feat: add vibecoded but working convert_json_jsonld.py

.gitignore

@@ -167,3 +167,7 @@ cython_debug/
 #.idea/
 
 else/
+DeepLabCutDeepLabCut.json
+MalloryWittwer.json
+output.jsonld
+sdsc-ordes.json

docs/JSONLD_CONVERSION_SUMMARY.md

@@ -0,0 +1,271 @@
+# JSON-LD Conversion Summary
+
+## Quick Reference: Key Property Mappings
+
+This document provides a quick reference for the most commonly used Pydantic→JSON-LD property mappings.
+
+### Core Repository Properties
+
+| Pydantic Field | JSON-LD Property | Notes |
+|----------------|------------------|-------|
+| `name` | `schema:name` | Repository name |
+| `description` | `schema:description` | Repository description |
+| `codeRepository` | `schema:codeRepository` | GitHub/GitLab URL |
+| `author` | `schema:author` | List of Person/Organization |
+| `license` | `schema:license` | SPDX license URL |
+| `discipline` | `pulse:discipline` | Wikidata discipline URIs |
+| `repositoryType` | `pulse:repositoryType` | PULSE enum values |
+
+### Person Properties
+
+| Pydantic Field | JSON-LD Property | Notes |
+|----------------|------------------|-------|
+| `name` | `schema:name` | Full name |
+| `email` | `pulse:email` | Email address |
+| `orcid` | `md4i:orcidId` | ORCID identifier |
+| `affiliation` | `schema:affiliation` | Institution/org |
+| `academicCatalogRelations` | `pulse:hasAcademicCatalogRelation` | Catalog links |
+
+### Organization Properties
+
+| Pydantic Field | JSON-LD Property | Notes |
+|----------------|------------------|-------|
+| `legalName` | `schema:legalName` | Official name |
+| `hasRorId` | `md4i:hasRorId` | ROR identifier URL |
+| `website` | `schema:url` | Organization website |
+
+### Academic Catalog Relations
+
+| Pydantic Field | JSON-LD Property | Notes |
+|----------------|------------------|-------|
+| `catalogType` | `pulse:catalogType` | infoscience, orcid, ror, wikidata |
+| `entityType` | `pulse:entityType` | person, organization, publication, project |
+| `entity` | `pulse:hasCatalogEntity` | The actual entity |
+| `confidence` | `pulse:confidence` | 0.0-1.0 |
+| `justification` | `pulse:justification` | Why this relation exists |
+| `matchedOn` | `pulse:matchedOn` | Fields used for matching |
+
+## Namespace Prefixes
+
+```turtle
+@prefix schema: <http://schema.org/> .
+@prefix sd: <https://w3id.org/okn/o/sd#> .
+@prefix pulse: <https://open-pulse.epfl.ch/ontology#> .
+@prefix md4i: <http://w3id.org/nfdi4ing/metadata4ing#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix wd: <http://www.wikidata.org/entity/> .
+```
+
+## Example JSON-LD Output
+
+### Repository with Author
+
+```json
+{
+  "@context": {
+    "schema": "http://schema.org/",
+    "pulse": "https://open-pulse.epfl.ch/ontology#",
+    "md4i": "http://w3id.org/nfdi4ing/metadata4ing#"
+  },
+  "@graph": [
+    {
+      "@id": "https://github.com/example/my-repo",
+      "@type": "schema:SoftwareSourceCode",
+      "schema:name": "My Research Software",
+      "schema:description": "A tool for scientific computing",
+      "schema:codeRepository": [
+        {"@id": "https://github.com/example/my-repo"}
+      ],
+      "schema:license": "https://spdx.org/licenses/MIT",
+      "schema:author": [
+        {
+          "@type": "schema:Person",
+          "schema:name": "Jane Doe",
+          "md4i:orcidId": {"@id": "https://orcid.org/0000-0002-1234-5678"},
+          "schema:affiliation": ["EPFL"]
+        }
+      ],
+      "pulse:repositoryType": "pulse:Software",
+      "pulse:discipline": [
+        {"@id": "wd:Q420"}  
+      ]
+    }
+  ]
+}
+```
+
+### Person with Academic Catalog Relations
+
+```json
+{
+  "@context": {
+    "schema": "http://schema.org/",
+    "pulse": "https://open-pulse.epfl.ch/ontology#",
+    "md4i": "http://w3id.org/nfdi4ing/metadata4ing#"
+  },
+  "@graph": [
+    {
+      "@type": "schema:Person",
+      "schema:name": "Jane Doe",
+      "pulse:email": "[email protected]",
+      "md4i:orcidId": "0000-0002-1234-5678",
+      "schema:affiliation": ["EPFL", "CVLAB"],
+      "pulse:hasAcademicCatalogRelation": [
+        {
+          "@type": "pulse:AcademicCatalogRelation",
+          "pulse:catalogType": "infoscience",
+          "pulse:entityType": "person",
+          "pulse:hasCatalogEntity": {
