper functions for getJobExitCode and to parse the bjobs status record """ @@ -224,7 +224,7 @@ class LSFBatchSystem(AbstractGridEngineBatchSystem): exit_info, job ) if "TERM_MEMLIMIT" in exit_reason: - return BatchJobExitReason.MEMLIMIT + return (exit_code if exit_code != 0 else EXIT_STATUS_UNAVAILABLE_VALUE, BatchJobExitReason.MEMLIMIT) return exit_code if process_status == "RUN": logger.debug( @@ -237,7 +237,7 @@ class LSFBatchSystem(AbstractGridEngineBatchSystem): return self.getJobExitCodeBACCT(job) - def getJobExitCodeBACCT(self,job): + def getJobExitCodeBACCT(self,job) -> Union[int, Tuple[int, Optional[BatchJobExitReason]], None]: # if not found in bjobs, then try bacct (slower than bjobs) logger.debug("bjobs failed to detect job - trying bacct: " "{}".format(job)) @@ -258,7 +258,7 @@ class LSFBatchSystem(AbstractGridEngineBatchSystem): "running: {}".format(job)) return None - def fallbackGetJobExitCode(self, job): + def fallbackGetJobExitCode(self, job) -> Union[int, Tuple[int, Optional[BatchJobExitReason]], None]: args = ["bjobs", "-l", str(job)] logger.debug(f"Checking job exit code for job via bjobs (fallback): {job}") stdout = call_command(args) diff --git a/src/toil/batchSystems/slurm.py b/src/toil/batchSystems/slurm.py index fc4c4941..6abdacb1 100644 --- a/src/toil/batchSystems/slurm.py +++ b/src/toil/batchSystems/slurm.py @@ -16,8 +16,9 @@ import math import os from argparse import ArgumentParser, _ArgumentGroup from shlex import quote -from typing import Dict, List, Optional, TypeVar, Union +from typing import Dict, List, Optional, Tuple, TypeVar, Union +from toil.batchSystems.abstractBatchSystem import BatchJobExitReason, EXIT_STATUS_UNAVAILABLE_VALUE from toil.batchSystems.abstractGridEngineBatchSystem import \ AbstractGridEngineBatchSystem from toil.batchSystems.options import OptionSetter @@ -97,12 +98,12 @@ class SlurmBatchSystem(AbstractGridEngineBatchSystem): logger.error("sbatch command failed") raise e - def coalesce_job_exit_codes(self, batch_job_id_list: list) -> list: + def coalesce_job_exit_codes(self, batch_job_id_list: list) -> List[Union[int, Tuple[int, Optional[BatchJobExitReason]], None]]: """ Collect all job exit codes in a single call. :param batch_job_id_list: list of Job ID strings, where each string has the form "<job>[.<task>]". - :return: list of job exit codes, associated with the list of job IDs. + :return: list of job exit codes or exit code, exit reason pairs associated with the list of job IDs. """ logger.debug("Getting exit codes for slurm jobs: %s", batch_job_id_list) # Convert batch_job_id_list to list of integer job IDs. @@ -113,7 +114,7 @@ class SlurmBatchSystem(AbstractGridEngineBatchSystem): exit_codes.append(self._get_job_return_code(status)) return exit_codes - def getJobExitCode(self, batchJobID: str) -> int: + def getJobExitCode(self, batchJobID: str) -> Union[int, Tuple[int, Optional[BatchJobExitReason]], None]: """ Get job exit code for given batch job ID. :param batchJobID: string of the form "<job>[.<task>]". @@ -140,18 +141,68 @@ class SlurmBatchSystem(AbstractGridEngineBatchSystem): status_dict = self._getJobDetailsFromScontrol(job_id_list) return status_dict - def _get_job_return_code(self, status: tuple) -> list: + def _get_job_return_code(self, status: tuple) -> Union[int, Tuple[int, Optional[BatchJobExitReason]], None]: """ + Given a Slurm return code, status pair, summarize them into a Toil return code, exit reason pair. + + The return code may have already been OR'd with the 128-offset + Slurm-reported signal. + + Slurm will report return codes of 0 even if jobs time out instead + of succeeding: + + 2093597|TIMEOUT|0:0 + 2093597.batch|CANCELLED|0:15 + + So we guarantee here that, if the Slurm status string is not a + successful one as defined in + <https://slurm.schedmd.com/squeue.html#SECTION_JOB-STATE-CODES>, we + will not return a successful return code. + Helper function for `getJobExitCode` and `coalesce_job_exit_codes`. - :param status: tuple containing the job's state and it's return code. - :return: the job's return code if it's completed, otherwise None. + :param status: tuple containing the job's state and it's return code from Slurm. + :return: the job's return code for Toil if it's completed, otherwise None. """ state, rc = status - # If job is in a running state, set return code to None to indicate we don't have - # an update. - if state in ('PENDING', 'RUNNING', 'CONFIGURING', 'COMPLETING', 'RESIZING', 'SUSPENDED'): - rc = None - return rc + + # If a job is in one of these states, Slurm can't run it anymore. + # We don't include states where the job is held or paused here; + # those mean it could run and needs to wait for someone to un-hold + # it, so Toil should wait for it. + # + # We map from each terminal state to the Toil-ontology exit reason. + TERMINAL_STATES: Dict[str, BatchJobExitReason] = { + "BOOT_FAIL": BatchJobExitReason.LOST, + "CANCELLED": BatchJobExitReason.KILLED, + "COMPLETED": BatchJobExitReason.FINISHED, + "DEADLINE": BatchJobExitReason.KILLED, + "FAILED": BatchJobExitReason.FAILED, + "NODE_FAIL": BatchJobExitReason.LOST, + "OUT_OF_MEMORY": BatchJobExitReason.MEMLIMIT, + "PREEMPTED": BatchJobExitReason.KILLED, + "TIMEOUT": BatchJobExitReason.KILLED + } + + if state not in TERMINAL_STATES: + # Don't treat the job as exited yet + return None + + exit_reason = TERMINAL_STATES[state] + + if exit_reason == BatchJobExitReason.FINISHED: + # The only state that should produce a 0 ever is COMPLETED. So + # if the job is COMPLETED and the exit reason is thus FINISHED, + # pass along the code it has. + return (rc, exit_reason) + + if rc == 0: + # The job claims to be in a state other than COMPLETED, but + # also to have not encountered a problem. Say the exit status + # is unavailable. + return (EXIT_STATUS_UNAVAILABLE_VALUE, exit_reason) + + # If the code is nonzero, pass it along. + return (rc, exit_reason) def _getJobDetailsFromSacct(self, job_id_list: list) -> dict: """ diff --git a/src/toil/leader.py b/src/toil/leader.py index 97a069b8..892cb3ad 100644 --- a/src/toil/leader.py +++ b/src/toil/leader.py @@ -28,7 +28,8 @@ import enlighten from toil import resolveEntryPoint from toil.batchSystems import DeadlockException from toil.batchSystems.abstractBatchSystem import (AbstractBatchSystem, - BatchJobExitReason) + BatchJobExitReason, + EXIT_STATUS_UNAVAILABLE_VALUE) from toil.bus import (JobCompletedMessage, JobFailedMessage, JobIssuedMessage, @@ -706,8 +707,9 @@ class Leader: if exitStatus == 0: logger.debug('Job ended: %s', updatedJob) else: - logger.warning(f'Job failed with exit value {exitStatus}: {updatedJob}\n' - f'Exit reason: {exitReason}') + status_string = str(exitStatus) if exitStatus != EXIT_STATUS_UNAVAILABLE_VALUE else "<UNAVAILABLE>" + logger.warning(f'Job failed with exit value {status_string}: {updatedJob}\n' + f'Exit reason: {BatchJobExitReason.to_string(exitReason)}') if exitStatus == CWL_UNSUPPORTED_REQUIREMENT_EXIT_CODE: # This is a CWL job informing us that the workflow is # asking things of us that Toil can't do. When we raise an

DataBiosphere/toil

7166aa20554e02638d8afc638d2fadc30e23066d

diff --git a/src/toil/test/batchSystems/test_slurm.py b/src/toil/test/batchSystems/test_slurm.py index d8b3ac32..0e68391f 100644 --- a/src/toil/test/batchSystems/test_slurm.py +++ b/src/toil/test/batchSystems/test_slurm.py @@ -4,6 +4,7 @@ from queue import Queue import pytest import toil.batchSystems.slurm +from toil.batchSystems.abstractBatchSystem import BatchJobExitReason, EXIT_STATUS_UNAVAILABLE_VALUE from toil.common import Config from toil.lib.misc import CalledProcessErrorStderr from toil.test import ToilTest @@ -284,7 +285,7 @@ class SlurmTest(ToilTest): def test_getJobExitCode_job_exists(self): self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_sacct) job_id = '785023' # FAILED - expected_result = 127 + expected_result = (127, BatchJobExitReason.FAILED) result = self.worker.getJobExitCode(job_id) assert result == expected_result, f"{result} != {expected_result}" @@ -303,7 +304,7 @@ class SlurmTest(ToilTest): self.monkeypatch.setattr(self.worker, "_getJobDetailsFromSacct", call_sacct_raises) self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_scontrol) job_id = '787204' # COMPLETED - expected_result = 0 + expected_result = (0, BatchJobExitReason.FINISHED) result = self.worker.getJobExitCode(job_id) assert result == expected_result, f"{result} != {expected_result}" @@ -329,7 +330,7 @@ class SlurmTest(ToilTest): def test_coalesce_job_exit_codes_one_exists(self): self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_sacct) job_ids = ['785023'] # FAILED - expected_result = [127] + expected_result = [(127, BatchJobExitReason.FAILED)] result = self.worker.coalesce_job_exit_codes(job_ids) assert result == expected_result, f"{result} != {expected_result}" @@ -347,7 +348,14 @@ class SlurmTest(ToilTest): '789724', # RUNNING, '789868', # PENDING, '789869'] # COMPLETED - expected_result = [0, 1, None, None, 0] # RUNNING and PENDING jobs should return None + # RUNNING and PENDING jobs should return None + expected_result = [ + (EXIT_STATUS_UNAVAILABLE_VALUE, BatchJobExitReason.KILLED), + (1, BatchJobExitReason.FAILED), + None, + None, + (0, BatchJobExitReason.FINISHED) + ] result = self.worker.coalesce_job_exit_codes(job_ids) assert result == expected_result, f"{result} != {expected_result}" @@ -358,7 +366,14 @@ class SlurmTest(ToilTest): '789724', # RUNNING, '999999', # Non-existent, '789869'] # COMPLETED - expected_result = [130, 2, None, None, 0] # RUNNING job should return None + # RUNNING job should return None + expected_result = [ + (130, BatchJobExitReason.FAILED), + (2, BatchJobExitReason.FAILED), + None, + None, + (0, BatchJobExitReason.FINISHED) + ] result = self.worker.coalesce_job_exit_codes(job_ids) assert result == expected_result, f"{result} != {expected_result}" @@ -370,7 +385,7 @@ class SlurmTest(ToilTest): self.monkeypatch.setattr(self.worker, "_getJobDetailsFromSacct", call_sacct_raises) self.monkeypatch.setattr(toil.batchSystems.slurm, "call_command", call_scontrol) job_ids = ['787204'] # COMPLETED - expected_result = [0] + expected_result = [(0, BatchJobExitReason.FINISHED)] result = self.worker.coalesce_job_exit_codes(job_ids) assert result == expected_result, f"{result} != {expected_result}"

Slurm job timeout doesn't seem to register as failure I just ran into the Slurm time limit for the first time. From the Toil logs, it looks like my job starts again, with no job failure or error message. Since there's nothing about deprecating `retryCount`, I suspect it may go on forever. It's only by looking in the `--batchLogsDir` that I can find a useful message like. ``` slurmstepd-phoenix-07: error: *** JOB 1449736 ON phoenix-07 CANCELLED AT 2023-12-03T12:47:09 DUE TO TIME LIMIT *** ``` From what I remember, if I have a job killed because of too much memory, even if I need to go into `batchLogs` to see why it was killed, the main Toil log at least shows the failure. It seems suspicious that this isn't the case here. ``` 2023-12-03 00:47:28.365363: Running the command: "vg index -t 72 -j /data/tmp/c75c5a6e213a5ccdbf30f0ea018ea009/7be9/6287/tmpuoenbd43/clip.t2t-apes-small-pangenome-nosplit-nov30.dist /data/tmp/c75c5a6e213a5ccdbf30f0ea018ea009/7be9/6287/tmpuoenbd43/clip.t2t-apes-small-pangenome-nosplit-nov30.gbz" 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run Issued job 'make_giraffe_indexes' kind-make_giraffe_indexes/instance-8p3w3wnh v1 with job batch system ID: 76 and disk: 381.3 Gi, memory: 1.5 Ti, cores: 72, accelerators: [], preemptible: False 2023-12-03 12:47:31.501711: Running the command: "vg index -t 72 -j /data/tmp/6e792d19fa1c5edbb77567d767580617/fb42/46cf/tmp9zvikqn9/clip.t2t-apes-small-pangenome-nosplit-nov30.dist /data/tmp/6e792d19fa1c5edbb77567d767580617/fb42/46cf/tmp9zvikqn9/clip.t2t-apes-small-pangenome-nosplit-nov30.gbz" 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run 1 jobs are running, 0 jobs are issued and waiting to run Issued job 'make_giraffe_indexes' kind-make_giraffe_indexes/instance-8p3w3wnh v1 with job batch system ID: 77 and disk: 381.3 Gi, memory: 1.5 Ti, cores: 72, accelerators: [], preemptible: False ``` ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1460) ┆Issue Number: TOIL-1460

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataBiosphere__toil-4805

diff --git a/src/toil/options/common.py b/src/toil/options/common.py index 61086f3d..5c041f3b 100644 --- a/src/toil/options/common.py +++ b/src/toil/options/common.py @@ -733,4 +733,4 @@ def add_base_toil_options(parser: ArgumentParser, jobstore_as_flag: bool = False # dest is set to enableCaching to not conflict with the current --caching destination caching.add_argument('--disableCaching', dest='enableCaching', action='store_false', help=SUPPRESS) - caching.set_defaults(disableCaching=None) + caching.set_defaults(enableCaching=None)

DataBiosphere/toil

6558c7f97fb37c6ef6f469c7ae614109050322f4

diff --git a/src/toil/test/options/__init__.py b/src/toil/test/options/__init__.py new file mode 100644 index 00000000..471fe7cd --- /dev/null +++ b/src/toil/test/options/__init__.py @@ -0,0 +1,13 @@ +# Copyright (C) 2015-2021 Regents of the University of California +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. diff --git a/src/toil/test/options/options.py b/src/toil/test/options/options.py new file mode 100644 index 00000000..c3c30749 --- /dev/null +++ b/src/toil/test/options/options.py @@ -0,0 +1,37 @@ +from configargparse import ArgParser + +from toil.common import addOptions, Toil +from toil.test import ToilTest + + +class OptionsTest(ToilTest): + """ + Class to test functionality of all Toil options + """ + def test_default_caching_slurm(self): + """ + Test to ensure that caching will be set to false when running on Slurm + :return: + """ + parser = ArgParser() + addOptions(parser, jobstore_as_flag=True, wdl=False, cwl=False) + test_args = ["--jobstore=example-jobstore", "--batchSystem=slurm"] + options = parser.parse_args(test_args) + with Toil(options) as toil: + caching_value = toil.config.caching + self.assertEqual(caching_value, False) + + def test_caching_option_priority(self): + """ + Test to ensure that the --caching option takes priority over the default_caching() return value + :return: + """ + parser = ArgParser() + addOptions(parser, jobstore_as_flag=True, wdl=False, cwl=False) + # the kubernetes batchsystem (and I think all batchsystems including singlemachine) return False + # for default_caching + test_args = ["--jobstore=example-jobstore", "--batchSystem=kubernetes", "--caching=True"] + options = parser.parse_args(test_args) + with Toil(options) as toil: + caching_value = toil.config.caching + self.assertEqual(caching_value, True)

FileJobStore's default_caching() result of False is not respected The `FileJobStore` is supposed to be able to set a default of no caching on the workflow: https://github.com/DataBiosphere/toil/blob/e45b27cb3086fc57f35653562357ab9537f45d4e/src/toil/jobStores/fileJobStore.py#L70-L78 But this no longer works. If I run a file job store workflow with a batch system that doesn't support caching (like Slurm until #928/#4775 gets fixed), I get a complaint that caching needs to manually be set to off. This didn't used to happen; I suspect that this is a regression introduced with the config file support. We should fix `default_caching()` to be respected again, and we should add a test to make sure it stays working. ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1490) ┆Issue Number: TOIL-1490

