Commit graph

132 commits

Author SHA1 Message Date
kempersc
f2b10fca19 fix: correct hallucinated PREMIS terms and Schema.org namespace mismatch
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PREMIS ontology fixes (8 schema files):
- Replace invalid premis:hasRepresentation with dcterms:hasFormat
- Replace invalid premis:hasAccessRestriction with odrl:hasPolicy
- Replace invalid premis:hasPreservationPolicy with dcterms:conformsTo
- Replace invalid premis:hasAccessPolicy with dcterms:accessRights
- Replace invalid premis:hasStoragePolicy with dcterms:conformsTo
- Replace invalid premis:ProcessingStatus with skos:Concept
- Add proper close_mappings to valid PREMIS classes (premis:Representation, etc.)
- Document hallucinated terms in Rule 51 (AGENTS.md) for future prevention

Schema.org namespace fixes (3 frontend files):
- Update OntologyTermPopup.tsx: add normalizeSchemaOrgUri() function
- Update ontology-loader.ts: change schema prefix to https://schema.org/
- Update linkml-schema-service.ts: change schema prefix to https://schema.org/
- The schemaorg.owl file uses https:// but code was using http://

These changes ensure ontology term lookups work correctly for Schema.org
terms and that LinkML schema files only reference valid ontology predicates.
2026-01-13 14:16:33 +01:00
kempersc
1fb924c412 feat: add ontology mappings to LinkML schema and enhance entity resolution
Schema enhancements (443 files):
- Add class_uri with proper ontology references (schema:, prov:, skos:, rico:)
- Add close_mappings, related_mappings per Rule 50 convention
- Replace stub hc: slot_uri with standard predicates (dcterms:identifier, skos:prefLabel)
- Improve descriptions with ontology mapping rationale
- Add prefixes blocks to all schema modules

Entity Resolution improvements:
- Add entity_resolution module with email semantics parsing
- Enhance build_entity_resolution.py with email-based matching signals
- Extend Entity Review API with filtering by signal types and count
- Add candidates caching and indexing for performance
- Add ReviewLoginPage component

New rules and documentation:
- Add Rule 51: No Hallucinated Ontology References
- Add .opencode/rules/no-hallucinated-ontology-references.md
- Add .opencode/rules/slot-ontology-mapping-reference.md
- Add adms.ttl and dqv.ttl ontology files

Frontend ontology support:
- Add RiC-O_1-1.rdf and schemaorg.owl to public/ontology
2026-01-13 13:51:02 +01:00
kempersc
c5fb9ec88e feat: add route for Entity Review page with lazy loading 2026-01-13 01:49:43 +01:00
kempersc
8d7aca0f98 Refactor code structure for improved readability and maintainability 2026-01-12 19:13:35 +01:00
kempersc
3b35f4aea5 Refactor code structure for improved readability and maintainability 2026-01-12 18:31:31 +01:00
kempersc
846a6cdcec Add new Record Set Types for various archival collections
- Introduced SoundArchiveRecordSetType, SpecialCollectionRecordSetType, SpecializedArchiveRecordSetType, SpecializedArchivesCzechiaRecordSetType, StateArchivesRecordSetType, StateArchivesSectionRecordSetType, StateDistrictArchiveRecordSetType, StateRegionalArchiveCzechiaRecordSetType, TelevisionArchiveRecordSetType, TradeUnionArchiveRecordSetType, UniversityArchiveRecordSetType, VereinsarchivRecordSetType, VerlagsarchivRecordSetType, VerwaltungsarchivRecordSetType, WebArchiveRecordSetType, and WomensArchivesRecordSetType.
- Each new type includes appropriate metadata, slots, and relationships to existing classes.
- Implemented a script to detect and fix Type class violations in LinkML files.
2026-01-12 15:20:29 +01:00
kempersc
5807840bbc fix: update generated timestamp in manifest.json
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2026-01-12 14:46:05 +01:00
kempersc
355d8be51d centralise slots 2026-01-12 14:33:56 +01:00
kempersc
f497be98d1 chore: update schema manifest after slot centralization
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2026-01-11 23:28:03 +01:00
kempersc
da5660cf4c chore: update schema manifest timestamp 2026-01-11 23:19:52 +01:00
kempersc
5d3d8530b0 chore: trigger DSPy eval workflow
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2026-01-11 22:40:23 +01:00
kempersc
56c373bba8 Implement fast WCMS migration script with state file checkpointing and batch processing 2026-01-11 22:26:37 +01:00
kempersc
174a420c08 refactor(schema): centralize 1515 inline slot definitions per Rule 48
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- Remove inline slot definitions from 144 class files
- Create 7 new centralized slot files in modules/slots/:
  - custodian_type_broader.yaml
  - custodian_type_narrower.yaml
  - custodian_type_related.yaml
  - definition.yaml
  - finding_aid_access_restriction.yaml
  - finding_aid_description.yaml
  - finding_aid_temporal_coverage.yaml
- Add centralize_inline_slots.py automation script
- Update manifest with new timestamp

