Integrate medical family with public CMS and DICOM samples

.gitattributes

@@ -7,3 +7,9 @@ native/tablespec/sources/** -text
 spec/domain-packs/medical*/sources/** -text
 spec/domain-packs/medical*/data/** -text
 spec/domain-packs/medical-terminology/sources/*.txt whitespace=cr-at-eol
+
+spec/domain-packs/medical-carrier/sources/cms-*.csv -text whitespace=cr-at-eol
+spec/domain-packs/medical-imaging/sources/*.dcm binary
+
+# Generated bundles may contain literal trailing spaces in dependency strings.
+docs/helix/05-deploy/microsite/dist/*.js whitespace=-blank-at-eol

.github/workflows/microsite.yml

@@ -8,6 +8,12 @@ on:
       - 'docs/helix/05-deploy/microsite/**'
       - 'src/**'
       - 'spec/**'
+      - 'scripts/build-medical-subpacks.ts'
+      - 'scripts/domain-pack-family.ts'
+      - 'scripts/export-domain-family.ts'
+      - 'scripts/export-domain-pack.ts'
+      - 'scripts/domain-packs/ontology.ts'
+      - 'tests/domain-packs/**'
       - 'patches/**'
       - 'package.json'
       - 'bun.lock'
@@ -19,6 +25,12 @@ on:
       - 'docs/helix/05-deploy/microsite/**'
       - 'src/**'
       - 'spec/**'
+      - 'scripts/build-medical-subpacks.ts'
+      - 'scripts/domain-pack-family.ts'
+      - 'scripts/export-domain-family.ts'
+      - 'scripts/export-domain-pack.ts'
+      - 'scripts/domain-packs/ontology.ts'
+      - 'tests/domain-packs/**'
       - 'patches/**'
       - 'package.json'
       - 'bun.lock'
@@ -42,6 +54,10 @@ jobs:
           bun-version: '1.3.14'
       - name: Install dependencies
         run: bun install --frozen-lockfile
+      - name: Verify medical family artifacts
+        run: |
+          bun scripts/build-medical-subpacks.ts --check
+          bun test tests/domain-packs
       - name: Build browser playground
         run: bun build docs/helix/05-deploy/microsite/demo.ts --target browser --minify --outfile docs/helix/05-deploy/microsite/dist/demo.js
       - name: Build schema explorer and domain-pack catalog

docs/helix/01-frame/features/FEAT-011-medical-domain-pack.md

@@ -80,3 +80,13 @@ First clinical profile, terminology distribution terms and source separation; FH
 ## Out of Scope
 
 Clinical decision support, medical advice, and population-valid simulation.
+
+## Medical family integration
+
+Clinical, carrier, epidemiology, imaging and terminology packs must be discoverable
+from one Medical overview. Preserve their independent versions and source namespaces.
+Carrier samples include qualified public CSV claim/enrollment excerpts alongside
+FHIR (Fast Healthcare Interoperability Resources) R4 originals. Imaging includes
+a rights-qualified public DICOM (Digital Imaging and Communications in Medicine)
+object alongside the synthetic private-tag control. Publish original-source and
+CSV downloads, source limitations and matching ontology/table navigation.

docs/helix/01-frame/user-stories/US-055-medical-subpacks.md

@@ -80,3 +80,14 @@ CONTRACT-001, CONTRACT-052, ADR-002, architecture, TD-055 and STP-055.
 Production carrier processing, clinical validation, patient identity matching,
 terminology equivalence, pixel codecs, live PACS and native graph-engine adoption.
 These retain separate FR-45 requirements and qualification gates.
+
+## Integrated family delivery
+
+Owner direction extends AC1/AC4/AC6 to qualified public samples and complete
+family discovery/export. Medical's clinical overview links each independently
+versioned subpack; each subpack links back. Exact public CMS CSV excerpts remain
+historical synthetic claims, distinct from the FHIR examples. A selected TCIA
+DICOM object keeps collection citation, rights and unchanged bytes. The explorer
+offers local source and CSV downloads and all four subpack ontology views.
+One explicit family export preserves separate pack directories and inventories;
+composition never invents patient linkage or combines populations.