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataBiosphere__toil-4809

diff --git a/src/toil/worker.py b/src/toil/worker.py index 13d9a668..2f086c9f 100644 --- a/src/toil/worker.py +++ b/src/toil/worker.py @@ -118,6 +118,14 @@ def nextChainable(predecessor: JobDescription, jobStore: AbstractJobStore, confi logger.debug("Next job is checkpoint, so finishing") return None + if not config.run_local_jobs_on_workers and predecessor.local and not successor.local: + # This job might be running on the leader, but the next job may not. + # + # TODO: Optimize by detecting whether we actually are on the leader, + # somehow. + logger.debug("Next job is not allowed to run on the leader, so finishing") + return None + # Made it through! This job is chainable. return successor

DataBiosphere/toil

c37f123ef2c67637f2aeec09ef2d6dddcfce90fd

diff --git a/src/toil/test/docs/scriptsTest.py b/src/toil/test/docs/scriptsTest.py index c1316a81..c1cd599b 100644 --- a/src/toil/test/docs/scriptsTest.py +++ b/src/toil/test/docs/scriptsTest.py @@ -5,6 +5,8 @@ import subprocess import sys import unittest +from typing import List + pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..')) # noqa sys.path.insert(0, pkg_root) # noqa @@ -36,9 +38,9 @@ class ToilDocumentationTest(ToilTest): unittest.TestCase.tearDown(self) """Just check the exit code""" - def checkExitCode(self, script): + def checkExitCode(self, script, extra_args: List[str] = []): program = os.path.join(self.directory, "scripts", script) - process = subprocess.Popen([python, program, "file:my-jobstore", "--clean=always"], + process = subprocess.Popen([python, program, "file:my-jobstore", "--clean=always"] + extra_args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) stdout, stderr = process.communicate() if isinstance(stdout, bytes): @@ -70,7 +72,8 @@ class ToilDocumentationTest(ToilTest): self.checkExitCode("tutorial_cwlexample.py") def testStats(self): - self.checkExitCode("tutorial_stats.py") + # This script asks for 4 cores but we might need to run the tests in only 3. + self.checkExitCode("tutorial_stats.py", ["--scale=0.5"]) def testDynamic(self): self.checkExitCode("tutorial_dynamic.py") diff --git a/src/toil/test/src/workerTest.py b/src/toil/test/src/workerTest.py index dcecace1..6df4f447 100644 --- a/src/toil/test/src/workerTest.py +++ b/src/toil/test/src/workerTest.py @@ -18,6 +18,8 @@ from toil.jobStores.fileJobStore import FileJobStore from toil.test import ToilTest from toil.worker import nextChainable +from typing import Optional + class WorkerTests(ToilTest): """Test miscellaneous units of the worker.""" @@ -32,7 +34,7 @@ class WorkerTests(ToilTest): def testNextChainable(self): """Make sure chainable/non-chainable jobs are identified correctly.""" - def createTestJobDesc(memory, cores, disk, preemptible, checkpoint): + def createTestJobDesc(memory, cores, disk, preemptible: bool = True, checkpoint: bool = False, local: Optional[bool] = None): """ Create a JobDescription with no command (representing a Job that has already run) and return the JobDescription. @@ -41,7 +43,16 @@ class WorkerTests(ToilTest): self.jobNumber += 1 descClass = CheckpointJobDescription if checkpoint else JobDescription - jobDesc = descClass(requirements={'memory': memory, 'cores': cores, 'disk': disk, 'preemptible': preemptible}, jobName=name) + jobDesc = descClass( + requirements={ + 'memory': memory, + 'cores': cores, + 'disk': disk, + 'preemptible': preemptible + }, + jobName=name, + local=local + ) # Assign an ID self.jobStore.assign_job_id(jobDesc) @@ -53,42 +64,64 @@ class WorkerTests(ToilTest): # Try with the branch point at both child and follow-on stages # Identical non-checkpoint jobs should be chainable. - jobDesc1 = createTestJobDesc(1, 2, 3, True, False) - jobDesc2 = createTestJobDesc(1, 2, 3, True, False) + jobDesc1 = createTestJobDesc(1, 2, 3) + jobDesc2 = createTestJobDesc(1, 2, 3) getattr(jobDesc1, successorType)(jobDesc2.jobStoreID) chainable = nextChainable(jobDesc1, self.jobStore, self.config) self.assertNotEqual(chainable, None) - self.assertEqual(jobDesc2.jobStoreID, chainable.jobStoreID) + self.assertEqual(chainable.jobStoreID, jobDesc2.jobStoreID) # Identical checkpoint jobs should not be chainable. - jobDesc1 = createTestJobDesc(1, 2, 3, True, False) - jobDesc2 = createTestJobDesc(1, 2, 3, True, True) + jobDesc1 = createTestJobDesc(1, 2, 3, checkpoint=True) + jobDesc2 = createTestJobDesc(1, 2, 3, checkpoint=True) + getattr(jobDesc1, successorType)(jobDesc2.jobStoreID) + self.assertEqual(nextChainable(jobDesc1, self.jobStore, self.config), None) + + # Changing checkpoint from false to true should make it not chainable. + jobDesc1 = createTestJobDesc(1, 2, 3, checkpoint=False) + jobDesc2 = createTestJobDesc(1, 2, 3, checkpoint=True) getattr(jobDesc1, successorType)(jobDesc2.jobStoreID) - self.assertEqual(None, nextChainable(jobDesc1, self.jobStore, self.config)) + self.assertEqual(nextChainable(jobDesc1, self.jobStore, self.config), None) # If there is no child we should get nothing to chain. - jobDesc1 = createTestJobDesc(1, 2, 3, True, False) - self.assertEqual(None, nextChainable(jobDesc1, self.jobStore, self.config)) + jobDesc1 = createTestJobDesc(1, 2, 3) + self.assertEqual(nextChainable(jobDesc1, self.jobStore, self.config), None) # If there are 2 or more children we should get nothing to chain. - jobDesc1 = createTestJobDesc(1, 2, 3, True, False) - jobDesc2 = createTestJobDesc(1, 2, 3, True, False) - jobDesc3 = createTestJobDesc(1, 2, 3, True, False) + jobDesc1 = createTestJobDesc(1, 2, 3) + jobDesc2 = createTestJobDesc(1, 2, 3) + jobDesc3 = createTestJobDesc(1, 2, 3) getattr(jobDesc1, successorType)(jobDesc2.jobStoreID) getattr(jobDesc1, successorType)(jobDesc3.jobStoreID) - self.assertEqual(None, nextChainable(jobDesc1, self.jobStore, self.config)) + self.assertEqual(nextChainable(jobDesc1, self.jobStore, self.config), None) # If there is an increase in resource requirements we should get nothing to chain. - reqs = {'memory': 1, 'cores': 2, 'disk': 3, 'preemptible': True, 'checkpoint': False} + base_reqs = {'memory': 1, 'cores': 2, 'disk': 3, 'preemptible': True, 'checkpoint': False} for increased_attribute in ('memory', 'cores', 'disk'): + reqs = dict(base_reqs) jobDesc1 = createTestJobDesc(**reqs) reqs[increased_attribute] += 1 jobDesc2 = createTestJobDesc(**reqs) getattr(jobDesc1, successorType)(jobDesc2.jobStoreID) - self.assertEqual(None, nextChainable(jobDesc1, self.jobStore, self.config)) + self.assertEqual(nextChainable(jobDesc1, self.jobStore, self.config), None) # A change in preemptability from True to False should be disallowed. - jobDesc1 = createTestJobDesc(1, 2, 3, True, False) - jobDesc2 = createTestJobDesc(1, 2, 3, False, True) + jobDesc1 = createTestJobDesc(1, 2, 3, preemptible=True) + jobDesc2 = createTestJobDesc(1, 2, 3, preemptible=False) + getattr(jobDesc1, successorType)(jobDesc2.jobStoreID) + self.assertEqual(nextChainable(jobDesc1, self.jobStore, self.config), None) + + # A change in local-ness from True to False should be disallowed. + jobDesc1 = createTestJobDesc(1, 2, 3, local=True) + jobDesc2 = createTestJobDesc(1, 2, 3, local=False) getattr(jobDesc1, successorType)(jobDesc2.jobStoreID) - self.assertEqual(None, nextChainable(jobDesc1, self.jobStore, self.config)) + self.assertEqual(nextChainable(jobDesc1, self.jobStore, self.config), None) + + # A change in local-ness from False to True should be allowed, + # since running locally is an optional optimization. + jobDesc1 = createTestJobDesc(1, 2, 3, local=False) + jobDesc2 = createTestJobDesc(1, 2, 3, local=True) + getattr(jobDesc1, successorType)(jobDesc2.jobStoreID) + chainable = nextChainable(jobDesc1, self.jobStore, self.config) + self.assertNotEqual(chainable, None) + self.assertEqual(chainable.jobStoreID, jobDesc2.jobStoreID)

toil-wdl-runner can run task containers on the leader @jeizenga has a workflow where the first task doesn't ask for more than the default amount of resources. So we kick off the `WDLRootJob` locally on the leader, and it chains to a call-a-task job, which chains to the actual task job, which doesn't need to reschedule itself for more resources, and starts up the container. The worker log goes something like: ``` [2024-02-02T11:10:19-0800] [MainThread] [D] [toil.worker] 'WDLWorkflowJob' kind-WDLRootJob/instance-87pqhjvf v4 would chain to ID kind-WDLWorkflowNodeJob/instance-e1oepvf7 [2024-02-02T11:10:19-0800] [MainThread] [I] [toil.worker] Chaining from 'WDLWorkflowJob' kind-WDLRootJob/instance-87pqhjvf v4 to 'WDLWorkflowNodeJob' call-formatAssembly kind-WDLWorkflowNodeJob/instance-e1oepvf7 v1 ... [2024-02-02T11:10:20-0800] [MainThread] [D] [toil.worker] 'WDLWorkflowNodeJob' call-formatAssembly kind-WDLRootJob/instance-87pqhjvf v6 would chain to ID kind-WDLTaskJob/instance-5ux5yawd [2024-02-02T11:10:20-0800] [MainThread] [I] [toil.worker] Chaining from 'WDLWorkflowNodeJob' call-formatAssembly kind-WDLRootJob/instance-87pqhjvf v6 to 'WDLTaskJob' centromereAnnotation.formatAssembly kind-WDLTaskJob/instance-5ux5yawd v1 ``` We probably want to make sure the WDLTaskJob itself isn't marked local and that chaining definitely refuses to go form a local job to a non-local one. ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1492) ┆Issue Number: TOIL-1492

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataBiosphere__toil-4873

diff --git a/src/toil/batchSystems/abstractGridEngineBatchSystem.py b/src/toil/batchSystems/abstractGridEngineBatchSystem.py index 98b48945..f41b3d0c 100644 --- a/src/toil/batchSystems/abstractGridEngineBatchSystem.py +++ b/src/toil/batchSystems/abstractGridEngineBatchSystem.py @@ -45,20 +45,21 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): A partial implementation of BatchSystemSupport for batch systems run on a standard HPC cluster. By default auto-deployment is not implemented. """ + class GridEngineThreadException(Exception): + pass - class Worker(Thread, metaclass=ABCMeta): - + class GridEngineThread(Thread, metaclass=ABCMeta): def __init__(self, newJobsQueue: Queue, updatedJobsQueue: Queue, killQueue: Queue, killedJobsQueue: Queue, boss: 'AbstractGridEngineBatchSystem') -> None: """ - Abstract worker interface class. All instances are created with five + Abstract thread interface class. All instances are created with five initial arguments (below). Note the Queue instances passed are empty. :param newJobsQueue: a Queue of new (unsubmitted) jobs :param updatedJobsQueue: a Queue of jobs that have been updated :param killQueue: a Queue of active jobs that need to be killed - :param killedJobsQueue: Queue of killed jobs for this worker + :param killedJobsQueue: Queue of killed jobs for this thread :param boss: the AbstractGridEngineBatchSystem instance that - controls this AbstractGridEngineWorker + controls this GridEngineThread """ Thread.__init__(self) @@ -77,6 +78,7 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): self.batchJobIDs: Dict[int, str] = dict() self._checkOnJobsCache = None self._checkOnJobsTimestamp = None + self.exception = None def getBatchSystemID(self, jobID: int) -> str: """ @@ -110,7 +112,7 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): """ Create a new job with the given attributes. - Implementation-specific; called by AbstractGridEngineWorker.run() + Implementation-specific; called by GridEngineThread.run() """ activity = False # Load new job id if present: @@ -146,7 +148,7 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): def killJobs(self): """ - Kill any running jobs within worker + Kill any running jobs within thread """ killList = list() while True: @@ -277,14 +279,17 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): while self._runStep(): pass except Exception as ex: - logger.error("GridEngine like batch system failure", exc_info=ex) - raise + self.exception = ex + logger.error("GridEngine like batch system failure: %s", ex) + # don't raise exception as is_alive will still be set to false, + # signalling exception in the thread as we expect the thread to + # always be running for the duration of the workflow def coalesce_job_exit_codes(self, batch_job_id_list: list) -> List[Union[int, Tuple[int, Optional[BatchJobExitReason]], None]]: """ Returns exit codes and possibly exit reasons for a list of jobs, or None if they are running. - Called by AbstractGridEngineWorker.checkOnJobs(). + Called by GridEngineThread.checkOnJobs(). This is an optional part of the interface. It should raise NotImplementedError if not actually implemented for a particular @@ -345,7 +350,7 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): def killJob(self, jobID): """ Kill specific job with the Toil job ID. Implementation-specific; called - by AbstractGridEngineWorker.killJobs() + by GridEngineThread.killJobs() :param string jobID: Toil job ID """ @@ -360,7 +365,7 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): If the job is not running but the exit code is not available, it will be EXIT_STATUS_UNAVAILABLE_VALUE. Implementation-specific; - called by AbstractGridEngineWorker.checkOnJobs(). + called by GridEngineThread.checkOnJobs(). The exit code will only be 0 if the job affirmatively succeeded. @@ -379,10 +384,10 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): self.updatedJobsQueue = Queue() self.killQueue = Queue() self.killedJobsQueue = Queue() - # get the associated worker class here - self.worker = self.Worker(self.newJobsQueue, self.updatedJobsQueue, - self.killQueue, self.killedJobsQueue, self) - self.worker.start() + # get the associated thread class here + self.background_thread = self.GridEngineThread(self.newJobsQueue, self.updatedJobsQueue, + self.killQueue, self.killedJobsQueue, self) + self.background_thread.start() self._getRunningBatchJobIDsTimestamp = None self._getRunningBatchJobIDsCache = {} @@ -428,7 +433,12 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): for jobID in jobIDs: self.killQueue.put(jobID) while jobIDs: - killedJobId = self.killedJobsQueue.get() + try: + killedJobId = self.killedJobsQueue.get(timeout=10) + except Empty: + if not self.background_thread.is_alive(): + raise self.GridEngineThreadException("Grid engine thread failed unexpectedly") from self.background_thread.exception + continue if killedJobId is None: break jobIDs.remove(killedJobId) @@ -460,7 +470,7 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): self.config.statePollingWait): batchIds = self._getRunningBatchJobIDsCache else: - batchIds = self.with_retries(self.worker.getRunningJobIDs) + batchIds = self.with_retries(self.background_thread.getRunningJobIDs) self._getRunningBatchJobIDsCache = batchIds self._getRunningBatchJobIDsTimestamp = datetime.now() batchIds.update(self.getRunningLocalJobIDs()) @@ -468,6 +478,11 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): def getUpdatedBatchJob(self, maxWait): local_tuple = self.getUpdatedLocalJob(0) + + if not self.background_thread.is_alive(): + # kill remaining jobs on the thread + self.background_thread.killJobs() + raise self.GridEngineThreadException("Unexpected GridEngineThread failure") from self.background_thread.exception if local_tuple: return local_tuple else: @@ -481,14 +496,14 @@ class AbstractGridEngineBatchSystem(BatchSystemCleanupSupport): def shutdown(self) -> None: """ - Signals worker to shutdown (via sentinel) then cleanly joins the thread + Signals thread to shutdown (via sentinel) then cleanly joins the thread """ self.shutdownLocal() newJobsQueue = self.newJobsQueue self.newJobsQueue = None newJobsQueue.put(None) - self.worker.join() + self.background_thread.join() def setEnv(self, name, value=None): if value and ',' in value: diff --git a/src/toil/batchSystems/gridengine.py b/src/toil/batchSystems/gridengine.py index 6250b491..17fe1838 100644 --- a/src/toil/batchSystems/gridengine.py +++ b/src/toil/batchSystems/gridengine.py @@ -28,7 +28,7 @@ logger = logging.getLogger(__name__) class GridEngineBatchSystem(AbstractGridEngineBatchSystem): - class Worker(AbstractGridEngineBatchSystem.Worker): + class GridEngineThread(AbstractGridEngineBatchSystem.GridEngineThread): """ Grid Engine-specific AbstractGridEngineWorker methods """ diff --git a/src/toil/batchSystems/htcondor.py b/src/toil/batchSystems/htcondor.py index 10504414..17b718bb 100644 --- a/src/toil/batchSystems/htcondor.py +++ b/src/toil/batchSystems/htcondor.py @@ -48,7 +48,7 @@ schedd_lock = Lock() class HTCondorBatchSystem(AbstractGridEngineBatchSystem): # When using HTCondor, the Schedd handles scheduling - class Worker(AbstractGridEngineBatchSystem.Worker): + class GridEngineThread(AbstractGridEngineBatchSystem.GridEngineThread): # Override the createJobs method so that we can use htcondor.Submit objects # and so that we can get disk allocation requests and ceil the CPU request. diff --git a/src/toil/batchSystems/lsf.py b/src/toil/batchSystems/lsf.py index 68dcef7a..5d44029a 100644 --- a/src/toil/batchSystems/lsf.py +++ b/src/toil/batchSystems/lsf.py @@ -44,8 +44,8 @@ logger = logging.getLogger(__name__) class LSFBatchSystem(AbstractGridEngineBatchSystem): - class Worker(AbstractGridEngineBatchSystem.Worker): - """LSF specific AbstractGridEngineWorker methods.""" + class GridEngineThread(AbstractGridEngineBatchSystem.GridEngineThread): + """LSF specific GridEngineThread methods.""" def getRunningJobIDs(self): times = {} diff --git a/src/toil/batchSystems/slurm.py b/src/toil/batchSystems/slurm.py index 3a624cf1..4a018654 100644 --- a/src/toil/batchSystems/slurm.py +++ b/src/toil/batchSystems/slurm.py @@ -70,7 +70,7 @@ NONTERMINAL_STATES: Set[str] = { class SlurmBatchSystem(AbstractGridEngineBatchSystem): - class Worker(AbstractGridEngineBatchSystem.Worker): + class GridEngineThread(AbstractGridEngineBatchSystem.GridEngineThread): def getRunningJobIDs(self): # Should return a dictionary of Job IDs and number of seconds @@ -135,7 +135,7 @@ class SlurmBatchSystem(AbstractGridEngineBatchSystem): logger.debug("sbatch submitted job %d", result) return result except OSError as e: - logger.error("sbatch command failed") + logger.error(f"sbatch command failed with error: {e}") raise e def coalesce_job_exit_codes(self, batch_job_id_list: list) -> List[Union[int, Tuple[int, Optional[BatchJobExitReason]], None]]: diff --git a/src/toil/batchSystems/torque.py b/src/toil/batchSystems/torque.py index 63fb18e9..308c7c2f 100644 --- a/src/toil/batchSystems/torque.py +++ b/src/toil/batchSystems/torque.py @@ -31,7 +31,7 @@ logger = logging.getLogger(__name__) class TorqueBatchSystem(AbstractGridEngineBatchSystem): # class-specific Worker - class Worker(AbstractGridEngineBatchSystem.Worker): + class GridEngineThread(AbstractGridEngineBatchSystem.GridEngineThread): def __init__( self, newJobsQueue, updatedJobsQueue, killQueue, killedJobsQueue, boss ): diff --git a/src/toil/lib/retry.py b/src/toil/lib/retry.py index b06481ba..f645724d 100644 --- a/src/toil/lib/retry.py +++ b/src/toil/lib/retry.py @@ -572,6 +572,8 @@ def old_retry( >>> i 1 """ + if timeout is None: + timeout = DEFAULT_TIMEOUT if timeout > 0: go = [ None ]

