Populate from gregor metadata #3990
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…ulate-from-gregor-metadata
…ulate-from-gregor-metadata
…ulate-from-gregor-metadata
…itute/seqr into populate-from-gregor-metadata
| return family_counts | ||
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| def _add_tag_type_counts(project_guid, project_variant_tags): |
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copy-pasted from proect_api, does not need review
| return num_new, len(update_tags) | ||
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| def _set_updated_tags(key: tuple[int, str], metadata: dict[str, dict], support_var_ids: list[str], |
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copy-paste from saummary_data_api, does not need review
| }, update_json | ||
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| def bulk_create_tagged_variants(family_variant_data, tag_name, get_metadata, user, project=None, load_new_variant_data=None): |
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adapted from summary_data_api, needs less thorough review
| if not is_google_bucket_file_path(gs_path): | ||
| raise Exception('A Google Storage path is expected.') | ||
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| # Anvil buckets are requester-pays and we bill them to the anvil project | ||
| google_project = get_google_project(gs_path) | ||
| google_project = get_google_project(gs_path) if not no_project else None |
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why aren't we including a billing project when importing the gregor metadata file?
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because that workspace is a special snowflake somehow and including the billing project causes it to fail shrug
| @@ -167,6 +167,8 @@ export const updateIndividuals = values => (dispatch, getState) => { | |||
| action = `save_individuals_table/${values.uploadedFileId}` | |||
| } else if (values.delete) { | |||
| action = 'delete_individuals' | |||
| } else if (values.workspaceName) { | |||
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Can you make uploadedFileId, delete, and workspaceName constants and use them wherever they're being defined originally? I know that workspaceName comes from a field on the uploaded Gregor metadata form but I haven't figured out yet where uploadedFileId comes from.
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I think fully refactoring a helper function used in several different place plus updating a whole lot of forms unrelated to this change to use those constants is outside the scope of this PR, but I am happy to add comments to make it clearer
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I agree that's out of scope, comments about where those fields come from would help too
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| def _iter_metadata_table(file_path, table_name, user, filter_row): | ||
| file_name = f'{file_path}/{table_name}.tsv' |
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Do these files come from the gregor report generated by seqr?
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Kind of. All the centers submit the same reports and then the DCC makes them into one big multi-site report. But in general, we want the schema for the report we generate to match the schema for the metadata we import here
| @@ -1087,6 +1342,10 @@ class LocalIndividualAPITest(AuthenticationTestCase, IndividualAPITest): | |||
| fixtures = ['users', '1kg_project', 'reference_data'] | |||
| HAS_EXTERNAL_PROJECT_ACCESS = False | |||
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| def test_import_gregor_metadata(self, *args): | |||
| # Importing gregor metadata does not work in local environment | |||
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should this be removed? looks like you do have another test_import_gregor_metadata
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So the way this test file is structured it has a base IndividualAPITest object thats not actually a runnable test case, and then it has LocalIndividualAPITest and AnvilIndividualAPITest that both inherit from that object plus from a different auth base class so that every test in the IndividualAPITest is by default run under both local install and anvil auth conditions. However, this test fails under local conditions because you can't import metadata from anvil buckets without anvil, so for the LocalIndividualAPITest we override this function so it doesn't run
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oh I missed that test_import_gregor_metadata is in a different *APITest class. thanks for explaining that
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