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Casabio integration handoff: green build/tests + complete SearchResult migration - #1

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Casabio integration handoff: green build/tests + complete SearchResult migration#1
capebio wants to merge 35 commits into
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alex/casabio-integration

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@capebio

@capebio capebio commented Jul 22, 2026

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Summary

Prepares JOSE (implementation, the NestJS backend) for Casabio integration handoff. Brings main's 34 unpushed commits + this branch to a green typecheck/build/test state, and commits the phylogeny module that was wired into app.module.ts but left untracked (a fresh clone would not have built).

Root cause of the red state was one half-finished refactor: feat/elastic-facets changed SearchPort.search() from SearchDoc[] → SearchResult { hits, total, facets } but not every consumer was migrated.

Changes

  • desk.service.ts — spread .hits instead of the SearchResult object. This was a real runtime bug: [...SearchResult] throws (non-iterable), so the Desk endpoint failed live, not only in tests.
  • search.spec — destructure .hits from query().
  • federation.spec — await resolvePerson (now async); wire ConfigService + persistence context (FederationModule now imports KnowledgeObjectModule for preprint ingest).
  • export.spec / review.spec — pass the new 4th constructor dependency (KnowledgeObjectRepo / KnowledgeObjectService).
  • phylogeny/ — commit the backend + frontend module (app.module.ts already imported it) so the repo builds from a clean clone; provide ConfigService in its spec.
  • Deferred implementation plans added.

Verification

  • tsc --noEmit -p tsconfig.json — clean
  • tsc -p tsconfig.build.json — clean
  • jest — 20 suites / 138 tests pass (was 7 suites / 6 tests failing)

Notes

  • The author.casabio.org deploy target is the separate jose-author app (Bun/SQLite), now at private repo capebio/jose-author — not this repo.
  • Production deploy work (OAuth, reverse proxy, persistent storage, Litestream, secrets, live smoke) remains and belongs to jose-author.

🤖 Generated with Claude Code

capebio and others added 30 commits July 13, 2026 00:57
@capebio @claude
feat(types): altText on ContentBlock+MediaObjectMeta, ROR/RRID/LSID o…
7cf5caa 
…n ExternalIdsDto

- Add altText?: string to ContentBlock (types.ts) and MediaObjectMeta (ports.ts)
  with WCAG 1.1.1 JSDoc; mirrors the authored-field-wins pattern.
- Add altText?: string to UploadMediaDto (media.dto.ts) with @IsOptional/@IsString.
- LightboxViewer: accept altText prop; when present it wins over the
  caption/taxon-derived fallback (backward compat preserved).
- Add ror, rrid, lsid optional string fields to ExternalIdsDto (identity-trust.dto.ts)
  with descriptive JSDoc; update IdentityRecord.externalIds comment in types.ts.
- Extend NomName.registration comment to include mycobank|lsid; same in
  CreateNameDto (taxonomy.dto.ts).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(taxonomy): synonymyOf + basionymOf fields on NomName
0b45336 
Adds structural synonym linkage — a junior/invalid name now points
directly to its accepted name and basionym. Previously "synonymy"
existed only as a free-text actType string on NomenclaturalAct.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat: D1 access-grant scope, D2 aiOriginalHash, taxon-aware map, phyl…
6baa31f 
…ogeny wiring

D1 (RESOLVED 2026-07-11 a): AccessGrant gains an explicit scope field
(AccessGrantScope) supporting per-KO working-set grants over a list of
observationIds. activeGrants in pg + memory repos match scope.observationIds.
Migration 003_access_grant_scope.sql adds the scope JSONB column.

D2: ContentBlock.aiOriginalHash pins the sha256 of AI-authored text at
first recording; origin.ts houses the D2 swap-point logic.

