Add longevitymap module (ported from Generation-I dna-seq/just_longevitymap)

data/longevitymap/annotations.parquet

@@ -1,3 +1,3 @@
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+size 22051

data/longevitymap/clin_sig_authority_calls.parquet

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+size 1138

data/longevitymap/clin_sig_concordance.parquet

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+oid sha256:0611079ba1ae139bf1b1c3038d0f784a798747436c88275b47e6e986d10fe9a6
+size 919

data/longevitymap/literature.parquet

@@ -1,3 +1,3 @@
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-size 7471
+oid sha256:ae43c8821d72ca1ee34431fe13933bcbbba9fbdee85c7a8104f577cbdf2f7d94
+size 10565

data/longevitymap/manifest.json

@@ -2,10 +2,11 @@
   "manifest_version": "1.0",
   "schema_version": "1.0",
   "identity": {
-    "namespace": null,
+    "namespace": "just-dna-seq",
     "name": "longevitymap",
-    "version": null,
-    "canonical_id": null
+    "version": "1.2.0",
+    "version_coerced_from": null,
+    "canonical_id": "just-dna-seq/longevitymap@1.2.0"
   },
   "display": {
     "title": "Longevity Map",
@@ -19,14 +20,16 @@
   "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": "2026-09-26T23:44:53Z",
   "stats": {
     "variant_count": 528,
-    "weights_rows": 1039,
+    "weights_rows": 1022,
     "study_count": 671,
     "gene_count": 272,
     "genes": [
@@ -323,62 +326,61 @@
   },
   "compilation": {
     "compile_success": true,
-    "compiled_by": null,
-    "compiler_version": "just-dna-compiler 0.5.1",
-    "ensembl_reference": null,
-    "compiled_at": "2026-08-09T17:55:09Z",
+    "compiled_by": "marketplace-server",
+    "compiler_version": "just-dna-compiler 0.7.0",
+    "ensembl_reference": "just-dna-seq/ensembl_variations",
+    "compiled_at": "2026-09-26T23:44:53Z",
     "warnings": [
-      "VRS allele identity covers 890/899 allele(s) in resolution.csv (99%) — 9 carry no ga4gh:VA. id. Anything keying on the VA sees only the covered fraction.",
-      "  9 allele(s): no coordinate to mint from (an unresolved row)",
-      "rs479744: not found in resolution table, position remains unset",
-      "rs479744: not found in resolution table, position remains unset",
-      "rs479744: not found in resolution table, position remains unset",
-      "rs479744: not found in resolution table, position remains unset",
-      "rs4880: not found in resolution table, position remains unset",
-      "rs4880: not found in resolution table, position remains unset",
-      "rs660339: not found in resolution table, position remains unset",
-      "rs660339: not found in resolution table, position remains unset",
-      "rs660339: not found in resolution table, position remains unset",
-      "rs660339: not found in resolution table, position remains unset",
-      "rs28940577: not found in resolution table, position remains unset",
-      "rs28940577: not found in resolution table, position remains unset",
-      "rs1050450: not found in resolution table, position remains unset",
-      "rs1050450: not found in resolution table, position remains unset",
-      "rs13181: not found in resolution table, position remains unset",
-      "rs11783247: not found in resolution table, position remains unset",
-      "rs11783247: not found in resolution table, position remains unset",
-      "rs3800358: not found in resolution table, position remains unset",
-      "rs3800358: not found in resolution table, position remains unset",
-      "rs1327533: not found in resolution table, position remains unset",
-      "rs1327533: not found in resolution table, position remains unset",
-      "literature.csv describes 36 citation(s) no study in this module cites: ['10583447', '11568114', '11602206', '11773214', '12152254', '12547486', '12954489', '14528043', '15569453', '16518704', '16611701', '16971231', '17182125', '18511746', '18761080', '19038839', '19249341', '20003469', '20304771', '20407924', '20800603', '21407828', '21782286', '21798861', '22008263', '22136229', '22456784', '22459618', '22912757', '22985084', '23128285', '23162014', '23186209', '24589862', '9170397', '9761238']",
-      "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).",
+      "verification.json records 1 finding(s) across 1 check(s): citation_existence (1 of 126). A finding is a disagreement between this module and a source, not a defect — the archive is the stale side often enough that this never fails a build. Read the record's `detail` for which rows, and record why the module is right in `provenance.json`'s `outranks` where it is.",
+      "12 genotype(s) at 6 site(s) have no row: a heterozygous genotype has no row, so a carrier matches nothing in this module. The module states two or more genotypes at each of those sites, so this is a gap in a set the author started rather than a rule that fires once — e.g. rs2755209 A/C; rs2755209 A/T; rs2277509 A/C (+9 more)",
+      "192 genotype(s) at 186 site(s) have no row: a homozygous alternate genotype has no row, so a subject carrying two copies matches nothing in this module — the row that would describe them is the one missing. The module states two or more genotypes at each of those sites, so this is a gap in a set the author started rather than a rule that fires once — e.g. rs2802292 T/T; rs9536314 A/A; rs9536314 G/G (+189 more)",