+            "@type": "pulse:CatalogEntity",
+            "pulse:uuid": "abc-123-def",
+            "schema:name": "Jane Doe",
+            "pulse:profileUrl": {
+              "@id": "https://infoscience.epfl.ch/entities/person/abc-123-def"
+            }
+          },
+          "pulse:confidence": 0.95,
+          "pulse:justification": "Matched on name and email",
+          "pulse:matchedOn": ["name", "email"]
+        }
+      ]
+    }
+  ]
+}
+```
+
+### Organization with ROR
+
+```json
+{
+  "@context": {
+    "schema": "http://schema.org/",
+    "md4i": "http://w3id.org/nfdi4ing/metadata4ing#"
+  },
+  "@graph": [
+    {
+      "@type": "schema:Organization",
+      "schema:legalName": "École Polytechnique Fédérale de Lausanne",
+      "md4i:hasRorId": {"@id": "https://ror.org/02s376052"},
+      "schema:url": {"@id": "https://www.epfl.ch"}
+    }
+  ]
+}
+```
+
+## Conversion Functions
+
+### Pydantic → JSON-LD
+
+```python
+from src.data_models.conversion import convert_pydantic_to_jsonld
+
+# Convert any Pydantic model to JSON-LD
+jsonld = convert_pydantic_to_jsonld(pydantic_model, base_url=optional_base_url)
+```
+
+The function:
+1. Automatically detects the model type
+2. Maps fields using `PYDANTIC_TO_ZOD_MAPPING`
+3. Handles nested models recursively
+4. Converts enums to proper values
+5. Formats dates as ISO 8601
+6. Converts ORCID IDs to URLs
+
+### JSON-LD → Pydantic
+
+```python
+from src.data_models.conversion import convert_jsonld_to_pydantic
+
+# Convert JSON-LD graph to Pydantic model
+model = convert_jsonld_to_pydantic(jsonld_graph)
+```
+
+The function:
+1. Parses the `@graph` array
+2. Identifies entity types via `@type`
+3. Maps JSON-LD properties to Pydantic fields using `JSONLD_TO_PYDANTIC_MAPPING`
+4. Resolves nested entity references
+5. Validates and constructs Pydantic models
+
+## Important Notes
+
+### ORCID Handling
+
+ORCID identifiers are stored as plain strings in Pydantic (`0000-0002-1234-5678`) but **always** converted to URL format in JSON-LD:
+
+```json
+"md4i:orcidId": {"@id": "https://orcid.org/0000-0002-1234-5678"}
+```
+
+### Discipline Values
+
+Disciplines are Wikidata entity URIs:
+- Biology: `wd:Q420`
+- Mathematics: `wd:Q395`
+- Physics: `wd:Q413`
+- Computer Engineering: `wd:Q428691`
+
+Full list in PULSE ontology documentation.
+
+### Repository Types
+
+Repository types use PULSE enum values:
+- Software: `pulse:Software`
+- Educational Resource: `pulse:EducationalResource`
+- Documentation: `pulse:Documentation`
+- Data: `pulse:Data`
+- Other: `pulse:Other`
+
+### Confidence Scores
+
+All confidence scores must be between 0.0 and 1.0 (inclusive). Used for:
+- `pulse:confidence` in academic catalog relations
+- `pulse:relatedToEPFLConfidence`
+- `Organization.attributionConfidence`
+
+### Justification Fields
+
+Multiple fields map to `pulse:justification`:
+- `disciplineJustification`
+- `repositoryTypeJustification`
+- `relatedToOrganizationJustification`
+- `relatedToEPFLJustification`
+- `AcademicCatalogRelation.justification`
+
+These are kept separate in Pydantic for context but may be merged in JSON-LD serialization.
+
+## Validation
+
+The PULSE ontology includes SHACL shapes for validation. Key rules:
+
+1. **Required fields**: Many properties are marked `sh:minCount 1`
+2. **Pattern constraints**: URLs must match `^http.*`
+3. **Length constraints**: `schema:name` has `sh:maxLength 60`
+4. **Cardinality**: Some fields are `sh:maxCount 1`
+5. **Enumerations**: `catalogType`, `entityType`, etc. have fixed value lists
+
+Run SHACL validation after conversion to ensure compliance.
+
+## Migration Notes
+
+### Changes from imaging-plaza to PULSE
+
+Key namespace changes:
+- `imag:` → `pulse:` for custom properties
+- `md4i:orcid` → `md4i:orcidId`
+- Added academic catalog relation support
+- Added Wikidata discipline mappings
+
+### Deprecated Properties
+
+- `imag:infoscienceEntities` → Use `pulse:hasAcademicCatalogRelation`
+- `imag:relatedToOrganization` → `pulse:relatedToOrganization`
+
+## See Also
+
+- [Full Mapping Documentation](./PYDANTIC_JSONLD_MAPPING.md)
+- [PULSE Ontology](https://open-pulse.epfl.ch/ontology#)
+- [Academic Catalog Integration](./ACADEMIC_CATALOG_OPTION_B_IMPLEMENTATION.md)