Map: locality.service.ts map() now includes micro-observations sharing
the treatment's taxon concept (not only direct ko matches), so the
flagship distribution map populates from linked micro-obs KOs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/type-model-additions: altText, ROR/RRID/LSID, MycoBank PID
c1589ba 
- altText on ContentBlock + MediaObjectMeta + UploadMediaDto + LightboxViewer
- ror/rrid/lsid fields on ExternalIdsDto (WCAG 1.1.1 + research resource PIDs)
- NomName.registration comment expanded to include mycobank|lsid
- IdentityRecord.externalIds comment updated with ror/rrid/lsid

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/synonymy-linkage: synonymyOf + basionymOf on NomName
fc2c906 
Resolved conflict: kept mycobank|lsid in registration comment (from
type-model-additions) and added synonymyOf/basionymOf fields (from
synonymy-linkage). Additive, non-overlapping changes.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(export): Darwin Core DwC endpoint GET /ko/:koId/dwc
8d07198 
Adds DwcRecord type + renderDwc() producing GBIF-compatible occurrence
records from ObservationPublic projections. Endpoint supports ?format=json
(default) and ?format=tsv. Coordinates are QDS-cell centroids (~14km
uncertainty) — precise coords never leave the system.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(search): Elastic faceted search with aggregations
871638c 
Replaces post-hoc soft filtering with proper Elastic bool+filter queries
and terms aggregations. SearchResult now includes hits + total + facets
(koType, tier, status, locality buckets). New filter params: tier, taxon,
localityQDS. Fixes localityQDS + tier population at index time.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/darwin-core: DwcRecord type + GET /export/ko/:id/dwc endpoint
73514c7 
GBIF-compatible occurrence export from ObservationPublic projections.
Supports ?format=json (default) and ?format=tsv. Coordinates are QDS
cell centroids (~14km uncertainty). Endpoint is @public (no JWT needed
for harvesters). scientificName + recordedBy TODO pending repo injections.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/elastic-facets: real Elastic aggs + SearchResult with facets
3ac6c51 
Replaces top-1000 soft-filter with bool+filter Elastic queries and
terms aggregations. SearchResult now includes hits/total/facets
(koType, tier, status, locality buckets). New filter params: tier,
taxon, localityQDS (prefix match). Fixes localityQDS+tier population
at index time for micro-observation and method KOs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(federation): BOLD, eBird, preprint servers, MycoBank connectors
c47bac5 
Adds BOLD (barcode/BIN), eBird observation, bioRxiv/EcoEvoRxiv/OSF
preprint, and MycoBank taxon stubs. All follow the offline-stub pattern;
live fetches gated behind federation.live (off in v1).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(types): CRediT contributor roles + ontology term annotation
4f26285 
Adds CreditRole union (14 CRediT types) and contributions field on
KnowledgeObjectContent. Adds ontologyTerms on Claim and TaxonConcept
for ENVO/PATO/GO controlled vocabulary binding.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(specimen): Digital Extended Specimen entity + POST/GET /specimens
5ac9f87 
Adds the DwC-aligned Specimen type, SpecimenRepo port, Pg and Memory
adapters, DB migration 005, and the /specimens module with upsert
semantics on (institutionCode, catalogNumber).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(stats): KO usage stats from provenance ledger + GET /ko/:id/stats
84af3e6 
Aggregates exportCount and citationCount from the provenance ledger
('exported' and 'cited' events). Public endpoint GET /ko/:id/stats
returns KoStats. Desk stats extended with totals.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(offline): observation outbox with online sync
2debee4 
Capture.tsx now queues observations in a local PouchDB outbox when
offline or when the API call fails. Auto-syncs on reconnect. Closes
the gap where UI promised local queuing but posted directly to the API.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(citation): citedBy graph endpoint from provenance ledger
bd0f13d 
Adds GET /citation/cited-by?ref=ko:… querying provenance 'cited' events
for inbound citations. CitationRepo gains citedBy() on both pg and memory
implementations.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/federation-extras: BOLD, eBird, preprints, MycoBank connec…
106bea4 
…tors

