From 2a9036caaa308bdd76367e8465cdc2a6f13c12bb Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Thu, 6 Jun 2024 13:38:59 -0400 Subject: [PATCH 01/11] fix drs --- CHANGELOG.rst | 7 + poetry.lock | 581 +++++++++++++++-------------- pyproject.toml | 2 +- src/encoded/tests/test_file_drs.py | 6 + src/encoded/types/file.py | 4 +- 5 files changed, 328 insertions(+), 272 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index e97009ed79..4542ec5554 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,13 @@ fourfront Change Log ---------- +7.5.2 +===== + +* Update DRS API to return JSON always +* Update DRS download URLs to return direct downloads to Open Data where applicable + + 7.5.1 ===== diff --git a/poetry.lock b/poetry.lock index b35e386134..fb35473c34 100644 --- a/poetry.lock +++ b/poetry.lock @@ -11,6 +11,17 @@ files = [ {file = "apipkg-3.0.2.tar.gz", hash = "sha256:c7aa61a4f82697fdaa667e70af1505acf1f7428b1c27b891d204ba7a8a3c5e0d"}, ] +[[package]] +name = "appdirs" +version = "1.4.4" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +optional = false +python-versions = "*" +files = [ + {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, + {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, +] + [[package]] name = "arrow" version = "1.3.0" @@ -92,18 +103,18 @@ wrapt = "*" [[package]] name = "awscli" -version = "1.32.85" +version = "1.33.2" description = "Universal Command Line Environment for AWS." optional = false python-versions = ">=3.8" files = [ - {file = "awscli-1.32.85-py3-none-any.whl", hash = "sha256:f3a94c6f603093ffc3b1e035f0dc7b6ec1db373023ca7b816c27b98864b0d565"}, - {file = "awscli-1.32.85.tar.gz", hash = "sha256:3b2bd24e0906f7e017aeae09660036fe5855367a25a5ea62df007f94c41e312f"}, + {file = "awscli-1.33.2-py3-none-any.whl", hash = "sha256:b8246ef8085df75ba20537c5ac0a621a4dbae1f084dc536bdc49cf2736fd0d3c"}, + {file = "awscli-1.33.2.tar.gz", hash = "sha256:4f692fff0e75fc2505f9a7cb613ec09426c6ed52bcd5a99246f58426b16a1bb6"}, ] [package.dependencies] -botocore = "1.34.85" -colorama = ">=0.2.5,<0.4.5" +botocore = "1.34.120" +colorama = ">=0.2.5,<0.4.7" docutils = ">=0.10,<0.17" PyYAML = ">=3.10,<6.1" rsa = ">=3.1.2,<4.8" @@ -132,13 +143,13 @@ lxml = ["lxml"] [[package]] name = "blinker" -version = "1.7.0" +version = "1.8.2" description = "Fast, simple object-to-object and broadcast signaling" optional = false python-versions = ">=3.8" files = [ - {file = "blinker-1.7.0-py3-none-any.whl", hash = "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9"}, - {file = "blinker-1.7.0.tar.gz", hash = "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182"}, + {file = "blinker-1.8.2-py3-none-any.whl", hash = "sha256:1779309f71bf239144b9399d06ae925637cf6634cf6bd131104184531bf67c01"}, + {file = 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["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [[package]] name = "zope-deprecation" diff --git a/pyproject.toml b/pyproject.toml index 9a94e70ef1..fa3df8b339 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "fourfront". name = "encoded" -version = "7.5.1" +version = "7.5.2" description = "4DN-DCIC Fourfront" authors = ["4DN-DCIC Team "] license = "MIT" diff --git a/src/encoded/tests/test_file_drs.py b/src/encoded/tests/test_file_drs.py index 9ce8412651..6754db23f5 100644 --- a/src/encoded/tests/test_file_drs.py +++ b/src/encoded/tests/test_file_drs.py @@ -74,3 +74,9 @@ def test_fastq_file_drs_access(testapp, file): assert drs_object_download == { 'url': f'https://localhost:80/{drs_object_uri}/@@download' } + + +def test_drs_always_returns_json(htmltestapp, file): + """ DRS is a JSON only API so should never not return this """ + drs_meta = htmltestapp.get(file['@id'] + '@@drs') + assert drs_meta.content_type == 'application/json' diff --git a/src/encoded/types/file.py b/src/encoded/types/file.py index 005abb022a..3f71b9b48f 100644 --- a/src/encoded/types/file.py +++ b/src/encoded/types/file.py @@ -1705,6 +1705,7 @@ def drs(context, request): """ DRS object implementation for file. """ rendered_object = request.embed(str(context.uuid), '@@object', as_user=True) accession = rendered_object['accession'] + open_data_url = rendered_object.get('open_data_url', None) drs_object_base = { 'id': rendered_object['@id'], 'created_time': rendered_object['date_created'], @@ -1714,12 +1715,13 @@ def drs(context, request): { # always prefer https 'access_url': { - 'url': f'https://{request.host}/{accession}/@@download' + 'url': open_data_url or f'https://{request.host}/{accession}/@@download' }, 'type': 'https' }, { # but provide http as well in case we are not on prod + # note that open data URLs will not work with http for obvious reasons 'access_url': { 'url': f'http://{request.host}/{accession}/@@download' }, From a49f832a6a06ee7badbf7ac6c0561667dccd7b9e Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Fri, 7 Jun 2024 12:15:37 -0400 Subject: [PATCH 02/11] bring in snovault, better testing --- poetry.lock | 8 ++--- pyproject.toml | 2 +- src/encoded/tests/test_file_drs.py | 53 +++++++++++++++++++----------- src/encoded/types/file.py | 18 ++++------ 4 files changed, 45 insertions(+), 36 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9780bff24f..aa6e3ecad5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1002,13 +1002,13 @@ tox = ["tox"] [[package]] name = "dcicsnovault" -version = "11.14.3" +version = "11.15.0" description = "Storage support for 4DN Data Portals." optional = false python-versions = "<3.12,>=3.8.1" files = [ - {file = "dcicsnovault-11.14.3-py3-none-any.whl", hash = "sha256:de48c89577872f6e4e7c4a2ee8dde7c435ac7998573b0804be2efc81ea6fcba6"}, - {file = "dcicsnovault-11.14.3.tar.gz", hash = "sha256:2b8720052f1ea617d4df554c4e30df0e6b211376a62311e6461d566df54beafc"}, + {file = "dcicsnovault-11.15.0-py3-none-any.whl", hash = "sha256:400fb2b5762f7233db17be9ebd8b6713a08d2df7acc007d8d83bb8e9d0cbc7c1"}, + {file = "dcicsnovault-11.15.0.tar.gz", hash = "sha256:9e459aff2abf9a3f481fc6ba7a58fcb74cb8a3983743458f93c00a9fe9adc30c"}, ] [package.dependencies] @@ -4040,4 +4040,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "66fb2f7bf93a4e76c738202f2c51d349f16d0962ccf30bfd764fb84ee5e8a74a" +content-hash = "0470628730c3ff9c7ec94327c5ae445da8681c25940289937909094ef3f71375" diff --git a/pyproject.toml b/pyproject.toml index 1385ae4598..f9ebc831fc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,7 +48,7 @@ colorama = "0.3.3" # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" -dcicsnovault = "^11.14.2" +dcicsnovault = "^11.15.0" dcicutils = "^8.0.0" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses diff --git a/src/encoded/tests/test_file_drs.py b/src/encoded/tests/test_file_drs.py index 6754db23f5..4a9fc96cc6 100644 --- a/src/encoded/tests/test_file_drs.py +++ b/src/encoded/tests/test_file_drs.py @@ -1,4 +1,5 @@ import pytest +from unittest import mock pytestmark = [pytest.mark.setone, pytest.mark.working] @@ -17,7 +18,7 @@ def mcool_file_json(award, experiment, lab, file_formats): 'md5sum': '00000000000000000000000000000000', 'content_md5sum': '00000000000000000000000000000000', 'filename': 'my.cool.mcool', - 'status': 'uploaded', + 'status': 'released', } return item @@ -32,7 +33,9 @@ def file(testapp, award, experiment, lab, file_formats): 'md5sum': '00000000000000000000000000000000', 'content_md5sum': '00000000000000000000000000000000', 'filename': 'my.fastq.gz', - 'status': 'uploaded', + 'status': 'released', + 'accession': 'TSTFI2896250', + 'uuid': '96115074-b6bd-4a1e-9564-14b708607e4c' } res = testapp.post_json('/file_fastq', item) return res.json['@graph'][0] @@ -51,32 +54,42 @@ def validate_drs_conversion(drs_obj, meta, uri=None): def test_processed_file_drs_view(testapp, mcool_file_json): """ Tests that processed mcool gives a valid DRS response """ - meta = testapp.post_json('/file_processed', mcool_file_json).json['@graph'][0] - drs_meta = testapp.get(meta['@id'] + '@@drs').json - validate_drs_conversion(drs_meta, meta) - drs_meta = testapp.get(f'{DRS_PREFIX}/{meta["uuid"]}').json - validate_drs_conversion(drs_meta, meta, uri=f'{DRS_PREFIX}/{meta["uuid"]}') + with mock.patch('encoded.types.file.File._head_s3', return_value=None): + meta = testapp.post_json('/file_processed', mcool_file_json).json['@graph'][0] + drs_meta = testapp.get(meta['@id'] + '@@drs').json + validate_drs_conversion(drs_meta, meta) + drs_meta = testapp.get(f'{DRS_PREFIX}/{meta["uuid"]}').json + validate_drs_conversion(drs_meta, meta, uri=f'{DRS_PREFIX}/{meta["uuid"]}') def test_fastq_file_drs_view(testapp, file): """ Tests that a fastq file has valid DRS response """ - drs_meta = testapp.get(file['@id'] + '@@drs').json - validate_drs_conversion(drs_meta, file) - drs_meta = testapp.get(f'{DRS_PREFIX}/{file["uuid"]}').json - validate_drs_conversion(drs_meta, file, uri=f'{DRS_PREFIX}/{file["uuid"]}') + with mock.patch('encoded.types.file.File._head_s3', return_value=None): + drs_meta = testapp.get(file['@id'] + '@@drs').json + validate_drs_conversion(drs_meta, file) + drs_meta = testapp.get(f'{DRS_PREFIX}/{file["uuid"]}').json + validate_drs_conversion(drs_meta, file, uri=f'{DRS_PREFIX}/{file["uuid"]}') def test_fastq_file_drs_access(testapp, file): """ Tests that access URLs are retrieved successfully """ - drs_meta = testapp.get(file['@id'] + '@@drs').json - drs_object_uri = drs_meta['drs_id'] - drs_object_download = testapp.get(f'/ga4gh/drs/v1/objects/{drs_object_uri}/access/').json - assert drs_object_download == { - 'url': f'https://localhost:80/{drs_object_uri}/@@download' - } + with mock.patch('encoded.types.file.File._head_s3', return_value=None): + drs_meta = testapp.get(file['@id'] + '@@drs').json + drs_object_uri = drs_meta['drs_id'] + drs_object_download = testapp.get(f'/ga4gh/drs/v1/objects/{drs_object_uri}/access/').json + assert drs_object_download == { + 'url': f'https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/' + f'96115074-b6bd-4a1e-9564-14b708607e4c/TSTFI2896250.fastq.gz' + } def test_drs_always_returns_json(htmltestapp, file): - """ DRS is a JSON only API so should never not return this """ - drs_meta = htmltestapp.get(file['@id'] + '@@drs') - assert drs_meta.content_type == 'application/json' + """ DRS is a JSON only API so should never not return html """ + with mock.patch('encoded.types.file.File._head_s3', return_value=None): + drs_meta = htmltestapp.get(file['@id'] + '@@drs') + assert drs_meta.content_type == 'application/json' + + +def test_drs_without_open_data_returns_404(testapp, file): + """ Tests that without open_data_url mocked, """ + testapp.get(file['@id'] + '@@drs', status=404) diff --git a/src/encoded/types/file.py b/src/encoded/types/file.py index 3f71b9b48f..399adc048a 100644 --- a/src/encoded/types/file.py +++ b/src/encoded/types/file.py @@ -20,6 +20,7 @@ from pyramid.threadlocal import get_current_request from pyramid.traversal import resource_path from pyramid.view import view_config +from pyramid.response import Response from snovault import ( AfterModified, BeforeModified, @@ -1706,6 +1707,9 @@ def drs(context, request): rendered_object = request.embed(str(context.uuid), '@@object', as_user=True) accession = rendered_object['accession'] open_data_url = rendered_object.get('open_data_url', None) + # TODO: implement access_id mechanism + if not open_data_url: + return Response('Access ID support planned for the future', status=404) drs_object_base = { 'id': rendered_object['@id'], 'created_time': rendered_object['date_created'], @@ -1713,20 +1717,12 @@ def drs(context, request): 'self_uri': f'drs://{request.host}{request.path}', 'access_methods': [ { - # always prefer https + # always use open data 'access_url': { - 'url': open_data_url or f'https://{request.host}/{accession}/@@download' + 'url': open_data_url }, 'type': 'https' - }, - { - # but provide http as well in case we are not on prod - # note that open data URLs will not work with http for obvious reasons - 'access_url': { - 'url': f'http://{request.host}/{accession}/@@download' - }, - 'type': 'http' - }, + } ] } return build_drs_object_from_props(drs_object_base, rendered_object) From 6aaa807668e12a0ab4d5d62c4cd0f95ea471b10f Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Fri, 7 Jun 2024 15:24:13 -0400 Subject: [PATCH 03/11] bring in fix --- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index aa6e3ecad5..d915efb431 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1002,13 +1002,13 @@ tox = ["tox"] [[package]] name = "dcicsnovault" -version = "11.15.0" +version = "11.15.1" description = "Storage support for 4DN Data Portals." optional = false python-versions = "<3.12,>=3.8.1" files = [ - {file = "dcicsnovault-11.15.0-py3-none-any.whl", hash = "sha256:400fb2b5762f7233db17be9ebd8b6713a08d2df7acc007d8d83bb8e9d0cbc7c1"}, - {file = "dcicsnovault-11.15.0.tar.gz", hash = "sha256:9e459aff2abf9a3f481fc6ba7a58fcb74cb8a3983743458f93c00a9fe9adc30c"}, + {file = "dcicsnovault-11.15.1-py3-none-any.whl", hash = "sha256:534767555e5f2053fb8db7a166496d053c2d114c5fe2fbd532af3e879efef0ad"}, + {file = "dcicsnovault-11.15.1.tar.gz", hash = "sha256:06f7dcd310ab2c68762a209557a1954aadb1025bb962f0365c145df1bb118e97"}, ] [package.dependencies] @@ -4040,4 +4040,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "0470628730c3ff9c7ec94327c5ae445da8681c25940289937909094ef3f71375" +content-hash = "d7a7c1e9e877317d5d70d7ddbc87d8f7b99d5ee2a1273f8c69e922b212d2fb7c" diff --git a/pyproject.toml b/pyproject.toml index f9ebc831fc..b1d496a325 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,7 +48,7 @@ colorama = "0.3.3" # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" -dcicsnovault = "^11.15.0" +dcicsnovault = "^11.15.1" dcicutils = "^8.0.0" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses From 9fde9b0ffd8343e1b28adfafa1248c47304dc9d3 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Thu, 27 Jun 2024 12:39:17 -0400 Subject: [PATCH 04/11] small changes --- src/encoded/tests/test_file_drs.py | 7 +++---- src/encoded/types/base.py | 22 ++++++---------------- src/encoded/types/file.py | 5 ++--- 3 files changed, 11 insertions(+), 23 deletions(-) diff --git a/src/encoded/tests/test_file_drs.py b/src/encoded/tests/test_file_drs.py index 4a9fc96cc6..2ca1b0f8bc 100644 --- a/src/encoded/tests/test_file_drs.py +++ b/src/encoded/tests/test_file_drs.py @@ -43,10 +43,9 @@ def file(testapp, award, experiment, lab, file_formats): def validate_drs_conversion(drs_obj, meta, uri=None): """ Validates drs object structure against the metadata in the db """ - assert drs_obj['id'] == meta['@id'] + assert drs_obj['id'] == meta['accession'] assert drs_obj['created_time'] == meta['date_created'] - assert drs_obj['drs_id'] == meta['accession'] - assert drs_obj['self_uri'] == f'drs://localhost:80{meta["@id"]}@@drs' if not uri else uri + assert drs_obj['self_uri'] == f'drs://localhost:80/{meta["accession"]}' if not uri else uri assert drs_obj['version'] == meta['md5sum'] assert drs_obj['name'] == meta['filename'] assert drs_obj['aliases'] == [meta['uuid']] @@ -75,7 +74,7 @@ def test_fastq_file_drs_access(testapp, file): """ Tests that access URLs are retrieved successfully """ with mock.patch('encoded.types.file.File._head_s3', return_value=None): drs_meta = testapp.get(file['@id'] + '@@drs').json - drs_object_uri = drs_meta['drs_id'] + drs_object_uri = drs_meta['id'] drs_object_download = testapp.get(f'/ga4gh/drs/v1/objects/{drs_object_uri}/access/').json assert drs_object_download == { 'url': f'https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/' diff --git a/src/encoded/types/base.py b/src/encoded/types/base.py index ca9a3bbb1a..e77a3ce7dc 100644 --- a/src/encoded/types/base.py +++ b/src/encoded/types/base.py @@ -26,18 +26,18 @@ def _award_viewing_group(award_uuid, root): # Item acls from ..acl import ( - ALLOW_CURRENT_AND_SUBMITTER_EDIT_ACL, + ALLOW_CURRENT_AND_SUBMITTER_EDIT_ACL, ALLOW_CURRENT_ACL, AWARD_MEMBER_ROLE, ALLOW_ANY_USER_ADD_ACL, - ALLOW_EVERYONE_VIEW_ACL, - ALLOW_LAB_MEMBER_VIEW_ACL, - ALLOW_LAB_SUBMITTER_EDIT_ACL, + ALLOW_EVERYONE_VIEW_ACL, + ALLOW_LAB_MEMBER_VIEW_ACL, + ALLOW_LAB_SUBMITTER_EDIT_ACL, ALLOW_LAB_VIEW_ADMIN_EDIT_ACL, ALLOW_OWNER_EDIT_ACL, ALLOW_SUBMITTER_ADD_ACL, - ALLOW_VIEWING_GROUP_LAB_SUBMITTER_EDIT_ACL, - ALLOW_VIEWING_GROUP_VIEW_ACL, + ALLOW_VIEWING_GROUP_LAB_SUBMITTER_EDIT_ACL, + ALLOW_VIEWING_GROUP_VIEW_ACL, DELETED_ACL, LAB_MEMBER_ROLE, LAB_SUBMITTER_ROLE, @@ -243,16 +243,6 @@ def _is_joint_analysis(props): roles[submitter] = OWNER_ROLE return roles - def unique_keys(self, properties): - """smth.""" - keys = super(Item, self).unique_keys(properties) - if 'accession' not in self.schema['properties']: - return keys - keys.setdefault('accession', []).extend(properties.get('alternate_accessions', [])) - if properties.get('status') != 'replaced' and 'accession' in properties: - keys['accession'].append(properties['accession']) - return keys - def _update(self, properties, sheets=None): props = {} try: diff --git a/src/encoded/types/file.py b/src/encoded/types/file.py index 399adc048a..3b0effcc1a 100644 --- a/src/encoded/types/file.py +++ b/src/encoded/types/file.py @@ -1711,10 +1711,9 @@ def drs(context, request): if not open_data_url: return Response('Access ID support planned for the future', status=404) drs_object_base = { - 'id': rendered_object['@id'], + 'id': accession, 'created_time': rendered_object['date_created'], - 'drs_id': accession, - 'self_uri': f'drs://{request.host}{request.path}', + 'self_uri': f'drs://{request.host}/{accession}', 'access_methods': [ { # always use open data From 797b3b91a0d0d6bed1cd0ff4ddff5c73fcb838b0 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Thu, 27 Jun 2024 12:57:03 -0400 Subject: [PATCH 05/11] bring in beta --- poetry.lock | 15 +++++++-------- pyproject.toml | 2 +- 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/poetry.lock b/poetry.lock index d915efb431..9d37d2c771 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1002,20 +1002,19 @@ tox = ["tox"] [[package]] name = "dcicsnovault" -version = "11.15.1" +version = "11.16.0.1b0" description = "Storage support for 4DN Data Portals." optional = false python-versions = "<3.12,>=3.8.1" files = [ - {file = "dcicsnovault-11.15.1-py3-none-any.whl", hash = "sha256:534767555e5f2053fb8db7a166496d053c2d114c5fe2fbd532af3e879efef0ad"}, - {file = "dcicsnovault-11.15.1.tar.gz", hash = "sha256:06f7dcd310ab2c68762a209557a1954aadb1025bb962f0365c145df1bb118e97"}, + {file = "dcicsnovault-11.16.0.1b0-py3-none-any.whl", hash = "sha256:cff494cc2c3e7f4fc53ff05d83ad7762ae33f4570dc5cb0a1e7f6202bb83dea0"}, ] [package.dependencies] aws_requests_auth = ">=0.4.1,<0.5.0" boto3 = ">=1.28.62" botocore = ">=1.31.62" -dcicutils = ">=8.8.5,<9.0.0" +dcicutils = ">=8.11.0,<9.0.0" elasticsearch = "7.13.4" elasticsearch_dsl = ">=7.4.0,<8.0.0" future = ">=0.15.2,<1" @@ -1058,13 +1057,13 @@ xlrd = ">=1.0.0,<2.0.0" [[package]] name = "dcicutils" -version = "8.9.0" +version = "8.12.0" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" optional = false python-versions = "<3.13,>=3.8" files = [ - {file = "dcicutils-8.9.0-py3-none-any.whl", hash = "sha256:6fb0a76d1f11b70f1b518d7b7f1f05d3d8aa3f762b99d5aaa4ce22b5eddba6e7"}, - {file = "dcicutils-8.9.0.tar.gz", hash = "sha256:9a78fad1137d7827d6155a7fd5982c25f482313f8f6cfbec577f69d61de63e09"}, + {file = "dcicutils-8.12.0-py3-none-any.whl", hash = "sha256:663283630f694a95b246817aa014fff66df06c5a92653af381ab5515af76f6ef"}, + {file = "dcicutils-8.12.0.tar.gz", hash = "sha256:402c2a123e66e12da72a38db0a164aa64871f003785a57468fa50ac221faf895"}, ] [package.dependencies] @@ -4040,4 +4039,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.8.1,<3.12" -content-hash = "d7a7c1e9e877317d5d70d7ddbc87d8f7b99d5ee2a1273f8c69e922b212d2fb7c" +content-hash = "03e9fef6bc6db18f7d65c472a125f7b9f0aceb6937bb5d8e6ab8cb311d9db486" diff --git a/pyproject.toml b/pyproject.toml index b1d496a325..6c533fb32f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -48,7 +48,7 @@ colorama = "0.3.3" # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" -dcicsnovault = "^11.15.1" +dcicsnovault = "11.16.0.1b0" dcicutils = "^8.0.0" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses From f9cc2aab33ffe5f78ac68f8bab0e5c96945bd413 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Fri, 16 Aug 2024 15:42:27 -0400 Subject: [PATCH 06/11] allow options call --- poetry.lock | 266 +++++++++++++++-------------- pyproject.toml | 2 +- src/encoded/tests/test_file_drs.py | 1 + src/encoded/types/file.py | 5 +- 4 files changed, 144 insertions(+), 130 deletions(-) diff --git a/poetry.lock b/poetry.lock index 98c58314ea..5f96769a8b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -102,17 +102,17 @@ wrapt = "*" [[package]] name = "awscli" -version = "1.33.42" +version = "1.33.44" description = "Universal Command Line Environment for AWS." optional = false python-versions = ">=3.8" files = [ - {file = "awscli-1.33.42-py3-none-any.whl", hash = "sha256:85c27c4ae58993a20dce76d9bc23ac9adda33d4a3bd84a1a4f8c9ee424f50a46"}, - {file = "awscli-1.33.42.tar.gz", hash = "sha256:975fe4d1e4733504ac5aa5e2bca8965c51c8d8f21f9bcb8f0147b9741114f73f"}, + {file = "awscli-1.33.44-py3-none-any.whl", hash = "sha256:7307ac7e0fdfeac7ec9d0da15898f708aa7a973e04bc707d3814fe7c85df2757"}, + {file = "awscli-1.33.44.tar.gz", hash = "sha256:b0910f3efa0dbbc56218b1a818122fd543f767eee1d829cf6a1a12ecd48617e8"}, ] [package.dependencies] -botocore = "1.34.160" +botocore = "1.34.162" colorama = ">=0.2.5,<0.4.7" docutils = ">=0.10,<0.17" PyYAML = ">=3.10,<6.1" @@ -164,17 +164,17 @@ files = [ [[package]] name = "boto3" -version = "1.34.160" +version = "1.34.162" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - {file = "boto3-1.34.160-py3-none-any.whl", hash = "sha256:bf3153bf5d66be2bb2112edc94eb143c0cba3fb502c5591437bd1c54f57eb559"}, - {file = "boto3-1.34.160.tar.gz", hash = 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python-versions = ">=3.9,<3.13" -content-hash = "fda9e4d048daaf2cfe6a0681be6f14858e59eddfa20772b0c3d141e08cbda9bf" +content-hash = "caa2ca22ef70579f11871d2ade9ed1e3c0a2cfa604881a4f03fe1807967a96de" diff --git a/pyproject.toml b/pyproject.toml index 0edf54d4a2..dc1838d153 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ colorama = "0.3.3" # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" -dcicsnovault = "11.21.1.0b0" +dcicsnovault = "11.21.1.0b1" dcicutils = "^8.13.3" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses diff --git a/src/encoded/tests/test_file_drs.py b/src/encoded/tests/test_file_drs.py index 2ca1b0f8bc..16fd2a237a 100644 --- a/src/encoded/tests/test_file_drs.py +++ b/src/encoded/tests/test_file_drs.py @@ -49,6 +49,7 @@ def validate_drs_conversion(drs_obj, meta, uri=None): assert drs_obj['version'] == meta['md5sum'] assert drs_obj['name'] == meta['filename'] assert drs_obj['aliases'] == [meta['uuid']] + assert drs_obj['access_methods'][0]['access_id'] == 'https' def test_processed_file_drs_view(testapp, mcool_file_json): diff --git a/src/encoded/types/file.py b/src/encoded/types/file.py index 2000af9aef..9ab7498f1c 100644 --- a/src/encoded/types/file.py +++ b/src/encoded/types/file.py @@ -570,7 +570,7 @@ def _get_file_experiment_info(self, request, currinfo): def track_and_facet_info(self, request, biosource_name=None): props = self.upgrade_properties() # order matters here at leat for last 2 fields - fields = ['experiment_type', 'assay_info', 'experimental_lab', 'dataset', 'condition', + fields = ['experiment_type', 'assay_info', 'experimental_lab', 'dataset', 'condition', 'biosource_name', 'replicate_info', 'experiment_bucket', 'lab_name', 'track_title'] # look for existing _props track_info = {field: props.get('override_' + field) for field in fields} @@ -1724,7 +1724,8 @@ def drs(context, request): 'access_url': { 'url': open_data_url }, - 'type': 'https' + 'type': 'https', + 'access_id': 'https' } ] } From 03b55991e36fa7d270e00e10f749935499176056 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Tue, 27 Aug 2024 14:02:51 -0400 Subject: [PATCH 07/11] another drs fix --- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5f96769a8b..f1714ebfcb 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1111,13 +1111,13 @@ files = [ [[package]] name = "dcicsnovault" -version = "11.21.1.0b1" +version = "11.21.1.0b2" description = "Storage support for 4DN Data Portals." optional = false python-versions = "<3.13,>=3.9" files = [ - {file = "dcicsnovault-11.21.1.0b1-py3-none-any.whl", hash = "sha256:38fa40891d0456b4f40a2002f1cdec7973ea4f18eb40725fdbddded5174a8a11"}, - {file = "dcicsnovault-11.21.1.0b1.tar.gz", hash = "sha256:cb1b37a7b6151cd7989071f69c14861b042093dc80512e65abb1021e58a9a0f6"}, + {file = "dcicsnovault-11.21.1.0b2-py3-none-any.whl", hash = "sha256:58995887c80017381fae4ec69a29982b24454cbe6ad7cc72c8c7adfd05a80902"}, + {file = "dcicsnovault-11.21.1.0b2.tar.gz", hash = "sha256:bb49b3dadd0685699a59167eca00aabb221a40a51558ba4593f6ed3b467b52d1"}, ] [package.dependencies] @@ -4483,4 +4483,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "caa2ca22ef70579f11871d2ade9ed1e3c0a2cfa604881a4f03fe1807967a96de" +content-hash = "132074033874560b8257e8a72fa29290aab135aad8386cb7bc3a138f2e22e79d" diff --git a/pyproject.toml b/pyproject.toml index dc1838d153..38d75f61e2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ colorama = "0.3.3" # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" -dcicsnovault = "11.21.1.0b1" +dcicsnovault = "11.21.1.0b2" dcicutils = "^8.13.3" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses From 2fa98c01b70f88510a74e21a5629be5f693aaca8 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Wed, 28 Aug 2024 14:22:40 -0400 Subject: [PATCH 08/11] allow another options path --- poetry.lock | 203 ++++++++++++++++++++++++++++++++++++++++++++++--- pyproject.toml | 2 +- 2 files changed, 195 insertions(+), 10 deletions(-) diff --git a/poetry.lock b/poetry.lock index f1714ebfcb..204faaf638 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. [[package]] name = "apipkg" version = "3.0.2" description = "apipkg: namespace control and lazy-import mechanism" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -15,6 +16,7 @@ files = [ name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" optional = false python-versions = "*" files = [ @@ -26,6 +28,7 @@ files = [ name = "arrow" version = "1.3.0" description = "Better dates & times for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -39,12 +42,13 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] +test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] [[package]] name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -56,6 +60,7 @@ files = [ name = "attrs" version = "22.2.