DataBiosphere/toil

c566f315393f65804ead58e8f3878b010fff1cfe

diff --git a/src/toil/test/batchSystems/test_slurm.py b/src/toil/test/batchSystems/test_slurm.py index 0e68391f..483e8fb0 100644 --- a/src/toil/test/batchSystems/test_slurm.py +++ b/src/toil/test/batchSystems/test_slurm.py @@ -193,7 +193,7 @@ class SlurmTest(ToilTest): def setUp(self): self.monkeypatch = pytest.MonkeyPatch() - self.worker = toil.batchSystems.slurm.SlurmBatchSystem.Worker( + self.worker = toil.batchSystems.slurm.SlurmBatchSystem.GridEngineThread( newJobsQueue=Queue(), updatedJobsQueue=Queue(), killQueue=Queue(),

Failed `sbatch` may hang a workflow Mira noticed that a workflow she was running reported a failed `sbatch` command, and then reported a long run of `squeue` commands succeeding while apparently doing nothing. It may be that a failed `sbatch` can kill a job submission thread that we need to be alive for the workflow not to get stuck. ┆Issue is synchronized with this [Jira Story](https://ucsc-cgl.atlassian.net/browse/TOIL-1533) ┆Issue Number: TOIL-1533

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataDog__datadog-lambda-python-214

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 0d00bfc..7d7884d 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -101,7 +101,7 @@ jobs: run: sudo yarn global add serverless@^2.72.2 --prefix /usr/local - name: Install Crossbuild Deps run: | - sudo apt-get update + sudo apt-get update --allow-releaseinfo-change --fix-missing sudo apt install -y qemu-user-static binfmt-support - name: Install dependencies diff --git a/.github/workflows/check-size.yml b/.github/workflows/check-size.yml index 69d578d..1c247e6 100644 --- a/.github/workflows/check-size.yml +++ b/.github/workflows/check-size.yml @@ -15,7 +15,9 @@ jobs: python-version: 3.7 - name: Install Crossbuild Deps - run: sudo apt install -y qemu-user-static binfmt-support + run: | + sudo apt-get update --allow-releaseinfo-change --fix-missing + sudo apt install -y qemu-user-static binfmt-support - name: Install dependencies run: | diff --git a/datadog_lambda/tag_object.py b/datadog_lambda/tag_object.py index 7ca8512..02dc3eb 100644 --- a/datadog_lambda/tag_object.py +++ b/datadog_lambda/tag_object.py @@ -3,6 +3,7 @@ # This product includes software developed at Datadog (https://www.datadoghq.com/). # Copyright 2021 Datadog, Inc. +from decimal import Decimal import json import logging @@ -26,7 +27,7 @@ def tag_object(span, key, obj, depth=0): except ValueError: redacted = _redact_val(key, obj[0:5000]) return span.set_tag(key, redacted) - if isinstance(obj, int) or isinstance(obj, float): + if isinstance(obj, int) or isinstance(obj, float) or isinstance(obj, Decimal): return span.set_tag(key, obj) if isinstance(obj, list): for k, v in enumerate(obj):

DataDog/datadog-lambda-python

1f59f3a8821aef37a02e5099a5112d938e57e9c1

diff --git a/tests/test_tag_object.py b/tests/test_tag_object.py index 0936f0c..cdb2941 100644 --- a/tests/test_tag_object.py +++ b/tests/test_tag_object.py @@ -1,4 +1,5 @@ import unittest +from decimal import Decimal try: from unittest.mock import MagicMock, patch, call @@ -82,3 +83,14 @@ class TestTagObject(unittest.TestCase): ], True, ) + + def test_decimal_tag_object(self): + payload = {"myValue": Decimal(500.50)} + spanMock = MagicMock() + tag_object(spanMock, "function.request", payload) + spanMock.set_tag.assert_has_calls( + [ + call("function.request.myValue", Decimal(500.50)), + ], + True, + )

When the response of lambda contain data of type Decimal, datadog raise except TypeError: 'decimal.Decimal' object is not iterable ## Expected Behavior When return response from DynamoDB and DynamoDB contains data of type Decimal ## Actual Behavior Get data of DynamoDB that contains data of type Decimal and raise next exception **except TypeError: 'decimal.Decimal' object is not iterable** ## Steps to Reproduce the Problem 1. Get data from Dynamodb inside handler and return response. In the code core de [datadog_lambda](https://github.com/DataDog/datadog-lambda-python/blob/main/datadog_lambda/tag_object.py) in the line 37 raises of exception because Decimal is instance of object, but this is not iterable ``` if isinstance(obj, object): for k in obj: v = obj.get(k) formatted_key = "{}.{}".format(key, k) tag_object(span, formatted_key, v, depth) return ``` ## Specifications - Datadog Lambda Layer version:  - Python version: 3.8 ## Stacktrace ``` File "/opt/python/lib/python3.8/site-packages/datadog_lambda/wrapper.py", line 203, in _after tag_object(self.span, "function.response", self.response) File "/opt/python/lib/python3.8/site-packages/datadog_lambda/tag_object.py", line 40, in tag_object tag_object(span, formatted_key, v, depth) File "/opt/python/lib/python3.8/site-packages/datadog_lambda/tag_object.py", line 40, in tag_object tag_object(span, formatted_key, v, depth) File "/opt/python/lib/python3.8/site-packages/datadog_lambda/tag_object.py", line 40, in tag_object tag_object(span, formatted_key, v, depth) [Previous line repeated 4 more times] File "/opt/python/lib/python3.8/site-packages/datadog_lambda/tag_object.py", line 37, in tag_object for k in obj: TypeError: 'decimal.Decimal' object is not iterable ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

apache-2.0

DataDog__datadogpy-382

diff --git a/datadog/api/resources.py b/datadog/api/resources.py index ad53a50..23b3663 100644 --- a/datadog/api/resources.py +++ b/datadog/api/resources.py @@ -373,7 +373,9 @@ class ActionAPIResource(object): resource_id=id, action_name=name ) - + if method == "GET": + # Do not add body to GET requests, it causes 400 Bad request responses on EU site + body = None return APIClient.submit(method, path, api_version, body, **params) @classmethod @@ -403,4 +405,7 @@ class ActionAPIResource(object): action_name=name, resource_id=id ) + if method == "GET": + # Do not add body to GET requests, it causes 400 Bad request responses on EU site + body = None return APIClient.submit(method, path, api_version, body)

DataDog/datadogpy

500e96369108eee6eef6378a64efbe2dab898f3b

diff --git a/tests/unit/api/helper.py b/tests/unit/api/helper.py index 4ba6cc4..c72ee09 100644 --- a/tests/unit/api/helper.py +++ b/tests/unit/api/helper.py @@ -143,8 +143,8 @@ class DatadogAPITestCase(unittest.TestCase): def request_called_with(self, method, url, data=None, params=None): (req_method, req_url), others = self.request_mock.call_args() - self.assertEquals(method, req_method, req_method) - self.assertEquals(url, req_url, req_url) + self.assertEqual(method, req_method, req_method) + self.assertEqual(url, req_url, req_url) if data: self.assertIn('data', others) @@ -155,7 +155,7 @@ class DatadogAPITestCase(unittest.TestCase): self.assertIn('params', others) for (k, v) in iteritems(params): self.assertIn(k, others['params'], others['params']) - self.assertEquals(v, others['params'][k]) + self.assertEqual(v, others['params'][k]) def assertIn(self, first, second, msg=None): msg = msg or "{0} not in {1}".format(first, second) diff --git a/tests/unit/api/test_api.py b/tests/unit/api/test_api.py index 3fc99a8..2ba1698 100644 --- a/tests/unit/api/test_api.py +++ b/tests/unit/api/test_api.py @@ -173,7 +173,7 @@ class TestInitialization(DatadogAPINoInitialization): self.assertEquals(getattr(api, attr_name), expected_value) @preserve_environ_datadog - def test_api_params_from_params(env_name, parameter, attr_name, value ): + def test_api_params_from_params(env_name, parameter, attr_name, value): """ Unset env_name environment variable Initialize API with parameter=value @@ -221,6 +221,8 @@ class TestResources(DatadogAPIWithInitialization): MyGetable.get(getable_object_id, otherparam="val") self.request_called_with('GET', "host/api/v1/getables/" + str(getable_object_id), params={'otherparam': "val"}) + _, kwargs = self.request_mock.call_args() + self.assertIsNone(kwargs["data"]) def test_listable(self): """ @@ -228,6 +230,8 @@ class TestResources(DatadogAPIWithInitialization): """ MyListable.get_all(otherparam="val") self.request_called_with('GET', "host/api/v1/listables", params={'otherparam': "val"}) + _, kwargs = self.request_mock.call_args() + self.assertIsNone(kwargs["data"]) def test_updatable(self): """ @@ -258,6 +262,8 @@ class TestResources(DatadogAPIWithInitialization): 'host/api/v1/resource_name/{0}/sub_resource_name'.format(resource_id), params={'otherparam': "val"} ) + _, kwargs = self.request_mock.call_args() + self.assertIsNone(kwargs["data"]) def test_addable_sub_resources(self): """ @@ -341,9 +347,10 @@ class TestResources(DatadogAPIWithInitialization): self.request_called_with( 'GET', 'host/api/v1/actionables/{0}/actionname'.format(str(actionable_object_id)), - params={'param1': 'val1', 'param2': 'val2'}, - data={} + params={'param1': 'val1', 'param2': 'val2'} ) + _, kwargs = self.request_mock.call_args() + self.assertIsNone(kwargs["data"]) MyActionable.trigger_action( 'POST', @@ -357,6 +364,18 @@ class TestResources(DatadogAPIWithInitialization): data={'mydata': "val"} ) + MyActionable.trigger_action( + 'GET', + 'actionname', + id=actionable_object_id, + ) + self.request_called_with( + 'GET', + 'host/api/v1/actionname/{0}'.format(actionable_object_id) + ) + _, kwargs = self.request_mock.call_args() + self.assertIsNone(kwargs["data"]) + class TestMetricResource(DatadogAPIWithInitialization): @@ -476,6 +495,7 @@ class TestMetricResource(DatadogAPIWithInitialization): serie = dict(metric='metric.numerical', points=point) self.submit_and_assess_metric_payload(serie) + class TestServiceCheckResource(DatadogAPIWithInitialization): def test_service_check_supports_none_parameters(self):

api.Monitor.search() returns "400 malformed request" html Any call to _api.Monitor.search()_ with parameters or without returns a 400 status code as response. For this call the request body is an empty JSON object('{}') rather than being _None_ (as for other 'GET' requests) and the headers accordingly contain _'Content-Type': 'application/json'_

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

DataDog__datadogpy-545

diff --git a/datadog/threadstats/base.py b/datadog/threadstats/base.py index ec89c3e..87421a0 100644 --- a/datadog/threadstats/base.py +++ b/datadog/threadstats/base.py @@ -7,20 +7,21 @@ performance. It collects metrics in the application thread with very little over and allows flushing metrics in process, in a thread or in a greenlet, depending on your application's needs. """ +import atexit +import logging +import os # stdlib from contextlib import contextmanager from functools import wraps from time import time -import atexit -import logging -import os # datadog from datadog.api.exceptions import ApiNotInitialized from datadog.threadstats.constants import MetricType from datadog.threadstats.events import EventsAggregator -from datadog.threadstats.metrics import MetricsAggregator, Counter, Gauge, Histogram, Timing,\ - Distribution +from datadog.threadstats.metrics import ( + MetricsAggregator, Counter, Gauge, Histogram, Timing, Distribution, Set +) from datadog.threadstats.reporters import HttpReporter # Loggers @@ -177,6 +178,18 @@ class ThreadStats(object): self._metric_aggregator.add_point(metric_name, tags, timestamp or time(), value, Gauge, sample_rate=sample_rate, host=host) + def set(self, metric_name, value, timestamp=None, tags=None, sample_rate=1, host=None): + """ + Add ``value`` to the current set. The length of the set is + flushed as a gauge to Datadog. Optionally, specify a set of + tags to associate with the metric. + + >>> stats.set('example_metric.set', "value_1", tags=['environement:dev']) + """ + if not self._disabled: + self._metric_aggregator.add_point(metric_name, tags, timestamp or time(), value, Set, + sample_rate=sample_rate, host=host) + def increment(self, metric_name, value=1, timestamp=None, tags=None, sample_rate=1, host=None): """ Increment the counter by the given ``value``. Optionally, specify a list of @@ -285,13 +298,16 @@ class ThreadStats(object): finally: stats.histogram('user.query.time', time.time() - start) """ + def wrapper(func): @wraps(func) def wrapped(*args, **kwargs): with self.timer(metric_name, sample_rate, tags, host): result = func(*args, **kwargs) return result + return wrapped + return wrapper def flush(self, timestamp=None): diff --git a/datadog/threadstats/metrics.py b/datadog/threadstats/metrics.py index 00ff71e..fe3a0b7 100644 --- a/datadog/threadstats/metrics.py +++ b/datadog/threadstats/metrics.py @@ -28,6 +28,25 @@ class Metric(object): raise NotImplementedError() +class Set(Metric): + """ A set metric. """ + + stats_tag = 'g' + + def __init__(self, name, tags, host): + self.name = name + self.tags = tags + self.host = host + self.set = set() + + def add_point(self, value): + self.set.add(value) + + def flush(self, timestamp, interval): + return [(timestamp, len(self.set), self.name, self.tags, + self.host, MetricType.Gauge, interval)] + + class Gauge(Metric): """ A gauge metric. """

