hvantk-resource-clingen

name: hvantk:resource-clingen description: Onboard, build, or update the ClinGen Gene-Disease Validity resource for hvantk status: provisional backend: hail domain: genomics

ClinGen Gene-Disease Validity resource skill

Read hvantk/skills/_conventions/SKILL.md first. This skill assumes its repository map, helpers, keying conventions, builder pattern, and validation contract.

1. Status & scope

This skill covers BUILD and UPDATE of the ClinGen Gene-Disease Validity Hail Table. It does NOT cover download (see hvantk/skills/clingen/cli.py) or downstream streamer logic. The per-plugin streamer subclass lives in hvantk/skills/clingen/streamers.py (ClinGenGeneDiseaseTableStreamer), built on the shared base GeneDiseaseTableStreamer in hvantk/core/streamers/gene_disease_table.py.

2. Source identity

Provider metadata (URL, license, citation) lives in the plugin's catalog/datasets.json (or query it with hvantk catalog show <accession> once a ClinGen catalog entry exists). The URL/version constants live in hvantk/skills/clingen/shared/constants.py (CLINGEN_BASE_URL, CLINGEN_DOWNLOADS_URL, CLINGEN_FILE_PREFIX, CLINGEN_HEADER_SKIP_LINES). Read those files; do not restate.

Stable provider notes the catalog will not capture:

• ClinGen serves a single rolling Gene-Disease Validity CSV; there are no dated archives. Freshness is determined by the file's HTTP Last-Modified header (when present) and by the values in the leading metadata block.
• The CSV is generated on demand from the live curation database, so two downloads minutes apart may differ.

3. Backend choice + reasoning

hail. ClinGen is small (~5k rows) and _conventions § 3 allows pandas for mapping tables, but every current consumer (ClinGenStreamer, gene-disease join points in PSROC, recipe-driven multi-table joins) reads it as a Hail Table — producing one avoids redundant materialization at every join site.

4. Raw format & gotchas

• File: comma-separated, double-quoted fields, 6-line metadata header before the column-header line (CLINGEN_HEADER_SKIP_LINES = 6). The column header begins with "GENE SYMBOL". Separator rows containing ++++++ are interleaved with the metadata block.
• Preprocessing: the builder streams the file via hl.hadoop_open and writes a cleaned temp CSV containing only the column header + data rows. This is required because hl.import_table cannot skip arbitrary leading metadata.
• Import: hl.import_table(delimiter=",", quote='"', impute=False, min_partitions=10). All fields stay as strings; no type inference.
• Field renaming is driven by CLINGEN_GENE_DISEASE_FIELDS (hvantk/skills/clingen/shared/constants.py). Notable renames: GENE SYMBOL → gene_symbol, GENE ID (HGNC) → hgnc_id, DISEASE LABEL → disease_label, DISEASE ID (MONDO) → mondo_id, MOI → mode_of_inheritance, CLASSIFICATION → classification, GCEP → gene_curation_expert_panel.
• ID prefix stripping: the builder strips the HGNC: and MONDO: prefixes from hgnc_id and mondo_id. This is asymmetric with the HGNC table (which keeps the prefix); downstream joins (e.g., clingen_streamer) account for this.
• Classification levels (CLINGEN_CLASSIFICATION_LEVELS, strongest first): Definitive, Strong, Moderate, Limited, Disputed, Refuted. The builder annotates classification_level as the numeric position (lower is stronger). Unknown values get len(CLINGEN_CLASSIFICATION_LEVELS).
• Keying: keyed by (hgnc_id, mondo_id).

5. Output contract

Hail Table at <output_path>.ht, keyed by (hgnc_id, mondo_id).

Row schema includes: hgnc_id, gene_symbol, disease_label, mondo_id, mode_of_inheritance, sop, classification, classification_level, classification_date, gene_curation_expert_panel, report_url.

