[SCHEMATIC-214] change data model and component #1556
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thomasyu888
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thomasyu888
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🔥 LGTM! Thanks for the quick work! Will we need to add any additional tests? Will let Andrew be final reviewer.
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@thomasyu888 thanks and no prob! |
andrewelamb
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… with the NA values argument (#1553) * Wrap pandas functions to support not including `None` with the NA values argument * Ignore types * pylint issues * ordering of ignore * Add to integration test to cover none in a manifest * Add additional test for manifest * [SCHEMATIC-210] Add attribute to nones data model (#1555) Update example_test_nones.model.csv component and add new invalid manifest with nones * first commit * ran black * add test for validateModelManifest * [SCHEMATIC-214] change data model and component (#1556) * add valid values to Patient attributes * update data model * add test manifests * update test for new model * update test for new valid value * change test to use new manifests * remove uneeded test file * revert file * revert file * change tests to use new manifests * remove uneeded manifests * ran black * add tests back in * ran black * revert manifest * Split up valid and errored test as separate testing functions * Remove unused import --------- Co-authored-by: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Co-authored-by: Andrew Lamb <andrewelamb@gmail.com> Co-authored-by: Thomas Yu <thomas.yu@sagebase.org>
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* add new tests * add unit tests * ran black * Update schematic/models/validate_attribute.py Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> * added tests * Update README.md * Update README.md * add unit tests * run black * Update README.md * temp commit * remove old tests * [FDS-2386] Synapse entity tracking and code concurrency updates (#1505) * [FDS-2386] Synapse entity tracking and code concurrency updates * ran black * Update CODEOWNERS * updated data model type rules to include error param * fix validate type attribute to use msg level param * added error handling * run black * create Node class * sat up Node class so that nodes with no displayName fields cause an error on creation * ran black * ran mypy * added new configs for CLI tests * added new manifests for testing CLI commands * automate manual CLI tests * ran black * Update CODEOWNERS * Update scan_repo.yml * Update .github/CODEOWNERS * Update .github/workflows/scan_repo.yml * Attach additional telemetry data to OTEL traces (#1519) * Attach additional telemetry data to OTEL traces * feat: added tracing for cross manifest validation and file name validation (#1509) * add tracing for GX validation * temp commit * Updating contribution doc to expect squash and merge (#1534) * [FDS-2491] Integration tests for Schematic API Test plan (#1512) Integration tests for Schematic API Test plan * [FDS-2500] Add Integration Tests for: Manifest Validation (#1516) * Add Integration Tests for: Manifest Validation * [FDS-2449] Lock `sphinx` version and update `poetry.lock` (#1530) Also install `typing-extensions` in the build * manual test files now being saved in manifests folder * manual test files now being saved in manifests folder * remove lines to delete json files that were under git control * ran black * add try finally blocks to remove created files * ran black * add lines to remove created json files * Update file annotation store process to require filename be present in order to annotate file * add lines to remove created json files * Revert "Update file annotation store process to require filename be present in order to annotate file" This reverts commit f57c718. * Don't attempt to annotate the table * add code in finally blocks to reset config to default values, when tests change them * complete submit manifest command test * ran black * add test for bug case * update test for table tidyness * remove unused import * remove etag column if already present when building temp file view * catch all exceptions to switch to sequential mode * update test for updated data * Revert "update test for updated data" This reverts commit 255e3c0. * Revert "catch all exceptions to switch to sequential mode" This reverts commit 68b0b24. * catch ValueErrors as well * Updates for integration test failures (#1537) * Updates for integration test failures, Config file reset and scope changes * add todos for removing config resets * [FDS-2525] Authenticated export of telemetry data (#1527) * Authenticated export of telemetry data, updating to HTTP otel library * temp reduce tests * restore tests * uncomment tests * redid how files are deleted, manual tests values are set * ran black * [SCHEMATIC-157] Make some dependencies required to avoid `schematic CLI` commands from potentially erroring when doing a pip install (#1540) * Make otel flash non-optional * Add dependencies as non-optional * Include schematic_api for now (#1547) * update toml version to 24.11.1 (#1548) * [SCHEMATIC-193] Support exporting telemetry data from GH integration test runs (#1550) * Support exporting telemetry data from GH run via access token retrieved via oauth2 * [SCHEMATIC-30, SCHEMATIC-200] Add version to click cli / use pathlib.Path module for checking cache size (#1542) * Add version to click cli * Add version * Run black * Reformat * Fix * Update schematic/schemas/data_model_parser.py * Add test for check_synapse_cache_size * Reformat * Fix tests * Remove unused parameter * Install all-extras for now * Make otel flash non-optional * Update dockerfile * Add dependencies as non-optional * Update pyproject toml * Fix trivy issue * Add service version * Run black * Move all utils.general tests into separate folder * Use pre-commit * Add updates to contribution doc * Fix * Add service version to log provider --------- Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> * [SCHEMATIC-212] Prevent traces from being combined (#1552) * Set instance id in github CI run, uninstrument flask auto during integration test run * [SCHEMATIC-163] Catch error when manifest is generated and existing one doesn't have `entityId` (#1551) * adds error handling * adds unit tests for _get_file_entityIds * updates error message * adds entityid check to parent func * updates docstring * [SCHEMATIC-183] Use paths from file view for manifest generation (#1529) source manifest file paths from synapse fileviews at generation * [SCHEMATIC-214] Wrap pandas functions to support not including `None` with the NA values argument (#1553) * Wrap pandas functions to support not including `None` with the NA values argument * Ignore types * pylint issues * ordering of ignore * Add to integration test to cover none in a manifest * Add additional test for manifest * [SCHEMATIC-210] Add attribute to nones data model (#1555) Update example_test_nones.model.csv component and add new invalid manifest with nones * first commit * ran black * add test for validateModelManifest * [SCHEMATIC-214] change data model and component (#1556) * add valid values to Patient attributes * update data model * add test manifests * update test for new model * update test for new valid value * change test to use new manifests * remove uneeded test file * revert file * revert file * change tests to use new manifests * remove uneeded manifests * ran black * add tests back in * ran black * revert manifest * Split up valid and errored test as separate testing functions * Remove unused import --------- Co-authored-by: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com> Co-authored-by: Andrew Lamb <andrewelamb@gmail.com> Co-authored-by: Thomas Yu <thomas.yu@sagebase.org> * incremented packge version number * Update publish.yml * Update test.yml * Update api_test.yml * Update pdoc.yml * Update version.py * updates publish.yml (#1558) (#1561) Co-authored-by: Brad Macdonald <52762200+BWMac@users.noreply.github.com> --------- Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com> Co-authored-by: Jenny V Medina <jenny.medina@sagebase.org> Co-authored-by: Thomas Yu <thomas.yu@sagebase.org> Co-authored-by: Lingling <55448354+linglp@users.noreply.github.com> Co-authored-by: GiaJordan <gianna.jordan@sagebase.org> Co-authored-by: Brad Macdonald <52762200+BWMac@users.noreply.github.com> Co-authored-by: Gianna Jordan <61707471+GiaJordan@users.noreply.github.com>
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I think it'd be better to use the
example.model.csvmodel andBiospecimencomponent for the tests of manifest"None"values given howMockComponentis used and the history of theexample_test_nones.model.csvmodel that @thomasyu888 pointed out.Included in this PR is updates to the data model (CSV and JSONLD forms) and both valid and invalid manifests that can be used for the integration tests.