DataDog/datadogpy

0ac41036382b9dc418afe367923ce14d7cdc4314

diff --git a/tests/unit/threadstats/test_threadstats.py b/tests/unit/threadstats/test_threadstats.py index 918a3b2..40c74a4 100644 --- a/tests/unit/threadstats/test_threadstats.py +++ b/tests/unit/threadstats/test_threadstats.py @@ -25,10 +25,6 @@ logger = logging.getLogger('dd.datadogpy') logger.setLevel(logging.ERROR) -def assert_equal(a, b): - assert a == b - - class MemoryReporter(object): """ A reporting class that reports to memory for testing. @@ -127,21 +123,21 @@ class TestUnitThreadStats(unittest.TestCase): """docstring""" return (a, b, c, d) - assert_equal(func.__name__, 'func') - assert_equal(func.__doc__, 'docstring') + assert func.__name__ == 'func' + assert func.__doc__ == 'docstring' result = func(1, 2, d=3) # Assert it handles args and kwargs correctly. - assert_equal(result, (1, 2, 1, 3)) + assert result == (1, 2, 1, 3) time.sleep(1) # Argh. I hate this. dog.flush() metrics = self.sort_metrics(reporter.metrics) - assert_equal(len(metrics), 8) + assert len(metrics) == 8 (_, _, _, _, avg, count, max_, min_) = metrics - assert_equal(avg['metric'], 'timed.test.avg') - assert_equal(count['metric'], 'timed.test.count') - assert_equal(max_['metric'], 'timed.test.max') - assert_equal(min_['metric'], 'timed.test.min') + assert avg['metric'] == 'timed.test.avg' + assert count['metric'] == 'timed.test.count' + assert max_['metric'] == 'timed.test.max' + assert min_['metric'] == 'timed.test.min' def test_event(self): dog = ThreadStats() @@ -159,10 +155,10 @@ class TestUnitThreadStats(unittest.TestCase): # Flush and test dog.flush() event1, event2 = reporter.events - assert_equal(event1['title'], event1_title) - assert_equal(event1['text'], event1_text) - assert_equal(event2['title'], event2_title) - assert_equal(event2['text'], event2_text) + assert event1['title'] == event1_title + assert event1['text'] == event1_text + assert event2['title'] == event2_title + assert event2['text'] == event2_text # Test more parameters reporter.events = [] @@ -175,11 +171,11 @@ class TestUnitThreadStats(unittest.TestCase): # Flush and test dog.flush() event, = reporter.events - assert_equal(event['title'], event1_title) - assert_equal(event['text'], event1_text) - assert_equal(event['priority'], event1_priority) - assert_equal(event['date_happened'], event1_date_happened) - assert_equal(event['tags'], [event1_tag]) + assert event['title'] == event1_title + assert event['text'] == event1_text + assert event['priority'] == event1_priority + assert event['date_happened'] == event1_date_happened + assert event['tags'] == [event1_tag] def test_event_constant_tags(self): constant_tag = 'type:constant' @@ -198,13 +194,13 @@ class TestUnitThreadStats(unittest.TestCase): # Flush and test dog.flush() event1, event2 = reporter.events - assert_equal(event1['title'], event1_title) - assert_equal(event1['text'], event1_text) - assert_equal(event1['tags'], [constant_tag]) - assert_equal(event2['title'], event2_title) - assert_equal(event2['text'], event2_text) - assert_equal(event2['text'], event2_text) - assert_equal(event2['tags'], [constant_tag]) + assert event1['title'] == event1_title + assert event1['text'] == event1_text + assert event1['tags'] == [constant_tag] + assert event2['title'] == event2_title + assert event2['text'] == event2_text + assert event2['text'] == event2_text + assert event2['tags'] == [constant_tag] # Test more parameters reporter.events = [] @@ -217,11 +213,11 @@ class TestUnitThreadStats(unittest.TestCase): # Flush and test dog.flush() event, = reporter.events - assert_equal(event['title'], event1_title) - assert_equal(event['text'], event1_text) - assert_equal(event['priority'], event1_priority) - assert_equal(event['date_happened'], event1_date_happened) - assert_equal(event['tags'], [event1_tag, constant_tag]) + assert event['title'] == event1_title + assert event['text'] == event1_text + assert event['priority'] == event1_priority + assert event['date_happened'] == event1_date_happened + assert event['tags'] == [event1_tag, constant_tag] def test_histogram(self): dog = ThreadStats() @@ -245,55 +241,55 @@ class TestUnitThreadStats(unittest.TestCase): # Flush and ensure they roll up properly. dog.flush(120.0) metrics = self.sort_metrics(reporter.metrics) - assert_equal(len(metrics), 24) + assert len(metrics) == 24 # Test histograms elsewhere. (h1751, h1851, h1951, h1991, h1avg1, h1cnt1, h1max1, h1min1, _, _, _, _, h2avg1, h2cnt1, h2max1, h2min1, h1752, _, _, h1992, h1avg2, h1cnt2, h1max2, h1min2) = metrics - assert_equal(h1avg1['metric'], 'histogram.1.avg') - assert_equal(h1avg1['points'][0][0], 100.0) - assert_equal(h1avg1['points'][0][1], 35) - assert_equal(h1cnt1['metric'], 'histogram.1.count') - assert_equal(h1cnt1['points'][0][0], 100.0) - assert_equal(h1cnt1['points'][0][1], 0.4) - assert_equal(h1min1['metric'], 'histogram.1.min') - assert_equal(h1min1['points'][0][1], 20) - assert_equal(h1max1['metric'], 'histogram.1.max') - assert_equal(h1max1['points'][0][1], 50) - assert_equal(h1751['metric'], 'histogram.1.75percentile') - assert_equal(h1751['points'][0][1], 40) - assert_equal(h1991['metric'], 'histogram.1.99percentile') - assert_equal(h1991['points'][0][1], 50) - - assert_equal(h1avg2['metric'], 'histogram.1.avg') - assert_equal(h1avg2['points'][0][0], 110.0) - assert_equal(h1avg2['points'][0][1], 40) - assert_equal(h1cnt2['metric'], 'histogram.1.count') - assert_equal(h1cnt2['points'][0][0], 110.0) - assert_equal(h1cnt2['points'][0][1], 0.3) - assert_equal(h1752['metric'], 'histogram.1.75percentile') - assert_equal(h1752['points'][0][0], 110.0) - assert_equal(h1752['points'][0][1], 40.0) - assert_equal(h1992['metric'], 'histogram.1.99percentile') - assert_equal(h1992['points'][0][0], 110.0) - assert_equal(h1992['points'][0][1], 50.0) - - assert_equal(h2avg1['metric'], 'histogram.2.avg') - assert_equal(h2avg1['points'][0][0], 100.0) - assert_equal(h2avg1['points'][0][1], 40) - assert_equal(h2cnt1['metric'], 'histogram.2.count') - assert_equal(h2cnt1['points'][0][0], 100.0) - assert_equal(h2cnt1['points'][0][1], 0.1) + assert h1avg1['metric'] == 'histogram.1.avg' + assert h1avg1['points'][0][0] == 100.0 + assert h1avg1['points'][0][1] == 35 + assert h1cnt1['metric'] == 'histogram.1.count' + assert h1cnt1['points'][0][0] == 100.0 + assert h1cnt1['points'][0][1] == 0.4 + assert h1min1['metric'] == 'histogram.1.min' + assert h1min1['points'][0][1] == 20 + assert h1max1['metric'] == 'histogram.1.max' + assert h1max1['points'][0][1] == 50 + assert h1751['metric'] == 'histogram.1.75percentile' + assert h1751['points'][0][1] == 40 + assert h1991['metric'] == 'histogram.1.99percentile' + assert h1991['points'][0][1] == 50 + + assert h1avg2['metric'] == 'histogram.1.avg' + assert h1avg2['points'][0][0] == 110.0 + assert h1avg2['points'][0][1] == 40 + assert h1cnt2['metric'] == 'histogram.1.count' + assert h1cnt2['points'][0][0] == 110.0 + assert h1cnt2['points'][0][1] == 0.3 + assert h1752['metric'] == 'histogram.1.75percentile' + assert h1752['points'][0][0] == 110.0 + assert h1752['points'][0][1] == 40.0 + assert h1992['metric'] == 'histogram.1.99percentile' + assert h1992['points'][0][0] == 110.0 + assert h1992['points'][0][1] == 50.0 + + assert h2avg1['metric'] == 'histogram.2.avg' + assert h2avg1['points'][0][0] == 100.0 + assert h2avg1['points'][0][1] == 40 + assert h2cnt1['metric'] == 'histogram.2.count' + assert h2cnt1['points'][0][0] == 100.0 + assert h2cnt1['points'][0][1] == 0.1 # Flush again ensure they're gone. dog.reporter.metrics = [] dog.flush(140.0) - assert_equal(len(dog.reporter.metrics), 8) + assert len(dog.reporter.metrics) == 8 dog.reporter.metrics = [] dog.flush(200.0) - assert_equal(len(dog.reporter.metrics), 0) + assert len(dog.reporter.metrics) == 0 def test_histogram_percentiles(self): dog = ThreadStats() @@ -312,10 +308,10 @@ class TestUnitThreadStats(unittest.TestCase): def assert_almost_equal(i, j, e=1): # Floating point math? assert abs(i - j) <= e, "%s %s %s" % (i, j, e) - assert_equal(len(metrics), 8) + assert len(metrics) == 8 p75, p85, p95, p99, _, _, _, _ = self.sort_metrics(metrics) - assert_equal(p75['metric'], 'percentiles.75percentile') - assert_equal(p75['points'][0][0], 1000.0) + assert p75['metric'] == 'percentiles.75percentile' + assert p75['points'][0][0] == 1000.0 assert_almost_equal(p75['points'][0][1], 75, 8) assert_almost_equal(p85['points'][0][1], 85, 8) assert_almost_equal(p95['points'][0][1], 95, 8) @@ -335,23 +331,61 @@ class TestUnitThreadStats(unittest.TestCase): # Assert they've been properly flushed. metrics = self.sort_metrics(reporter.metrics) - assert_equal(len(metrics), 2) + assert len(metrics) == 2 (first, second) = metrics - assert_equal(first['metric'], 'test.gauge.1') - assert_equal(first['points'][0][0], 100.0) - assert_equal(first['points'][0][1], 22) - assert_equal(second['metric'], 'test.gauge.2') + assert first['metric'] == 'test.gauge.1' + assert first['points'][0][0] == 100.0 + assert first['points'][0][1] == 22 + assert second['metric'] == 'test.gauge.2' # Flush again and make sure we're progressing. reporter.metrics = [] dog.flush(130.0) - assert_equal(len(reporter.metrics), 1) + assert len(reporter.metrics) == 1 + + # Finally, make sure we've flushed all metrics. + reporter.metrics = [] + dog.flush(150.0) + assert len(reporter.metrics) == 0 + + def test_set(self): + # Create some fake metrics. + dog = ThreadStats() + dog.start(roll_up_interval=10, flush_in_thread=False) + reporter = dog.reporter = MemoryReporter() + + dog.set('test.set.1', "a string", 100.0) + dog.set('test.set.1', frozenset(), 105.0) + dog.set('test.set.2', 30, 115.0) + dog.set('test.set.3', 30, 125.0) + dog.flush(120.0) + + # Assert they've been properly flushed. + metrics = self.sort_metrics(reporter.metrics) + assert len(metrics) == 2 + + (first, second) = metrics + assert first['metric'] == 'test.set.1' + assert first['points'][0][0] == 100.0 + assert first['points'][0][1] == 2 + assert second['metric'] == 'test.set.2' + assert second['points'][0][0] == 110.0 + assert second['points'][0][1] == 1 + + # Flush again and make sure we're progressing. + reporter.metrics = [] + dog.flush(130.0) + metrics = self.sort_metrics(reporter.metrics) + assert len(metrics) == 1 + assert metrics[0]['metric'] == 'test.set.3' + assert metrics[0]['points'][0][0] == 120.0 + assert metrics[0]['points'][0][1] == 1 # Finally, make sure we've flushed all metrics. reporter.metrics = [] dog.flush(150.0) - assert_equal(len(reporter.metrics), 0) + assert len(reporter.metrics) == 0 def test_counter(self): # Create some fake metrics. @@ -367,12 +401,12 @@ class TestUnitThreadStats(unittest.TestCase): # Assert they've been properly flushed. metrics = self.sort_metrics(reporter.metrics) - assert_equal(len(metrics), 2) + assert len(metrics) == 2 (first, second) = metrics - assert_equal(first['metric'], 'test.counter.1') - assert_equal(first['points'][0][0], 1000.0) - assert_equal(first['points'][0][1], 0.3) - assert_equal(second['metric'], 'test.counter.2') + assert first['metric'] == 'test.counter.1' + assert first['points'][0][0] == 1000.0 + assert first['points'][0][1] == 0.3 + assert second['metric'] == 'test.counter.2' # Test decrement dog.increment('test.counter.1', value=10, timestamp=1000.0) @@ -381,22 +415,22 @@ class TestUnitThreadStats(unittest.TestCase): dog.flush(1021.0) metrics = self.sort_metrics(reporter.metrics) - assert_equal(len(metrics), 1) + assert len(metrics) == 1 first, = metrics - assert_equal(first['metric'], 'test.counter.1') - assert_equal(first['points'][0][0], 1000.0) - assert_equal(first['points'][0][1], 0.8) - assert_equal(second['metric'], 'test.counter.2') + assert first['metric'] == 'test.counter.1' + assert first['points'][0][0] == 1000.0 + assert first['points'][0][1] == 0.8 + assert second['metric'] == 'test.counter.2' # Flush again and make sure we're progressing. reporter.metrics = [] dog.flush(1030.0) - assert_equal(len(reporter.metrics), 1) + assert len(reporter.metrics) == 1 # Finally, make sure we've flushed all metrics. reporter.metrics = [] dog.flush(1050.0) - assert_equal(len(reporter.metrics), 0) + assert len(reporter.metrics) == 0 def test_distribution(self): # Create some fake metrics. @@ -412,23 +446,23 @@ class TestUnitThreadStats(unittest.TestCase): # Assert they've been properly flushed. dists = self.sort_metrics(reporter.distributions) - assert_equal(len(dists), 2) + assert len(dists) == 2 (first, second) = dists - assert_equal(first['metric'], 'test.dist.1') - assert_equal(first['points'][0][0], 100.0) - assert_equal(first['points'][0][1], [20, 22]) - assert_equal(second['metric'], 'test.dist.2') + assert first['metric'] == 'test.dist.1' + assert first['points'][0][0] == 100.0 + assert first['points'][0][1] == [20, 22] + assert second['metric'] == 'test.dist.2' # Flush again and make sure we're progressing. reporter.distributions = [] dog.flush(130.0) - assert_equal(len(reporter.distributions), 1) + assert len(reporter.distributions) == 1 # Finally, make sure we've flushed all metrics. reporter.distributions = [] dog.flush(150.0) - assert_equal(len(reporter.distributions), 0) + assert len(reporter.distributions) == 0 def test_default_host_and_device(self): dog = ThreadStats() @@ -447,8 +481,8 @@ class TestUnitThreadStats(unittest.TestCase): dog.gauge('my.gauge', 1, 100.0, host='host') dog.flush(1000) metric = reporter.metrics[0] - assert_equal(metric['device'], 'dev') - assert_equal(metric['host'], 'host') + assert metric['device'] == 'dev' + assert metric['host'] == 'host' def test_tags(self): dog = ThreadStats() @@ -467,24 +501,28 @@ class TestUnitThreadStats(unittest.TestCase): dog.flush(200.0) metrics = self.sort_metrics(reporter.metrics) - assert_equal(len(metrics), 6) + assert len(metrics) == 6 [c1, c2, c3, g1, g2, g3] = metrics - (assert_equal(c['metric'], 'counter') for c in [c1, c2, c3]) - assert_equal(c1['tags'], None) - assert_equal(c1['points'][0][1], 0.1) - assert_equal(c2['tags'], ['env:production', 'db']) - assert_equal(c2['points'][0][1], 0.1) - assert_equal(c3['tags'], ['env:staging']) - assert_equal(c3['points'][0][1], 0.1) - - (assert_equal(c['metric'], 'gauge') for c in [g1, g2, g3]) - assert_equal(g1['tags'], None) - assert_equal(g1['points'][0][1], 10) - assert_equal(g2['tags'], ['env:production', 'db']) - assert_equal(g2['points'][0][1], 15) - assert_equal(g3['tags'], ['env:staging']) - assert_equal(g3['points'][0][1], 20) + assert c1['metric'] == 'counter' + assert c2['metric'] == 'counter' + assert c3['metric'] == 'counter' + assert c1['tags'] is None + assert c1['points'][0][1] == 0.1 + assert c2['tags'] == ['env:production', 'db'] + assert c2['points'][0][1] == 0.1 + assert c3['tags'] == ['env:staging'] + assert c3['points'][0][1] == 0.1 + + assert g1['metric'] == 'gauge' + assert g2['metric'] == 'gauge' + assert g3['metric'] == 'gauge' + assert g1['tags'] is None + assert g1['points'][0][1] == 10 + assert g2['tags'] == ['env:production', 'db'] + assert g2['points'][0][1] == 15 + assert g3['tags'] == ['env:staging'] + assert g3['points'][0][1] == 20 def test_constant_tags(self): """ @@ -579,27 +617,31 @@ class TestUnitThreadStats(unittest.TestCase): dog.flush(200.0) metrics = self.sort_metrics(reporter.metrics) - assert_equal(len(metrics), 6) + assert len(metrics) == 6 [c1, c2, c3, g1, g2, g3] = metrics - (assert_equal(c['metric'], 'counter') for c in [c1, c2, c3]) - assert_equal(c1['host'], None) - assert_equal(c1['tags'], None) - assert_equal(c1['points'][0][1], 0.2) - assert_equal(c2['host'], 'test') - assert_equal(c2['tags'], None) - assert_equal(c2['points'][0][1], 0.1) - assert_equal(c3['host'], 'test') - assert_equal(c3['tags'], ['tag']) - assert_equal(c3['points'][0][1], 0.2) - - (assert_equal(g['metric'], 'gauge') for g in [g1, g2, g3]) - assert_equal(g1['host'], None) - assert_equal(g1['points'][0][1], 10) - assert_equal(g2['host'], '') - assert_equal(g2['points'][0][1], 12) - assert_equal(g3['host'], 'test') - assert_equal(g3['points'][0][1], 15) + assert c1['metric'] == 'counter' + assert c2['metric'] == 'counter' + assert c3['metric'] == 'counter' + assert c1['host'] is None + assert c1['tags'] is None + assert c1['points'][0][1] == 0.2 + assert c2['host'] == 'test' + assert c2['tags'] is None + assert c2['points'][0][1] == 0.1 + assert c3['host'] == 'test' + assert c3['tags'] == ['tag'] + assert c3['points'][0][1] == 0.2 + + assert g1['metric'] == 'gauge' + assert g2['metric'] == 'gauge' + assert g3['metric'] == 'gauge' + assert g1['host'] is None + assert g1['points'][0][1] == 10 + assert g2['host'] == '' + assert g2['points'][0][1] == 12 + assert g3['host'] == 'test' + assert g3['points'][0][1] == 15 # Ensure histograms work as well. @dog.timed('timed', host='test') @@ -658,13 +700,13 @@ class TestUnitThreadStats(unittest.TestCase): # Flush and test dog.flush() event1, event2 = reporter.events - assert_equal(event1['title'], event1_title) - assert_equal(event1['text'], event1_text) - assert_equal(event1['tags'], test_tags) - assert_equal(event2['title'], event2_title) - assert_equal(event2['text'], event2_text) - assert_equal(event2['text'], event2_text) - assert_equal(event2['tags'], test_tags) + assert event1['title'] == event1_title + assert event1['text'] == event1_text + assert event1['tags'] == test_tags + assert event2['title'] == event2_title + assert event2['text'] == event2_text + assert event2['text'] == event2_text + assert event2['tags'] == test_tags # Test more parameters reporter.events = [] @@ -677,11 +719,11 @@ class TestUnitThreadStats(unittest.TestCase): # Flush and test dog.flush() event, = reporter.events - assert_equal(event['title'], event1_title) - assert_equal(event['text'], event1_text) - assert_equal(event['priority'], event1_priority) - assert_equal(event['date_happened'], event1_date_happened) - assert_equal(event['tags'], [event1_tag] + test_tags) + assert event['title'] == event1_title + assert event['text'] == event1_text + assert event['priority'] == event1_priority + assert event['date_happened'] == event1_date_happened + assert event['tags'] == [event1_tag] + test_tags dog.start(flush_interval=1, roll_up_interval=1) def test_tags_from_environment_and_constant(self): @@ -704,13 +746,13 @@ class TestUnitThreadStats(unittest.TestCase): # Flush and test dog.flush() event1, event2 = reporter.events - assert_equal(event1['title'], event1_title) - assert_equal(event1['text'], event1_text) - assert_equal(event1['tags'], constant_tags + test_tags) - assert_equal(event2['title'], event2_title) - assert_equal(event2['text'], event2_text) - assert_equal(event2['text'], event2_text) - assert_equal(event2['tags'], constant_tags + test_tags) + assert event1['title'] == event1_title + assert event1['text'] == event1_text + assert event1['tags'] == constant_tags + test_tags + assert event2['title'] == event2_title + assert event2['text'] == event2_text + assert event2['text'] == event2_text + assert event2['tags'] == constant_tags + test_tags # Test more parameters reporter.events = [] @@ -723,11 +765,11 @@ class TestUnitThreadStats(unittest.TestCase): # Flush and test dog.flush() event, = reporter.events - assert_equal(event['title'], event1_title) - assert_equal(event['text'], event1_text) - assert_equal(event['priority'], event1_priority) - assert_equal(event['date_happened'], event1_date_happened) - assert_equal(event['tags'], [event1_tag] + constant_tags + test_tags) + assert event['title'] == event1_title + assert event['text'] == event1_text + assert event['priority'] == event1_priority + assert event['date_happened'] == event1_date_happened + assert event['tags'] == [event1_tag] + constant_tags + test_tags dog.start(flush_interval=1, roll_up_interval=1) def test_metric_type(self): @@ -748,16 +790,16 @@ class TestUnitThreadStats(unittest.TestCase): (first, second, p75, p85, p95, p99, avg, cnt, max_, min_) = self.sort_metrics(reporter.metrics) # Assert Metric type - assert_equal(first['type'], 'rate') - assert_equal(second['type'], 'gauge') - assert_equal(p75['type'], 'gauge') - assert_equal(p85['type'], 'gauge') - assert_equal(p95['type'], 'gauge') - assert_equal(p99['type'], 'gauge') - assert_equal(avg['type'], 'gauge') - assert_equal(cnt['type'], 'rate') - assert_equal(max_['type'], 'gauge') - assert_equal(min_['type'], 'gauge') + assert first['type'] == 'rate' + assert second['type'] == 'gauge' + assert p75['type'] == 'gauge' + assert p85['type'] == 'gauge' + assert p95['type'] == 'gauge' + assert p99['type'] == 'gauge' + assert avg['type'] == 'gauge' + assert cnt['type'] == 'rate' + assert max_['type'] == 'gauge' + assert min_['type'] == 'gauge' # Test lambda_wrapper (uses ThreadStats under the hood) def test_basic_lambda_decorator(self): @@ -769,9 +811,9 @@ class TestUnitThreadStats(unittest.TestCase): _lambda_stats.reporter = self.reporter basic_wrapped_function() - assert_equal(_lambda_stats.reporter.dist_flush_counter, 1) + assert _lambda_stats.reporter.dist_flush_counter == 1 dists = self.sort_metrics(_lambda_stats.reporter.distributions) - assert_equal(len(dists), 1) + assert len(dists) == 1 def test_embedded_lambda_decorator(self): """ @@ -789,7 +831,7 @@ class TestUnitThreadStats(unittest.TestCase): _lambda_stats.reporter = self.reporter wrapped_function_2() - assert_equal(_lambda_stats.reporter.dist_flush_counter, 1) + assert _lambda_stats.reporter.dist_flush_counter == 1 dists = self.sort_metrics(_lambda_stats.reporter.distributions) - assert_equal(len(dists), 2) + assert len(dists) == 2

