Add pharmgkb module (ported from Generation-I dna-seq/just_pharmgkb)

data/pharmgkb/manifest.json

@@ -0,0 +1,145 @@
+{
+  "manifest_version": "1.0",
+  "schema_version": "1.0",
+  "identity": {
+    "namespace": null,
+    "name": "pharmgkb",
+    "version": "1.0.0",
+    "canonical_id": null
+  },
+  "display": {
+    "title": "Pharmacogenomics",
+    "description": "Drug response by genotype, from the ClinPGx (PharmGKB) clinical annotations at evidence levels 1A/1B/2A/2B",
+    "report_title": "Drug Response",
+    "icon": "pill",
+    "icon_set": "fomantic",
+    "color": "#a333c8"
+  },
+  "genome_build": "GRCh38",
+  "curator": "ai-module-creator",
+  "method": "literature-review",
+  "license": "CC-BY-SA-4.0",
+  "owner": null,
+  "authors": [],
+  "authorship": [
+    {
+      "who": "just-dna-seq",
+      "role": "created",
+      "kind": [
+        "human",
+        "ai"
+      ],
+      "at": null
+    }
+  ],
+  "created_at": null,
+  "published_at": null,
+  "stats": {
+    "variant_count": 0,
+    "weights_rows": 0,
+    "study_count": 0,
+    "gene_count": 0,
+    "genes": [],
+    "categories": [],
+    "clinvar_count": 0,
+    "pathogenic_count": 0,
+    "benign_count": 0
+  },
+  "compilation": {
+    "compile_success": true,
+    "compiled_by": null,
+    "compiler_version": "just-dna-compiler 0.5.1",
+    "ensembl_reference": null,
+    "compiled_at": "2026-08-09T17:43:43Z",
+    "warnings": [
+      "rs11322783 allele CG: vrs_id ga4gh:VA.F3v_lEqvSi3_93m6iBnsYsGc7vfv8sSW could not be verified — CTT>CG is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified.",
+      "rs11322783 allele CT: vrs_id ga4gh:VA.oP5cClGlw9R11DDh_FGUdUw7KwQAOndA could not be verified — CTT>CT is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified.",
+      "rs72549303: vrs_id ga4gh:VA.xtTu0h437Gtu9jSFmnpgUKARsBHaDqMN could not be verified — GG>G is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified."
+    ],
+    "resolution_mode": null,
+    "fully_resolved": true,
+    "resolution_signature": null,
+    "resolution_sources": [],
+    "vrs_alleles": 262,
+    "vrs_alleles_identified": 262
+  },
+  "frequency": null,
+  "gene_metrics": null,
+  "literature": null,
+  "sources": {
+    "signature": "sha256:bce1234aadb985c72485181b73d85d499994859d8cbb5f0fef80bc22fb466c40",
+    "sources": [
+      "clinpgx",
+      "ensembl"
+    ],
+    "layers": [
+      "annotation",
+      "resolution"
+    ],
+    "licenses": [
+      "Apache-2.0",
+      "CC-BY-SA-4.0"
+    ],
+    "attributions": [
+      "ClinPGx (https://www.clinpgx.org/page/citingClinpgx)",
+      "Ensembl (https://www.ensembl.org)"
+    ],
+    "notices": [
+      "ShareAlike; ClinPGx data may not be sold for private or commercial use."
+    ],
+    "share_alike_layers": [
+      "annotation"
+    ],
+    "noncommercial_layers": [
+      "annotation"
+    ],
+    "unknown_terms_sources": [],
+    "nonredistributable_layers": [],
+    "declared_uses": [
+      "non_commercial",
+      "unstated"
+    ],
+    "commercial_use": false,
+    "redistribution": true,
+    "row_count": 2
+  },
+  "inputs": [
+    {
+      "name": "module_spec.yaml",
+      "sha256": "sha256:f6f563dea57664c9f2be14516591f92cdc7b8ff5e437ab3696040b5ca5bb1a12",
+      "size": 582
+    },
+    {
+      "name": "pharm_variants.csv",
+      "sha256": "sha256:1e34ef298f4d96bc98e63e71940067ef0e41a5c85b915c960659d8dc9142d054",
+      "size": 624633
+    }
+  ],
+  "content_signature": "sha256:964c15cc1ed1e44132ef1f3c8f71bfabb1833e80cff456cd0059c870f0c6daa9",
+  "artifact": {
+    "digest": "sha256:cef74d5bc26ffbfbd1becd652bf43b3a1799d38ce0a9674532873876f1bb12bf",
+    "files": [
+      {
+        "name": "pharm_variants.parquet",
+        "sha256": "sha256:b1942e61aa707bf94bacca76969a3301469fdc468526ef5f2e6cec9c32ca7f46",
+        "size": 25092
+      },
+      {
+        "name": "sources.parquet",
+        "sha256": "sha256:c3b47dfcfc88c378326a6c2cc7754d1a9030f3bb5ca9a9b87d8f1d9d0c60f496",
+        "size": 6391
+      }
+    ]
+  },
+  "logs": [
+    {
+      "name": "pharmgkb.log",
+      "sha256": "sha256:fe9930c2daa0e428f9b7cf3253d62f65d4df4278e0f2646decc210b83fd6510d",
+      "size": 713
+    }
+  ],
+  "provenance": null,
+  "panel": null,
+  "logo": null,
+  "signature": null
+}

data/pharmgkb/pharm_variants.parquet

@@ -0,0 +1,3 @@
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+oid sha256:b1942e61aa707bf94bacca76969a3301469fdc468526ef5f2e6cec9c32ca7f46
+size 25092

data/pharmgkb/sources.parquet

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+oid sha256:c3b47dfcfc88c378326a6c2cc7754d1a9030f3bb5ca9a9b87d8f1d9d0c60f496
+size 6391