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Use when changing the GenCC SQLite schema. Coordinates schema.sql, the ingest builder/aggregates, and the repository together, then rebuilds the database and updates tests and fixtures.
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Use when adding, renaming, or modifying this backend's FastAPI routes, dependencies, middleware, or response behavior.
Use when CI fails on a PR or main in gencc-link. Walks through reproducing make ci-local locally and root-causing without bypassing checks.
Use when adding, renaming, or removing an MCP tool in gencc-link. Walks through the tool module, facade registration, the capabilities TOOLS tuple, tests, and the README/connection-guide tables.
Use when preparing a versioned release of gencc-link. Walks through the pre-release checklist — ci-local green, CHANGELOG, version bump, valid docker config — then tagging and watching the release workflow.
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| name | data-schema-change |
| description | Use when changing the GenCC SQLite schema. Coordinates schema.sql, the ingest builder/aggregates, and the repository together, then rebuilds the database and updates tests and fixtures. |
Use this skill when changing the shape of the local SQLite store — columns,
tables, indexes, FTS5 config, or the aggregated gene_disease roll-up. These
three layers must change together or queries will break at runtime.
gencc_link/data/schema.sql — the DDL: submissions, genes,
diseases, submitters, the aggregated gene_disease table, the
genes_fts / diseases_fts FTS5 indexes, and the single-row meta table.gencc_link/ingest/ — the builder that populates the schema:
parser.py parses the 31-column TSV (header validated against the column
order in gencc_link/constants.py);aggregates.py computes per-gene / per-disease / per-submitter and
per-(gene, disease) roll-ups, including consensus and conflict;builder.py writes rows + aggregates + FTS, sets the meta row, and does
the atomic rename.gencc_link/data/repository.py (+ queries.py) — the read-only query
layer that selects from those tables. Every changed column/table must be
reflected in the SQL here.Bump the schema version. If the change is not backward compatible with an
existing built database, bump SCHEMA_VERSION in gencc_link/constants.py
so stale databases are detected.
Edit schema.sql. Add/alter the table, column, index, or FTS definition.
Keep FTS5 columns and tokenizer consistent with the search queries.
Update the ingest builder. Adjust parser.py (if the source columns
changed — also update SUBMISSION_COLUMNS in constants.py),
aggregates.py (if a derived/aggregated value changed — consensus and
conflict logic lives in gencc_link/services/consensus.py and is applied at
build time), and builder.py (the INSERT/index/FTS population).
Update the repository. Edit repository.py / queries.py so reads match
the new schema. Update the service layer (gencc_link/services/) and any
Pydantic records (gencc_link/models/records.py) consuming the new fields.
Rebuild. Run make data (gencc-link-data build) to rebuild the live
database, then make data-info to confirm provenance and counts. Regenerate
the test fixture database if the schema changed (see the tests/fixtures/
sample TSV + built SQLite).
Tests. Update unit tests that assert table shape, repository results,
aggregates, consensus/conflict, and shaping. Run make test.
Docs. Update the data-store and consensus sections of
docs/architecture.md if the change is user-visible, and add a
CHANGELOG.md entry.
CI. Run make ci-local.