Release - family external ids and misc fixes #980
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Contributor
dancoates
commented
Oct 29, 2024
dancoates
commented
- Code quality uplift
- Permissions fixes
- Family external ids
* Add tests directory to sonarqube config file * Hide db backup folder results * Fix test exclusion for code coverage settings * Address all current metamist bugs * Fix security issues, including exclusive use of formatMoney with resistent regex * formatMoney bug fix * Fix the ValueFilter so that the useState is called in the same order in every render * Change so that the nonroot user is used in the db dockerfile * Change so that the nonroot user is used in the api dockerfile * Fix default logging level to warning to reduce the leak of secure information * Add merge_group to the test workflow * Fix web pages format using prettier * Fix web pages format using prettier - npm ci ran first * Add referenceBranch to sonar-project.properties * Update test workflow to include metamist dev branch version in analysis * Add Sonarqube scan to deploy check, update db Dockerfile based on comments * Fix run fastapi command in api Dockerfile
* Create family_external_id database table * Replace family.external_id with external_ids etc * In api/graphql/schema.py, add external_ids alongside external_id * In ParticipantGridRow.tsx, reuse prepareExternalIds() to handle family multiple extids * Complete rewrite of insert_or_update_multiple_families() The previous INSERT ... ON DUPLICATE KEY UPDATE code inserts a new family or, if the same project+external_id entry already exists, updates description and coded_phenotype -- as external_id is part of the key used to locate the record, it can't be updated. With external_id moving to a separate table, we need to write this logic out explicitly. We search by any external id, but only insert the primary external id for new records. (At present, this functionality is used only by FamilyLayer.import_families(), which parses only the primary external id.) * Use transactions in create_family() and update_family() * FamilyTable.get_id_map_by_internal_ids() returns only primary extids Most users of this function want a single external id (per internal id) that they can use to populate a pedigree or for use with seqr. (The call in ParticipantLayer.generic_individual_metadata_importer() has complex wants but is mostly similar.) Hence, at least for now, it is simplest to keep the 1:1 map return type and return only the primary external ids.
* fix error in translating old permissions to new this would have allowed read access permissions to upsert samples * fix other permission inconsistencies
* remove duplicated unittest workflow definition from deploy * switch dockerfile CMD back to shell form as exec form wasn't working
this was accidentally removed in PR #957
jmarshall
approved these changes
Oct 29, 2024
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