docs/helix/01-frame/user-stories/US-062-medical-domain-pack.md

@@ -28,7 +28,7 @@ The pack's conceptual scope is Patients; organizations; practitioners; encounter
 
 ## Delivered Subset
 
-The completed medical pack is an official fixed example corpus, not a longitudinal generator: 17 HL7 R4 resources, eight projections, exact originals/literals and explicit source provenance. [Evidence](../../04-build/evidence/medical-domain-pack.md) records typed ZIP and local Sail/Spark checks. Medication is a resource, not an inferred order/administration. Conditions, allergies, procedures, notes and claims remain desired expansions. CMS records are reference-only until selected bytes and reuse terms are established. AC4/AC5 apply to future generated supplementation; they must not force cloning published clinical records or be marked passed by fixed corpus ingestion.
+The completed medical pack is an official fixed example corpus, not a longitudinal generator: 17 HL7 R4 resources, eight projections, exact originals/literals and explicit source provenance. [Evidence](../../04-build/evidence/medical-domain-pack.md) records typed ZIP and local Sail/Spark checks. Medication is a resource, not an inferred order/administration. Conditions, allergies, procedures and notes remain desired expansions. US-055 separately qualifies carrier FHIR/CSV examples and bounded CMS DE-SynPUF excerpts; these do not establish the longitudinal generated scenario in this story. Medical 1.1.0 links that independent carrier pack and the imaging, epidemiology and terminology packs while retaining the unchanged clinical sources. AC4/AC5 apply to future generated supplementation; they must not force cloning published clinical records or be marked passed by fixed corpus ingestion.
 
 ## Pilot Question
 

docs/helix/02-design/contracts/CONTRACT-052-domain-packs.md

@@ -368,3 +368,41 @@ This selection MUST NOT mark rights cleared or permit redistributable source ZIP
 export. Mixed processing MUST generate only synthetic bindings through a trusted
 generator, ingest observed bindings unchanged and refuse unresolved bindings or
 cross-boundary references before target writes.
+
+## Medical family composition and public fixture delivery
+
+Optional `family` metadata is `{id,version,label}`. Optional `composition` is
+`{version:"1.0.0",components:[{id,version,label,checksum:{algorithm:"sha256",value}}]}`.
+Component IDs use lowercase letters, digits and hyphens, start with a letter and
+contain no path separators. Identity is exact pack ID/version. Duplicate or self
+components, malformed descriptors and unsupported composition versions refuse
+admission. Unknown annotation fields remain retained. These additive metadata
+fields use the existing extensible domain-pack 1.0.0 envelope.
+
+Composition resolves only caller-selected local sibling pack directories. Each
+component's manifest hash, exact identity and matching `family` declaration must
+agree. Components cannot themselves contain compositions. No implicit fetching,
+patient matching or cross-source joins occur. `export-domain-family.ts --pack
+<pack.json> --output <directory> [--include-sources] [--check]` exports the root
+and components into independent ID/version directories using the shared exporter;
+it preflights every component before publishing and writes `family.json` with
+exact manifest hashes. Rights, hash and path errors refuse the whole preflight.
+
+Subpacks expose CONTRACT-053 fixed tabular and graph targets. Ontologies are
+declared schema companions of their exact tables, not native graph-engine or
+clinical-conformance evidence. CSV/FHIR/DICOM originals stay source authorities.
+
+The schema explorer resolves exact composition identities and hashes within its
+built catalog, shows family links and publishes only checksum-verified local
+sources with explicit allowed redistribution. Row bindings link a selected table
+to its CSV; source cards identify format, origin, release and qualification.
+Downloads preserve exact bytes; no remote metadata URL triggers retrieval.
+
+CMS DE-SynPUF excerpts preserve native columns and tokens, empty cells and ICD-9
+era semantics; they are published synthetic data, not real beneficiary records.
+The selected TCIA LIDC-IDRI object retains original binary and separate pydicom
+JSON metadata; pixel/file-meta representation differences remain explicit.
+Collection-specific CC BY 3.0 attribution accompanies redistribution. Public
+source selection and native inspection are development evidence; the portable
+library performs no binary parsing or pixel decoding. Live PACS/DICOMweb and
+production carrier processing retain their separate future designs.