Rule 48: Class files must NOT define inline slots - all slots
must be imported from modules/slots/ directory.

Note: Pre-existing IdentifierFormat duplicate class definition
(in Standard.yaml and IdentifierFormat.yaml) not addressed in
this commit - requires separate schema refactor.
2026-01-11 22:02:14 +01:00
kempersc
3e6c2367ad feat(linkml-viewer): UX improvements - entry counts, deep links, settings persistence
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- Add entry count badge next to schema file name showing (xC, yE, zS) counts
- Add tooltip explaining LinkML file names vs class names
- Remove redundant section headers (Classes, Enums, Slots collapsible sections)
- Add URL params for enum (?enum=) and slot (?slot=) deep linking
- Persist category filters, dev tools visibility, and legend visibility to localStorage
- Set 'Main Schema' filter to OFF by default (confusing for users)
- Add Rule 48: Class files must not define inline slots
2026-01-11 21:42:35 +01:00
kempersc
eff3153f3f feat(schema): add Environmental Zone Type slot definitions
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Add 4 slot files for EnvironmentalZoneType class:
- environmental_zone_type_id: URI identifier slot
- environmental_zone_type_code: code slot for zone type codes
- environmental_zone_type_label: human-readable label
- environmental_zone_type_description: detailed description

Update manifest.json with new slot count (2084 slots total)
2026-01-11 21:22:44 +01:00
kempersc
95d79d0078 fix: update manifest with new generated timestamp and file counts; add EnvironmentalZoneType classes and new slot requirements
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2026-01-11 21:15:49 +01:00
kempersc
10bb5b69c5 Add Environmental Zone Type Enumeration and related slots
- Introduced EnvironmentalZoneTypeEnum.yaml to classify climate-controlled storage zones with detailed descriptions and recommended conditions for various materials.
- Created slots for environmental zone type code, description, ID, label, and HC preset URI to facilitate structured data representation.
- Implemented boolean slots for specific environmental requirements including dark storage, dust-free environment, ESD protection, and UV filtering, referencing relevant ISO standards.
- Enhanced documentation for each slot to clarify usage and preservation context.
2026-01-11 21:14:59 +01:00
kempersc
66ab2908d0 fix: remove deprecated AnnotationMotivationEnum, add European surname data
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- Move deprecated AnnotationMotivationEnum to archive-deprecated/ (outside served paths)
- Add French, Italian, Polish, Spanish surname datasets for entity resolution
- Update name_commonality.py with expanded European surname detection
- Triggers GitOps workflow to test Forgejo Actions runner
2026-01-11 16:03:18 +01:00
kempersc
fd792fce2c Refactor code structure for improved readability and maintainability
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2026-01-11 15:27:14 +01:00
kempersc
0f7fbf1ca0 feat(ci): add Forgejo Actions workflow for auto-deploy on LinkML schema changes
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Infrastructure changes to enable automatic frontend deployment when schemas change:

- Add .forgejo/workflows/deploy-frontend.yml workflow triggered by:
  - Changes to frontend/** or schemas/20251121/linkml/**
  - Manual workflow dispatch