Threadstatsd set metric There appears to be a disconnect between dogstatd and threadstatsd. the `set` method is not supported. What is the equivalent in the thread version? https://github.com/DataDog/datadogpy/blob/master/datadog/dogstatsd/base.py#L227

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

DataDog__datadogpy-555

diff --git a/datadog/dogshell/wrap.py b/datadog/dogshell/wrap.py index 022b333..a454d33 100644 --- a/datadog/dogshell/wrap.py +++ b/datadog/dogshell/wrap.py @@ -211,8 +211,9 @@ def build_event_body(cmd, returncode, stdout, stderr, notifications): ) if notifications: + notifications = notifications.decode("utf-8", "replace") if isinstance(notifications, bytes) else notifications fmt_notifications = u"**>>>> NOTIFICATIONS <<<<**\n\n {notifications}\n".format( - notifications=notifications.decode("utf-8", "replace") + notifications=notifications ) return \

DataDog/datadogpy

6319ebde0e6bce51c5f6c21f253204c3a13f4d92

diff --git a/tests/unit/dogwrap/test_dogwrap.py b/tests/unit/dogwrap/test_dogwrap.py index e4cd2a3..02341ca 100644 --- a/tests/unit/dogwrap/test_dogwrap.py +++ b/tests/unit/dogwrap/test_dogwrap.py @@ -47,6 +47,11 @@ class TestDogwrap(unittest.TestCase): event_body = build_event_body(cmd, returncode, stdout, stderr, notifications) self.assertEqual(expected_body, event_body) + # notifications can be unicode already in py3, make sure we don't try decoding + notifications = notifications.decode("utf-8", "replace") + event_body = build_event_body(cmd, returncode, stdout, stderr, notifications) + self.assertEqual(expected_body, event_body) + def test_parse_options(self): options, cmd = parse_options([]) self.assertEqual(cmd, '')

String decode in dogwrap **Describe the bug** The parameters `notify_success`, `notify_warning` and `notify_error` cause the `AttributeError` shown below to be thrown when used. ``` Traceback (most recent call last): File "/usr/local/bin/dogwrap", line 8, in <module> sys.exit(main()) File "/usr/local/lib/python3.7/site-packages/datadog/dogshell/wrap.py", line 377, in main event_body = build_event_body(cmd, returncode, stdout, stderr, notifications) File "/usr/local/lib/python3.7/site-packages/datadog/dogshell/wrap.py", line 209, in build_event_body notifications=notifications.decode("utf-8", "replace") AttributeError: 'str' object has no attribute 'decode' ``` Line 209 attempts to call a decode method on a string. To my knowledge, this method has been removed in python3. **To Reproduce** Steps to reproduce the behavior: 1. Install datadog for python3 2. Execute the `dogwrap` command with the `--notify_error` flag set to any string and a command that causes an error 3. Get an exception **Expected behavior** The datadog event to be logged with the string specified by `--notify_error` in after `**>>>> NOTIFICATIONS <<<<**` **Screenshots** ``` $ dogwrap -n "Example Error" -k ${API_KEY} --submit_mode errors --notify_error "test notification" "pwd -h" Traceback (most recent call last): File "/usr/local/bin/dogwrap", line 8, in <module> sys.exit(main()) File "/usr/local/lib/python3.7/site-packages/datadog/dogshell/wrap.py", line 377, in main event_body = build_event_body(cmd, returncode, stdout, stderr, notifications) File "/usr/local/lib/python3.7/site-packages/datadog/dogshell/wrap.py", line 209, in build_event_body notifications=notifications.decode("utf-8", "replace") AttributeError: 'str' object has no attribute 'decode' ``` **Environment and Versions (please complete the following information):** ``` $ python3 --version Python 3.7.6 $ dogwrap --version dogwrap 0.34.1 ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

DataDog__datadogpy-609

diff --git a/datadog/threadstats/aws_lambda.py b/datadog/threadstats/aws_lambda.py index fa24951..5a3c6de 100644 --- a/datadog/threadstats/aws_lambda.py +++ b/datadog/threadstats/aws_lambda.py @@ -44,6 +44,9 @@ class _LambdaDecorator(object): # This avoids adding execution time at the end of the lambda run t = Thread(target=_init_api_client) t.start() + + # Make sure the global ThreadStats has been created + _get_lambda_stats() cls._counter = cls._counter + 1 @classmethod @@ -63,7 +66,7 @@ class _LambdaDecorator(object): if cls._counter > 0: should_flush = False if should_flush: - _lambda_stats.flush(float("inf")) + _get_lambda_stats().flush(float("inf")) def __call__(self, *args, **kw): warnings.warn("datadog_lambda_wrapper() is relocated to https://git.io/fjy8o", DeprecationWarning) @@ -74,14 +77,22 @@ class _LambdaDecorator(object): _LambdaDecorator._close() -_lambda_stats = ThreadStats() -_lambda_stats.start(flush_in_greenlet=False, flush_in_thread=False) +_lambda_stats = None datadog_lambda_wrapper = _LambdaDecorator +def _get_lambda_stats(): + global _lambda_stats + # This is not thread-safe, it should be called first by _LambdaDecorator + if _lambda_stats is None: + _lambda_stats = ThreadStats() + _lambda_stats.start(flush_in_greenlet=False, flush_in_thread=False) + return _lambda_stats + + def lambda_metric(*args, **kw): """ Alias to expose only distributions for lambda functions""" - _lambda_stats.distribution(*args, **kw) + _get_lambda_stats().distribution(*args, **kw) def _init_api_client():

DataDog/datadogpy

1d796ec40d2e48b2059e9370b27bc1add4d5b1e1

diff --git a/tests/unit/threadstats/test_threadstats.py b/tests/unit/threadstats/test_threadstats.py index 40c74a4..bc1b9c1 100644 --- a/tests/unit/threadstats/test_threadstats.py +++ b/tests/unit/threadstats/test_threadstats.py @@ -17,7 +17,7 @@ from mock import patch # datadog from datadog import ThreadStats, lambda_metric, datadog_lambda_wrapper -from datadog.threadstats.aws_lambda import _lambda_stats +from datadog.threadstats.aws_lambda import _get_lambda_stats from tests.util.contextmanagers import preserve_environment_variable # Silence the logger. @@ -808,11 +808,11 @@ class TestUnitThreadStats(unittest.TestCase): def basic_wrapped_function(): lambda_metric("lambda.somemetric", 100) - _lambda_stats.reporter = self.reporter + _get_lambda_stats().reporter = self.reporter basic_wrapped_function() - assert _lambda_stats.reporter.dist_flush_counter == 1 - dists = self.sort_metrics(_lambda_stats.reporter.distributions) + assert _get_lambda_stats().reporter.dist_flush_counter == 1 + dists = self.sort_metrics(_get_lambda_stats().reporter.distributions) assert len(dists) == 1 def test_embedded_lambda_decorator(self): @@ -829,9 +829,9 @@ class TestUnitThreadStats(unittest.TestCase): wrapped_function_1() lambda_metric("lambda.dist.2", 30) - _lambda_stats.reporter = self.reporter + _get_lambda_stats().reporter = self.reporter wrapped_function_2() - assert _lambda_stats.reporter.dist_flush_counter == 1 + assert _get_lambda_stats().reporter.dist_flush_counter == 1 - dists = self.sort_metrics(_lambda_stats.reporter.distributions) + dists = self.sort_metrics(_get_lambda_stats().reporter.distributions) assert len(dists) == 2

"import datadog" executes statements **Describe the bug** `import datadog` executes statements. In particular, it runs `atexit.register(lambda: self.flush(float('inf')))` in `datadog/threadstats/base.py`. This results in errors in our unit tests because the exit handler, `datadog.threadstats.ThreadStats.flush`, calls `log.debug` after the logging capture file has been closed. **To Reproduce** Steps to reproduce the behavior: 1. Create a Python file, p.py, containing only `import datadog` 2. Run pdb on p.py 3. Set a breakpoint on `.../datadog/threadstats/base.py:337` 4. Enter `c` to start execution 5. Once the breakpoint is hit, enter `bt` to see the backtrace leading back to `import datadog` **Expected behavior** `import datadog` should not execute any statements. **Environment and Versions (please complete the following information):** - datadogpy 0.36.0 - python 3.7