docs/helix/02-design/technical-designs/TD-055-medical-subpacks.md

@@ -97,3 +97,20 @@ slice; no persisted core migration or cross-repository port is required.
 Public examples may not agree financially or resolve references. Retain originals
 and unresolved relationships. Public code availability does not grant unrestricted
 terminology rights. Source-specific notices and local licensed bindings apply.
+
+## Family integration and public sources
+
+Follow CONTRACT-052 composition metadata and family export. The deterministic
+builder adds fixed execution profiles and table-derived ontology schemas to
+each subpack, then fingerprints component manifests from Medical's overview.
+CMS native CSV excerpts get separate schemas and source lineage without FHIR
+conversion or ICD crosswalks. A TCIA object gets a separate source namespace,
+recursive metadata views and unchanged binary source. Source qualification is
+checked in; regeneration and browser/catalog builds never download sources.
+
+The explorer links family overviews, table/ontology counterparts and pinned
+local original/row downloads. Site asset construction uses shared rights/hash
+checks. Export preserves one directory per pack and preflights before writes.
+Bun rejects stale or escaping members; Chromium exercises direct links, downloads,
+search and mobile layout. Independent TableSpec and pydicom checks verify public
+CSV cells, local-only joins, recursive DICOM metadata and exact archived originals.

docs/helix/03-test/acceptance-criteria-ledger.json

@@ -4091,6 +4091,7 @@
       "story": "docs/helix/01-frame/user-stories/US-055-medical-subpacks.md",
       "status": "SATISFIED",
       "evidence": [
+        "tests/domain-packs/medical-family.test.ts:11",
         "tests/domain-packs/medical-subpacks.test.ts:17"
       ],
       "rationale": "A live Bun test carries a canonical citation."
@@ -4119,6 +4120,7 @@
       "story": "docs/helix/01-frame/user-stories/US-055-medical-subpacks.md",
       "status": "SATISFIED",
       "evidence": [
+        "tests/domain-packs/medical-family.test.ts:11",
         "tests/domain-packs/medical-subpacks.test.ts:66"
       ],
       "rationale": "A live Bun test carries a canonical citation."
@@ -4128,6 +4130,7 @@
       "story": "docs/helix/01-frame/user-stories/US-055-medical-subpacks.md",
       "status": "SATISFIED",
       "evidence": [
+        "tests/domain-packs/medical-family.test.ts:24",
         "tests/domain-packs/medical-subpacks.test.ts:113",
         "tests/domain-packs/medical-subpacks.test.ts:81",
         "tests/domain-packs/medical-subpacks.test.ts:97"
@@ -4139,6 +4142,8 @@
       "story": "docs/helix/01-frame/user-stories/US-055-medical-subpacks.md",
       "status": "SATISFIED",
       "evidence": [
+        "tests/domain-packs/medical-family.test.ts:11",
+        "tests/domain-packs/medical-family.test.ts:24",
         "tests/domain-packs/medical-subpacks.test.ts:113",
         "tests/domain-packs/medical-subpacks.test.ts:97"
       ],

docs/helix/03-test/test-plans/STP-055-medical-subpacks.md

@@ -63,3 +63,17 @@ suppression/zero/unknown, exact money and nested private DICOM content.
 Follow TD-055: source qualification, projections, pack artifacts, consumer checks.
 Done requires all six criteria to pass their named scoped checks, with versions and
 limits recorded. Full native equivalence and live services remain unclaimed.
+
+## Integrated public-source and family checks
+
+AC1: independently compare every selected CMS CSV cell and historical native
+column against the retained excerpt; show its synthetic source separately from
+FHIR. AC4: pydicom checks the selected TCIA UIDs, metadata, native sequences and
+original bytes without treating the private-tag synthetic case as public evidence.
+AC6: validate all five fixed profiles and ontologies; export/check all family
+members; reject wrong hashes, versions, duplicates, traversal, missing members
+and uncleared sources before output. Chromium follows Medical-to-subpack and
+back links, every table/ontology pair, CSV/FHIR/DICOM downloads, search, direct
+links and mobile containment. TableSpec ingests every tabular target and recovers
+both schemas and original attachments. Historical broader obligations remain
+separate from acceptance of this requested sample/integration slice.

