Add thrombophilia module (ported from Generation-I dna-seq/just_thrombophilia)

data/thrombophilia/annotations.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:29f5d2c467fe2c69425a1692b64fcb5a43e8116be49eec1c199bd09f3184e079
-size 3979
+oid sha256:2b2483fb5394bc98da57a18ae6c52fae2f5218ddc3c57f8ba9f4c601f28a2a08
+size 4318

data/thrombophilia/clin_sig_authority_calls.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:233b40fd79c7da73a9989ef4f7442886fd11d4495fbab9fe3a8d630855c9a1d4
+size 1138

data/thrombophilia/clin_sig_concordance.parquet

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

data/thrombophilia/literature.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:9865b7939038652cd12c48993edec0dee84343f964235b5abd94aadf752ad115
-size 5277
+oid sha256:0740b3ff2a5dc62f3073f92f75e8afd7470f6f0d89084f3a34cb379cf5c9e4fd
+size 7331

data/thrombophilia/manifest.json

@@ -2,10 +2,11 @@
   "manifest_version": "1.0",
   "schema_version": "1.0",
   "identity": {
-    "namespace": null,
+    "namespace": "just-dna-seq",
     "name": "thrombophilia",
-    "version": null,
-    "canonical_id": null
+    "version": "1.1.0",
+    "version_coerced_from": null,
+    "canonical_id": "just-dna-seq/thrombophilia@1.1.0"
   },
   "display": {
     "title": "Thrombophilia",
@@ -19,11 +20,13 @@
   "curator": "just-dna-seq",
   "method": "expert-curated",
   "license": null,
-  "owner": null,
+  "authority_precedence": [],
+  "weighting": null,
+  "owner": "just-dna-seq",
   "authors": [],
   "authorship": [],
   "created_at": null,
-  "published_at": null,
+  "published_at": "2026-09-26T23:44:13Z",
   "stats": {
     "variant_count": 8,
     "weights_rows": 24,
@@ -46,38 +49,53 @@
   },
   "compilation": {
     "compile_success": true,
-    "compiled_by": null,
-    "compiler_version": "just-dna-compiler 0.5.1",
-    "ensembl_reference": null,
-    "compiled_at": "2026-08-09T17:52:49Z",
+    "compiled_by": "marketplace-server",
+    "compiler_version": "just-dna-compiler 0.7.0",
+    "ensembl_reference": "just-dna-seq/ensembl_variations",
+    "compiled_at": "2026-09-26T23:44:13Z",
     "warnings": [
-      "literature.csv describes 1 citation(s) no study in this module cites: ['22672568']",
-      "sources.csv has no row for 1 source(s) the module's fact tables cite: ['pubmed'] — their terms are unrecorded."
+      "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)."
     ],
-    "resolution_mode": "best_effort",
+    "carried": [],
+    "warnings_summary": {
+      "module_not_closed": 1
+    },
+    "dropped_rows": {},
+    "resolution_mode": "strict",
     "fully_resolved": true,
+    "resolution_subjects": 24,
+    "expanded_keys": 0,
+    "expanded_rows": 0,
     "resolution_signature": "sha256:25223241b8f875afcd3822e0ff384cf60b9201e16b2c1257117e3bef3a6b4e40",
     "resolution_sources": [
       "cache"
     ],
     "vrs_alleles": 12,
-    "vrs_alleles_identified": 12
+    "vrs_alleles_identified": 12,
+    "positional_rows": 0,
+    "positional_rows_placed": 0
   },
   "frequency": null,
   "gene_metrics": null,
+  "gene_validity": null,
+  "clinical_assertions": null,
+  "gwas_effects": null,
+  "expression_effects": null,
   "literature": {
-    "signature": "sha256:5432d514674531dd8c2410cc1b0db8c065b113e0eb8ff5a489de54be4b62bc0b",
+    "signature": "sha256:d386c156a366be298cc8c116756af29e583cbacd8f525f945997fc8396b724bc",
     "sources": [
       "pubmed"
     ],
-    "row_count": 25,
-    "resolved_count": 25,
+    "row_count": 24,
+    "resolved_count": 24,
     "missing_count": 0,
     "open_access_count": 3,
     "abstract_only_count": 0,
     "quotes_authored": 0,
-    "quotes_found": 0
+    "quotes_found": 0,
+    "quotes_unchecked": 24
   },
+  "clin_sig_concordance": null,
   "sources": {
     "signature": "sha256:b1c5043ccc97b5c15683fcdc1c63de32c6da8e270295619f2c4954817ed8332f",
     "sources": [
@@ -104,11 +122,141 @@
     "redistribution": true,
     "row_count": 1
   },
+  "verification": {
+    "signature": "sha256:e90ed43899a088b63a9dc1c5040de40f99fd78081a47e64a45d4ccaf404e6418",