+      "307 genotype(s) at 307 site(s) have no row: the reference homozygote has no row, so a subject carrying neither alternate matches nothing in this module. The module states two or more genotypes at each of those sites, so this is a gap in a set the author started rather than a rule that fires once — e.g. rs7412 C/C; rs429358 T/T; rs9536314 T/T (+304 more)"
     ],
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-    "fully_resolved": false,
-    "resolution_signature": "sha256:b593ac914749f4fc3e5c78498902f56b047de6d472ec2b4cef7ab2c37b55782a",
+    "carried": [
+      "verification.json records 1 finding(s) across 1 check(s): citation_existence (1 of 126). A finding is a disagreement between this module and a source, not a defect — the archive is the stale side often enough that this never fails a build. Read the record's `detail` for which rows, and record why the module is right in `provenance.json`'s `outranks` where it is."
+    ],
+    "warnings_summary": {
+      "genotype_coverage_gap": 3,
+      "module_not_closed": 1,
+      "verification_findings_recorded": 1
+    },
+    "dropped_rows": {},
+    "resolution_mode": "strict",
+    "fully_resolved": true,
+    "resolution_subjects": 1022,
+    "expanded_keys": 0,
+    "expanded_rows": 0,
+    "resolution_signature": "sha256:8d49dae7a51680776c2c3b0f6ec4e8edb1e5d6a3611e33e5c5accd2e1c9938b2",
     "resolution_sources": [
-      "cache",
-      "ensembl"
+      "cache"
     ],
-    "vrs_alleles": 899,
-    "vrs_alleles_identified": 890
+    "vrs_alleles": 900,
+    "vrs_alleles_identified": 900,
+    "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": {
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+    "signature": "sha256:8a18462371b9e8bb07255f5d7f48b7ae602fa325e1a784700411e685376c90d6",
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       "pubmed"
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-    "resolved_count": 162,
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     "missing_count": 0,
-    "open_access_count": 16,
+    "open_access_count": 12,
     "abstract_only_count": 0,
     "quotes_authored": 0,
-    "quotes_found": 0
+    "quotes_found": 0,
+    "quotes_unchecked": 126
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     "sources": [
@@ -405,59 +407,231 @@
     "redistribution": true,
     "row_count": 1
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+    "module_hash": "sha256:d58a825c858f9d6c81142aa851c5603cf6513b0348fd504de8156cb93251d7ef",
+    "producer": "just-dna-enricher 0.7.0",
+    "produced_at": "2026-09-26T23:44:52Z",
+    "closure": null,
+    "checks": [
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+        "check": "citation_existence",
+        "subjects": 126,
+        "findings": 1,
+        "skipped": null,
+        "detail": "1 cited DOI(s) do not resolve in Crossref",
+        "source": "pubmed",
+        "release": null,
+        "checked_at": "2026-09-26T17:39:42Z",
+        "producer": "just-dna-enricher 0.7.2"
+      },
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+        "subjects": 0,
+        "findings": 0,
+        "skipped": "nothing_to_check",
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+        "source": "pubmed",
+        "release": null,
+        "checked_at": "2026-09-26T17:39:42Z",
+        "producer": "just-dna-enricher 0.7.2"
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+        "source": "clinvar",
+        "release": "clinvar_2026-06-27",
+        "checked_at": "2026-09-26T23:44:52Z",
+        "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": "2026-09-26T23:44:52Z",
+        "producer": "just-dna-enricher 0.7.0"
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+        "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": "2026-09-26T23:44:52Z",
+        "producer": "just-dna-enricher 0.7.0"
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+        "subjects": 0,
+        "findings": 0,
+        "skipped": "offline",
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+        "source": "ensembl-grch37",
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+        "checked_at": "2026-09-26T23:44:52Z",
+        "producer": "just-dna-enricher 0.7.0"
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+        "release": null,
+        "checked_at": "2026-09-26T17:39:42Z",
+        "producer": "just-dna-enricher 0.7.2"
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+        "source": "civic",
+        "release": "civic_01-Sep-2026",
+        "checked_at": "2026-09-26T23:44:52Z",
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+        "source": "seqrepo",
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+        "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": "2026-09-26T23:44:52Z",
+        "producer": "just-dna-enricher 0.7.0"
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+        "producer": "just-dna-enricher 0.7.2"
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@@ -467,5 +641,6 @@
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   "signature": null
 }

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