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

data/pharmgkb/clin_sig_authority_calls.parquet

@@ -0,0 +1,3 @@
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+oid sha256:233b40fd79c7da73a9989ef4f7442886fd11d4495fbab9fe3a8d630855c9a1d4
+size 1138

data/pharmgkb/clin_sig_concordance.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0611079ba1ae139bf1b1c3038d0f784a798747436c88275b47e6e986d10fe9a6
+size 919

data/pharmgkb/manifest.json

@@ -2,10 +2,11 @@
   "manifest_version": "1.0",
   "schema_version": "1.0",
   "identity": {
-    "namespace": null,
+    "namespace": "just-dna-seq",
     "name": "pharmgkb",
     "version": "1.0.0",
-    "canonical_id": null
+    "version_coerced_from": null,
+    "canonical_id": "just-dna-seq/pharmgkb@1.0.0"
   },
   "display": {
     "title": "Pharmacogenomics",
@@ -19,7 +20,9 @@
   "curator": "ai-module-creator",
   "method": "literature-review",
   "license": "CC-BY-SA-4.0",
-  "owner": null,
+  "authority_precedence": [],
+  "weighting": null,
+  "owner": "just-dna-seq",
   "authors": [],
   "authorship": [
     {
@@ -33,13 +36,49 @@
     }
   ],
   "created_at": null,
-  "published_at": null,
+  "published_at": "2026-09-26T23:45:19Z",
   "stats": {
     "variant_count": 0,
     "weights_rows": 0,
     "study_count": 0,
-    "gene_count": 0,
-    "genes": [],
+    "gene_count": 35,
+    "genes": [
+      "ABCG2",
+      "ACE",
+      "ADD1",
+      "ADRB2",
+      "ALDH2",
+      "APOE",
+      "ATIC",
+      "CACNA1S",
+      "CES1",
+      "CFTR",
+      "CHRNA5",
+      "CYP2B6",
+      "CYP3A4",
+      "CYP4F2",
+      "DPYD",
+      "EGFR",
+      "F2",
+      "F5",
+      "FCGR3A",
+      "IFNL3",
+      "IFNL3;IFNL4",
+      "IFNL4",
+      "ITPA",
+      "MT-RNR1",
+      "MTHFR",
+      "NUDT15",
+      "RYR1",
+      "SCN1A",
+      "SLC19A1",
+      "SLC28A3",
+      "SLCO1B1",
+      "TNF",
+      "UGT1A1",
+      "VKORC1",
+      "XRCC1"
+    ],
     "categories": [],
     "clinvar_count": 0,
     "pathogenic_count": 0,
@@ -47,27 +86,62 @@
   },
   "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",
+    "compiled_by": "marketplace-server",
+    "compiler_version": "just-dna-compiler 0.7.0",
+    "ensembl_reference": "just-dna-seq/ensembl_variations",
+    "compiled_at": "2026-09-26T23:45:19Z",
     "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."
+      "1 allele(s): vrs_id could not be verified — A>ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs1799752).",
+      "1 allele(s): vrs_id could not be verified — ATGAA>A is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs72549309).",
+      "1 allele(s): vrs_id 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 CG).",
+      "1 allele(s): vrs_id 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 (rs11322783 allele CT).",
+      "1 allele(s): vrs_id 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 (rs72549303).",
+      "1 allele(s): vrs_id could not be verified — GGAG>G is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs121918596).",
+      "1 allele(s): vrs_id could not be verified — TCTT>T is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs113993960 allele T).",
+      "1 allele(s): vrs_id could not be verified — TCTT>TCTTCTT is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs113993960 allele TCTTCTT).",
+      "This module records no closure: nothing in it states that authoring is finished, so a consumer cannot tell a spec still being edited from one its author considers done. Run `just-dna-compiler close <spec-dir>` when the module is complete — closing is a deliberate act, it is never stamped by a passing check, and editing any authored file afterwards drops the closure again. Compiling without one is a warning today; requiring it is filed for 1.0 (RM73).",
+      "1 gene cell(s) contain a list separator and are published as single gene names: 'IFNL3;IFNL4' (33 row(s)). `stats.genes` is what a registry's gene index reads, so a composite value becomes a gene nobody will search for, beside its parts. Nothing is split here — a composite may legitimately name the locus — so either give the row one symbol, or leave it and know the index will not find the module by either part."
+    ],
+    "carried": [
+      "1 allele(s): vrs_id could not be verified — A>ATACAGTCACTTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCA is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs1799752).",
+      "1 allele(s): vrs_id could not be verified — ATGAA>A is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs72549309).",
+      "1 allele(s): vrs_id 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 CG).",
+      "1 allele(s): vrs_id 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 (rs11322783 allele CT).",
+      "1 allele(s): vrs_id 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 (rs72549303).",
+      "1 allele(s): vrs_id could not be verified — GGAG>G is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs121918596).",
+      "1 allele(s): vrs_id could not be verified — TCTT>T is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs113993960 allele T).",
+      "1 allele(s): vrs_id could not be verified — TCTT>TCTTCTT is not a single-base substitution, so justifying it needs the reference sequence — minted upstream by the enricher, not recomputable here; carried unverified (rs113993960 allele TCTTCTT)."
     ],
+    "warnings_summary": {
+      "composite_gene_cell": 1,
+      "module_not_closed": 1,
+      "vrs_id_unverifiable": 8