+    "module_hash": "sha256:5fce340f69e54da9c3b8ce633dda98e2774af88876f91b4f4f8866a638a33b81",
+    "producer": "just-dna-enricher 0.7.0",
+    "produced_at": "2026-09-26T23:44:11Z",
+    "closure": null,
+    "checks": [
+      {
+        "check": "citation_existence",
+        "subjects": 24,
+        "findings": 0,
+        "skipped": null,
+        "detail": null,
+        "source": "pubmed",
+        "release": null,
+        "checked_at": "2026-09-26T17:33:06Z",
+        "producer": "just-dna-enricher 0.7.2"
+      },
+      {
+        "check": "citation_identifier",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": "nothing_to_check",
+        "detail": "none of 24 citation(s) carries an authored DOI or PMC id, so there was nothing to compare against PubMed's own",
+        "source": "pubmed",
+        "release": null,
+        "checked_at": "2026-09-26T17:33:06Z",
+        "producer": "just-dna-enricher 0.7.2"
+      },
+      {
+        "check": "clinical_significance",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": null,
+        "detail": null,
+        "source": "clinvar",
+        "release": "clinvar_2026-06-27",
+        "checked_at": "2026-09-26T23:44:11Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
+        "check": "dataset_currency",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": "nothing_to_check",
+        "detail": "the module records no release, so it makes no claim about where its rows came from",
+        "source": null,
+        "release": null,
+        "checked_at": "2026-09-26T23:44:11Z",
+        "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": "2026-09-26T23:44:11Z",
+        "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": "2026-09-26T23:44:11Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
+        "check": "provenance_quote",
+        "subjects": 0,
+        "findings": 0,
+        "skipped": "nothing_to_check",
+        "detail": "no provenance quote or regex on any citation, so none of them asked this question",
+        "source": "europepmc",
+        "release": null,
+        "checked_at": "2026-09-26T17:33:06Z",
+        "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": "2026-09-26T23:44:11Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
+        "check": "reference_allele",
+        "subjects": 8,
+        "findings": 0,
+        "skipped": null,
+        "detail": null,
+        "source": "seqrepo",
+        "release": null,
+        "checked_at": "2026-09-26T17:32:59Z",
+        "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": "2026-09-26T23:44:11Z",
+        "producer": "just-dna-enricher 0.7.0"
+      },
+      {
+        "check": "rsid_currency",
+        "subjects": 8,
+        "findings": 0,
+        "skipped": null,
+        "detail": null,
+        "source": "dbsnp",
+        "release": null,
+        "checked_at": "2026-09-26T17:32:59Z",
+        "producer": "just-dna-enricher 0.7.2"
+      }
+    ]
+  },
   "inputs": [
     {
       "name": "module_spec.yaml",
-      "sha256": "sha256:d9a92eeccfe11a436f4891e85a0774ad6ef140da68705409ac600b927cd63f5d",
-      "size": 428
+      "sha256": "sha256:7052dc47117cb129b07d19951ef073dee6ba885dfaffd02c38902014f8bd4b73",
+      "size": 470
     },
     {
       "name": "variants.csv",
@@ -117,46 +265,88 @@
     },
     {
       "name": "studies.csv",
-      "sha256": "sha256:170872b6b5c463b0b5e60b0eb1c7ca15a795e69efa186a8c7e0836ca494cf479",
-      "size": 10505
+      "sha256": "sha256:f5b1136a4737ae9ef7c48579c054dc20836c6a467018c48f3d100a8b286efad4",
+      "size": 10773
     }
   ],
-  "content_signature": "sha256:0d2588945101345a926ba5e4a6a1235801017cdaa88deb40c9c9a3aaf3c0b26c",
+  "content_signature": "sha256:19c8a0c93476e4720ea3c033636e7de8a8d720471c24b98de5fb09c57633fc44",
   "artifact": {
-    "digest": "sha256:294eb72e152e57b6366329674d2a0ab60ebb321f60e8e2b78b141a8d36568ab2",
+    "digest": "sha256:6bd966c7fd96cffae582794977e3fdae8bf05faf66ebc29c239a1b048c2d6c42",
     "files": [
       {
