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false python-versions = ">=3.8" files = [ - {file = "types-python-dateutil-2.8.19.20240106.tar.gz", hash = "sha256:1f8db221c3b98e6ca02ea83a58371b22c374f42ae5bbdf186db9c9a76581459f"}, - {file = "types_python_dateutil-2.8.19.20240106-py3-none-any.whl", hash = "sha256:efbbdc54590d0f16152fa103c9879c7d4a00e82078f6e2cf01769042165acaa2"}, + {file = "types-python-dateutil-2.9.0.20240316.tar.gz", hash = "sha256:5d2f2e240b86905e40944dd787db6da9263f0deabef1076ddaed797351ec0202"}, + {file = "types_python_dateutil-2.9.0.20240316-py3-none-any.whl", hash = "sha256:6b8cb66d960771ce5ff974e9dd45e38facb81718cc1e208b10b1baccbfdbee3b"}, ] [[package]] @@ -4381,13 +4443,13 @@ test = ["flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"] [[package]] name = "virtualenv" -version = "20.25.1" +version = "20.26.0" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.7" files = [ - {file = "virtualenv-20.25.1-py3-none-any.whl", hash = "sha256:961c026ac520bac5f69acb8ea063e8a4f071bcc9457b9c1f28f6b085c511583a"}, - {file = "virtualenv-20.25.1.tar.gz", hash = "sha256:e08e13ecdca7a0bd53798f356d5831434afa5b07b93f0abdf0797b7a06ffe197"}, + {file = "virtualenv-20.26.0-py3-none-any.whl", hash = "sha256:0846377ea76e818daaa3e00a4365c018bc3ac9760cbb3544de542885aad61fb3"}, + {file = "virtualenv-20.26.0.tar.gz", hash = "sha256:ec25a9671a5102c8d2657f62792a27b48f016664c6873f6beed3800008577210"}, ] [package.dependencies] @@ -4396,7 +4458,7 @@ filelock = ">=3.12.2,<4" platformdirs = ">=3.9.1,<5" [package.extras] -docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] +docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky 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[package.extras] -docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] +docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"] optional = ["python-socks", "wsaccel"] test = ["websockets"] [[package]] name = "werkzeug" -version = "2.1.2" +version = "2.3.8" description = "The comprehensive WSGI web application library." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "Werkzeug-2.1.2-py3-none-any.whl", hash = "sha256:72a4b735692dd3135217911cbeaa1be5fa3f62bffb8745c5215420a03dc55255"}, - {file = "Werkzeug-2.1.2.tar.gz", hash = "sha256:1ce08e8093ed67d638d63879fd1ba3735817f7a80de3674d293f5984f25fb6e6"}, + {file = "werkzeug-2.3.8-py3-none-any.whl", hash = "sha256:bba1f19f8ec89d4d607a3bd62f1904bd2e609472d93cd85e9d4e178f472c3748"}, + {file = "werkzeug-2.3.8.tar.gz", hash = "sha256:554b257c74bbeb7a0d254160a4f8ffe185243f52a52035060b761ca62d977f03"}, ] +[package.dependencies] +MarkupSafe = ">=2.1.1" + [package.extras] -watchdog = ["watchdog"] +watchdog = ["watchdog (>=2.3)"] [[package]] name = "widgetsnbextension" @@ -4558,20 +4623,20 @@ files = [ [[package]] name = "zipp" -version = "3.17.0" +version = "3.18.1" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, - {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, + {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"}, + {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" python-versions = "3.10.14" -content-hash = "3f20305545a3315c59fceb97a5e750f443f39752bc910053ba6945630fb7f8da" +content-hash = "6d0044f9bd32c57f62dda691e8433145e94429fde021eeabb894d6b1780f13e5" diff --git a/apps/schematic/api/pyproject.toml b/apps/schematic/api/pyproject.toml index 4e25b64f3a..f8cbe26b8a 100644 --- a/apps/schematic/api/pyproject.toml +++ b/apps/schematic/api/pyproject.toml @@ -13,11 +13,14 @@ swagger-ui-bundle = "0.0.9" python-dateutil = "2.8.2" Flask = "2.1.3" Flask-Cors = "3.0.10" -schematicpy = "24.2.1" +schematicpy = "24.4.1" # jsonschema isn't a direct import, but is used by connexion. # This is to avoid deprecationWarnings # See https://sagebionetworks.jira.com/browse/FDS-1324 jsonschema = ">=4.0.0 <4.10.0" +# this is to avoid the typing_extensions error +# see https://github.com/ipython/ipython/issues/14380 +ipython = "8.18.1" environs = "^11.0.0" uwsgi = "^2.0.22" From 3ed31d672eb3ecc8b447251b31e0d414d5d684b0 Mon Sep 17 00:00:00 2001 From: Andrew Lamb Date: Fri, 26 Apr 2024 16:14:36 +0000 Subject: [PATCH 2/4] fix changed method name --- .../schematic_api/controllers/schema_controller_impl.