Feature/pds registration#4

Merged

JamesKane merged 31 commits intomainfrom

feature/pds-registration

Dec 6, 2025

Commits on Dec 5, 2025

Commits on Dec 6, 2025

Update API Extension Design to reflect CitizenBiosample segregation strategy
JamesKane
committed
Add Firehose API Specification section to API Extension Design
JamesKane
committed
Remove detailed DTO definitions from API Extension Design document
JamesKane
committed
Implement Firehose API for Citizen Biosamples and Projects
JamesKane
committed
Add Tapir endpoint definitions for CitizenBiosamples and Projects
JamesKane
committed
Update Atmosphere_Lexicon to make citizenDid a required field
JamesKane
committed
Add atUri field to record schema in Atmosphere_Lexicon.md
JamesKane
committed
Refactor CitizenBiosample to use atUri instead of citizenBiosampleDid
JamesKane
committed
Refactor API to use atUri for Citizen Biosamples and Projects
JamesKane
committed
Require atUri in Atmosphere Lexicon for biosample and project records
JamesKane
committed
Update haplogroup data structures to use robust JSONB model across all biosample types
JamesKane
committed
Fix haplogroup type mismatch errors
JamesKane
committed
Support top-level haplogroup assignments for Citizen Biosamples
JamesKane
committed
Align SpecimenDonor and PDSRegistrationService with Lexicon atUri and full flow diagram
JamesKane
committed
Fix SpecimenDonor geocoord parameter in GenomicStudyMappers
JamesKane
committed
Add lease management fields and index to pds_registrations table
JamesKane
committed
Introduce Specimen Donor linkage for Citizen Biosamples
JamesKane
committed
Introduce Specimen Donor linkage for Citizen Biosamples
JamesKane
committed
Refactor CitizenBiosampleService to delegate Firehose event handling to new event-driven CitizenBiosampleEventHandler. Introduce unified FirehoseEvent abstraction for Create, Update, and Delete ope…
JamesKane
committed
Add test coverage for CitizenBiosampleEventHandler, CitizenBiosampleService, and PDSRegistrationService
JamesKane
committed

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Feature/pds registration#4

Feature/pds registration#4
JamesKane merged 31 commits intomainfrom
feature/pds-registration

Commits on Dec 5, 2025

Adding initial PDS registration work

Add flow diagram for sync

Fixing config for new metadata db

feat: Support Atmosphere BGS integration with Citizen/PDS linking

Update the integration plan and add lexicon draft

feat: Implement Upsert logic for external biosample submission

feat: Implement DELETE endpoint for external biosamples

feat: Enhance security for DELETE biosample endpoint

fix: Compilation errors in BGS integration code

Lexicon updates

Lexicon updates

Commits on Dec 6, 2025

Update API Extension Design to reflect CitizenBiosample segregation strategy

Add Firehose API Specification section to API Extension Design

Remove detailed DTO definitions from API Extension Design document

Implement Firehose API for Citizen Biosamples and Projects

Add Tapir endpoint definitions for CitizenBiosamples and Projects

Update Atmosphere_Lexicon to make citizenDid a required field

Add atUri field to record schema in Atmosphere_Lexicon.md

Refactor CitizenBiosample to use atUri instead of citizenBiosampleDid

Refactor API to use atUri for Citizen Biosamples and Projects

Require atUri in Atmosphere Lexicon for biosample and project records

Update haplogroup data structures to use robust JSONB model across all biosample types

Fix haplogroup type mismatch errors

Support top-level haplogroup assignments for Citizen Biosamples

Align SpecimenDonor and PDSRegistrationService with Lexicon atUri and full flow diagram

Fix SpecimenDonor geocoord parameter in GenomicStudyMappers

Add lease management fields and index to pds_registrations table

Introduce Specimen Donor linkage for Citizen Biosamples

Introduce Specimen Donor linkage for Citizen Biosamples

Refactor CitizenBiosampleService to delegate Firehose event handling to new event-driven CitizenBiosampleEventHandler. Introduce unified FirehoseEvent abstraction for Create, Update, and Delete ope…

Add test coverage for CitizenBiosampleEventHandler, CitizenBiosampleService, and PDSRegistrationService