- Rewrite generate-schema-manifest.cjs to properly scan all schema directories
  - Recursively scans classes, enums, slots, modules directories
  - Uses singular category names (class, enum, slot) matching TypeScript types
  - Includes all 4 main schemas at root level
  - Skips archive directories and backup files

- Update schema-loader.ts to match new manifest format
  - Add SchemaCategory interface
  - Update SchemaManifest to use categories as array
  - Add flattenCategories() helper function
  - Add getSchemaCategories() and getSchemaCategoriesSync() functions

The workflow builds frontend with updated manifest and deploys to bronhouder.nl
2026-01-11 14:16:57 +01:00
kempersc
329b341bb1 refactor(schema): sync AnnotationMotivationType changes to frontend public schemas
- Update VideoAnnotation class with new motivation type references
- Add AnnotationMotivationType and AnnotationMotivationTypes class files
- Add motivation_type slots (description, id, name)
- Archive deprecated AnnotationMotivationEnum
- Update slot references for derived_from_entity, has_observation, has_person_observation
2026-01-11 14:16:39 +01:00
kempersc
9726cc7917 feat(frontend): Add AnnotationMotivationType to LinkML schema manifest
Add new AnnotationMotivationType and AnnotationMotivationTypes to the
SCHEMA_FILES array so they appear in the /linkml viewer.
2026-01-11 13:56:11 +01:00
kempersc
0a888ec682 chore: add node_modules to .gitignore and remove from tracking
- Add node_modules/ and .pnpm-store/ to .gitignore
- Remove 76k node_modules files from git tracking
- Update frontend manifest
2026-01-11 00:41:21 +01:00
kempersc
a4184cb805 feat(infra): add webhook-based schema deployment pipeline
- Add FastAPI webhook receiver for Forgejo push events
- Add setup script for server deployment
- Add Caddy snippet for webhook endpoint
- Add local sync-schemas.sh helper script
- Sync frontend schemas with source (archived deprecated slots)

Infrastructure scripts staged for optional webhook deployment.
Current deployment uses: ./infrastructure/deploy.sh --frontend
2026-01-10 21:45:02 +01:00
kempersc
6c19ef8661 feat(rag): add Rule 46 epistemic provenance tracking
Track full lineage of RAG responses: WHERE data comes from, WHEN it was
retrieved, HOW it was processed (SPARQL/vector/LLM).

Backend changes:
- Add provenance.py with EpistemicProvenance, DataTier, SourceAttribution
- Integrate provenance into MultiSourceRetriever.merge_results()
- Return epistemic_provenance in DSPyQueryResponse

Frontend changes:
- Pass EpistemicProvenance through useMultiDatabaseRAG hook
- Display provenance in ConversationPage (for cache transparency)

Schema fixes:
- Fix truncated example in has_observation.yaml slot definition

References:
- Pavlyshyn's Context Graphs and Data Traces paper
- LinkML ProvenanceBlock schema pattern
2026-01-10 18:42:43 +01:00
kempersc
28c3aaf33f enrich profiles 2026-01-10 17:31:02 +01:00
kempersc
13938c92ca chore(schemas): sync LinkML schemas to frontend apps
Copies authoritative schemas from schemas/20251121/ to:
- frontend/public/schemas/20251121/
- apps/archief-assistent/public/schemas/20251121/

This ensures slot definitions with corrected ontology property
references (commit 2808dad6cd) are available to frontend apps.
2026-01-10 15:02:25 +01:00
kempersc
8a475d5c02 refactor(linkml): apply RiC-O slot naming conventions (Rule 39)
Rename slots to follow Records in Contexts (RiC-O) style naming:
- Add 'has_' prefix for possession predicates (has_acquisition_method)
- Add 'is_or_was_' prefix for temporal relationships
- Add 'has_or_had_' for bidirectional temporal relations

Key changes across 496 schema files:
- acquisition_method → has_acquisition_method
- acquisition_date → has_acquisition_date
- acquisition_source → has_acquisition_source
- access_policy_ref → has_access_policy_reference
- arrangement → has_arrangement
- parent_custodian → is_or_was_suborganization_of (hierarchy)
- parent_custodian → associated_custodian (event association)

Also adds new slots following RiC-O patterns:
- is_or_was_aggregated_by
- is_or_was_allocated_by
- is_or_was_archive_department_of
- was_approved_by, was_archived_at, was_asserted_by

This aligns with AGENTS.md Rule 39: Slot Naming Convention (RiC-O Style)
for accurate temporal semantics in heritage custodian ontology.