6. hvantk integration points

• Plugin manifest: hvantk/skills/clingen/plugin.yaml (the loader resolves this dataset via get_registry().get_dataset("clingen:gene-disease"); top-level builds run through run_builder_for_spec in hvantk/core/plugin/run_builder.py).
• Builder: build_clingen_gene_disease in hvantk/skills/clingen/builder.py. Signature (parsed_input, ctx, *, min_classification=None, fields=None) -> AnnotationTable. The table is built inline (hl.import_table + renames/transforms); the only shared helper is cleanup_temp_file from hvantk/core/utils/hail_helpers.py.
• Downloader CLI: download_cmd (Click clingen-download) in hvantk/skills/clingen/cli.py; lifecycle entry-point download_dataset(raw_dir=...) (declared under lifecycle.download in plugin.yaml).
• Dataset class: ClinGenGeneDiseaseDataset in hvantk/skills/clingen/shared/datasets.py.
• Build CLI: hvantk reprocess clingen:gene-disease --raw-dir <dir> --output <path>.ht (pass builder kwargs via --plugin-arg key=value, e.g. --plugin-arg min_classification=Strong).
• Streamer (per-plugin): ClinGenGeneDiseaseTableStreamer in hvantk/skills/clingen/streamers.py, subclass of GeneDiseaseTableStreamer (hvantk/core/streamers/gene_disease_table.py).
• Constants: CLINGEN_BASE_URL, CLINGEN_DOWNLOADS_URL, CLINGEN_FILE_PREFIX, CLINGEN_HEADER_SKIP_LINES, CLINGEN_GENE_DISEASE_FIELDS, CLINGEN_CLASSIFICATION_LEVELS in hvantk/skills/clingen/shared/constants.py.
• Tests: hvantk/skills/clingen/tests/test_downloader.py, test_drift_probe.py, test_streamer.py.

7. Workflow steps

When invoked to build or update:

1. Verify Hail is available (defer to the SessionStart hook).
2. Confirm the raw CSV is present at <raw_dir>/Clingen-Gene-Disease-Summary-<YYYY-MM-DD>.csv. If absent, run the plugin downloader (Click clingen-download, e.g. hvantk download clingen --output-dir <raw_dir>).
3. The builder keys the output by (hgnc_id, mondo_id). Optionally pass min_classification to drop weaker associations, and fields to select a column subset.
4. Build via CLI: hvantk reprocess clingen:gene-disease --raw-dir <dir> --output <path>.ht [--plugin-arg min_classification=Strong].
5. Sanity-check the output: row count plausible (~5k associations live, 11 in fixture); key fields present; HGNC/MONDO prefixes stripped on at least one known row (e.g., BRCA1 → hgnc_id == "1100", not "HGNC:1100").
6. Run validation: pytest hvantk/skills/clingen/tests -m hail.

8. Update playbook

When ClinGen publishes an updated snapshot (any download is effectively a new snapshot):

1. Re-download: hvantk download clingen --output-dir <raw_dir> --overwrite. Capture the Last-Modified header (or the snapshot date label) in the PR description.
2. Diff the new CSV header against the previous fixture header. New columns alone are non-breaking — they will not appear in the built table unless added to CLINGEN_GENE_DISEASE_FIELDS. Removed/renamed columns require updating CLINGEN_GENE_DISEASE_FIELDS.
3. Drift-probe diff: regenerate hvantk/skills/clingen/tests/drift_fingerprint.json and inspect for column-list changes or hash changes.
4. If the fixture (hvantk/skills/clingen/tests/testdata/raw/clingen/clingen_test_sample.csv) is no longer representative (new classification value, new GCEP under test), refresh it from a curated sub-sample.
5. Re-run the plugin tests (pytest hvantk/skills/clingen/tests -m hail); expected diffs: new optional columns, refreshed classification_date values. Unexpected diffs (changed key semantics, stripped prefixes leaking back in) require investigation before commit.
6. Open PR; reviewer checks the diff narrative.

9. Validation contract

• fixture: hvantk/skills/clingen/tests/testdata/raw/clingen/clingen_test_sample.csv
• drift_fingerprint: hvantk/skills/clingen/tests/drift_fingerprint.json
• test_command: pytest hvantk/skills/clingen/tests -m hail

Snapshot status: the tests/snapshots/schema.json and tests/snapshots/sample_rows.json paths declared in plugin.yaml have NOT yet been seeded for this plugin (the tests/snapshots/ directory does not exist yet). Until seeded, there is no fixed-schema round-trip check; the live tests are test_downloader.py, test_drift_probe.py, and test_streamer.py.