BOLD (barcode/BIN), eBird, bioRxiv/EcoEvoRxiv/OSF preprints, MycoBank.
All offline stubs; live fetches gated behind federation.live (off v1).
PreprintParamDto + GET /federation/preprint/:system/:id endpoint.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/offline-outbox: PouchDB outbox + auto-sync on reconnect
23555a1 
Capture.tsx now queues observations locally when offline or on API
failure. jose_outbox PouchDB db. Auto-syncs on online event, component
mount, and app startup. Closes gap where UI promised local queuing but
posted straight to the API.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/usage-metrics: KoStats + GET /ko/:id/stats + Desk totals
28747c9 
KoStats interface (exportCount, citationCount, viewCount, lastActivity).
statsForKo() fans out to provenance events per version. Public endpoint
GET /ko/:koId/stats. Desk stats extended with totalExports + totalCitations.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/citation-graph: citedBy endpoint from provenance ledger
0dc3fcb 
CitedByEntry type + citedBy() on CitationRepo (pg + memory). GET
/citation/cited-by?ref=ko:… (query param avoids colon routing issues).
createSnippet now stores citingKo+citingVersion in provenance detail.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/credit-ontology: CRediT roles + ontologyTerms on TaxonConcept
af7eb10 
CreditRole union type (14 terms), contributions on KnowledgeObjectContent,
ontologyTerms on TaxonConcept (stored in circumscription JSONB, no migration).
SetContributionsDto + ContributorRolesDto; taxonomy DTOs/service/controller pass
ontologyTerms through.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/specimen-entity: Specimen entity + voucher linking
d2bf3ec 
Specimen type + SpecimenRepo port + PgSpecimenRepo/MemorySpecimenRepo adapters.
SpecimenModule: POST /specimens (verified), GET /specimens/:id and ?institution=CODE (public).
DB migration 005_specimen.sql. Wired into persistence.module.ts + app.module.ts.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio
feat(export): CRediT contributor roles in JATS contrib-group + Markdown
8d368bd 
JATS output gains <contrib-group> with <role vocab="credit"> elements per
CRediT spec (NISO). Markdown export appends a "Contributor roles" line.
Uses version.content.contributions (Record<authorRef, CreditRole[]>).
@capebio @claude
Merge feat/credit-jats: CRediT roles in JATS contrib-group + Markdown
986e71c 
JATS output gains <contrib-group> with <role vocab="credit"> per NISO spec.
creditTermUrl() maps role name to NISO URI. Markdown appends contributor
roles line. Uses version.content.contributions Record<authorRef, CreditRole[]>.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio
feat(retraction): propagate retraction notices to citing KOs and fork…
3b07db8 
… descendants

Adds KnowledgeObjectRepo.listForkDescendants(). VersioningService.retract()
now fans out 'cited-retracted' and 'fork-source-retracted' provenance events
to all KOs that cited or forked from the retracted content. Two new
ProvenanceAction values added to the union type.
@capebio @claude
Merge feat/retraction-propagation: fan-out retraction to citing KOs +…
774262f 
… forks

listForkDescendants() on KnowledgeObjectRepo (memory + Couch adapters).
retract() fans out 'cited-retracted' and 'fork-source-retracted' provenance
events to all KOs that cited or forked from the retracted content.
Two new ProvenanceAction values added to the union type.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio
feat(release): DataCite DOI registration + schema.org JSON-LD + Revie…
3cc7f94 
…w-as-KO

DoiRegistrar port (stub + live DataCite API v2). VersioningService.tagVoR
calls registrar after transaction commits. GET /ko/:id/schema.org returns
JSON-LD ScholarlyArticle/Dataset. POST /reviews/:id/mint-ko mints peer
reviews as citable KOs.
@capebio @claude
Merge feat/release-pipeline: DataCite DOI registration + schema.org +…
8ee1637 
… Review-as-KO

DoiRegistrar port with DataCiteRegistrar (live) and NoopDoiRegistrar (test).
tagVoR calls registrar outside the UoW transaction so a DataCite failure
never rolls back the DB. GET /export/:koId/schema.org returns JSON-LD
ScholarlyArticle/Dataset. POST /reviews/:id/mint-ko mints peer reviews as
citable KOs of type 'review'.