docs/helix/04-build/evidence/medical-subpacks.md

@@ -123,3 +123,73 @@ TypeScript checks, 61 extension-package and 349 JSON Schema audits, the browser
 build, 60 Chromium library checks, and all 19 explorer checks including every
 catalog schema and all eighteen medical subpack schemas. This supplements the
 source and native-oracle evidence above; it does not broaden native support.
+
+## Integrated medical family 1.1.0 — 2026-10-08
+
+The requested sample integration is complete under US-055/TD-055/STP-055. Five
+1.1.0 packs preserve the unchanged clinical originals, separately versioned
+carrier/epidemiology/imaging/terminology content and source namespaces. There are
+29 tables, five table-derived ontology schemas and 517 projected rows. The
+Medical overview and each child/schema link the whole family; old 1.0.0 browser
+bookmarks redirect to the qualified current subset. One preflighted family export
+retains independent directories and an exact manifest inventory. Historical
+1.0.0 archives and the earlier evidence above remain available.
+
+Public sources add three CMS DE-SynPUF beneficiaries, five inpatient claims and
+five carrier claims as exact native CSV excerpts. These are published synthetic
+2008/2008–2010 data. The selection excludes numeric CPT/Level I HCPCS carrier
+rows, preserves every selected native column and ICD-9-era token, and retains
+upstream/member/subset hashes and original record numbers. CMS rights qualification
+is limited to this subset and does not grant dictionary redistribution. FHIR R4
+originals and separately authored eligibility/authorization/payment scenarios
+remain independent; no CMS-to-FHIR clinical equivalence is claimed.
+
+Imaging adds one unchanged, publisher-deidentified TCIA LIDC-IDRI CT slice under
+CC BY 3.0, DOI 10.7937/K9/TCIA.2015.LO9QL9SX. Collection attribution and selection
+are supplied with the original binary and derived pydicom JSON. This is one of
+133 series instances, not a full study. Its native DICOM edition and burned-in
+annotation declaration are unavailable. Three private elements are retained and
+recorded; no independent deidentification certification is asserted. Native DS/IS
+spellings and file/pixel bytes remain in the binary; JSON numeric normalization
+and local opaque pixel BulkDataURI are explicit projection differences.
+
+Executed integration gates:
+
+- Bun 1.4.2: 48 domain-pack/traceability tests, 3,146 assertions, zero failures.
+  Family version/hash/rights errors refuse before output; all source bytes recover.
+- Both TypeScript configurations, browser ESM/declarations, 61 extension packages,
+  349 canonical schemas, medical regeneration and acceptance inventory pass.
+- Chromium 153.0.8010.12: 68 portable-library checks, including public DICOM
+  preservation; 24 explorer checks navigate all 24 packs/273 catalog entries.
+  Family links, four ontology/table pairs, exact CSV/FHIR/DICOM hashes and actual
+  downloads, old bookmarks, search and mobile containment pass.
+- TableSpec installed metadata 0.0.6.post6.dev0+d2ee70a / Python 3.12.15:
+  all five fixed profiles ingest; 29 tables/517 rows, 96 original attachments,
+  every schema and typed archive row recover. Two archives per pack match bytes.
+  Independent Python CSV reads compare every CMS native cell to projected cells.
+- pydicom 3.0.2 / Python 3.13.16: 24 native assertions pass across synthetic and
+  public objects, including UIDs, transfer syntax, private content and exact bytes.
+- All five published HTML signatures remain valid; no HTML seal/key change is
+  needed. The publication workflow now checks medical regeneration and pack
+  regressions, then constructs allowed sample downloads with the shared exporter.
+
+The [machine record](../../../../fixtures/validation/medical-family-integration-evidence.json)
+fingerprints source, schema, row, tooling, catalog and new archive files.
+Reproduction: `bun scripts/build-medical-subpacks.ts --check`,
+`bun test tests/domain-packs tests/traceability`,
+`bun docs/helix/05-deploy/microsite/build-explorer.ts`,
+`bun docs/helix/05-deploy/microsite/verify-explorer.ts` with the local preview,
+`bun scripts/domain-pack-browser.ts` with the browser library build, and the
+existing native oracle with `--dicom-only` or `--output fixtures/domain-packs`.
+`collect-medical-public-samples.py --cache <directory>` regenerates public selections
+from the explicitly downloaded archives after verifying their pinned hashes. It
+never fetches from browser/pack operations.
+
+Initial verification found a comma in the local DICOM tag fragment, a tooling
+type error, stale browser version selectors and the expected traceability snapshot
+change. These were corrected and the affected gates rerun. An intermediate browser
+run also compared a loaded catalog with a concurrently regenerated manifest; the
+final sequential catalog/browser run passes. Full repository/native replay, full
+terminology dictionaries/maps, graph storage, live PACS/DICOMweb/X12 and production
+carrier behavior remain separate obligations; this delivery completes the
+requested public sample and browser/family integration slice.