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -74,6 +79,7 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy name = "aws-requests-auth" version = "0.4.3" description = "AWS signature version 4 signing process for the python requests module" +category = "main" optional = false python-versions = "*" files = [ @@ -88,6 +94,7 @@ requests = ">=0.14.0" name = "aws-xray-sdk" version = "0.95" description = "The AWS X-Ray SDK for Python (the SDK) enables Python developers to record and emit information from within their applications to the AWS X-Ray service." +category = "dev" optional = false python-versions = "*" files = [ @@ -104,6 +111,7 @@ wrapt = "*" name = "awscli" version = "1.33.44" description = "Universal Command Line Environment for AWS." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -123,6 +131,7 @@ s3transfer = ">=0.10.0,<0.11.0" name = "beautifulsoup4" version = "4.12.3" description = "Screen-scraping library" +category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -144,6 +153,7 @@ lxml = ["lxml"] name = "blinker" version = "1.8.2" description = "Fast, simple object-to-object and broadcast signaling" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -155,6 +165,7 @@ files = [ name = "boto" version = "2.49.0" description = "Amazon Web Services Library" +category = "dev" optional = false python-versions = "*" files = [ @@ -166,6 +177,7 @@ files = [ name = "boto3" version = "1.34.162" description = "The AWS SDK for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -185,6 +197,7 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] name = "boto3-stubs" version = "1.34.162" description = "Type annotations for boto3 1.34.162 generated with mypy-boto3-builder 7.26.0" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -592,6 +605,7 @@ xray = ["mypy-boto3-xray (>=1.34.0,<1.35.0)"] name = "botocore" version = "1.34.162" description = "Low-level, data-driven core of boto 3." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -614,6 +628,7 @@ crt = ["awscrt (==0.21.2)"] name = "botocore-stubs" version = "1.34.162" description = "Type annotations and code completion for botocore" +category = "dev" optional = false python-versions = "<4.0,>=3.8" files = [ @@ -631,6 +646,7 @@ botocore = ["botocore"] name = "certifi" version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -642,6 +658,7 @@ files = [ name = "cffi" version = "1.17.0" description = "Foreign Function Interface for Python calling C code." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -721,6 +738,7 @@ pycparser = "*" name = "chardet" version = "5.2.0" description = "Universal encoding detector for Python 3" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -732,6 +750,7 @@ files = [ name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -831,6 +850,7 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -845,6 +865,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "codacy-coverage" version = "1.3.11" description = "Codacy coverage reporter for Python" +category = "dev" optional = false python-versions = "*" files = [ @@ -863,6 +884,7 @@ test = ["coverage", "nosetests"] name = "codeguru-profiler-agent" version = "1.2.5" description = "The Python agent to be used for Amazon CodeGuru Profiler" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -877,6 +899,7 @@ boto3 = ">=1.14.0" name = "colorama" version = "0.3.3" description = "Cross-platform colored terminal text." +category = "main" optional = false python-versions = "*" files = [ @@ -887,6 +910,7 @@ files = [ name = "coverage" version = "7.6.1" description = "Code coverage measurement for Python" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -974,6 +998,7 @@ toml = ["tomli"] name = "coveralls" version = "4.0.1" description = "Show coverage stats online via coveralls.io" +category = "dev" optional = false python-versions = "<3.13,>=3.8" files = [ @@ -982,7 +1007,7 @@ files = [ ] [package.dependencies] -coverage = {version = ">=5.0,<6.0.dev0 || >6.1,<6.1.1 || >6.1.1,<8.0", extras = ["toml"]} +coverage = {version = ">=5.0,<6.0.0 || >6.1,<6.1.1 || >6.1.1,<8.0", extras = ["toml"]} docopt = ">=0.6.1,<0.7.0" requests = ">=1.0.0,<3.0.0" @@ -993,6 +1018,7 @@ yaml = ["pyyaml (>=3.10,<7.0)"] name = "cryptography" version = "39.0.2" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1038,6 +1064,7 @@ tox = ["tox"] name = "cython" version = "3.0.11" description = "The Cython compiler for writing C extensions in the Python language." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" files = [ @@ -1111,13 +1138,14 @@ files = [ [[package]] name = "dcicsnovault" -version = "11.21.1.0b2" +version = "11.21.1.0b3" description = "Storage support for 4DN Data Portals." +category = "main" optional = false python-versions = "<3.13,>=3.9" files = [ - {file = "dcicsnovault-11.21.1.0b2-py3-none-any.whl", hash = "sha256:58995887c80017381fae4ec69a29982b24454cbe6ad7cc72c8c7adfd05a80902"}, - {file = "dcicsnovault-11.21.1.0b2.tar.gz", hash = "sha256:bb49b3dadd0685699a59167eca00aabb221a40a51558ba4593f6ed3b467b52d1"}, + {file = "dcicsnovault-11.21.1.0b3-py3-none-any.whl", hash = "sha256:3de7d666d905badbcd7832dca130c8c9578e85924ceaa1a36a9327e95ab6c59d"}, + {file = "dcicsnovault-11.21.1.0b3.tar.gz", hash = "sha256:7554fe967237a0a94f17b35998e1bd41d5221d5c22d1138f74ae7943605d463e"}, ] [package.dependencies] @@ -1171,6 +1199,7 @@ xlrd = ">=1.0.0,<2.0.0" name = "dcicutils" version = "8.14.0" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" +category = "main" optional = false python-versions = "<3.13,>=3.8.1" files = [ @@ -1212,6 +1241,7 @@ webtest = ">=2.0.34,<3.0.0" name = "docker" version = "4.4.4" description = "A Python library for the Docker Engine API." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1233,6 +1263,7 @@ tls = ["cryptography (>=1.3.4)", "idna (>=2.0.0)", "pyOpenSSL (>=17.5.0)"] name = "docopt" version = "0.6.2" description = "Pythonic argument parser, that will make you smile" +category = "dev" optional = false python-versions = "*" files = [ @@ -1243,6 +1274,7 @@ files = [ name = "docutils" version = "0.16" description = "Docutils -- Python Documentation Utilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1254,6 +1286,7 @@ files = [ name = "ecdsa" version = "0.19.0" description = "ECDSA cryptographic signature library (pure python)" +category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.6" files = [ @@ -1272,6 +1305,7 @@ gmpy2 = ["gmpy2"] name = "elasticsearch" version = "7.13.4" description = "Python client for Elasticsearch" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4" files = [ @@ -1293,6 +1327,7 @@ requests = ["requests (>=2.4.0,<3.0.0)"] name = "elasticsearch-dsl" version = "7.4.1" description = "Python client for Elasticsearch" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1312,6 +1347,7 @@ develop = ["coverage (<5.0.0)", "mock", "pytest (>=3.0.0)", "pytest-cov", "pytes name = "et-xmlfile" version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1323,6 +1359,7 @@ files = [ name = "events" version = "0.5" description = "Bringing the elegance of C# EventHandler to Python" +category = "main" optional = false python-versions = "*" files = [ @@ -1333,6 +1370,7 @@ files = [ name = "exceptiongroup" version = "1.2.2" description = "Backport of PEP 654 (exception groups)" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1347,6 +1385,7 @@ test = ["pytest (>=6)"] name = "execnet" version = "1.4.1" description = "execnet: rapid multi-Python deployment" +category = "main" optional = false python-versions = "*" files = [ @@ -1361,6 +1400,7 @@ apipkg = ">=1.4" name = "flake8" version = "7.1.1" description = "the modular source code checker: pep8 pyflakes and co" +category = "dev" optional = false python-versions = ">=3.8.1" files = [ @@ -1377,6 +1417,7 @@ pyflakes = ">=3.2.0,<3.3.0" name = "flaky" version = "3.8.1" description = "Plugin for pytest that automatically reruns flaky tests." +category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1388,6 +1429,7 @@ files = [ name = "flask" version = "3.0.3" description = "A simple framework for building complex web applications." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1411,6 +1453,7 @@ dotenv = ["python-dotenv"] name = "fqdn" version = "1.5.1" description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" +category = "main" optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" files = [ @@ -1422,6 +1465,7 @@ files = [ name = "future" version = "0.18.3" description = "Clean single-source support for Python 3 and 2" +category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1432,6 +1476,7 @@ files = [ name = "gitdb" version = "4.0.11" description = "Git Object Database" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1446,6 +1491,7 @@ smmap = ">=3.0.1,<6" name = "gitpython" version = "3.1.43" description = "GitPython is a Python library used to interact with Git repositories" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1464,6 +1510,7 @@ test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", name = "greenlet" version = "3.0.3" description = "Lightweight in-process concurrent programming" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1535,6 +1582,7 @@ test = ["objgraph", "psutil"] name = "html5lib" version = "1.1" description = "HTML parser based on the WHATWG HTML specification" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1556,6 +1604,7 @@ lxml = ["lxml"] name = "humanfriendly" version = "1.44.9" description = "Human friendly output for text interfaces using Python" +category = "main" optional = false python-versions = "*" files = [ @@ -1567,6 +1616,7 @@ files = [ name = "hupper" version = "1.12.1" description = "Integrated process monitor for developing and reloading daemons." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1582,6 +1632,7 @@ testing = ["mock", "pytest", "pytest-cov", "watchdog"] name = "idna" version = "2.10" description = "Internationalized Domain Names in Applications (IDNA)" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1593,6 +1644,7 @@ files = [ name = "importlib-metadata" version = "8.2.0" description = "Read metadata from Python packages" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1612,6 +1664,7 @@ test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "p name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1623,6 +1676,7 @@ files = [ name = "isodate" version = "0.6.0" description = "An ISO 8601 date/time/duration parser and formatter" +category = "main" optional = false python-versions = "*" files = [ @@ -1637,6 +1691,7 @@ six = "*" name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1651,6 +1706,7 @@ arrow = ">=0.15.0" name = "itsdangerous" version = "2.2.0" description = "Safely pass data to untrusted environments and back." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1662,6 +1718,7 @@ files = [ name = "jinja2" version = "3.1.4" description = "A very fast and expressive template engine." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1679,6 +1736,7 @@ i18n = ["Babel (>=2.7)"] name = "jmespath" version = "0.9.0" description = "JSON Matching Expressions" +category = "main" optional = false python-versions = "*" files = [ @@ -1690,6 +1748,7 @@ files = [ name = "joblib" version = "1.4.2" description = "Lightweight pipelining with Python functions" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1701,6 +1760,7 @@ files = [ name = "jsonc-parser" version = "1.1.5" description = "A lightweight, native tool for parsing .jsonc files" +category = "main" optional = false python-versions = ">=3.5" files = [ @@ -1712,6 +1772,7 @@ files = [ name = "jsondiff" version = "1.1.1" description = "Diff JSON and JSON-like structures in Python" +category = "dev" optional = false python-versions = "*" files = [ @@ -1722,6 +1783,7 @@ files = [ name = "jsonpickle" version = "3.2.2" description = "Python library for serializing arbitrary object graphs into JSON" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1738,6 +1800,7 @@ testing = ["bson", "ecdsa", "feedparser", "gmpy2", "numpy", "pandas", "pymongo", name = "jsonpointer" version = "3.0.0" description = "Identify specific nodes in a JSON document (RFC 6901)" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1749,6 +1812,7 @@ files = [ name = "jsonschema" version = "4.23.0" description = "An implementation of JSON Schema validation for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1778,6 +1842,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.12.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1792,6 +1857,7 @@ referencing = ">=0.31.0" name = "lorem-text" version = "2.1" description = "Dummy lorem ipsum text generator" +category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1806,6 +1872,7 @@ Click = ">=7.0" name = "markdown" version = "3.7" description = "Python implementation of John Gruber's Markdown." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1824,6 +1891,7 @@ testing = ["coverage", "pyyaml"] name = "markupsafe" version = "2.1.5" description = "Safely add untrusted strings to HTML/XML markup." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1893,6 +1961,7 @@ files = [ name = "mccabe" version = "0.7.0" description = "McCabe checker, plugin for flake8" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1904,6 +1973,7 @@ files = [ name = "mock" version = "5.1.0" description = "Rolling backport of unittest.mock for all Pythons" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1920,6 +1990,7 @@ test = ["pytest", "pytest-cov"] name = "moto" version = "1.3.7" description = "A library that allows your python tests to easily mock out the boto library" +category = "dev" optional = false python-versions = "*" files = [ @@ -1954,6 +2025,7 @@ server = ["flask"] name = "netaddr" version = "0.10.1" description = "A network address manipulation library for Python" +category = "main" optional = false python-versions = "*" files = [ @@ -1965,6 +2037,7 @@ files = [ name = "numpy" version = "1.26.4" description = "Fundamental package for array computing in Python" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2010,6 +2083,7 @@ files = [ name = "openpyxl" version = "3.1.5" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2024,6 +2098,7 @@ et-xmlfile = "*" name = "opensearch-py" version = "2.6.0" description = "Python client for OpenSearch" +category = "main" optional = false python-versions = "<4,>=3.8" files = [ @@ -2052,6 +2127,7 @@ kerberos = ["requests-kerberos"] name = "packaging" version = "24.1" description = "Core utilities for Python packages" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2063,6 +2139,7 @@ files = [ name = "pandas" version = "2.2.2" description = "Powerful data structures for data analysis, time series, and statistics" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2136,6 +2213,7 @@ xml = ["lxml (>=4.9.2)"] name = "passlib" version = "1.7.4" description = "comprehensive password hashing framework supporting over 30 schemes" +category = "main" optional = false python-versions = "*" files = [ @@ -2153,6 +2231,7 @@ totp = ["cryptography"] name = "pastedeploy" version = "3.1.0" description = "Load, configure, and compose WSGI applications and servers" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2169,6 +2248,7 @@ testing = ["Paste", "pytest", "pytest-cov"] name = "patsy" version = "0.5.6" description = "A Python package for describing statistical models and for building design matrices." +category = "main" optional = false python-versions = "*" files = [ @@ -2187,6 +2267,7 @@ test = ["pytest", "pytest-cov", "scipy"] name = "pbkdf2" version = "1.3" description = "PKCS#5 v2.0 PBKDF2 Module" +category = "main" optional = false python-versions = "*" files = [ @@ -2197,6 +2278,7 @@ files = [ name = "pillow" version = "9.5.0" description = "Python Imaging Library (Fork)" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2276,6 +2358,7 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa name = "pip" version = "24.2" description = "The PyPA recommended tool for installing Python packages." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2287,6 +2370,7 @@ files = [ name = "pip-licenses" version = "3.5.5" description = "Dump the software license list of Python packages installed with pip." +category = "dev" optional = false python-versions = "~=3.7" files = [ @@ -2304,6 +2388,7 @@ test = ["docutils", "pytest-cov", "pytest-pycodestyle", "pytest-runner"] name = "pipdeptree" version = "2.23.1" description = "Command line utility to show dependency tree of packages." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2323,6 +2408,7 @@ test = ["covdefaults (>=2.3)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pyte name = "plaster" version = "1.0" description = "A loader interface around multiple config file formats." +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2341,6 +2427,7 @@ testing = ["pytest", "pytest-cov"] name = "plaster-pastedeploy" version = "0.6" description = "A loader implementing the PasteDeploy syntax to be used by plaster." +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2359,6 +2446,7 @@ testing = ["pytest", "pytest-cov"] name = "pluggy" version = "1.5.0" description = "plugin and hook calling mechanisms for python" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2374,6 +2462,7 @@ testing = ["pytest", "pytest-benchmark"] name = "pmdarima" version = "2.0.4" description = "Python's forecast::auto.arima equivalent" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2425,6 +2514,7 @@ urllib3 = "*" name = "psutil" version = "5.9.8" description = "Cross-platform lib for process and system monitoring in Python." +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -2453,6 +2543,7 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "psycopg2-binary" version = "2.9.9" description = "psycopg2 - Python-PostgreSQL Database Adapter" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2534,6 +2625,7 @@ files = [ name = "ptable" version = "0.9.2" description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format" +category = "dev" optional = false python-versions = "*" files = [ @@ -2544,6 +2636,7 @@ files = [ name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2555,6 +2648,7 @@ files = [ name = "pyaml" version = "24.7.0" description = "PyYAML-based module to produce a bit more pretty and readable YAML-serialized data" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2572,6 +2666,7 @@ anchors = ["unidecode"] name = "pyasn1" version = "0.6.0" description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2583,6 +2678,7 @@ files = [ name = "pybrowserid" version = "0.10.0" description = "Python library for the BrowserID Protocol" +category = "main" optional = false python-versions = "*" files = [ @@ -2596,6 +2692,7 @@ requests = "*" name = "pycodestyle" version = "2.12.1" description = "Python style guide checker" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2607,6 +2704,7 @@ files = [ name = "pycparser" version = "2.22" description = "C parser in Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2618,6 +2716,7 @@ files = [ name = "pycryptodome" version = "3.20.0" description = "Cryptographic library for Python" +category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2659,6 +2758,7 @@ files = [ name = "pyflakes" version = "3.2.0" description = "passive checker of Python programs" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2670,6 +2770,7 @@ files = [ name = "pygments" version = "2.18.0" description = "Pygments is a syntax highlighting package written in Python." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2684,6 +2785,7 @@ windows-terminal = ["colorama (>=0.4.6)"] name = "pyjwt" version = "2.9.0" description = "JSON Web Token implementation in Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2701,6 +2803,7 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"] name = "pyopenssl" version = "23.2.0" description = "Python wrapper module around the OpenSSL library" +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2719,6 +2822,7 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"] name = "pyparsing" version = "2.4.7" description = "Python parsing module" +category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -2730,6 +2834,7 @@ files = [ name = "pyperclip" version = "1.9.0" description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)" +category = "main" optional = false python-versions = "*" files = [ @@ -2740,6 +2845,7 @@ files = [ name = "pyramid" version = "1.10.8" description = "The Pyramid Web Framework, a Pylons project" +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2766,6 +2872,7 @@ testing = ["coverage", "nose", "virtualenv", "webtest (>=1.3.1)", "zope.componen name = "pyramid-multiauth" version = "0.9.0" description = "pyramid_multiauth" +category = "main" optional = false python-versions = "*" files = [ @@ -2780,6 +2887,7 @@ pyramid = "*" name = "pyramid-retry" version = "1.0" description = "An execution policy for Pyramid that supports retrying requests after certain failure exceptions." +category = "main" optional = false python-versions = "*" files = [ @@ -2799,6 +2907,7 @@ testing = ["WebTest", "pytest", "pytest-cov"] name = "pyramid-tm" version = "2.5" description = "A package which allows Pyramid requests to join the active transaction" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2818,6 +2927,7 @@ testing = ["WebTest", "coverage (>=5.0)", "pytest", "pytest-cov"] name = "pyramid-translogger" version = "0.1" description = "access log logger tween (almost stolen from Paste.translogger)" +category = "main" optional = false python-versions = "*" files = [ @@ -2831,6 +2941,7 @@ setuptools = "*" name = "pytest" version = "7.4.4" description = "pytest: simple powerful testing with Python" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2853,6 +2964,7 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-cov" version = "5.0.0" description = "Pytest plugin for measuring coverage." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2871,6 +2983,7 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"] name = "pytest-instafail" version = "0.5.0" description = "pytest plugin to show failures instantly" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2885,6 +2998,7 @@ pytest = ">=5" name = "pytest-mock" version = "3.14.0" description = "Thin-wrapper around the mock package for easier use with pytest" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2902,6 +3016,7 @@ dev = ["pre-commit", "pytest-asyncio", "tox"] name = "pytest-timeout" version = "2.3.1" description = "pytest plugin to abort hanging tests" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2916,6 +3031,7 @@ pytest = ">=7.0.0" name = "pytest-xdist" version = "3.5.0" description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2936,6 +3052,7 @@ testing = ["filelock"] name = "python-dateutil" version = "2.9.0.post0" description = "Extensions to the standard Python datetime module" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -2950,6 +3067,7 @@ six = ">=1.5" name = "python-jose" version = "2.0.2" description = "JOSE implementation in Python" +category = "dev" optional = false python-versions = "*" files = [ @@ -2971,6 +3089,7 @@ pycrypto = ["pycrypto (>=2.6.0,<2.7.0)"] name = "python-magic" version = "0.4.27" description = "File type identification using libmagic" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2982,6 +3101,7 @@ files = [ name = "pytz" version = "2024.1" description = "World timezone definitions, modern and historical" +category = "main" optional = false python-versions = "*" files = [ @@ -2993,6 +3113,7 @@ files = [ name = "pywin32" version = "227" description = "Python for Window Extensions" +category = "main" optional = false python-versions = "*" files = [ @@ -3014,6 +3135,7 @@ files = [ name = "pyyaml" version = "6.0.2" description = "YAML parser and emitter for Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3076,6 +3198,7 @@ files = [ name = "rdflib" version = "4.2.2" description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information." +category = "main" optional = false python-versions = "*" files = [ @@ -3095,6 +3218,7 @@ sparql = ["SPARQLWrapper"] name = "rdflib-jsonld" version = "0.6.0" description = "rdflib extension adding JSON-LD parser and serializer" +category = "main" optional = false python-versions = "*" files = [ @@ -3109,6 +3233,7 @@ rdflib = "*" name = "redis" version = "4.6.0" description = "Python client for Redis database and key-value store" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3127,6 +3252,7 @@ ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)" name = "referencing" version = "0.35.1" description = "JSON Referencing + Python" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3142,6 +3268,7 @@ rpds-py = ">=0.7.0" name = "repoze-debug" version = "1.1" description = "Forensic debugging WSGI middleware" +category = "dev" optional = false python-versions = "*" files = [ @@ -3160,6 +3287,7 @@ testing = ["WebOb", "coverage", "nose"] name = "requests" version = "2.31.0" description = "Python HTTP for Humans." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3181,6 +3309,7 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "responses" version = "0.25.3" description = "A utility library for mocking out the `requests` Python library." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3200,6 +3329,7 @@ tests = ["coverage (>=6.0.0)", "flake8", "mypy", "pytest (>=7.0.0)", "pytest-asy name = "rfc3339-validator" version = "0.1.4" description = "A pure python RFC3339 validator" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3214,6 +3344,7 @@ six = "*" name = "rfc3986" version = "1.5.0" description = "Validating URI References per RFC 3986" +category = "main" optional = false python-versions = "*" files = [ @@ -3228,6 +3359,7 @@ idna2008 = ["idna"] name = "rfc3986-validator" version = "0.1.1" description = "Pure python rfc3986 validator" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3239,6 +3371,7 @@ files = [ name = "rpds-py" version = "0.20.0" description = "Python bindings to Rust's persistent data structures (rpds)" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3351,6 +3484,7 @@ files = [ name = "rsa" version = "3.3" description = "Pure-Python RSA implementation" +category = "main" optional = false python-versions = "*" files = [ @@ -3365,6 +3499,7 @@ pyasn1 = ">=0.1.3" name = "rutter" version = "0.4" description = "Py3k-compatible fork of Paste's urlmap" +category = "main" optional = false python-versions = "*" files = [ @@ -3382,6 +3517,7 @@ testing = ["WebTest", "coverage", "pytest", "pytest-cov"] name = "s3transfer" version = "0.10.2" description = "An Amazon S3 Transfer Manager" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3399,6 +3535,7 @@ crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"] name = "scikit-learn" version = "1.5.1" description = "A set of python modules for machine learning and data mining" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3444,6 +3581,7 @@ tests = ["black (>=24.3.0)", "matplotlib (>=3.3.4)", "mypy (>=1.9)", "numpydoc ( name = "scipy" version = "1.13.1" description = "Fundamental algorithms for scientific computing in Python" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3486,6 +3624,7 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po name = "semantic-version" version = "2.10.0" description = "A library implementing the 'SemVer' scheme." +category = "main" optional = false python-versions = ">=2.7" files = [ @@ -3501,6 +3640,7 @@ doc = ["Sphinx", "sphinx-rtd-theme"] name = "sentry-sdk" version = "1.45.1" description = "Python client for Sentry (https://sentry.io)" +category = "main" optional = false python-versions = "*" files = [ @@ -3548,6 +3688,7 @@ tornado = ["tornado (>=5)"] name = "setuptools" version = "72.2.