+    },
+    "dropped_rows": {},
     "resolution_mode": null,
     "fully_resolved": true,
-    "resolution_signature": null,
-    "resolution_sources": [],
-    "vrs_alleles": 262,
-    "vrs_alleles_identified": 262
+    "resolution_subjects": 0,
+    "expanded_keys": null,
+    "expanded_rows": null,
+    "resolution_signature": "sha256:c699850a98ee2797575bc633ace061986d589e26e23003133529f98f865bd43d",
+    "resolution_sources": [
+      "cache"
+    ],
+    "vrs_alleles": 270,
+    "vrs_alleles_identified": 270,
+    "positional_rows": 1531,
+    "positional_rows_placed": 1531
   },
   "frequency": null,
   "gene_metrics": null,
+  "gene_validity": null,
+  "clinical_assertions": null,
+  "gwas_effects": null,
+  "expression_effects": null,
   "literature": null,
+  "clin_sig_concordance": null,
   "sources": {
-    "signature": "sha256:bce1234aadb985c72485181b73d85d499994859d8cbb5f0fef80bc22fb466c40",
+    "signature": "sha256:798f5dae0ee12581e522f8099d66d7dd12b0bd07c9d2c69eb156bd99bc1d93ea",
     "sources": [
       "clinpgx",
       "ensembl"
@@ -103,43 +177,193 @@
     "redistribution": true,
     "row_count": 2
   },
+  "verification": {
+    "signature": "sha256:92e2e55e846b7c567f4ec0cd311e81c8a0c192fe016ac921e78cbf58426e2426",
+    "module_hash": "sha256:63c8df71c259269f05486a12c21e738361fc976cd9e25c045493b5293d463d7e",
+    "producer": "just-dna-enricher 0.7.0",
+    "produced_at": "2026-09-26T23:45:18Z",
+    "closure": null,
+    "checks": [
+      {
+        "check": "clinical_significance",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": null,
+        "detail": null,
+        "source": "clinvar",
+        "release": "clinvar_2026-06-27",
+        "checked_at": "2026-09-26T23:45:18Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
+        "check": "dataset_currency",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": "offline",
+        "detail": "1 recorded release(s) unchecked (offline): clinpgx clinpgx_2025-07-05",
+        "source": null,
+        "release": null,
+        "checked_at": "2026-09-26T23:45:18Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
+        "check": "evidence_status_currency",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": "nothing_to_check",
+        "detail": "this module records no citation drafted from CIViC's API, so there is no recorded curation status to re-ask about",
+        "source": "civic",
+        "release": null,
+        "checked_at": "2026-09-26T23:45:18Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
+        "check": "genome_build_agreement",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": "offline",
+        "detail": "the GRCh37 service is the only thing that can tell an old-assembly coordinate from a wrong ref, and there is no local GRCh37 data",
+        "source": "ensembl-grch37",
+        "release": null,
+        "checked_at": "2026-09-26T23:45:18Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
+        "check": "pgx_evidence_level",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": "tautology",
+        "detail": "ClinPGx evidence-level check not run: this module's licence row records that these annotations were drafted from clinpgx_2025-07-05, the snapshot this check reads, and every authored evidence_level still hashes to what the drafter wrote — so each is a copy of the value it would be compared against. Edit any of them and it runs again.",
+        "source": "clinpgx",
+        "release": null,
+        "checked_at": "2026-09-26T17:22:57Z",
+        "producer": "just-dna-enricher 0.7.2"
+      },
+      {
+        "check": "published_refutation",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": null,
+        "detail": "no authored direction sits beside a published refutation (basis accepted)",
+        "source": "civic",
+        "release": "civic_01-Sep-2026",
+        "checked_at": "2026-09-26T23:45:18Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
+        "check": "reference_allele",
+        "subjects": 154,
+        "findings": 0,
+        "skipped": null,
+        "detail": null,
+        "source": "seqrepo",
+        "release": null,
+        "checked_at": "2026-09-26T17:23:59Z",
+        "producer": "just-dna-enricher 0.7.2"
+      },
+      {
+        "check": "rsid_coordinate_agreement",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": "nothing_to_check",
+        "detail": "no row authors both an rsID and a coordinate, so the module makes no pair claim to compare — this is not a comparison that found nothing",
+        "source": "ensembl",
+        "release": null,
+        "checked_at": "2026-09-26T23:45:18Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
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+        "findings": 0,
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+        "detail": null,
+        "source": "dbsnp",
+        "release": null,
+        "checked_at": "2026-09-26T17:23:59Z",
+        "producer": "just-dna-enricher 0.7.2"
+      }
+    ]
+  },
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     {
       "name": "pharm_variants.csv",
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+      "size": 738
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   "panel": null,
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+    "name": "logo.png",
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   "signature": null
 }

data/pharmgkb/pharm_variants.parquet

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