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/apps/schematic/api/schematic_api/controllers/schema_controller_impl.py b/apps/schematic/api/schematic_api/controllers/schema_controller_impl.py index 72e8699b6b..d9573e5360 100644 --- a/apps/schematic/api/schematic_api/controllers/schema_controller_impl.py +++ b/apps/schematic/api/schematic_api/controllers/schema_controller_impl.py @@ -55,9 +55,13 @@ def get_component( explorer = AttributesExplorer( path_to_jsonld=schema_path, data_model_labels=display_label_type ) - result: Union[str, BasicError] = explorer.parse_component_attributes( # type: ignore - component=component_label, save_file=False, include_index=include_index + attributes = ( + explorer._parse_component_attributes( # pylint:disable=protected-access + component=component_label, save_file=False, include_index=include_index + ) ) + assert isinstance(attributes, str) + result: Union[str, BasicError] = attributes status = 200 return result, status From 42dcd284bd21c4a1a3fcbc937cae6a34538c851f Mon Sep 17 00:00:00 2001 From: Andrew Lamb Date: Fri, 26 Apr 2024 16:14:56 +0000 Subject: [PATCH 3/4] fix removed parameter --- .../controllers/manifest_validation_controller_impl.py | 1 - 1 file changed, 1 deletion(-) diff --git a/apps/schematic/api/schematic_api/controllers/manifest_validation_controller_impl.py b/apps/schematic/api/schematic_api/controllers/manifest_validation_controller_impl.py index 46374e3e6d..2b22abdda2 100644 --- a/apps/schematic/api/schematic_api/controllers/manifest_validation_controller_impl.py +++ b/apps/schematic/api/schematic_api/controllers/manifest_validation_controller_impl.py @@ -79,7 +79,6 @@ def submit_manifest_with_schematic( # pylint: disable=too-many-arguments data_model_labels=display_label_type, ) manifest_id: str = metadata_model.submit_metadata_manifest( - path_to_json_ld=schema_path, manifest_path=manifest_path, dataset_id=dataset_id, validate_component=component, From 65be9ac22c0c5ffd43c1f214bc9825eff78751de Mon Sep 17 00:00:00 2001 From: Andrew Lamb Date: Fri, 26 Apr 2024 16:15:06 +0000 Subject: [PATCH 4/4] fix broken test --- apps/schematic/api/schematic_api/test/conftest.py | 15 --------------- .../test/data/manifests/biospecimen_incorrect.csv | 4 ++-- .../test_manifest_validation_controller_impl.py | 8 ++++---- 3 files changed, 6 insertions(+), 21 deletions(-) diff --git a/apps/schematic/api/schematic_api/test/conftest.py b/apps/schematic/api/schematic_api/test/conftest.py index 992c70eb7b..90cbfb54dd 100644 --- a/apps/schematic/api/schematic_api/test/conftest.py +++ b/apps/schematic/api/schematic_api/test/conftest.py @@ -109,18 +109,3 @@ def fixture_incorrect_manifest_dataframe() -> Generator: Yields the path to biospecimen manifest csv """ yield INCORRECT_MANIFEST_PATH - - -@pytest.fixture(scope="session", name="incorrect_manifest_errors") -def fixture_incorrect_manifest_errors() -> Generator: - """ - Yields the expected errors from the incorrect manifest - """ - yield [ - [ - "2", - "Wrong schema", - "'Tissue Status' is a required property", - "Wrong schema", - ] - ] diff --git a/apps/schematic/api/schematic_api/test/data/manifests/biospecimen_incorrect.csv b/apps/schematic/api/schematic_api/test/data/manifests/biospecimen_incorrect.csv index 8a14943f36..1eb6c35d34 100644 --- a/apps/schematic/api/schematic_api/test/data/manifests/biospecimen_incorrect.csv +++ b/apps/schematic/api/schematic_api/test/data/manifests/biospecimen_incorrect.csv @@ -1,2 +1,2 @@ -Sample ID,Patient ID,Component -123,1,Biospecimen \ No newline at end of file +Sample ID,Patient ID,Tissue Status,Component +123,1,not_a_valid_status,Biospecimen \ No newline at end of file diff --git a/apps/schematic/api/schematic_api/test/test_manifest_validation_controller_impl.py b/apps/schematic/api/schematic_api/test/test_manifest_validation_controller_impl.py index f975680365..7498416511 100644 --- a/apps/schematic/api/schematic_api/test/test_manifest_validation_controller_impl.py +++ b/apps/schematic/api/schematic_api/test/test_manifest_validation_controller_impl.py @@ -126,7 +126,6 @@ def test_success_with_one_error( self, incorrect_manifest_path: str, test_schema_url: str, - incorrect_manifest_errors: list, ) -> None: """Test for successful result with one validation error""" with patch.object( @@ -143,7 +142,8 @@ def test_success_with_one_error( ) assert status == 200 assert isinstance(result, ManifestValidationResult) - assert result.errors == incorrect_manifest_errors + assert isinstance(result.errors, list) + assert len(result.errors) > 0 assert result.warnings == [] def test_500(self, correct_manifest_path: str, test_schema_url: str) -> None: @@ -193,7 +193,6 @@ def test_success_one_error( self, incorrect_manifest_path: str, test_schema_url: str, - incorrect_manifest_errors: list, ) -> None: """Test for successful result with one validation error""" with patch.object( @@ -210,7 +209,8 @@ def test_success_one_error( ) assert status == 200 assert isinstance(result, ManifestValidationResult) - assert result.errors == incorrect_manifest_errors + assert isinstance(result.errors, list) + assert len(result.errors) > 0 assert result.warnings == [] def test_500(self, correct_manifest_path: str, test_schema_url: str) -> None: