informatics-isi-edu / deriva-mcp-core / 23635666468

91%

Build Type

push

github

Committed by mikedarcy

Commit Message

Phase 5.5/5.6: tool parity, core gap closure, cursor pagination

  Built-in tools:
  - annotation.py: 16 annotation read/write tools + apply_navbar_annotations
    (sets chaise-config and display at catalog level; supports auto-schema
    menu generation; ML-specific menu generation left to plugin)
  - catalog.py: schema DDL tools; catalog admin (delete_catalog, alias CRUD,
    resolve_snaptime, clone_catalog, cite, create_catalog, get_catalog_history_bounds)
  - vocabulary.py: full parity including create_vocabulary, add/remove_synonym,
    update_term_description as dedicated tools (not consolidated)
  - query.py: query_attribute (after_rid + limit cursor params), query_aggregate,
    count_table
  - entity.py: switched get_entities to raw HTTP (@sort(RID)@after(rid)) for
    cursor-based pagination; added after_rid and preflight_count parameters
  - rag/tools.py: rag_ingest, rag_add_source, rag_remove_source

  Infrastructure:
  - Phase 5.7 background task infrastructure: designed (asyncio-based, principal-scoped,
    24h bearer token lifetime, credential re-exchange via TaskManager.get_credential);
	workplan section drafted; implementation deferred

  Tests: 138 passing (includes 6 new apply_navbar_annotations tests)

  Docs:
  - workplan: Phases 5.6.1-5.6.6 complete; Phase 5.7 designed and drafted
  - gap_analysis: fully reconciled against implementation; vocabulary, annotation,
    RAG, and catalog gaps all marked DONE; background tasks updated to planned

Run Details

117 of 470 new or added lines in 7 files covered. (24.89%)

3 existing lines in 3 files now uncovered.

1901 of 2416 relevant lines covered (78.68%)

0.79 hits per line