         "name": "weights.parquet",
-        "sha256": "sha256:98bc06b3c5eb040106db63ed43beda4ea7bdf0899a078919390f3787c49c0cc7",
-        "size": 12692
+        "sha256": "sha256:8031b81c47b5edee959a700acb91898f9bd13ef186d0d31b169eb8b63dedb685",
+        "size": 13350
       },
       {
         "name": "annotations.parquet",
-        "sha256": "sha256:29f5d2c467fe2c69425a1692b64fcb5a43e8116be49eec1c199bd09f3184e079",
-        "size": 3979
+        "sha256": "sha256:2b2483fb5394bc98da57a18ae6c52fae2f5218ddc3c57f8ba9f4c601f28a2a08",
+        "size": 4318
       },
       {
         "name": "studies.parquet",
-        "sha256": "sha256:2f9995a0623ecf24cbc8bcf9b575a8c958f0a7612f7b9f1fdebeaed079488598",
-        "size": 10094
+        "sha256": "sha256:4e6f6c1a4133f6bf420cfaa6e0a24df74c45d07fdaed138d9042b0009163991a",
+        "size": 11807
       },
       {
         "name": "literature.parquet",
-        "sha256": "sha256:9865b7939038652cd12c48993edec0dee84343f964235b5abd94aadf752ad115",
-        "size": 5277
+        "sha256": "sha256:0740b3ff2a5dc62f3073f92f75e8afd7470f6f0d89084f3a34cb379cf5c9e4fd",
+        "size": 7331
+      },
+      {
+        "name": "clin_sig_concordance.parquet",
+        "sha256": "sha256:0611079ba1ae139bf1b1c3038d0f784a798747436c88275b47e6e986d10fe9a6",
+        "size": 919
+      },
+      {
+        "name": "clin_sig_authority_calls.parquet",
+        "sha256": "sha256:233b40fd79c7da73a9989ef4f7442886fd11d4495fbab9fe3a8d630855c9a1d4",
+        "size": 1138
       },
       {
         "name": "sources.parquet",
-        "sha256": "sha256:9c716764e0c5b87b3743f5bb3057e865c99025c49c9543d29a83043d2d4fb050",
-        "size": 5443
+        "sha256": "sha256:fd6913c2b6d909e0fa354fcde37d95aea6ae4d236b06b22e7047dbe4fdf024f1",
+        "size": 5725
       }
     ]
   },
   "logs": [
     {
       "name": "v1_port.log",
-      "sha256": "sha256:0d32bc96edd0f36c925303af5377ef29b1d1daa4ffd766da9643b4806cce832e",
-      "size": 352
+      "sha256": "sha256:2176f12edfdc1f530ef323cfae4ef49d9b5a1f1f947b63cb199c59747bb65ab2",
+      "size": 983
+    }
+  ],
+  "derived": [
+    {
+      "name": "resolution.csv",
+      "sha256": "sha256:f0748b1b7bd5096ad2d0f53f6046b6e64087619bc66f44b222f52a0f744441b2",
+      "size": 1328
+    },
+    {
+      "name": "verification.json",
+      "sha256": "sha256:cedd36956d2f5556a348b3e66f364b0dee9419cf5f2ac569f25260b17216d57d",
+      "size": 4196
+    },
+    {
+      "name": "literature.csv",
+      "sha256": "sha256:d3033a06fdcd687f5b185165dbc71beea0fbb6f99b0b94da17f6186fcd6cd58e",
+      "size": 3381
+    },
+    {
+      "name": "clin_sig_concordance.csv",
+      "sha256": "sha256:ff2fbcd4a536aff6577458b75e00602b79623361583187e4412dcb01449ac891",
+      "size": 99
+    },
+    {
+      "name": "clin_sig_authority_calls.csv",
+      "sha256": "sha256:9845268c423f16dc3528bc568f25f2633066af2b8155e76185e4395c9dd0a9f0",
+      "size": 107
+    },
+    {
+      "name": "licensing.csv",
+      "sha256": "sha256:288b7c81407b72e49f2581af04efca839f54f6a70d7919cd1940c582b498a1bd",
+      "size": 327
     }
   ],
   "provenance": null,
@@ -166,5 +356,6 @@
     "sha256": "sha256:50f4a2f72b123a4e78f30acd074e21c80dc10843298da17fe3a645a5cd18f216",
     "size": 109928
   },
+  "readme": null,
   "signature": null
 }

data/thrombophilia/sources.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:9c716764e0c5b87b3743f5bb3057e865c99025c49c9543d29a83043d2d4fb050
-size 5443
+oid sha256:fd6913c2b6d909e0fa354fcde37d95aea6ae4d236b06b22e7047dbe4fdf024f1
+size 5725

data/thrombophilia/studies.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:2f9995a0623ecf24cbc8bcf9b575a8c958f0a7612f7b9f1fdebeaed079488598
-size 10094
+oid sha256:4e6f6c1a4133f6bf420cfaa6e0a24df74c45d07fdaed138d9042b0009163991a
+size 11807

data/thrombophilia/weights.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:98bc06b3c5eb040106db63ed43beda4ea7bdf0899a078919390f3787c49c0cc7
-size 12692
+oid sha256:8031b81c47b5edee959a700acb91898f9bd13ef186d0d31b169eb8b63dedb685
+size 13350