Feature/pds registration #4
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- Added BGS Integration Plan document. - Updated to include and . - Updated to find donors by DID + Identifier. - Updated to auto-provision or link Specimen Donors for Atmosphere samples.
- Modified update method to include more fields. - Added to for efficient sequence file cleanup. - Implemented in to handle full replacement of sequencing data. - Refactored to perform an upsert (update or insert) based on , including Specimen Donor and full sequence data replacement.
- Added method to for direct deletion by ID. - Added to and for cascading deletions. - Implemented in to orchestrate a hard delete of a biosample and all its dependent data. - Added to to provide service-level deletion by accession. - Exposed a endpoint in for BGS server initiated deletion.
- Updated endpoint in to require parameter. - Updated to verify that the biosample belongs to the provided before deletion. - Prevents ID collision and ensures ownership verification for BGS-initiated deletions.
- Fixed syntax errors in (mismatched braces/parentheses). - Added missing import in . - Verified successful compilation with [info] welcome to sbt 1.10.11 (Red Hat, Inc. Java 21.0.9) [info] loading global plugins from /home/jkane/.sbt/1.0/plugins [info] loading settings for project decodingus-build from plugins.sbt... [info] loading project definition from /home/jkane/devel/scala3/decodingus/project [info] loading settings for project root from build.sbt... [info] __ __ [info] \ \ ____ / /____ _ __ __ [info] \ \ / __ \ / // __ `// / / / [info] / / / /_/ // // /_/ // /_/ / [info] /_/ / .___//_/ \__,_/ \__, / [info] /_/ /____/ [info] [info] Version 3.0.9 running Java 21.0.9 [info] [info] Play is run entirely by the community. Please consider contributing and/or donating: [info] https://www.playframework.com/sponsors [info] [info] Executing in batch mode. For better performance use sbt's shell [success] Total time: 0 s, completed Dec 5, 2025, 8:47:48 AM.
…l biosample types
… full flow diagram
- Add `specimenDonorId` field and foreign key in `citizen_biosample` table. - Enable resolving or creating Specimen Donors during biosample creation and updates. - Update `CitizenBiosampleService` to handle Specimen Donor associations.
- Add `specimenDonorId` field and foreign key in `citizen_biosample` table. - Enable resolving or creating Specimen Donors during biosample creation and updates. - Update `CitizenBiosampleService` to handle Specimen Donor associations.
…to new event-driven CitizenBiosampleEventHandler. Introduce unified FirehoseEvent abstraction for Create, Update, and Delete operations.
…ervice, and PDSRegistrationService - Introduce unit tests for `CitizenBiosampleEventHandler`, covering Create, Update, Delete operations, and edge cases like conflicts and not found scenarios. - Add service-level tests for `CitizenBiosampleService`, handling delegation to the event handler and proper result translations. - Implement tests for `PDSRegistrationService`, including new registration, conflict detection, and PDS retrieval by DID/handle.
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