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3558,12 +3699,13 @@ files = [ [package.extras] core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"] -test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (>=1.11.0,<1.12.0)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] [[package]] name = "shortuuid" version = "1.0.13" description = "A generator library for concise, unambiguous and URL-safe UUIDs." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3575,6 +3717,7 @@ files = [ name = "simplejson" version = "3.19.3" description = "Simple, fast, extensible JSON encoder/decoder for Python" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.5" files = [ @@ -3694,6 +3837,7 @@ files = [ name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3705,6 +3849,7 @@ files = [ name = "smmap" version = "5.0.1" description = "A pure Python implementation of a sliding window memory map manager" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3716,6 +3861,7 @@ files = [ name = "soupsieve" version = "2.6" description = "A modern CSS selector implementation for Beautiful Soup." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3727,6 +3873,7 @@ files = [ name = "sparqlwrapper" version = "1.8.5" description = "SPARQL Endpoint interface to Python" +category = "main" optional = false python-versions = "*" files = [ @@ -3745,6 +3892,7 @@ keepalive = ["keepalive (>=0.5)"] name = "sqlalchemy" version = "1.4.41" description = "Database Abstraction Library" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -3792,7 +3940,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and platform_machine == \"aarch64\" or python_version >= \"3\" and platform_machine == \"ppc64le\" or python_version >= \"3\" and platform_machine == \"x86_64\" or python_version >= \"3\" and platform_machine == \"amd64\" or python_version >= \"3\" and platform_machine == \"AMD64\" or python_version >= \"3\" and platform_machine == \"win32\" or python_version >= \"3\" and platform_machine == \"WIN32\""} [package.extras] aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] @@ -3819,6 +3967,7 @@ sqlcipher = ["sqlcipher3-binary"] name = "statsmodels" version = "0.14.2" description = "Statistical computations and models for Python" +category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3864,6 +4013,7 @@ docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "n name = "structlog" version = "19.2.0" description = "Structured Logging for Python" +category = "main" optional = false python-versions = "*" files = [ @@ -3884,6 +4034,7 @@ tests = ["coverage", "freezegun (>=0.2.8)", "pretend", "pytest (>=3.3.0)", "pyth name = "submit4dn" version = "4.1.0" description = "Utility package for submitting data to the 4DN Data Portal" +category = "main" optional = false python-versions = "<3.13,>=3.8.1" files = [ @@ -3902,6 +4053,7 @@ python-magic = ">=0.4.12,<1" name = "subprocess-middleware" version = "0.3" description = "Subprocess WSGI middleware and Pyramid tween." +category = "main" optional = false python-versions = "*" files = [ @@ -3918,6 +4070,7 @@ test = ["WebTest", "pyramid", "pytest"] name = "supervisor" version = "4.2.5" description = "A system for controlling process state under UNIX" +category = "main" optional = false python-versions = "*" files = [ @@ -3935,6 +4088,7 @@ testing = ["pytest", "pytest-cov"] name = "threadpoolctl" version = "3.5.0" description = "threadpoolctl" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3946,6 +4100,7 @@ files = [ name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" +category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3957,6 +4112,7 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3968,6 +4124,7 @@ files = [ name = "tqdm" version = "4.66.5" description = "Fast, Extensible Progress Meter" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3988,6 +4145,7 @@ telegram = ["requests"] name = "transaction" version = "3.1.0" description = "Transaction management for Python" +category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" files = [ @@ -4007,6 +4165,7 @@ testing = ["coverage", "mock", "nose"] name = "translationstring" version = "1.3" description = "Utility library for i18n relied on by various Repoze and Pyramid packages" +category = "main" optional = false python-versions = "*" files = [ @@ -4018,6 +4177,7 @@ files = [ name = "types-awscrt" version = "0.21.2" description = "Type annotations and code completion for awscrt" +category = "dev" optional = false python-versions = "<4.0,>=3.7" files = [ @@ -4029,6 +4189,7 @@ files = [ name = "types-python-dateutil" version = "2.9.0.20240316" description = "Typing stubs for python-dateutil" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4040,6 +4201,7 @@ files = [ name = "types-s3transfer" version = "0.10.1" description = "Type annotations and code completion for s3transfer" +category = "dev" optional = false python-versions = "<4.0,>=3.8" files = [ @@ -4051,6 +4213,7 @@ files = [ name = "typing-extensions" version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4062,6 +4225,7 @@ files = [ name = "tzdata" version = "2024.1" description = "Provider of IANA time zone data" +category = "main" optional = false python-versions = ">=2" files = [ @@ -4073,6 +4237,7 @@ files = [ name = "uptime" version = "3.0.1" description = "Cross-platform uptime library" +category = "main" optional = false python-versions = "*" files = [ @@ -4083,6 +4248,7 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4097,6 +4263,7 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "urllib3" version = "1.26.19" description = "HTTP library with thread-safe connection pooling, file post, and more." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -4113,6 +4280,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "venusian" version = "3.1.0" description = "A library for deferring decorator actions" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4128,6 +4296,7 @@ testing = ["coverage", "pytest", "pytest-cov"] name = "waitress" version = "2.1.2" description = "Waitress WSGI server" +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -4143,6 +4312,7 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] name = "webcolors" version = "24.8.0" description = "A library for working with the color formats defined by HTML and CSS." +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4158,6 +4328,7 @@ tests = ["coverage[toml]"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" +category = "main" optional = false python-versions = "*" files = [ @@ -4169,6 +4340,7 @@ files = [ name = "webob" version = "1.8.8" description = "WSGI request and response object" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -4184,6 +4356,7 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] name = "websocket-client" version = "1.8.0" description = "WebSocket client for Python with low level API options" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4200,6 +4373,7 @@ test = ["websockets"] name = "webtest" version = "2.0.35" description = "Helper to test WSGI applications" +category = "main" optional = false python-versions = "*" files = [ @@ -4221,6 +4395,7 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu name = "werkzeug" version = "3.0.3" description = "The comprehensive WSGI web application library." +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -4238,6 +4413,7 @@ watchdog = ["watchdog (>=2.3)"] name = "wheel" version = "0.40.0" description = "A built-package format for Python" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4252,6 +4428,7 @@ test = ["pytest (>=6.0.0)"] name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4331,6 +4508,7 @@ files = [ name = "wsgiproxy2" version = "0.4.2" description = "UNKNOWN" +category = "main" optional = false python-versions = "*" files = [ @@ -4345,6 +4523,7 @@ webob = "*" name = "xlrd" version = "1.2.0" description = "Library for developers to extract data from Microsoft Excel (tm) spreadsheet files" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -4356,6 +4535,7 @@ files = [ name = "xlwt" version = "1.2.0" description = "Library to create spreadsheet files compatible with MS Excel 97/2000/XP/2003 XLS files, on any platform, with Python 2.6, 2.7, 3.3+" +category = "main" optional = false python-versions = "*" files = [ @@ -4367,6 +4547,7 @@ files = [ name = "xmltodict" version = "0.13.0" description = "Makes working with XML feel like you are working with JSON" +category = "dev" optional = false python-versions = ">=3.4" files = [ @@ -4378,6 +4559,7 @@ files = [ name = "zipp" version = "3.20.0" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4393,6 +4575,7 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", name = "zope-deprecation" version = "4.4.0" description = "Zope Deprecation Infrastructure" +category = "main" optional = false python-versions = "*" files = [ @@ -4411,6 +4594,7 @@ test = ["zope.testrunner"] name = "zope-interface" version = "5.5.2" description = "Interfaces for Python" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -4464,6 +4648,7 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] name = "zope-sqlalchemy" version = "1.6" description = "Minimal Zope/SQLAlchemy transaction integration" +category = "main" optional = false python-versions = "*" files = [ @@ -4483,4 +4668,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "132074033874560b8257e8a72fa29290aab135aad8386cb7bc3a138f2e22e79d" +content-hash = "155efb7061eda8a9032996202030ecca56891e61f266441fc2b60045591065e7" diff --git a/pyproject.toml b/pyproject.toml index 38d75f61e2..006bf9d518 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ colorama = "0.3.3" # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" -dcicsnovault = "11.21.1.0b2" +dcicsnovault = "11.21.1.0b3" dcicutils = "^8.13.3" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses From ac82d861cf05fcc8f637bec8b510d46830ad33cb Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Wed, 28 Aug 2024 15:17:06 -0400 Subject: [PATCH 09/11] update again --- poetry.lock | 203 +++---------------------------------------------- pyproject.toml | 2 +- 2 files changed, 10 insertions(+), 195 deletions(-) diff --git a/poetry.lock b/poetry.lock index 204faaf638..20d49bafcd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. [[package]] name = "apipkg" version = "3.0.2" description = "apipkg: namespace control and lazy-import mechanism" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -16,7 +15,6 @@ files = [ name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" optional = false python-versions = "*" files = [ @@ -28,7 +26,6 @@ files = [ name = "arrow" version = "1.3.0" description = "Better dates & times for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -42,13 +39,12 @@ types-python-dateutil = ">=2.8.10" [package.extras] doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"] -test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (>=3.0.0,<4.0.0)"] +test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"] [[package]] name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -60,7 +56,6 @@ files = [ name = "attrs" version = "22.2.0" description = "Classes Without Boilerplate" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -79,7 +74,6 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy name = "aws-requests-auth" version = "0.4.3" description = "AWS signature version 4 signing process for the python requests module" -category = "main" optional = false python-versions = "*" files = [ @@ -94,7 +88,6 @@ requests = ">=0.14.0" name = "aws-xray-sdk" version = "0.95" description = "The AWS X-Ray SDK for Python (the SDK) enables Python developers to record and emit information from within their applications to the AWS X-Ray service." -category = "dev" optional = false python-versions = "*" files = [ @@ -111,7 +104,6 @@ wrapt = "*" name = "awscli" version = "1.33.44" description = "Universal Command Line Environment for AWS." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -131,7 +123,6 @@ s3transfer = ">=0.10.0,<0.11.0" name = "beautifulsoup4" version = "4.12.3" description = "Screen-scraping library" -category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -153,7 +144,6 @@ lxml = ["lxml"] name = "blinker" version = "1.8.2" description = "Fast, simple object-to-object and broadcast signaling" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -165,7 +155,6 @@ files = [ name = "boto" version = "2.49.0" description = "Amazon Web Services Library" -category = "dev" optional = false python-versions = "*" files = [ @@ -177,7 +166,6 @@ files = [ name = "boto3" version = "1.34.162" description = "The AWS SDK for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -197,7 +185,6 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] name = "boto3-stubs" version = "1.34.162" description = "Type annotations for boto3 1.34.162 generated with mypy-boto3-builder 7.26.0" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -605,7 +592,6 @@ xray = ["mypy-boto3-xray (>=1.34.0,<1.35.0)"] name = "botocore" version = "1.34.162" description = "Low-level, data-driven core of boto 3." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -628,7 +614,6 @@ crt = ["awscrt (==0.21.2)"] name = "botocore-stubs" version = "1.34.162" description = "Type annotations and code completion for botocore" -category = "dev" optional = false python-versions = "<4.0,>=3.8" files = [ @@ -646,7 +631,6 @@ botocore = ["botocore"] name = "certifi" version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -658,7 +642,6 @@ files = [ name = "cffi" version = "1.17.0" description = "Foreign Function Interface for Python calling C code." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -738,7 +721,6 @@ pycparser = "*" name = "chardet" version = "5.2.0" description = "Universal encoding detector for Python 3" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -750,7 +732,6 @@ files = [ name = "charset-normalizer" version = "3.3.2" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -850,7 +831,6 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -865,7 +845,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "codacy-coverage" version = "1.3.11" description = "Codacy coverage reporter for Python" -category = "dev" optional = false python-versions = "*" files = [ @@ -884,7 +863,6 @@ test = ["coverage", "nosetests"] name = "codeguru-profiler-agent" version = "1.2.5" description = "The Python agent to be used for Amazon CodeGuru Profiler" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -899,7 +877,6 @@ boto3 = ">=1.14.0" name = "colorama" version = "0.3.3" description = "Cross-platform colored terminal text." -category = "main" optional = false python-versions = "*" files = [ @@ -910,7 +887,6 @@ files = [ name = "coverage" version = "7.6.1" description = "Code coverage measurement for Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -998,7 +974,6 @@ toml = ["tomli"] name = "coveralls" version = "4.0.1" description = "Show coverage stats online via coveralls.io" -category = "dev" optional = false python-versions = "<3.13,>=3.8" files = [ @@ -1007,7 +982,7 @@ files = [ ] [package.dependencies] -coverage = {version = ">=5.0,<6.0.0 || >6.1,<6.1.1 || >6.1.1,<8.0", extras = ["toml"]} +coverage = {version = ">=5.0,<6.0.dev0 || >6.1,<6.1.1 || >6.1.1,<8.0", extras = ["toml"]} docopt = ">=0.6.1,<0.7.0" requests = ">=1.0.0,<3.0.0" @@ -1018,7 +993,6 @@ yaml = ["pyyaml (>=3.10,<7.0)"] name = "cryptography" version = "39.0.2" description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1064,7 +1038,6 @@ tox = ["tox"] name = "cython" version = "3.0.11" description = "The Cython compiler for writing C extensions in the Python language." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" files = [ @@ -1138,14 +1111,13 @@ files = [ [[package]] name = "dcicsnovault" -version = "11.21.1.0b3" +version = "11.21.1.0b4" description = "Storage support for 4DN Data Portals." -category = "main" optional = false python-versions = "<3.13,>=3.9" files = [ - {file = "dcicsnovault-11.21.1.0b3-py3-none-any.whl", hash = "sha256:3de7d666d905badbcd7832dca130c8c9578e85924ceaa1a36a9327e95ab6c59d"}, - {file = "dcicsnovault-11.21.1.0b3.tar.gz", hash = "sha256:7554fe967237a0a94f17b35998e1bd41d5221d5c22d1138f74ae7943605d463e"}, + {file = "dcicsnovault-11.21.1.0b4-py3-none-any.whl", hash = "sha256:a6f1e2ffde265891009d464c6becdb04e2ad964b0a5f6e52a3f03be78b2aac34"}, + {file = "dcicsnovault-11.21.1.0b4.tar.gz", hash = "sha256:aeac5a31ef183f144a53e161c6938c00165329e58a9cf9effdc4a2168a4a5bb9"}, ] [package.dependencies] @@ -1199,7 +1171,6 @@ xlrd = ">=1.0.0,<2.0.0" name = "dcicutils" version = "8.14.0" description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources" -category = "main" optional = false python-versions = "<3.13,>=3.8.1" files = [ @@ -1241,7 +1212,6 @@ webtest = ">=2.0.34,<3.0.0" name = "docker" version = "4.4.4" description = "A Python library for the Docker Engine API." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1263,7 +1233,6 @@ tls = ["cryptography (>=1.3.4)", "idna (>=2.0.0)", "pyOpenSSL (>=17.5.0)"] name = "docopt" version = "0.6.2" description = "Pythonic argument parser, that will make you smile" -category = "dev" optional = false python-versions = "*" files = [ @@ -1274,7 +1243,6 @@ files = [ name = "docutils" version = "0.16" description = "Docutils -- Python Documentation Utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1286,7 +1254,6 @@ files = [ name = "ecdsa" version = "0.19.0" description = "ECDSA cryptographic signature library (pure python)" -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.6" files = [ @@ -1305,7 +1272,6 @@ gmpy2 = ["gmpy2"] name = "elasticsearch" version = "7.13.4" description = "Python client for Elasticsearch" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4" files = [ @@ -1327,7 +1293,6 @@ requests = ["requests (>=2.4.0,<3.0.0)"] name = "elasticsearch-dsl" version = "7.4.1" description = "Python client for Elasticsearch" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1347,7 +1312,6 @@ develop = ["coverage (<5.0.0)", "mock", "pytest (>=3.0.0)", "pytest-cov", "pytes name = "et-xmlfile" version = "1.1.0" description = "An implementation of lxml.xmlfile for the standard library" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1359,7 +1323,6 @@ files = [ name = "events" version = "0.5" description = "Bringing the elegance of C# EventHandler to Python" -category = "main" optional = false python-versions = "*" files = [ @@ -1370,7 +1333,6 @@ files = [ name = "exceptiongroup" version = "1.2.2" description = "Backport of PEP 654 (exception groups)" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1385,7 +1347,6 @@ test = ["pytest (>=6)"] name = "execnet" version = "1.4.1" description = "execnet: rapid multi-Python deployment" -category = "main" optional = false python-versions = "*" files = [ @@ -1400,7 +1361,6 @@ apipkg = ">=1.4" name = "flake8" version = "7.1.1" description = "the modular source code checker: pep8 pyflakes and co" -category = "dev" optional = false python-versions = ">=3.8.1" files = [ @@ -1417,7 +1377,6 @@ pyflakes = ">=3.2.0,<3.3.0" name = "flaky" version = "3.8.1" description = "Plugin for pytest that automatically reruns flaky tests." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1429,7 +1388,6 @@ files = [ name = "flask" version = "3.0.3" description = "A simple framework for building complex web applications." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1453,7 +1411,6 @@ dotenv = ["python-dotenv"] name = "fqdn" version = "1.5.1" description = "Validates fully-qualified domain names against RFC 1123, so that they are acceptable to modern bowsers" -category = "main" optional = false python-versions = ">=2.7, !=3.0, !=3.1, !=3.2, !=3.3, !=3.4, <4" files = [ @@ -1465,7 +1422,6 @@ files = [ name = "future" version = "0.18.3" description = "Clean single-source support for Python 3 and 2" -category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1476,7 +1432,6 @@ files = [ name = "gitdb" version = "4.0.11" description = "Git Object Database" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1491,7 +1446,6 @@ smmap = ">=3.0.1,<6" name = "gitpython" version = "3.1.43" description = "GitPython is a Python library used to interact with Git repositories" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1510,7 +1464,6 @@ test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", name = "greenlet" version = "3.0.3" description = "Lightweight in-process concurrent programming" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1582,7 +1535,6 @@ test = ["objgraph", "psutil"] name = "html5lib" version = "1.1" description = "HTML parser based on the WHATWG HTML specification" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -1604,7 +1556,6 @@ lxml = ["lxml"] name = "humanfriendly" version = "1.44.9" description = "Human friendly output for text interfaces using Python" -category = "main" optional = false python-versions = "*" files = [ @@ -1616,7 +1567,6 @@ files = [ name = "hupper" version = "1.12.1" description = "Integrated process monitor for developing and reloading daemons." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1632,7 +1582,6 @@ testing = ["mock", "pytest", "pytest-cov", "watchdog"] name = "idna" version = "2.10" description = "Internationalized Domain Names in Applications (IDNA)" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1644,7 +1593,6 @@ files = [ name = "importlib-metadata" version = "8.2.0" description = "Read metadata from Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1664,7 +1612,6 @@ test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "p name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1676,7 +1623,6 @@ files = [ name = "isodate" version = "0.6.0" description = "An ISO 8601 date/time/duration parser and formatter" -category = "main" optional = false python-versions = "*" files = [ @@ -1691,7 +1637,6 @@ six = "*" name = "isoduration" version = "20.11.0" description = "Operations with ISO 8601 durations" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1706,7 +1651,6 @@ arrow = ">=0.15.0" name = "itsdangerous" version = "2.2.0" description = "Safely pass data to untrusted environments and back." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1718,7 +1662,6 @@ files = [ name = "jinja2" version = "3.1.4" description = "A very fast and expressive template engine." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1736,7 +1679,6 @@ i18n = ["Babel (>=2.7)"] name = "jmespath" version = "0.9.0" description = "JSON Matching Expressions" -category = "main" optional = false python-versions = "*" files = [ @@ -1748,7 +1690,6 @@ files = [ name = "joblib" version = "1.4.2" description = "Lightweight pipelining with Python functions" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1760,7 +1701,6 @@ files = [ name = "jsonc-parser" version = "1.1.5" description = "A lightweight, native tool for parsing .jsonc files" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -1772,7 +1712,6 @@ files = [ name = "jsondiff" version = "1.1.1" description = "Diff JSON and JSON-like structures in Python" -category = "dev" optional = false python-versions = "*" files = [ @@ -1783,7 +1722,6 @@ files = [ name = "jsonpickle" version = "3.2.2" description = "Python library for serializing arbitrary object graphs into JSON" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1800,7 +1738,6 @@ testing = ["bson", "ecdsa", "feedparser", "gmpy2", "numpy", "pandas", "pymongo", name = "jsonpointer" version = "3.0.0" description = "Identify specific nodes in a JSON document (RFC 6901)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1812,7 +1749,6 @@ files = [ name = "jsonschema" version = "4.23.0" description = "An implementation of JSON Schema validation for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1842,7 +1778,6 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- name = "jsonschema-specifications" version = "2023.12.1" description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1857,7 +1792,6 @@ referencing = ">=0.31.0" name = "lorem-text" version = "2.1" description = "Dummy lorem ipsum text generator" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1872,7 +1806,6 @@ Click = ">=7.0" name = "markdown" version = "3.7" description = "Python implementation of John Gruber's Markdown." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -1891,7 +1824,6 @@ testing = ["coverage", "pyyaml"] name = "markupsafe" version = "2.1.5" description = "Safely add untrusted strings to HTML/XML markup." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1961,7 +1893,6 @@ files = [ name = "mccabe" version = "0.7.0" description = "McCabe checker, plugin for flake8" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1973,7 +1904,6 @@ files = [ name = "mock" version = "5.1.0" description = "Rolling backport of unittest.mock for all Pythons" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1990,7 +1920,6 @@ test = ["pytest", "pytest-cov"] name = "moto" version = "1.3.7" description = "A library that allows your python tests to easily mock out the boto library" -category = "dev" optional = false python-versions = "*" files = [ @@ -2025,7 +1954,6 @@ server = ["flask"] name = "netaddr" version = "0.10.1" description = "A network address manipulation library for Python" -category = "main" optional = false python-versions = "*" files = [ @@ -2037,7 +1965,6 @@ files = [ name = "numpy" version = "1.26.4" description = "Fundamental package for array computing in Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2083,7 +2010,6 @@ files = [ name = "openpyxl" version = "3.1.5" description = "A Python library to read/write Excel 2010 xlsx/xlsm files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2098,7 +2024,6 @@ et-xmlfile = "*" name = "opensearch-py" version = "2.6.0" description = "Python client for OpenSearch" -category = "main" optional = false python-versions = "<4,>=3.8" files = [ @@ -2127,7 +2052,6 @@ kerberos = ["requests-kerberos"] name = "packaging" version = "24.1" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2139,7 +2063,6 @@ files = [ name = "pandas" version = "2.2.2" description = "Powerful data structures for data analysis, time series, and statistics" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -2213,7 +2136,6 @@ xml = ["lxml (>=4.9.2)"] name = "passlib" version = "1.7.4" description = "comprehensive password hashing framework supporting over 30 schemes" -category = "main" optional = false python-versions = "*" files = [ @@ -2231,7 +2153,6 @@ totp = ["cryptography"] name = "pastedeploy" version = "3.1.0" description = "Load, configure, and compose WSGI applications and servers" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2248,7 +2169,6 @@ testing = ["Paste", "pytest", "pytest-cov"] name = "patsy" version = "0.5.6" description = "A Python package for describing statistical models and for building design matrices." -category = "main" optional = false python-versions = "*" files = [ @@ -2267,7 +2187,6 @@ test = ["pytest", "pytest-cov", "scipy"] name = "pbkdf2" version = "1.3" description = "PKCS#5 v2.0 PBKDF2 Module" -category = "main" optional = false python-versions = "*" files = [ @@ -2278,7 +2197,6 @@ files = [ name = "pillow" version = "9.5.0" description = "Python Imaging Library (Fork)" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2358,7 +2276,6 @@ tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "pa name = "pip" version = "24.2" description = "The PyPA recommended tool for installing Python packages." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2370,7 +2287,6 @@ files = [ name = "pip-licenses" version = "3.5.5" description = "Dump the software license list of Python packages installed with pip." -category = "dev" optional = false python-versions = "~=3.7" files = [ @@ -2388,7 +2304,6 @@ test = ["docutils", "pytest-cov", "pytest-pycodestyle", "pytest-runner"] name = "pipdeptree" version = "2.23.1" description = "Command line utility to show dependency tree of packages." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2408,7 +2323,6 @@ test = ["covdefaults (>=2.3)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pyte name = "plaster" version = "1.0" description = "A loader interface around multiple config file formats." -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2427,7 +2341,6 @@ testing = ["pytest", "pytest-cov"] name = "plaster-pastedeploy" version = "0.6" description = "A loader implementing the PasteDeploy syntax to be used by plaster." -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2446,7 +2359,6 @@ testing = ["pytest", "pytest-cov"] name = "pluggy" version = "1.5.0" description = "plugin and hook calling mechanisms for python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2462,7 +2374,6 @@ testing = ["pytest", "pytest-benchmark"] name = "pmdarima" version = "2.0.4" description = "Python's forecast::auto.arima equivalent" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2514,7 +2425,6 @@ urllib3 = "*" name = "psutil" version = "5.9.8" description = "Cross-platform lib for process and system monitoring in Python." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -2543,7 +2453,6 @@ test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"] name = "psycopg2-binary" version = "2.9.9" description = "psycopg2 - Python-PostgreSQL Database Adapter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2625,7 +2534,6 @@ files = [ name = "ptable" version = "0.9.2" description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format" -category = "dev" optional = false python-versions = "*" files = [ @@ -2636,7 +2544,6 @@ files = [ name = "py" version = "1.11.0" description = "library with cross-python path, ini-parsing, io, code, log facilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2648,7 +2555,6 @@ files = [ name = "pyaml" version = "24.7.0" description = "PyYAML-based module to produce a bit more pretty and readable YAML-serialized data" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2666,7 +2572,6 @@ anchors = ["unidecode"] name = "pyasn1" version = "0.6.0" description = "Pure-Python implementation of ASN.1 types and DER/BER/CER codecs (X.208)" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2678,7 +2583,6 @@ files = [ name = "pybrowserid" version = "0.10.0" description = "Python library for the BrowserID Protocol" -category = "main" optional = false python-versions = "*" files = [ @@ -2692,7 +2596,6 @@ requests = "*" name = "pycodestyle" version = "2.12.1" description = "Python style guide checker" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2704,7 +2607,6 @@ files = [ name = "pycparser" version = "2.22" description = "C parser in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2716,7 +2618,6 @@ files = [ name = "pycryptodome" version = "3.20.0" description = "Cryptographic library for Python" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -2758,7 +2659,6 @@ files = [ name = "pyflakes" version = "3.2.0" description = "passive checker of Python programs" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2770,7 +2670,6 @@ files = [ name = "pygments" version = "2.18.0" description = "Pygments is a syntax highlighting package written in Python." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2785,7 +2684,6 @@ windows-terminal = ["colorama (>=0.4.6)"] name = "pyjwt" version = "2.9.0" description = "JSON Web Token implementation in Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -2803,7 +2701,6 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"] name = "pyopenssl" version = "23.2.0" description = "Python wrapper module around the OpenSSL library" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -2822,7 +2719,6 @@ test = ["flaky", "pretend", "pytest (>=3.0.1)"] name = "pyparsing" version = "2.4.7" description = "Python parsing module" -category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -2834,7 +2730,6 @@ files = [ name = "pyperclip" version = "1.9.0" description = "A cross-platform clipboard module for Python. (Only handles plain text for now.)" -category = "main" optional = false python-versions = "*" files = [ @@ -2845,7 +2740,6 @@ files = [ name = "pyramid" version = "1.10.8" description = "The Pyramid Web Framework, a Pylons project" -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" files = [ @@ -2872,7 +2766,6 @@ testing = ["coverage", "nose", "virtualenv", "webtest (>=1.3.1)", "zope.componen name = "pyramid-multiauth" version = "0.9.0" description = "pyramid_multiauth" -category = "main" optional = false python-versions = "*" files = [ @@ -2887,7 +2780,6 @@ pyramid = "*" name = "pyramid-retry" version = "1.0" description = "An execution policy for Pyramid that supports retrying requests after certain failure exceptions." -category = "main" optional = false python-versions = "*" files = [ @@ -2907,7 +2799,6 @@ testing = ["WebTest", "pytest", "pytest-cov"] name = "pyramid-tm" version = "2.5" description = "A package which allows Pyramid requests to join the active transaction" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -2927,7 +2818,6 @@ testing = ["WebTest", "coverage (>=5.0)", "pytest", "pytest-cov"] name = "pyramid-translogger" version = "0.1" description = "access log logger tween (almost stolen from Paste.translogger)" -category = "main" optional = false python-versions = "*" files = [ @@ -2941,7 +2831,6 @@ setuptools = "*" name = "pytest" version = "7.4.4" description = "pytest: simple powerful testing with Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2964,7 +2853,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-cov" version = "5.0.0" description = "Pytest plugin for measuring coverage." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -2983,7 +2871,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"] name = "pytest-instafail" version = "0.5.0" description = "pytest plugin to show failures instantly" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -2998,7 +2885,6 @@ pytest = ">=5" name = "pytest-mock" version = "3.14.0" description = "Thin-wrapper around the mock package for easier use with pytest" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3016,7 +2902,6 @@ dev = ["pre-commit", "pytest-asyncio", "tox"] name = "pytest-timeout" version = "2.3.1" description = "pytest plugin to abort hanging tests" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3031,7 +2916,6 @@ pytest = ">=7.0.0" name = "pytest-xdist" version = "3.5.0" description = "pytest xdist plugin for distributed testing, most importantly across multiple CPUs" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -3052,7 +2936,6 @@ testing = ["filelock"] name = "python-dateutil" version = "2.9.0.post0" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -3067,7 +2950,6 @@ six = ">=1.5" name = "python-jose" version = "2.0.2" description = "JOSE implementation in Python" -category = "dev" optional = false python-versions = "*" files = [ @@ -3089,7 +2971,6 @@ pycrypto = ["pycrypto (>=2.6.0,<2.7.0)"] name = "python-magic" version = "0.4.27" description = "File type identification using libmagic" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3101,7 +2982,6 @@ files = [ name = "pytz" version = "2024.1" description = "World timezone definitions, modern and historical" -category = "main" optional = false python-versions = "*" files = [ @@ -3113,7 +2993,6 @@ files = [ name = "pywin32" version = "227" description = "Python for Window Extensions" -category = "main" optional = false python-versions = "*" files = [ @@ -3135,7 +3014,6 @@ files = [ name = "pyyaml" version = "6.0.2" description = "YAML parser and emitter for Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3198,7 +3076,6 @@ files = [ name = "rdflib" version = "4.2.2" description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information." -category = "main" optional = false python-versions = "*" files = [ @@ -3218,7 +3095,6 @@ sparql = ["SPARQLWrapper"] name = "rdflib-jsonld" version = "0.6.0" description = "rdflib extension adding JSON-LD parser and serializer" -category = "main" optional = false python-versions = "*" files = [ @@ -3233,7 +3109,6 @@ rdflib = "*" name = "redis" version = "4.6.0" description = "Python client for Redis database and key-value store" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3252,7 +3127,6 @@ ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)" name = "referencing" version = "0.35.1" description = "JSON Referencing + Python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3268,7 +3142,6 @@ rpds-py = ">=0.7.0" name = "repoze-debug" version = "1.1" description = "Forensic debugging WSGI middleware" -category = "dev" optional = false python-versions = "*" files = [ @@ -3287,7 +3160,6 @@ testing = ["WebOb", "coverage", "nose"] name = "requests" version = "2.31.0" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3309,7 +3181,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "responses" version = "0.25.3" description = "A utility library for mocking out the `requests` Python library." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -3329,7 +3200,6 @@ tests = ["coverage (>=6.0.0)", "flake8", "mypy", "pytest (>=7.0.0)", "pytest-asy name = "rfc3339-validator" version = "0.1.4" description = "A pure python RFC3339 validator" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3344,7 +3214,6 @@ six = "*" name = "rfc3986" version = "1.5.0" description = "Validating URI References per RFC 3986" -category = "main" optional = false python-versions = "*" files = [ @@ -3359,7 +3228,6 @@ idna2008 = ["idna"] name = "rfc3986-validator" version = "0.1.1" description = "Pure python rfc3986 validator" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -3371,7 +3239,6 @@ files = [ name = "rpds-py" version = "0.20.0" description = "Python bindings to Rust's persistent data structures (rpds)" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3484,7 +3351,6 @@ files = [ name = "rsa" version = "3.3" description = "Pure-Python RSA implementation" -category = "main" optional = false python-versions = "*" files = [ @@ -3499,7 +3365,6 @@ pyasn1 = ">=0.1.3" name = "rutter" version = "0.4" description = "Py3k-compatible fork of Paste's urlmap" -category = "main" optional = false python-versions = "*" files = [ @@ -3517,7 +3382,6 @@ testing = ["WebTest", "coverage", "pytest", "pytest-cov"] name = "s3transfer" version = "0.10.2" description = "An Amazon S3 Transfer Manager" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3535,7 +3399,6 @@ crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"] name = "scikit-learn" version = "1.5.1" description = "A set of python modules for machine learning and data mining" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3581,7 +3444,6 @@ tests = ["black (>=24.3.0)", "matplotlib (>=3.3.4)", "mypy (>=1.9)", "numpydoc ( name = "scipy" version = "1.13.1" description = "Fundamental algorithms for scientific computing in Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -3624,7 +3486,6 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po name = "semantic-version" version = "2.10.0" description = "A library implementing the 'SemVer' scheme." -category = "main" optional = false python-versions = ">=2.7" files = [ @@ -3640,7 +3501,6 @@ doc = ["Sphinx", "sphinx-rtd-theme"] name = "sentry-sdk" version = "1.45.1" description = "Python client for Sentry (https://sentry.io)" -category = "main" optional = false python-versions = "*" files = [ @@ -3688,7 +3548,6 @@ tornado = ["tornado (>=5)"] name = "setuptools" version = "72.2.0" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3699,13 +3558,12 @@ files = [ [package.extras] core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier", "towncrier (<24.7)"] -test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (>=1.11.0,<1.12.0)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] +test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"] [[package]] name = "shortuuid" version = "1.0.13" description = "A generator library for concise, unambiguous and URL-safe UUIDs." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -3717,7 +3575,6 @@ files = [ name = "simplejson" version = "3.19.3" description = "Simple, fast, extensible JSON encoder/decoder for Python" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.5" files = [ @@ -3837,7 +3694,6 @@ files = [ name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -3849,7 +3705,6 @@ files = [ name = "smmap" version = "5.0.1" description = "A pure Python implementation of a sliding window memory map manager" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -3861,7 +3716,6 @@ files = [ name = "soupsieve" version = "2.6" description = "A modern CSS selector implementation for Beautiful Soup." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -3873,7 +3727,6 @@ files = [ name = "sparqlwrapper" version = "1.8.5" description = "SPARQL Endpoint interface to Python" -category = "main" optional = false python-versions = "*" files = [ @@ -3892,7 +3745,6 @@ keepalive = ["keepalive (>=0.5)"] name = "sqlalchemy" version = "1.4.41" description = "Database Abstraction Library" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -3940,7 +3792,7 @@ files = [ ] [package.dependencies] -greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and platform_machine == \"aarch64\" or python_version >= \"3\" and platform_machine == \"ppc64le\" or python_version >= \"3\" and platform_machine == \"x86_64\" or python_version >= \"3\" and platform_machine == \"amd64\" or python_version >= \"3\" and platform_machine == \"AMD64\" or python_version >= \"3\" and platform_machine == \"win32\" or python_version >= \"3\" and platform_machine == \"WIN32\""} +greenlet = {version = "!=0.4.17", markers = "python_version >= \"3\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"} [package.extras] aiomysql = ["aiomysql", "greenlet (!=0.4.17)"] @@ -3967,7 +3819,6 @@ sqlcipher = ["sqlcipher3-binary"] name = "statsmodels" version = "0.14.2" description = "Statistical computations and models for Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -4013,7 +3864,6 @@ docs = ["ipykernel", "jupyter-client", "matplotlib", "nbconvert", "nbformat", "n name = "structlog" version = "19.2.0" description = "Structured Logging for Python" -category = "main" optional = false python-versions = "*" files = [ @@ -4034,7 +3884,6 @@ tests = ["coverage", "freezegun (>=0.2.8)", "pretend", "pytest (>=3.3.0)", "pyth name = "submit4dn" version = "4.1.0" description = "Utility package for submitting data to the 4DN Data Portal" -category = "main" optional = false python-versions = "<3.13,>=3.8.1" files = [ @@ -4053,7 +3902,6 @@ python-magic = ">=0.4.12,<1" name = "subprocess-middleware" version = "0.3" description = "Subprocess WSGI middleware and Pyramid tween." -category = "main" optional = false python-versions = "*" files = [ @@ -4070,7 +3918,6 @@ test = ["WebTest", "pyramid", "pytest"] name = "supervisor" version = "4.2.5" description = "A system for controlling process state under UNIX" -category = "main" optional = false python-versions = "*" files = [ @@ -4088,7 +3935,6 @@ testing = ["pytest", "pytest-cov"] name = "threadpoolctl" version = "3.5.0" description = "threadpoolctl" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4100,7 +3946,6 @@ files = [ name = "toml" version = "0.10.2" description = "Python Library for Tom's Obvious, Minimal Language" -category = "main" optional = false python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -4112,7 +3957,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -4124,7 +3968,6 @@ files = [ name = "tqdm" version = "4.66.5" description = "Fast, Extensible Progress Meter" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4145,7 +3988,6 @@ telegram = ["requests"] name = "transaction" version = "3.1.0" description = "Transaction management for Python" -category = "main" optional = false python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" files = [ @@ -4165,7 +4007,6 @@ testing = ["coverage", "mock", "nose"] name = "translationstring" version = "1.3" description = "Utility library for i18n relied on by various Repoze and Pyramid packages" -category = "main" optional = false python-versions = "*" files = [ @@ -4177,7 +4018,6 @@ files = [ name = "types-awscrt" version = "0.21.2" description = "Type annotations and code completion for awscrt" -category = "dev" optional = false python-versions = "<4.0,>=3.7" files = [ @@ -4189,7 +4029,6 @@ files = [ name = "types-python-dateutil" version = "2.9.0.20240316" description = "Typing stubs for python-dateutil" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4201,7 +4040,6 @@ files = [ name = "types-s3transfer" version = "0.10.1" description = "Type annotations and code completion for s3transfer" -category = "dev" optional = false python-versions = "<4.0,>=3.8" files = [ @@ -4213,7 +4051,6 @@ files = [ name = "typing-extensions" version = "4.12.2" description = "Backported and Experimental Type Hints for Python 3.8+" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4225,7 +4062,6 @@ files = [ name = "tzdata" version = "2024.1" description = "Provider of IANA time zone data" -category = "main" optional = false python-versions = ">=2" files = [ @@ -4237,7 +4073,6 @@ files = [ name = "uptime" version = "3.0.1" description = "Cross-platform uptime library" -category = "main" optional = false python-versions = "*" files = [ @@ -4248,7 +4083,6 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4263,7 +4097,6 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "urllib3" version = "1.26.19" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -4280,7 +4113,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "venusian" version = "3.1.0" description = "A library for deferring decorator actions" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4296,7 +4128,6 @@ testing = ["coverage", "pytest", "pytest-cov"] name = "waitress" version = "2.1.2" description = "Waitress WSGI server" -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -4312,7 +4143,6 @@ testing = ["coverage (>=5.0)", "pytest", "pytest-cover"] name = "webcolors" version = "24.8.0" description = "A library for working with the color formats defined by HTML and CSS." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4328,7 +4158,6 @@ tests = ["coverage[toml]"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" -category = "main" optional = false python-versions = "*" files = [ @@ -4340,7 +4169,6 @@ files = [ name = "webob" version = "1.8.8" description = "WSGI request and response object" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -4356,7 +4184,6 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"] name = "websocket-client" version = "1.8.0" description = "WebSocket client for Python with low level API options" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4373,7 +4200,6 @@ test = ["websockets"] name = "webtest" version = "2.0.35" description = "Helper to test WSGI applications" -category = "main" optional = false python-versions = "*" files = [ @@ -4395,7 +4221,6 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu name = "werkzeug" version = "3.0.3" description = "The comprehensive WSGI web application library." -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -4413,7 +4238,6 @@ watchdog = ["watchdog (>=2.3)"] name = "wheel" version = "0.40.0" description = "A built-package format for Python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -4428,7 +4252,6 @@ test = ["pytest (>=6.0.0)"] name = "wrapt" version = "1.16.0" description = "Module for decorators, wrappers and monkey patching." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -4508,7 +4331,6 @@ files = [ name = "wsgiproxy2" version = "0.4.2" description = "UNKNOWN" -category = "main" optional = false python-versions = "*" files = [ @@ -4523,7 +4345,6 @@ webob = "*" name = "xlrd" version = "1.2.0" description = "Library for developers to extract data from Microsoft Excel (tm) spreadsheet files" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -4535,7 +4356,6 @@ files = [ name = "xlwt" version = "1.2.0" description = "Library to create spreadsheet files compatible with MS Excel 97/2000/XP/2003 XLS files, on any platform, with Python 2.6, 2.7, 3.3+" -category = "main" optional = false python-versions = "*" files = [ @@ -4547,7 +4367,6 @@ files = [ name = "xmltodict" version = "0.13.0" description = "Makes working with XML feel like you are working with JSON" -category = "dev" optional = false python-versions = ">=3.4" files = [ @@ -4559,7 +4378,6 @@ files = [ name = "zipp" version = "3.20.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -4575,7 +4393,6 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", name = "zope-deprecation" version = "4.4.0" description = "Zope Deprecation Infrastructure" -category = "main" optional = false python-versions = "*" files = [ @@ -4594,7 +4411,6 @@ test = ["zope.testrunner"] name = "zope-interface" version = "5.5.2" description = "Interfaces for Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -4648,7 +4464,6 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"] name = "zope-sqlalchemy" version = "1.6" description = "Minimal Zope/SQLAlchemy transaction integration" -category = "main" optional = false python-versions = "*" files = [ @@ -4668,4 +4483,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "155efb7061eda8a9032996202030ecca56891e61f266441fc2b60045591065e7" +content-hash = "ccc7ee8654e0dd07544fcd26c3eee943d16a8c6413b9ccb5e6f7d02cd2a81cf4" diff --git a/pyproject.toml b/pyproject.toml index 006bf9d518..39ce6fb97f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ colorama = "0.3.3" # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" -dcicsnovault = "11.21.1.0b3" +dcicsnovault = "11.21.1.0b4" dcicutils = "^8.13.3" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses From f4e24131fa34c1f262099fcbe113e61f07463693 Mon Sep 17 00:00:00 2001 From: William Ronchetti Date: Thu, 29 Aug 2024 09:29:52 -0400 Subject: [PATCH 10/11] ignore content type for options --- poetry.lock | 8 ++++---- pyproject.toml | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/poetry.lock b/poetry.lock index 20d49bafcd..fac8c23b25 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1111,13 +1111,13 @@ files = [ [[package]] name = "dcicsnovault" -version = "11.21.1.0b4" +version = "11.21.1.0b5" description = "Storage support for 4DN Data Portals." optional = false python-versions = "<3.13,>=3.9" files = [ - {file = "dcicsnovault-11.21.1.0b4-py3-none-any.whl", hash = "sha256:a6f1e2ffde265891009d464c6becdb04e2ad964b0a5f6e52a3f03be78b2aac34"}, - {file = "dcicsnovault-11.21.1.0b4.tar.gz", hash = "sha256:aeac5a31ef183f144a53e161c6938c00165329e58a9cf9effdc4a2168a4a5bb9"}, + {file = "dcicsnovault-11.21.1.0b5-py3-none-any.whl", hash = "sha256:ab9fe33871386094d642a5a495377eff53616a7209f4d044d6b5fb1979c3867e"}, + {file = "dcicsnovault-11.21.1.0b5.tar.gz", hash = "sha256:fd383ba89f459ca673df82d3c704fcae54b140f4920f010500a71545b4cbac99"}, ] [package.dependencies] @@ -4483,4 +4483,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "ccc7ee8654e0dd07544fcd26c3eee943d16a8c6413b9ccb5e6f7d02cd2a81cf4" +content-hash = "85bbe4be4399c8a19d142acf88470f1d10a66b3d525df99b2459cb911f43fd6b" diff --git a/pyproject.toml b/pyproject.toml index 39ce6fb97f..f9d18ee87e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -49,7 +49,7 @@ colorama = "0.3.3" # we get odd 'pyo3_runtime.PanicException: Python API call failed' error on import # of cryptography.hazmat.bindings._rust in cryptography package. 2023-04-21. cryptography = "39.0.2" -dcicsnovault = "11.21.1.0b4" +dcicsnovault = "11.21.1.0b5" dcicutils = "^8.13.3" elasticsearch = "7.13.4" elasticsearch-dsl = "^7.0.0" # TODO: port code from cgap-portal to get rid of uses From a6087e2823ad548a928030d25b75f5d94c2c1ee3 Mon Sep 17 00:00:00 2001 From: David Michaels Date: Wed, 9 Oct 2024 17:03:16 -0400 Subject: [PATCH 11/11] added pkill opensearch to kill target in makefile --- Makefile | 1 + 1 file changed, 1 insertion(+) diff --git a/Makefile b/Makefile index 0ba48b2d66..8bd3199b35 100644 --- a/Makefile +++ b/Makefile @@ -133,6 +133,7 @@ kibana-stop: kill: # kills back-end processes associated with the application. Use with care. pkill -f postgres & + pkill -f opensearch & pkill -f elasticsearch & pkill -f moto_server &