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

DataDog__datadogpy-625

diff --git a/datadog/threadstats/base.py b/datadog/threadstats/base.py index 5fc8a4e..84041bb 100644 --- a/datadog/threadstats/base.py +++ b/datadog/threadstats/base.py @@ -31,6 +31,12 @@ from datadog.threadstats.reporters import HttpReporter # Loggers log = logging.getLogger('datadog.threadstats') +DD_ENV_TAGS_MAPPING = { + 'DD_ENV': 'env', + 'DD_SERVICE': 'service', + 'DD_VERSION': 'version', +} + class ThreadStats(object): @@ -48,11 +54,27 @@ class ThreadStats(object): :type compress_payload: bool :envvar DATADOG_TAGS: Tags to attach to every metric reported by ThreadStats client - :type DATADOG_TAGS: list of strings + :type DATADOG_TAGS: comma-delimited string + + :envvar DD_ENV: the env of the service running the ThreadStats client. + If set, it is appended to the constant (global) tags of the client. + :type DD_ENV: string + + :envvar DD_SERVICE: the name of the service running the ThreadStats client. + If set, it is appended to the constant (global) tags of the client. + :type DD_SERVICE: string + + :envvar DD_VERSION: the version of the service running the ThreadStats client. + If set, it is appended to the constant (global) tags of the client. + :type DD_VERSION: string """ # Parameters self.namespace = namespace env_tags = [tag for tag in os.environ.get('DATADOG_TAGS', '').split(',') if tag] + for var, tag_name in DD_ENV_TAGS_MAPPING.items(): + value = os.environ.get(var, '') + if value: + env_tags.append('{name}:{value}'.format(name=tag_name, value=value)) if constant_tags is None: constant_tags = [] self.constant_tags = constant_tags + env_tags

DataDog/datadogpy

b9449d6ae2a378ed6986b7977ed547f2c63beeef

diff --git a/tests/unit/threadstats/test_threadstats.py b/tests/unit/threadstats/test_threadstats.py index bc1b9c1..998633b 100644 --- a/tests/unit/threadstats/test_threadstats.py +++ b/tests/unit/threadstats/test_threadstats.py @@ -18,7 +18,7 @@ from mock import patch # datadog from datadog import ThreadStats, lambda_metric, datadog_lambda_wrapper from datadog.threadstats.aws_lambda import _get_lambda_stats -from tests.util.contextmanagers import preserve_environment_variable +from tests.util.contextmanagers import preserve_environment_variable, EnvVars # Silence the logger. logger = logging.getLogger('dd.datadogpy') @@ -772,6 +772,31 @@ class TestUnitThreadStats(unittest.TestCase): assert event['tags'] == [event1_tag] + constant_tags + test_tags dog.start(flush_interval=1, roll_up_interval=1) + def test_tags_from_environment_env_service_version(self): + test_tags = set(['env:staging', 'service:food', 'version:1.2.3']) + with EnvVars( + env_vars={ + "DD_ENV": "staging", + "DD_VERSION": "1.2.3", + "DD_SERVICE": "food", + } + ): + dog = ThreadStats() + dog.start(roll_up_interval=10, flush_in_thread=False) + reporter = dog.reporter = MemoryReporter() + + # Add two events + event1_title = "Event 1 title" + event1_text = "Event 1 text" + dog.event(event1_title, event1_text) + + # Flush and test + dog.flush() + [event1] = reporter.events + assert event1['title'] == event1_title + assert event1['text'] == event1_text + assert set(event1['tags']) == test_tags + def test_metric_type(self): """ Checks the submitted metric's metric type.

DD_ENV (SERVICE, VERSION) are not used in ThreadStats https://github.com/DataDog/datadogpy/pull/548 added support for taking unified tags from env vars, but it doesn't works when using ThreadStats in the following way: ``` >>> from datadog import initialize, ThreadStats >>> initialize(api_key='my_api_key') >>> stats = ThreadStats() >>> stats.start() ```

2401580b6f41fe72f1360493ee46e8a842bd04ba

bsd-3-clause

Deltares__pyflwdir-18

diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c0327c7..f240f71 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -2,6 +2,16 @@ Change Log ########### +Unreleased +******************** + +Improved +--------- +* prioritize non-boundary cells with same elevation over boundary cells in dem.fill_depressions, #17 + +Bugfix +------ + 0.5.3 (18-Nov-2021) ******************** diff --git a/pyflwdir/dem.py b/pyflwdir/dem.py index 0d6876e..cb77f81 100644 --- a/pyflwdir/dem.py +++ b/pyflwdir/dem.py @@ -76,25 +76,27 @@ def fill_depressions( # initiate queue if idxs_pit is None: # with edge cells queued = gis_utils.get_edge(~done, structure=struct) - else: # with user difinfed outlet cells + else: # with user defined outlet cells queued = np.array([bool(0) for s in range(elevtn.size)]).reshape((nrow, ncol)) for idx in idxs_pit: queued.flat[idx] = True - q = [(elevtn[0, 0], np.uint32(0), np.uint32(0)) for _ in range(0)] + # queue contains (elevation, boundary, row, col) + # boundary is included to favor non-boundary cells over boundary cells with same elevation + q = [(elevtn[0, 0], np.uint8(1), np.uint32(0), np.uint32(0)) for _ in range(0)] heapq.heapify(q) for r, c in zip(*np.where(queued)): - heapq.heappush(q, (elevtn[r, c], np.uint32(r), np.uint32(c))) + heapq.heappush(q, (elevtn[r, c], np.uint8(1), np.uint32(r), np.uint32(c))) # restrict queue to global edge mimimum (single outlet) if outlets == "min": q = [heapq.heappop(q)] queued[:, :] = False - queued[q[0][1], q[0][2]] = True + queued[q[0][-2], q[0][-1]] = True # loop over cells and neighbors with ascending cell elevation. drs, dcs = np.where(struct) drs, dcs = drs - 1, dcs - 1 while len(q) > 0: - z0, r0, c0 = heapq.heappop(q) + z0, _, r0, c0 = heapq.heappop(q) for dr, dc in zip(drs, dcs): r = r0 + dr c = c0 + dc @@ -104,7 +106,7 @@ def fill_depressions( dz = z0 - z1 # local depression if dz > 0 if max_depth >= 0: # if positive max_depth: don't fill when dz > max_depth if dz >= max_depth: - heapq.heappush(q, (z1, np.uint32(r), np.uint32(c))) + heapq.heappush(q, (z1, np.uint8(0), np.uint32(r), np.uint32(c))) queued[r, c] = True for dr, dc in zip(drs, dcs): # (re)visit neighbors done[r + dr, c + dc] = False @@ -116,7 +118,7 @@ def fill_depressions( delv[r, c] = dz z1 += dz if ~queued[r, c]: # add to queue - heapq.heappush(q, (z1, np.uint32(r), np.uint32(c))) + heapq.heappush(q, (z1, np.uint8(0), np.uint32(r), np.uint32(c))) queued[r, c] = True done[r, c] = True d8[r, c] = core_d8._us[dr + 1, dc + 1]

Deltares/pyflwdir

90be06f24c7d7ce9bbeeccf19b1452d5be8859d2

diff --git a/tests/test_dem.py b/tests/test_dem.py index 8d7449a..39ec1d4 100644 --- a/tests/test_dem.py +++ b/tests/test_dem.py @@ -24,12 +24,13 @@ def test_from_dem(): ) # NOTE: compared to paper same a_filled, but difference # in flowdir because row instead of col first .. + # and priority of non-boundary cells with same elevation d8 = np.array( [ [2, 2, 4, 8, 1, 0, 16], [1, 1, 2, 2, 128, 64, 32], [128, 128, 1, 1, 2, 2, 4], - [64, 128, 128, 128, 1, 1, 0], + [128, 128, 128, 128, 1, 1, 0], [64, 128, 64, 32, 128, 128, 64], ], dtype=np.uint8,

prioritize non-boundary cells with same elevation over boundary cells in dem.fill_depressions

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

Deric-W__ascii_progress-9

diff --git a/ascii_progress/__main__.py b/ascii_progress/__main__.py index f5d1e15..b550f91 100644 --- a/ascii_progress/__main__.py +++ b/ascii_progress/__main__.py @@ -16,7 +16,7 @@ for frames in ( (">))'>", " >))'>", " >))'>", " <'((<", " <'((<", "<'((<") ): sys.stdout.write("Working ") - with Spinner(frames) as spinner: + with Spinner(frames).handle_exceptions("Done", "Exception") as spinner: for _ in map(spinner.set_progress, range(1, 15)): time.sleep(0.2) @@ -29,6 +29,6 @@ for bar_format in map( ) ): sys.stdout.write("Working ") - with bar_format.bar(75) as bar: + with bar_format.bar(75).handle_exceptions("Done", "Exception") as bar: for _ in bar: time.sleep(0.02) diff --git a/ascii_progress/bar.py b/ascii_progress/bar.py index e660116..b5f0903 100644 --- a/ascii_progress/bar.py +++ b/ascii_progress/bar.py @@ -9,11 +9,23 @@ import sys import math from abc import abstractmethod from string import Formatter -from typing import Callable, Sequence, TextIO, Tuple, Iterator, ContextManager, Mapping, Any, Union +from typing import ( + Callable, + Sequence, + TextIO, + Tuple, + Iterator, + ContextManager, + Mapping, + Any, + Union, + TypeVar +) __all__ = ( "LazyFormatter", "LAZY_FORMATTER", + "BarContext", "Bar", "ThresholdDecorator", "PercentDecorator", @@ -36,8 +48,48 @@ class LazyFormatter(Formatter): LAZY_FORMATTER = LazyFormatter() +T = TypeVar("T", bound="Bar") + + +class BarContext(ContextManager[T]): + """context manager which handles exceptions while using a bar""" + + bar: T + + message: str + + error: str + + __slots__ = ("bar", "message", "error") + + def __init__(self, bar: T, message: str, error: str) -> None: + self.bar = bar + self.message = message + self.error = error + + def __eq__(self, other: object) -> bool: + if isinstance(other, BarContext): + return self.bar == other.bar \ + and self.message == other.message \ + and self.error == other.error + return NotImplemented + + def __enter__(self) -> T: + return self.bar + + def __exit__(self, type, value, traceback) -> bool: # type: ignore + if type is None: + self.bar.replace(self.message, end="\n") + elif type is KeyboardInterrupt: + # add 2 \b and 2 spaces to handle additional ^C + # add 2 additional spaces to make up for missing padding + self.bar.replace("\b\b" + self.error, end=" \n") + else: + self.bar.replace(self.error, end="\n") + return False # we dont handle exceptions + -class Bar(ContextManager["Bar"], Iterator[None]): +class Bar(Iterator[None]): """abstract base class for progress bars""" __slots__ = () @@ -49,16 +101,6 @@ class Bar(ContextManager["Bar"], Iterator[None]): and self.width() == other.width() return NotImplemented - def __enter__(self) -> "Bar": - return self - - def __exit__(self, type, value, traceback) -> bool: # type: ignore - if type is KeyboardInterrupt: # handle ^C - self.replace("\b\bKeyboardInterrupt", end=" \n") - else: - self.replace("Finished") - return False # we dont handle exceptions - def __iter__(self) -> "Bar": return self @@ -97,6 +139,10 @@ class Bar(ContextManager["Bar"], Iterator[None]): """return the size of the bar""" raise NotImplementedError + def handle_exceptions(self: T, message: str, error: str) -> BarContext[T]: + """return a context manager which replaces the bar with message or error if a exceptions is raised""" + return BarContext(self, message, error) + def ratio(self) -> float: """return the ration progress / target""" return self.progress() / self.target() @@ -271,16 +317,14 @@ class PercentDecorator(ThresholdDecorator): @classmethod def with_inferred_thresholds(cls, bar: Bar) -> "PercentDecorator": """create an instance with inferred thresholds""" - lower_threshold, upper_threshold = calculate_thresholds(bar, 100) - return cls( - bar, - lower_threshold, - upper_threshold, - ) + return cls(bar, *calculate_thresholds(bar, 100)) def update_thresholds(self) -> None: """update lower and upper thresholds""" - self.lower_threshold, self.upper_threshold = calculate_thresholds(self.bar, 100) + self.lower_threshold, self.upper_threshold = calculate_thresholds( + self.bar, + 100 + ) class BarDecorator(ThresholdDecorator): @@ -291,16 +335,14 @@ class BarDecorator(ThresholdDecorator): @classmethod def with_inferred_thresholds(cls, bar: Bar) -> "BarDecorator": """create an instance with inferred thresholds""" - lower_threshold, upper_threshold = calculate_thresholds(bar, bar.width()) - return cls( - bar, - lower_threshold, - upper_threshold, - ) + return cls(bar, *calculate_thresholds(bar, bar.width())) def update_thresholds(self) -> None: """update lower and upper thresholds""" - self.lower_threshold, self.upper_threshold = calculate_thresholds(self.bar, self.bar.width()) + self.lower_threshold, self.upper_threshold = calculate_thresholds( + self.bar, + self.bar.width() + ) class BarFormat: diff --git a/ascii_progress/spinner.py b/ascii_progress/spinner.py index 17edecd..c3fc287 100644 --- a/ascii_progress/spinner.py +++ b/ascii_progress/spinner.py @@ -6,14 +6,55 @@ # SPDX-License-Identifier: MIT import sys -from typing import ContextManager, Iterator, TextIO, Sequence +from typing import ContextManager, Iterator, TextIO, Sequence, TypeVar __all__ = ( - "Spinner", + "SpinnerContext", + "Spinner" ) +T = TypeVar("T", bound="Spinner") -class Spinner(ContextManager, Iterator[None]): + +class SpinnerContext(ContextManager[T]): + """context manager which handles exceptions while using the spinner""" + + spinner: T + + message: str + + error: str + + __slots__ = ("spinner", "message", "error") + + def __init__(self, spinner: T, message: str, error: str) -> None: + self.spinner = spinner + self.message = message + self.error = error + + def __eq__(self, other: object) -> bool: + if isinstance(other, SpinnerContext): + return self.spinner == other.spinner \ + and self.message == other.message \ + and self.error == other.error + return NotImplemented + + def __enter__(self) -> T: + return self.spinner + + def __exit__(self, type, value, traceback) -> bool: # type: ignore + if type is None: + self.spinner.replace(self.message, end="\n") + elif type is KeyboardInterrupt: + # add 2 \b and 2 spaces to handle additional ^C + # add 2 additional spaces to make up for missing padding + self.spinner.replace("\b\b" + self.error, end=" \n") + else: + self.spinner.replace(self.error, end="\n") + return False # we dont handle exceptions + + +class Spinner(Iterator[None]): """class for creating a spinning animation""" frames: Sequence[str] @@ -43,16 +84,6 @@ class Spinner(ContextManager, Iterator[None]): and self.file is other.file return NotImplemented - def __enter__(self) -> "Spinner": - return self - - def __exit__(self, type, value, traceback) -> bool: # type: ignore - if type is KeyboardInterrupt: # add 2 \b and 2 spaces to handle additional ^C - self.replace("\b\bKeyboardInterrupt", end=" \n") - else: - self.replace("Finished") - return False # we dont handle exceptions - def __iter__(self) -> "Spinner": return self @@ -102,3 +133,7 @@ class Spinner(ContextManager, Iterator[None]): # pad message to fully overwrite old frame and add end self.file.write(message + " " * (len(self.current_frame) - len(message)) + end) self.file.flush() + + def handle_exceptions(self: T, message: str, error: str) -> SpinnerContext[T]: + """return a context manager which replaces the spinner with message or error if a exceptions is raised""" + return SpinnerContext(self, message, error)