Conflict resolved: versioning.service.ts imports CitationRepo + DoiRegistrar
(both branches added distinct injections — merged additively).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
docs(plans): add implementation plans for deferred complex features
0cbd0b0 
plan-vector-search.md: pgvector semantic search with embedding service
plan-casa-wasm.md: WASM media pipeline (EXIF strip + JXL derivatives)
plan-ai-triage.md: async AI review triage + species ID via vision model
plan-preservation.md: CLOCKSS SFTP deposit after tagVoR

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(versioning): preregistration lifecycle state + POST /ko/:id/prer…
717a5c7 
…egister

Adds 'preregistered' to VersionStatus and ProvenanceAction unions.
VersioningService.preregister() mints a public timestamped version with
status='preregistered' -- the immutable registered report record.
POST /ko/:id/preregister endpoint added (verified assurance required).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
feat(federation): ORCID live verification via pub.orcid.org v3.0 API
13c1014 
FederationService gains ConfigService injection. resolvePerson() goes live
for ORCID when federation.live=true, calling pub.orcid.org/v3.0/{id}/record.
Falls back gracefully to stub with liveAttempted:true on API failure.
GET /identity/verify-orcid/:id added (verified assurance required).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
capebio and others added 5 commits July 14, 2026 03:54
@capebio @claude
Merge feat/preregistration: preregistration lifecycle state
2671140 
'preregistered' added to VersionStatus and 'preregister' to ProvenanceAction.
VersioningService.preregister() mints a public immutable version with
status='preregistered'. POST /ko/:id/preregister added (verified required).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
Merge feat/orcid-live: ORCID live verification via pub.orcid.org v3.0
8532b64 
FederationService gains ConfigService. resolvePerson() goes live for ORCID
when federation.live=true, fetching pub.orcid.org/v3.0/{id}/record.
Graceful fallback to stub with liveAttempted:true on API failure.
GET /identity/verify-orcid/:id added (verified assurance required).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio
feat(federation): preprint ingest -> POST /federation/preprint/:syste…
f5aa059 
…m/:id/ingest

buildPreprintContent() produces stub KnowledgeObjectContent from a preprint
reference. POST endpoint mints a private Commons KO of type ''article'' from
the stub, returning federatedRef + entity + version. Requires verified
assurance.
@capebio @claude
Merge feat/preprint-ingest: preprint stub ingest via POST /federation…
24951e3 
…/preprint/:system/:id/ingest

buildPreprintContent() produces stub KnowledgeObjectContent from a preprint
reference. POST endpoint mints a private Commons 'article' KO from the stub,
returning federatedRef + entity + version. Requires verified assurance.
KnowledgeObjectModule imported into FederationModule via forwardRef.

Conflict resolved: federation.service.ts imports ConfigService (orcid-live)
+ KnowledgeObjectContent type (preprint-ingest) — both additive.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@capebio @claude
fix: complete SearchResult migration + commit phylogeny module (green…
eceb8bc 
… build/tests)

The elastic-facets change made SearchPort.search() return SearchResult
{hits,total,facets} instead of SearchDoc[], but not all consumers were
migrated, leaving main red (typecheck + build + 7 failing test suites).

- desk.service.ts: spread .hits (was spreading a non-iterable SearchResult
  -> the Desk endpoint threw at runtime, not only in tests)
- search.spec: destructure .hits from query()
- federation.spec: await resolvePerson (now async) and wire ConfigService +
  persistence context (FederationModule now imports KnowledgeObjectModule)
- export.spec / review.spec: pass the new 4th constructor dependency
  (KnowledgeObjectRepo / KnowledgeObjectService)
- commit the phylogeny module (backend + frontend) that app.module.ts already
  imported but was left untracked, so a fresh clone builds

Result: tsc --noEmit clean, tsc -p tsconfig.build.json clean,
jest 20 suites / 138 tests pass.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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