Net change: +2,063 lines (new slots added, old patterns consolidated)
2026-01-10 10:33:51 +01:00
kempersc
004d342935 chore: minor updates and evaluation results
- auth.setup.ts: require env vars for test credentials (no hardcoded defaults)
- manifest.json: update schema manifest
- full_evaluation_results.json: add RAG evaluation results
- petra-links.json: update birth date from web claim
2026-01-09 21:10:55 +01:00
kempersc
f7bd3e9edc feat(linkml-viewer): add slot_usage side-by-side comparison view
- Add 'Compare' toggle button next to slots with slot_usage overrides
- Show generic slot definition vs class-specific override in 3-column grid
- Highlight changed properties with green 'changed' badge
- Display '(inherited)' when override matches generic definition
- Display '(not defined)' when generic has no value for property
- Compare: range, description, required, multivalued, slot_uri, pattern, identifier
- Full i18n support (Dutch/English translations)
- Responsive design: stacks vertically on mobile (<640px)
2026-01-09 21:02:14 +01:00
kempersc
9e67d0f967 enrich profiles 2026-01-09 20:35:19 +01:00
kempersc
932ec5438c add person profiles with PPID 2026-01-09 18:26:58 +01:00
kempersc
1ad717767a feat(linkml-viewer): add visual indicators for slot_usage overrides
- Add green 'slot_usage' badge for slots with class-specific overrides
- Add ✦ markers next to properties that are overridden vs inherited
- Add green left border styling for slots with slot_usage
- Add i18n translations (nl/en) for override indicators
- Merge generic slot definitions with class-specific slot_usage properties

This helps users understand which slot properties come from the generic
slot definition vs which are overridden at the class level via slot_usage.
2026-01-09 18:23:21 +01:00
kempersc
35a057981c chore(frontend): sync schema files with custodian_type → has_or_had_custodian_type refactor
- Remove deprecated slots: custodian_type.yaml, custodian_types.yaml,
  custodian_type_broader/narrower/related.yaml, custodian_types_primary/rationale.yaml
- Add new unified slot: has_or_had_custodian_type.yaml
- Sync all 236+ class files with updated slot references
- Update manifest.json
2026-01-09 12:15:32 +01:00
kempersc
c88fd3af70 Refactor code structure for improved readability and maintainability 2026-01-09 11:05:26 +01:00
kempersc
0393b321c9 refactor(schema): unify custodian_type slots into has_or_had_custodian_type (Rule 39, 43)
- Migrate 236+ class files from custodian_types to has_or_had_custodian_type
- Archive deprecated slots: custodian_type, custodian_types, custodian_type_broader/narrower/related
- Update main schema and manifest imports
- Fix Custodian.yaml class to use new slot
- Fix annotation format (list→scalar) in has_or_had_custodian_type.yaml

Rules applied:
- Rule 39: RiC-O naming convention (hasOrHad pattern)
- Rule 43: Slot nouns must be singular (multivalued:true for cardinality)
- Rule 38: Slot centralization with semantic URI
2026-01-09 10:55:21 +01:00
kempersc
6608a207d4 update frontend 2026-01-08 15:56:28 +01:00
kempersc
0b0ea75070 feat(rag): add factual query fast path - skip LLM for count/list queries
- Add ontology cache warming at startup in lifespan() function
- Add is_factual_query() detection in template_sparql.py (12 templates)
- Add factual_result and sparql_query fields to DSPyQueryResponse
- Skip LLM generation for factual templates (count, list, compare)
- Execute SPARQL directly and return results as table (~15s → ~2s latency)
- Update ConversationPanel.tsx to render factual results table
- Add CSS styling for factual results with green theme

For queries like 'hoeveel archieven zijn er in Den Haag', the SPARQL
results ARE the answer - no need for expensive LLM prose generation.
2026-01-08 13:34:23 +01:00
kempersc
9b769f1ca2 Update manifest timestamp and minor class fixes 2026-01-07 22:04:29 +01:00
kempersc
81da4ede50 Add comprehensive slot visualization to LinkML viewer
- Add standalone Slots section in visual view alongside Classes and Enums
- Display slot_uri, range, identifier badge, description, pattern
- Show examples with value/description pairs
- Color-coded SKOS mapping tags (exact/close/narrow/broad/related)
- Yellow highlighted comments section
- Custodian type filtering works with slots
- Shared renderSlotDetails() function for consistency
2026-01-07 22:03:08 +01:00
kempersc
d19822f958 Remove redundant sections from class descriptions
- Created cleanup_class_descriptions_v2.py script using text-based regex
- Removed 134 class files' redundant sections:
  - dual_class_pattern: 80 occurrences
  - ontological_alignment: 35 occurrences
  - ontology_alignment_upper: 33 occurrences
  - multilingual_labels: 26 occurrences
  - glamorcubes_category: 6 occurrences
  - example_structure: 6 occurrences
- Fixed ArchiveOrganizationType.yaml parse error after cleanup
- Added 49 new slot definition files
- All 395 class files validate as correct YAML
- Deployed to bronhouder.nl/linkml
2026-01-07 13:50:14 +01:00
kempersc
dfa667c90f Fix LinkML schema for valid RDF generation with proper slot_uri
Summary:
- Create 46 missing slot definition files with proper slot_uri values
- Add slot imports to main schema (01_custodian_name_modular.yaml)
- Fix YAML examples sections in 116+ class and slot files
- Fix PersonObservation.yaml examples section (nested objects → string literals)

Technical changes:
- All slots now have explicit slot_uri mapping to base ontologies (RiC-O, Schema.org, SKOS)
- Eliminates malformed URIs like 'custodian/:slot_name' in generated RDF
- gen-owl now produces valid Turtle with 153,166 triples

New slot files (46):
- RiC-O slots: rico_note, rico_organizational_principle, rico_has_or_had_holder, etc.
- Scope slots: scope_includes, scope_excludes, archive_scope
- Organization slots: organization_type, governance_authority, area_served
- Platform slots: platform_type_category, portal_type_category
- Social media slots: social_media_platform_category, post_type_*
- Type hierarchy slots: broader_type, narrower_types, custodian_type_broader
- Wikidata slots: wikidata_equivalent, wikidata_mapping

Generated output:
- schemas/20251121/rdf/01_custodian_name_modular_20260107_134534_clean.owl.ttl (6.9MB)
- Validated with rdflib: 153,166 triples, no malformed URIs
2026-01-07 13:48:03 +01:00
kempersc
98c42bf272 Fix LinkML URI conflicts and generate RDF outputs
- Fix scope_note → finding_aid_scope_note in FindingAid.yaml
- Remove duplicate wikidata_entity slot from CustodianType.yaml (import instead)
- Remove duplicate rico_record_set_type from class_metadata_slots.yaml
- Fix range types for equals_string compatibility (uriorcurie → string)
- Move class names from close_mappings to see_also in 10 RecordSetTypes files
- Generate all RDF formats: OWL, N-Triples, RDF/XML, N3, JSON-LD context
- Sync schemas to frontend/public/schemas/

Files: 1,151 changed (includes prior CustodianType migration)
2026-01-07 12:32:59 +01:00
kempersc
6c6810fa43 Replace CustodianTypeCodeEnum with CustodianType class references
- Remove deprecated CustodianTypeCodeEnum from class_metadata_slots.yaml
- Update custodian_types slot to use uriorcurie range (references CustodianType subclasses)
- Update custodian_types_primary slot similarly
- Add migration note for legacy string format ['A'] vs new URI format

Per Rule 9: Enum-to-Class Promotion - Single Source of Truth
2026-01-06 12:37:40 +01:00
kempersc
b34992b1d3 Migrate all 293 class files to ontology-aligned slots
Extends migration to all class types (museums, libraries, galleries, etc.)