Deric-W/ascii_progress

a5f5f2815ba25cdfdcf57a0f02c025ef9dc2a3b0

diff --git a/tests/test_bar.py b/tests/test_bar.py index bfab94b..bc53278 100644 --- a/tests/test_bar.py +++ b/tests/test_bar.py @@ -5,8 +5,10 @@ import unittest import unittest.mock from io import StringIO +from typing import ContextManager from ascii_progress.bar import ( LAZY_FORMATTER, + BarContext, Bar, ASCIIBar, ThresholdDecorator, @@ -42,6 +44,58 @@ class TestLazyFormatter(unittest.TestCase): ) +class BarSpinnerContext(unittest.TestCase): + """tests for BarContext""" + + def test_eq(self) -> None: + """test BarContext.__eq__""" + format = BarFormat(("-[", "]-"), (" ", "=="), 5) + bar = ASCIIBar(format, file=StringIO()) + contexts = [ + BarContext(bar, "1", "2"), + BarContext(bar, "2", "2"), + BarContext(bar, "1", "1"), + BarContext(ASCIIBar(format, file=StringIO()), "1", "1") + ] + for context in contexts: + self.assertEqual( + [context], + [c for c in contexts if c == context] + ) + self.assertNotEqual(contexts[0], 42) + + def test_context(self) -> None: + """test SpinnerContext as context manager""" + output = StringIO() + bar = ASCIIBar(BarFormat(("[", "]"), (" ", "="), 3, format="{bar}"), file=output) + with BarContext(bar, "1", "2") as context: + self.assertIsInstance(context, Bar) + context.set_progress(34) + context.update() + with self.assertRaises(RuntimeError): + with BarContext(bar, "1", "2") as context: + context.set_progress(67) + context.update() + raise RuntimeError + with self.assertRaises(KeyboardInterrupt): + with BarContext(bar, "1", "2") as context: + context.set_progress(100) + context.update() + raise KeyboardInterrupt + self.assertEqual( + output.getvalue(), + "\b\b\b\b\b".join(( + "[ ]", + "[= ]", + "1 \n", + "[== ]", + "2 \n", + "[===]", + "\b\b2 \n" + )) + ) + + class TestBar(unittest.TestCase): """Tests for Bar""" @@ -76,18 +130,11 @@ class TestBar(unittest.TestCase): break self.assertEqual(next(iterations), 11) - def test_enter(self) -> None: - """test Bar.__enter__ and __exit__""" - mock = unittest.mock.Mock(spec=Bar) - self.assertIs(Bar.__enter__(mock), mock) - self.assertFalse(Bar.__exit__(mock, None, None, None)) - self.assertFalse(Bar.__exit__(mock, KeyboardInterrupt, KeyboardInterrupt(), None)) - self.assertEqual( - mock.replace.call_args_list, - [ - unittest.mock.call("Finished"), - unittest.mock.call("\b\bKeyboardInterrupt", end=" \n") - ] + def test_handle_exceptions(self) -> None: + """test Bar.handle_exceptions""" + self.assertIsInstance( + Bar.handle_exceptions(None, "", ""), + ContextManager ) diff --git a/tests/test_spinner.py b/tests/test_spinner.py index 037d43c..0cffa5b 100644 --- a/tests/test_spinner.py +++ b/tests/test_spinner.py @@ -5,7 +5,48 @@ import unittest import unittest.mock from io import StringIO -from ascii_progress.spinner import Spinner +from typing import ContextManager +from ascii_progress.spinner import Spinner, SpinnerContext + + +class TestSpinnerContext(unittest.TestCase): + """tests for SpinnerContext""" + + def test_eq(self) -> None: + """test SpinnerContext.__eq__""" + spinner = Spinner("abc", StringIO()) + contexts = [ + SpinnerContext(spinner, "1", "2"), + SpinnerContext(spinner, "2", "2"), + SpinnerContext(spinner, "1", "1"), + SpinnerContext(Spinner("abc", StringIO()), "1", "2") + ] + for context in contexts: + self.assertEqual( + [context], + [c for c in contexts if c == context] + ) + self.assertNotEqual(contexts[0], 42) + + def test_context(self) -> None: + """test SpinnerContext as context manager""" + output = StringIO() + spinner = Spinner("abc", output) + with SpinnerContext(spinner, "1", "2") as context: + self.assertIsInstance(context, Spinner) + context.current_frame = "b" + with self.assertRaises(RuntimeError): + with SpinnerContext(spinner, "1", "2") as context: + context.current_frame = "c" + raise RuntimeError + with self.assertRaises(KeyboardInterrupt): + with SpinnerContext(spinner, "1", "2") as context: + context.current_frame = "a" + raise KeyboardInterrupt + self.assertEqual( + output.getvalue(), + "a\bb\b1\n\bc\b2\n\ba\b\b\b2 \n" + ) class TestSpinner(unittest.TestCase): @@ -31,27 +72,13 @@ class TestSpinner(unittest.TestCase): ) self.assertNotEqual(spinners[0], 42) - def test_context(self) -> None: - """test Spinner __enter__ and __exit__""" - output = StringIO() - with Spinner("abc", output) as spinner: - self.assertIsInstance(spinner, Spinner) - self.assertEqual(output.getvalue(), "a") - self.assertEqual(output.getvalue(), "a\bFinished\n") - output.seek(0) - output.truncate(0) - with self.assertRaises(KeyboardInterrupt): - with Spinner("abc", output) as spinner: - raise KeyboardInterrupt - self.assertEqual(output.getvalue(), "a\b\b\bKeyboardInterrupt \n") - def test_iter(self) -> None: """test Spinner __iter__ and __exit__""" output = StringIO() - with Spinner("abc", output) as spinner: - for _ in zip(range(6), spinner): - pass - self.assertEqual(output.getvalue(), "a\bb\bc\ba\bb\bc\ba\bFinished\n") + spinner = Spinner("abc", output) + for _ in zip(range(6), spinner): + pass + self.assertEqual(output.getvalue(), "a\bb\bc\ba\bb\bc\ba") def test_with_padding(self) -> None: """test Spinner.with_padding""" @@ -63,14 +90,14 @@ class TestSpinner(unittest.TestCase): def test_current_frame(self) -> None: """test Spinner.current_frame""" output = StringIO() - with Spinner("abc", output) as spinner: - self.assertEqual(spinner.current_frame, "a") - spinner.set_progress(1) - self.assertEqual(spinner.current_frame, "b") - spinner.current_frame = "a" - with self.assertRaises(ValueError): - spinner.current_frame = "x" - self.assertEqual(output.getvalue(), "a\bb\ba\bFinished\n") + spinner = Spinner("abc", output) + self.assertEqual(spinner.current_frame, "a") + spinner.set_progress(1) + self.assertEqual(spinner.current_frame, "b") + spinner.current_frame = "a" + with self.assertRaises(ValueError): + spinner.current_frame = "x" + self.assertEqual(output.getvalue(), "a\bb\ba") def test_update(self) -> None: """test Spinner.update""" @@ -96,11 +123,13 @@ class TestSpinner(unittest.TestCase): def test_set_progress(self) -> None: """test Spinner.set_progress""" - output = StringIO() - with Spinner("abc", output) as spinner: - spinner.set_progress(2) - spinner.set_progress(4) - self.assertEqual(output.getvalue(), "a\bc\bb\bFinished\n") + output = unittest.mock.Mock(wraps=StringIO()) + spinner = Spinner("abc", output) + output.reset_mock() + spinner.set_progress(2) + output.flush.assert_called() + spinner.set_progress(4) + self.assertEqual(output.getvalue(), "a\bc\bb") def test_replace(self) -> None: """test Spinner.replace""" @@ -110,3 +139,10 @@ class TestSpinner(unittest.TestCase): Spinner(("testtest", ""), output).replace("test", "42") self.assertEqual(output.flush.call_count, 2) self.assertEqual(output.getvalue(), "testtest\b\b\b\b\b\b\b\btest 42") + + def test_handle_exceptions(self) -> None: + """test Spinner.handle_exceptions""" + self.assertIsInstance( + Spinner("abc", file=StringIO()).handle_exceptions("", ""), + ContextManager + )

improved context managers Problem: The messages displayed when using `Spinner` or `Bar` as context managers are hard coded. Solution: Add a `.handle_exceptions(message, error)` method to both classes which returns a context manager.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DevoInc__python-sdk-113

diff --git a/CHANGELOG.md b/CHANGELOG.md index 28e86d5..6686fd3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * `Lookup.send_headers` method not working as expected with key_index parameter * Add `type_of_key` parameter to `Lookup.send_headers` method * Avoid lookups' key element to be deleted when `Lookup.send_data_line` is invoked. - +### Added + * Double quotes on lookups can be escaped by adding `"escape_quotes": true` to the config file. ## [3.4.2] - 2021-05-18 ### Added diff --git a/devo/sender/lookup.py b/devo/sender/lookup.py index d92908e..db089e3 100644 --- a/devo/sender/lookup.py +++ b/devo/sender/lookup.py @@ -6,6 +6,7 @@ import sys import time + def find_key_index(value=None, headers=None): """Find index of key value in a list""" for index, val in enumerate(headers): @@ -43,7 +44,7 @@ class Lookup: CONTROL_TABLE = "my.lookup.control" def __init__(self, name="example", historic_tag=None, - con=None, delay=5): + con=None, delay=5, escape_quotes=False): if not re.match(r"^[A-Za-z0-9_]+$", name): raise Exception('Devo Lookup: The name of the lookup is incorrect,' @@ -58,6 +59,7 @@ class Lookup: self.historic_tag = historic_tag self.name = name.replace(" ", "_") self.delay = delay + self.escape_quotes = escape_quotes # Helper methods # -------------------------------------------------------------------------- @@ -92,9 +94,11 @@ class Lookup: :return: """ # TODO: Deprecate this if with list_to_fields in v4 - p_fields = Lookup.list_to_fields(fields=fields, key=key) \ + p_fields = Lookup.list_to_fields(fields=fields, key=key, + escape_quotes=self.escape_quotes) \ if key_index is None \ - else Lookup.process_fields(fields=fields, key_index=key_index) + else Lookup.process_fields(fields=fields, key_index=key_index, + escape_quotes=self.escape_quotes) self.send_data(row=p_fields, delete=delete) @staticmethod @@ -206,8 +210,10 @@ class Lookup: if delete_index is not None: for fields in spam_reader: field_action = fields.pop(delete_index) - p_fields = Lookup.process_fields(fields=fields, - key_index=key_index) + p_fields = Lookup.process_fields( + fields=fields, + key_index=key_index, + escape_quotes=self.escape_quotes) self.send_data(row=p_fields, delete=field_action == "delete" or field_action == "DELETE") @@ -218,8 +224,10 @@ class Lookup: counter += 1 else: for fields in spam_reader: - p_fields = Lookup.process_fields(fields=fields, - key_index=key_index) + p_fields = Lookup.process_fields( + fields=fields, + key_index=key_index, + escape_quotes=self.escape_quotes) self.send_data(row=p_fields) # Send full log for historic @@ -351,16 +359,16 @@ class Lookup: return out @staticmethod - def field_to_str(field): + def field_to_str(field, escape_quotes=False): """ Convert one value to STR, cleaning it :param field: field to clean :return: """ - return ',%s' % Lookup.clean_field(field) + return ',%s' % Lookup.clean_field(field, escape_quotes) @staticmethod - def process_fields(fields=None, key_index=None): + def process_fields(fields=None, key_index=None, escape_quotes=False): """ Method to convert list with one row/fields to STR to send :param fields: fields list @@ -368,23 +376,23 @@ class Lookup: :return: """ # First the key - out = '%s' % Lookup.clean_field(fields[key_index]) + out = '%s' % Lookup.clean_field(fields[key_index], escape_quotes) # The rest of the fields for item in fields[:key_index] + fields[key_index + 1:]: - out += Lookup.field_to_str(item) + out += Lookup.field_to_str(item, escape_quotes) return out # TODO: Deprecated @staticmethod - def list_to_fields(fields=None, key="key"): + def list_to_fields(fields=None, key="key", escape_quotes=False): """ Transform list item to the object we need send to Devo for each row :param list fields: list of field names :param str key: key name, optional :result str """ - key = Lookup.clean_field(key) + key = Lookup.clean_field(key, escape_quotes) # First the key out = '%s' % key @@ -393,7 +401,7 @@ class Lookup: # The rest of the fields for item in fields: - item = Lookup.clean_field(item) + item = Lookup.clean_field(item, escape_quotes) # If file is the key don't add if item == key: continue @@ -401,7 +409,7 @@ class Lookup: return out @staticmethod - def clean_field(field=None): + def clean_field(field=None, escape_quotes=False): """ Strip and quotechar the fields :param str field: field for clean @@ -414,6 +422,9 @@ class Lookup: if Lookup.is_number(field): return field + if escape_quotes: + field = field.replace('"', '""') + return '"%s"' % field @staticmethod diff --git a/docs/sender/lookup.md b/docs/sender/lookup.md index 3cde900..04105a4 100644 --- a/docs/sender/lookup.md +++ b/docs/sender/lookup.md @@ -18,13 +18,15 @@ object into the _lookup_ variable with the new parameters or add in the CLI flag Example: ``` -{ sender": { +{ + sender": { ... }, "lookup": { "name": "Test_Lookup_of_180306_02", "file": "test_lookup.csv", "lkey": "KEY" + "escape_quotes": true } } ``` @@ -225,3 +227,24 @@ You can use config file to send types list: .... }} ``` +##### Double quotes in the field value + +Any double quotes inside the field value can cause trouble when sending the lookup if this is not escaped. +An example of this case can be seen below: + +`lookup.send_data_line(key="11", fields=["11", 'double quotes must escaped"'])` + +That lookup creation will fail because that double quote will be interpreted as a field termination and +the number of fields for that row will unmatch the corresponding number of columns. To avoid this, +add `"escape_quotes": true` to the lookup configuration file and `escape_quotes=True` to the `Lookup` constructor. +Below, an example for the constructor is shown: + +``` +`lookup = Lookup(name=self.lookup_name, historic_tag=None, con=con, escape_quotes=True)` +``` + +To see an example for the lookup configuration please refer to the one shown at the start of the document. + +This will escape ALL double quotes in the field value by adding a second double quote to it. + +The default behavior is to NOT escape any double quotes. \ No newline at end of file

DevoInc/python-sdk

3fa89f73be41307044fec587eb13b563201cd8f9

diff --git a/tests/sender/send_lookup.py b/tests/sender/send_lookup.py index 4e7e416..a0937a8 100644 --- a/tests/sender/send_lookup.py +++ b/tests/sender/send_lookup.py @@ -243,6 +243,96 @@ class TestLookup(unittest.TestCase): self.assertEqual(fields, ["a", "b", "c"]) self.assertEqual(processed_fields, '"b","a","c"') + # Clean field + def test_clean_field_parametrized(self): + test_params = [ + ("No double quotes", False, '"No double quotes"'), + ("No double quotes", True, '"No double quotes"'), + ('Double quotes"', False, '"Double quotes""'), + ('Double quotes"', True, '"Double quotes"""') + ] + for field, escape_quotes, expected_result in test_params: + with self.subTest( + field=field, + escape_quotes=escape_quotes, + expected_result=expected_result + ): + result = Lookup.clean_field(field, escape_quotes) + self.assertEqual(result, expected_result) + + # Test to make sure escape_quotes is propagated correctly + def test_escape_quotes_in_send_data_line_key(self): + engine_config = SenderConfigSSL( + address=(self.server, self.port), + key=self.key, + cert=self.cert, + ) + con = Sender(engine_config) + + lookup = Lookup(name=self.lookup_name, historic_tag=None, con=con, + escape_quotes=True) + + with mock.patch.object(Lookup, 'clean_field', + wraps=Lookup.clean_field) as clean_field: + lookup.send_data_line(key="11", fields=["11", 'Double quotes"']) + clean_field.assert_called_with('Double quotes"', True) + + # Test to make sure escape_quotes is propagated correctly + def test_escape_quotes_in_send_data_line(self): + engine_config = SenderConfigSSL( + address=(self.server, self.port), + key=self.key, + cert=self.cert, + ) + con = Sender(engine_config) + + lookup = Lookup(name=self.lookup_name, historic_tag=None, con=con, + escape_quotes=True) + + with mock.patch.object(Lookup, 'clean_field', + wraps=Lookup.clean_field) as clean_field: + lookup.send_data_line(fields=["11", 'Double quotes"']) + clean_field.assert_called_with('Double quotes"', True) + + # Test to make sure escape_quotes is propagated correctly + + def test_escape_quotes_in_send_csv(self): + engine_config = SenderConfigSSL( + address=(self.server, self.port), + key=self.key, + cert=self.cert, + ) + con = Sender(engine_config) + + lookup = Lookup(name=self.lookup_name, historic_tag=None, con=con, + escape_quotes=True) + + with mock.patch.object(Lookup, 'clean_field', + wraps=Lookup.clean_field) as clean_field: + lookup.send_csv(path=self.lookup_file, + has_header=True, + key=self.lookup_key) + clean_field.assert_called_with('ffffff', True) + + # Test to make sure escape_quotes is propagated correctly + + def test_escape_quotes_in_send_csv_delete_index(self): + engine_config = SenderConfigSSL( + address=(self.server, self.port), + key=self.key, + cert=self.cert, + ) + con = Sender(engine_config) + + lookup = Lookup(name=self.lookup_name, historic_tag=None, con=con, + escape_quotes=True) + + with mock.patch.object(Lookup, 'clean_field', + wraps=Lookup.clean_field) as clean_field: + lookup.send_csv(path=self.lookup_file, + has_header=True, + key=self.lookup_key, delete_field="Green") + clean_field.assert_called_with('ffffff', True) if __name__ == "__main__": unittest.main()

Lookup API is unable to send records with a double quote character in their content Right now, the `Lookup.clean_field` method wraps the field's content in double quotes, unless it is a number: https://github.com/DevoInc/python-sdk/blob/84a4e2c9da8d3013cd8f012e4399994d64817035/devo/sender/lookup.py#L400-L414 However, it does not check the existence of double quotes present in the field's value itself. This leads to a problem in which a code like this: ```python lookup.send_headers(headers=['KEY', 'VALUE'], key='KEY', event='START', action="INC") lookup.send_data_line(key="11", fields=["11", 'double quote: "']) lookup.send_headers(headers=['KEY', 'VALUE'], key='KEY', event='END', action="INC") ``` Makes the update process fail silently, without any notice from the client's perspective. I think we need to ensure that double quotes are escaped by replacing them like this: ```python field.replace('"', '""') ``` Or at least inform in the documentation that double quotes need to be escaped with two double quotes.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit

DiCarloLab-Delft__PycQED_py3-284

diff --git a/examples/Setting up a basic measurement using the MC.ipynb b/examples/Setting up a basic measurement using the MC.ipynb index 95f8b96a..69639e6f 100644 --- a/examples/Setting up a basic measurement using the MC.ipynb +++ b/examples/Setting up a basic measurement using the MC.ipynb @@ -7,18 +7,12 @@ "collapsed": false }, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "WARNING:root:Setting datadir to default location\n" - ] - }, { "name": "stdout", "output_type": "stream", "text": [ - "Data directory set to: None\n" + "Data directory set to: /Users/Adriaan/Documents/Testing/Data\n", + "Could not import msvcrt (used for detecting keystrokes)\n" ] } ], @@ -71,15 +65,7 @@ "metadata": { "collapsed": false }, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "WARNING:root:Error getting or interpreting *IDN?: ''\n" - ] - } - ], + "outputs": [], "source": [ "from pycqed.instrument_drivers.virtual_instruments import instrument_monitor as im \n", "IM = im.InstrumentMonitor('IM', station)\n", @@ -88,6 +74,17 @@ "MC.instrument_monitor('IM')" ] }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "IM.update()" + ] + }, { "cell_type": "markdown", "metadata": {}, @@ -98,9 +95,10 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "metadata": { - "collapsed": false + "collapsed": false, + "scrolled": true }, "outputs": [ { @@ -109,7 +107,7 @@ "'dummy_instrument'" ] }, - "execution_count": 4, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -130,7 +128,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "metadata": { "collapsed": false, "scrolled": false @@ -166,7 +164,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "metadata": { "collapsed": false }, @@ -178,37 +176,7 @@ "Starting measurement: dummy_hard persistent\n", "Sweep function: None_Sweep\n", "Detector function: Dummy_Detector\n", - " 100% completed \telapsed time: 1.4s \ttime left: 0.0s\n", - "[[ 0.00000000e+00 -8.41805618e-03 9.52221751e-01]\n", - " [ 3.44827592e-01 5.64679876e-02 9.63823080e-01]\n", - " [ 6.89655185e-01 2.71647215e-01 9.90496159e-01]\n", - " [ 1.03448272e+00 3.58638942e-01 9.83597755e-01]\n", - " [ 1.37931037e+00 4.11285490e-01 8.58026862e-01]\n", - " [ 1.72413790e+00 4.77858633e-01 7.64453173e-01]\n", - " [ 2.06896544e+00 6.31779075e-01 7.80045271e-01]\n", - " [ 2.41379309e+00 6.28673434e-01 7.12422073e-01]\n", - " [ 2.75862074e+00 8.28549922e-01 6.89963996e-01]\n", - " [ 3.10344839e+00 8.08600903e-01 5.54980338e-01]\n", - " [ 3.44827580e+00 8.77372682e-01 4.91556764e-01]\n", - " [ 3.79310346e+00 9.23762381e-01 4.19212967e-01]\n", - " [ 4.13793087e+00 9.73725736e-01 2.85644293e-01]\n", - " [ 4.48275852e+00 9.79517102e-01 7.03447387e-02]\n", - " [ 4.82758617e+00 1.05004179e+00 5.40984496e-02]\n", - " [ 5.17241383e+00 1.08093548e+00 -8.87244269e-02]\n", - " [ 5.51724148e+00 1.00360012e+00 -1.67943716e-01]\n", - " [ 5.86206913e+00 9.49792027e-01 -3.16440761e-01]\n", - " [ 6.20689678e+00 9.28232491e-01 -4.36341375e-01]\n", - " [ 6.55172396e+00 9.33600187e-01 -4.78987128e-01]\n", - " [ 6.89655161e+00 7.27082551e-01 -6.07001722e-01]\n", - " [ 7.24137926e+00 7.72163808e-01 -6.35885179e-01]\n", - " [ 7.58620691e+00 6.45901322e-01 -7.35407114e-01]\n", - " [ 7.93103456e+00 5.10887504e-01 -9.08347905e-01]\n", - " [ 8.27586174e+00 4.88061309e-01 -7.98481047e-01]\n", - " [ 8.62068939e+00 4.13446218e-01 -9.27012920e-01]\n", - " [ 8.96551704e+00 3.15337449e-01 -1.00892162e+00]\n", - " [ 9.31034470e+00 1.65451705e-01 -1.01685059e+00]\n", - " [ 9.65517235e+00 1.13537371e-01 -1.01554918e+00]\n", - " [ 1.00000000e+01 -4.30937521e-02 -9.94131565e-01]]\n" + " 100% completed \telapsed time: 1.5s \ttime left: 0.0s\n" ] } ], @@ -218,8 +186,7 @@ "MC.set_sweep_points(np.linspace(0, 10, 30))\n", "MC.set_detector_function(det.Dummy_Detector_Hard(noise=0.5, delay=.02))\n", "dat2 = MC.run('dummy_hard persistent')\n", - "data_set2 = dat2['dset']\n", - "print(data_set2)" + "data_set2 = dat2['dset']" ] }, { @@ -230,24 +197,6 @@ "A soft measurement is a a measurement where the data acquisition loop occurs in the **soft**ware" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": true - }, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": true - }, - "outputs": [], - "source": [] - }, { "cell_type": "code", "execution_count": 8, @@ -274,11 +223,11 @@ "Starting measurement: 1D test\n", "Sweep function: x\n", "Detector function: parabola\n", - " 100% completed \telapsed time: 6.6s \ttime left: 0.0s\n", + " 100% completed \telapsed time: 6.3s \ttime left: 0.0s\n", "Starting measurement: 1D test-persist\n", "Sweep function: x\n", "Detector function: parabola\n", - " 100% completed \telapsed time: 7.5s \ttime left: 0.0s\n" + " 100% completed \telapsed time: 6.5s \ttime left: 0.0s\n" ] } ], @@ -331,7 +280,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 11, "metadata": { "collapsed": false }, @@ -344,7 +293,7 @@ "Sweep function 0: x\n", "Sweep function 1: Sweep_function\n", "Detector function: parabola\n", - " 100% completed \telapsed time: 5.2s \ttime left: 0.0ss\n" + " 100% completed \telapsed time: 3.9s \ttime left: 0.0s\n" ] } ], @@ -374,7 +323,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 12, "metadata": { "collapsed": false }, @@ -387,7 +336,7 @@ "Sweep function 0: None_Sweep\n", "Sweep function 1: None_Sweep\n", "Detector function: Dummy_Detector\n", - " 100% completed \telapsed time: 14.0s \ttime left: 0.0s\n" + " 100% completed \telapsed time: 11.4s \ttime left: 0.0s\n" ] } ], @@ -424,7 +373,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 13, "metadata": { "collapsed": false }, @@ -436,7 +385,7 @@ "Starting measurement: dummy_hard\n", "Sweep function: None_Sweep\n", "Detector function: Dummy_Detector\n", - " 100% completed \telapsed time: 1.1s \ttime left: 0.0s\n" + " 100% completed \telapsed time: 0.9s \ttime left: 0.0s\n" ] } ], @@ -459,7 +408,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 16, "metadata": { "collapsed": false }, @@ -472,7 +421,7 @@ "Sweep function 0: None_Sweep\n", "Sweep function 1: None_Sweep\n", "Detector function: Dummy_Detector\n", - " 100% completed \telapsed time: 16.7s \ttime left: 0.0s\n" + " 100% completed \telapsed time: 13.6s \ttime left: 0.0s\n" ] } ], @@ -501,7 +450,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 15, "metadata": { "collapsed": false }, @@ -514,7 +463,7 @@ "Sweep function 0: module\n", "Sweep function 1: module\n", "Detector function: parabola\n", - "Optimization completed in 1.564s\n" + "Optimization completed in 1.357s\n" ] } ], @@ -530,15 +479,6 @@ "dat = MC.run('1D test', mode='adaptive')\n", "data_set = dat['dset']" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": true - }, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/pycqed/analysis/tools/plotting.py b/pycqed/analysis/tools/plotting.py index 72814d22..35b3b62f 100644 --- a/pycqed/analysis/tools/plotting.py +++ b/pycqed/analysis/tools/plotting.py @@ -85,6 +85,30 @@ def SI_prefix_and_scale_factor(val, unit=None): return scale_factor, unit +def SI_val_to_msg_str(val: float, unit: str=None): + """ + Takes in a value with optional unit and returns a string tuple consisting + of (value_str, unit) where the value and unit are rescaled according to + SI prefixes. + """ + validtypes = (float, int, np.integer, np.floating) + if unit in SI_UNITS and isinstance(val, validtypes): + if val == 0: + prefix_power = 0 + else: + # The defined prefixes go down to -24 but this is below + # the numerical precision of python + prefix_power = np.clip(-15, (np.log10(abs(val))//3 * 3), 24) + # Determine SI prefix, number 8 corresponds to no prefix + SI_prefix_idx = int(prefix_power/3 + 8) + prefix = SI_PREFIXES[SI_prefix_idx] + # Convert the unit + val = val*10**-prefix_power + unit = prefix+unit + + value_str = str(val) + return value_str, unit + def data_to_table_png(data: list, filename: str, title: str='', close_fig: bool=True): """ @@ -110,7 +134,7 @@ def data_to_table_png(data: list, filename: str, title: str='', if close_fig: plt.close(fig) - + def annotate_point_pair(ax, text, xy_start, xy_end, xycoords='data', text_offset=(-10, -5), arrowprops=None, **kw): ''' diff --git a/pycqed/instrument_drivers/virtual_instruments/ins_mon/qc_snapshot_widget.py b/pycqed/instrument_drivers/virtual_instruments/ins_mon/qc_snapshot_widget.py index 4392940c..49f38825 100644 --- a/pycqed/instrument_drivers/virtual_instruments/ins_mon/qc_snapshot_widget.py +++ b/pycqed/instrument_drivers/virtual_instruments/ins_mon/qc_snapshot_widget.py @@ -1,15 +1,6 @@ # -*- coding: utf-8 -*- from pyqtgraph.Qt import QtGui -from pycqed.analysis.tools.plotting import SI_UNITS, SI_PREFIXES -import types -import traceback -import numpy as np - -try: - import metaarray - HAVE_METAARRAY = True -except Exception: - HAVE_METAARRAY = False +from pycqed.analysis.tools.plotting import SI_val_to_msg_str class QcSnaphotWidget(QtGui.QTreeWidget): @@ -25,10 +16,12 @@ class QcSnaphotWidget(QtGui.QTreeWidget): self.setData(data) self.setColumnCount(4) self.setHeaderLabels(['Name', 'Value', 'Unit', 'Last update']) + self.nodes = {} def setData(self, data): - """data should be a QCoDes snapshot of a station.""" - self.clear() + """ + data should be a QCoDes snapshot of a station. + """ self.buildTreeSnapshot(snapshot=data) self.resizeColumnToContents(0) @@ -40,72 +33,35 @@ class QcSnaphotWidget(QtGui.QTreeWidget): for ins in sorted(snapshot.keys()): ins_snapshot = snapshot[ins] - node = QtGui.QTreeWidgetItem([ins, "", ""]) - parent.addChild(node) + if ins not in self.nodes: + self.nodes[ins] = QtGui.QTreeWidgetItem([ins, "", ""]) + parent.addChild(self.nodes[ins]) + + node = self.nodes[ins] for par_name in sorted(ins_snapshot['parameters'].keys()): par_snap = ins_snapshot['parameters'][par_name] # Depending on the type of data stored in value do different - # things. + # things, currently only blocks non-dicts if not isinstance(par_snap['value'], dict): - value_str, unit = par_val_to_msg(par_snap['value'], - par_snap['unit']) + value_str, unit = SI_val_to_msg_str(par_snap['value'], + par_snap['unit']) # Omits printing of the date to make it more readable if par_snap['ts'] is not None: latest_str = par_snap['ts'][11:] else: latest_str = '' - par_node = QtGui.QTreeWidgetItem( - [par_name, value_str, unit, latest_str]) - node.addChild(par_node) - - def buildTree(self, data, parent, name='', hideRoot=False): - if hideRoot: - node = parent - else: - typeStr = type(data).__name__ - if typeStr == 'instance': - typeStr += ": " + data.__class__.__name__ - node = QtGui.QTreeWidgetItem([name, typeStr, ""]) - parent.addChild(node) - - # convert traceback to a list of strings - if isinstance(data, types.TracebackType): - data = list( - map(str.strip, traceback.format_list( - traceback.extract_tb(data)))) - elif HAVE_METAARRAY and (hasattr(data, 'implements') - and data.implements('MetaArray')): - data = { - 'data': data.view(np.ndarray), - 'meta': data.infoCopy() - } - - if isinstance(data, dict): - for k in data.keys(): - self.buildTree(data[k], node, str(k)) - elif isinstance(data, list) or isinstance(data, tuple): - for i, d in enumerate(data): - self.buildTree(d, node, str(i)) - else: - node.setText(2, str(data)) - - -def par_val_to_msg(val, unit=None): - validtypes = (float, int, np.integer, np.floating) - if unit in SI_UNITS and isinstance(val, validtypes): - if val == 0: - prefix_power = 0 - else: - # The defined prefixes go down to -24 but this is below - # the numerical precision of python - prefix_power = np.clip(-15, (np.log10(abs(val))//3 * 3), 24) - # Determine SI prefix, number 8 corresponds to no prefix - SI_prefix_idx = int(prefix_power/3 + 8) - prefix = SI_PREFIXES[SI_prefix_idx] - # Convert the unit - val = val*10**-prefix_power - unit = prefix+unit - value_str = str(val) - return value_str, unit + # Name of the node in the self.nodes dictionary + param_node_name = '{}.{}'.format(ins, par_name) + # If node does not yet exist, create a node + if param_node_name not in self.nodes: + param_node = QtGui.QTreeWidgetItem( + [par_name, value_str, unit, latest_str]) + node.addChild(param_node) + self.nodes[param_node_name] = param_node + else: # else update existing node + param_node = self.nodes[param_node_name] + param_node.setData(1, 0, value_str) + param_node.setData(2, 0, unit) + param_node.setData(3, 0, latest_str) diff --git a/pycqed/instrument_drivers/virtual_instruments/instrument_monitor.py b/pycqed/instrument_drivers/virtual_instruments/instrument_monitor.py index 12bf89f8..980a97b9 100644 --- a/pycqed/instrument_drivers/virtual_instruments/instrument_monitor.py +++ b/pycqed/instrument_drivers/virtual_instruments/instrument_monitor.py @@ -46,7 +46,6 @@ class InstrumentMonitor(Instrument): snapshot = self.station.snapshot() self.tree.setData(snapshot['instruments']) - def _init_qt(self): # starting the process for the pyqtgraph plotting # You do not want a new process to be created every time you start a @@ -57,7 +56,6 @@ class InstrumentMonitor(Instrument): ins_mon_mod = 'pycqed.instrument_drivers.virtual_instruments.ins_mon.qc_snapshot_widget' self.__class__.rpg = self.proc._import(ins_mon_mod) - def create_tree(self, figsize=(1000, 600)): self.tree = self.rpg.QcSnaphotWidget()

DiCarloLab-Delft/PycQED_py3

8c50aff24fc47d6fd986ee6925d7e274f5da4f9e

diff --git a/pycqed/tests/test_unit_conversions.py b/pycqed/tests/test_unit_conversions.py index b43958d4..0a8dd82d 100644 --- a/pycqed/tests/test_unit_conversions.py +++ b/pycqed/tests/test_unit_conversions.py @@ -3,6 +3,7 @@ import numpy as np import matplotlib.pyplot as plt from pycqed.analysis.tools.plotting import SI_prefix_and_scale_factor from pycqed.analysis.tools.plotting import set_xlabel, set_ylabel +from pycqed.analysis.tools.plotting import SI_val_to_msg_str class Test_SI_prefix_scale_factor(unittest.TestCase): @@ -56,3 +57,10 @@ class test_SI_unit_aware_labels(unittest.TestCase): ytick_label_vals = [float(yl.get_text()) for yl in ytick_labels] for yt, yl in zip(yticks, ytick_label_vals): self.assertAlmostEqual(yt*1e6, yl) + + def test_SI_val_to_msg_str(self): + val, unit = SI_val_to_msg_str(1030, 'm') + self.assertEqual(val, str(1.03)) + self.assertEqual(unit, 'km') + +

Instrument monitor folds on update First reported by @fluthi , Makes it quite annoying to effectively use this in a real life scenario. Instrument monitor folds on every update.

2401580b6f41fe72f1360493ee46e8a842bd04ba

mit