docs/helix/04-build/implementation-plan.md

@@ -5644,3 +5644,13 @@ input/output switching, YAML generation and existing explorer preservation and
 navigation checks; see the schema-explorer evidence. Public deployment is not
 performed. Changed playground HTML requires its Innsigle signature to be renewed
 before publication. Rollback restores the prior viewer and rebuilds bundles.
+
+### Integrated medical family and public samples
+
+Owner direction completes the sample integration under US-055/TD-055/STP-055:
+qualify bounded public CMS CSV and TCIA DICOM sources, retain exact native meaning
+and originals, add all subpack fixed profiles/ontology companions, link the
+Medical family in the explorer and expose allowed original/row downloads.
+Preflight and export the complete family in separate versioned directories; run
+Bun, actual Chromium, independent TableSpec/pydicom and deployment gates before
+merging. Live PACS and production carrier services remain separate future scope.

docs/helix/05-deploy/microsite/.gitignore

@@ -2,3 +2,5 @@
 !dist/**
 .sites-checkout/
 .sites-checkout-*/
+
+/dist/pack-assets/

docs/helix/05-deploy/microsite/README.md

@@ -152,3 +152,25 @@ text and downloads retain their exact bytes. JSON Schema and OpenAPI generated
 files default to YAML with an explicit JSON option. Avro and Spark previews use
 YAML for reading; their native downloads and the interchange report bundle stay
 JSON. SQL, GraphQL and Protobuf keep their native syntax.
+
+
+## Integrated medical sample family 1.1.0
+
+The Medical overview and each medical-family schema link Clinical, Carrier,
+Epidemiology, Imaging and Terminology. All five fixed profiles have ontology/table
+companions; the family contains 29 tables/five ontologies. The catalog remains
+24 packs and now has 273 entries. Legacy 1.0.0 medical bookmarks redirect to the
+current 1.1.0 subset. Source namespaces are never merged or matched implicitly.
+
+Local source-inclusive export constructs `dist/pack-assets/` during every build.
+Only checksum-verified local samples with allowed rights are published; source
+metadata never causes a remote fetch. Overviews download original CSV/FHIR/DICOM
+files and notices; selected table pages link their bound CSV. The public CMS
+synthetic excerpts retain ICD-9 meanings; TCIA LIDC-IDRI contributes one
+CC BY 3.0 native CT slice with separate metadata and explicit projection losses.
+`Sample scope` exposes limits while composition/execution metadata stays available
+in a collapsed source detail. Deployment regenerates assets rather than committing
+duplicate originals. 24 Chromium explorer checks pass, including actual public
+sample downloads/hash equality, all catalog entries, family navigation, ontology
+links, old bookmarks and mobile containment. Detailed reproduction and native
+checks are in `../../04-build/evidence/medical-subpacks.md`.