New slots added to class_metadata_slots.yaml:
- RiC-O: rico_record_set_type, rico_organizational_principle,
  rico_has_or_had_holder, rico_note
- Multilingual: label_de, label_es, label_fr, label_nl, label_it, label_pt
- Scope: scope_includes, scope_excludes, custodian_only,
  organizational_level, geographic_restriction
- Notes: privacy_note, preservation_note, legal_note

Migration script now handles 30+ annotation types.
All migrated schemas pass linkml-validate.

Total: 387 class files now use proper slots instead of annotations.
2026-01-06 12:24:54 +01:00
kempersc
aa763dab25 Migrate 94 archive class annotations to ontology-aligned slots
- Add migration script: scripts/migrate_annotations_to_slots.py
- Convert custodian_types, wikidata, skos_broader, specificity_* annotations
- Replace with proper slots mapped to SKOS, PROV-O, RiC-O predicates
- Add ../slots/class_metadata_slots import to all migrated files
- Remove AcademicArchive_refactored.yaml (main file now migrated)
- Sync changes to frontend/public/schemas/

Migration converts:
  - custodian_types → hc:custodianTypes slot
  - wikidata/wikidata_label → wikidata_alignment structured slot
  - skos_broader → skos:broader slot
  - specificity_* → specificity_annotation structured slot
  - dual_class_pattern → dual_class_link structured slot
  - template_specificity → template_specificity slot

All 94 migrated schemas pass linkml-validate.
2026-01-06 11:25:37 +01:00
kempersc
f37f5208ca Copy class metadata slots to frontend public folder for deployment 2026-01-06 11:17:12 +01:00
kempersc
11983014bb Enhance specificity scoring system integration with existing infrastructure
- Updated documentation to clarify integration points with existing components in the RAG pipeline and DSPy framework.
- Added detailed mapping of SPARQL templates to context templates for improved specificity filtering.
- Implemented wrapper patterns around existing classifiers to extend functionality without duplication.
- Introduced new tests for the SpecificityAwareClassifier and SPARQLToContextMapper to ensure proper integration and functionality.
- Enhanced the CustodianRDFConverter to include ISO country and subregion codes from GHCID for better geospatial data handling.
2026-01-05 17:37:49 +01:00
kempersc
41d8905661 Fix Turtle parser multi-line string handling for PiCo ontology
- Fixed bug where closing triple-quotes (""") would incorrectly re-trigger
  multi-line string detection, causing subsequent class definitions to be skipped
- Added lineToProcess variable to track which portion of line to process after
  closing a multi-line string, preventing re-detection of opening quotes
- Moved UML large diagram confirmation logic from OntologyViewerPage to
  UMLVisualization component for better encapsulation
- PiCo ontology now correctly shows all 8 classes instead of 2

Deployed and verified on https://bronhouder.nl/ontology?ontology=PiCo
2026-01-05 11:25:43 +01:00
kempersc
242bc8bb35 Add new slots for heritage custodian entities
- Created deliverables_slot for expected or achieved deliverable outputs.
- Introduced event_id_slot for persistent unique event identifiers.
- Added follow_up_date_slot for scheduled follow-up action dates.
- Implemented object_ref_slot for references to heritage objects.
- Established price_slot for price information across entities.
- Added price_currency_slot for currency codes in price information.
- Created protocol_slot for API protocol specifications.
- Introduced provenance_text_slot for full provenance entry text.
- Added record_type_slot for classification of record types.
- Implemented response_formats_slot for supported API response formats.
- Established status_slot for current status of entities or activities.
- Added FactualCountDisplay component for displaying count query results.
- Introduced ReplyTypeIndicator component for visualizing reply types.
- Created approval_date_slot for formal approval dates.
- Added authentication_required_slot for API authentication status.
- Implemented capacity_items_slot for maximum storage capacity.
- Established conservation_lab_slot for conservation laboratory information.
- Added cost_usd_slot for API operation costs in USD.
2026-01-05 00:49:05 +01:00