feat: add vibecoded but working convert_json_jsonld.py

[caviri]

Note

Medium Risk
Moderate risk due to contract changes to core models (emails, structured Affiliation, linkedEntities) and pipeline behavior/documented execution order, which can break cached data and downstream API consumers if not migrated.

Overview
Introduces a new scripts/convert_json_jsonld.py CLI (and scripts/README.md) to convert extractor outputs between Pydantic JSON and JSON-LD, including basic model-type detection (repo/user/org) and optional --base-url for @id generation; adds a Tentris upload test script.

Refactors/renames academic-catalog enrichment to linked entities across docs and rules, and documents an atomic multi-stage LLM pipeline with optional author-level linked-entity enrichment and a new union-field reconciliation guideline.

Updates data-model guidance to support structured Affiliation objects with provenance, switches Person.email to Person.emails with automatic email anonymization, simplifies Organization fields, and bumps project baseline to Python >=3.10; also fixes just test commands to run tests/ with PYTHONPATH=src and refreshes devcontainer onboarding/docs.

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[caviri]

Hi @rmfranken, I can see the conversion for repositories what about the conversion for user, and organization?

[rmfranken]

Here are the conversion commands for each type - they are pretty much the same:
A person:
python scripts/convert_json_jsonld.py to-jsonld MalloryWittwer.json output.jsonld --base-url https://github.com/MalloryWittwer

A organization:
python scripts/convert_json_jsonld.py to-jsonld sdsc-ordes.json sdsc-ordes.jsonld --base-url https://github.com/sdsc-ordes
A software:
python scripts/convert_json_jsonld.py to-jsonld DeepLabCutDeepLabCut.json DeepLabCutDeepLabCut.jsonld --base-url https://github.com/DeepLabCut/DeepLabCut

The script auto-detects what kind of entity it's dealing with and processes it accordingly. The base-url is a bit too safe maybe - but we can see how easy it is to inject that into the call that we build.

[rmfranken]

I think I want to make the URI's hashed - not blank nodes. Tentris is not dealing super well with them - not sure why - will investigate tomorrow.

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Cursor Bugbot has reviewed your changes and found 4 potential issues.

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[cursor]

Gemini CLI added to shared devcontainer Dockerfile

Low Severity

The devcontainer Dockerfile now installs Node.js 24 and @google/gemini-cli globally. This appears to be personal development tooling (the comment references copying personal credentials). It adds significant image size and an external dependency to the shared devcontainer that isn't related to the project's core functionality.

 

[cursor]

Environment variable uses inconsistent casing convention

Low Severity

The environment variable linked_entities_ENRICHMENT_MODELS mixes lowercase and uppercase, breaking the standard SCREAMING_SNAKE_CASE convention for environment variables. Grep confirmed this same name is used in the actual source code at src/llm/model_config.py. All other env vars in this file follow SCREAMING_SNAKE_CASE (e.g., USER_ENRICHMENT_MODELS, ORG_ENRICHMENT_MODELS).

 

[cursor]

Mermaid diagram broken by stroke-width.md typo

Low Severity

The mermaid diagram style definitions use stroke-width.md:2px instead of stroke-width:2px on three lines. The .md suffix was erroneously inserted (likely from the filename), making the CSS property invalid. This will cause the mermaid renderer to fail to apply the intended styling to nodes Z, Y, and the agentNode class definition.

 

[cursor]

PR's featured script convert_json_jsonld.py missing from commit

High Severity

The PR title is "feat: add vibecoded but working convert_json_jsonld.py" and this commit adds extensive documentation for scripts/convert_json_jsonld.py (a full CLI guide in docs/JSON_JSONLD_CONVERSION_CLI.md, usage examples in scripts/README.md and docs/JSONLD_MAPPING_UPDATE.md), but the actual script file is absent from the commit. Grep confirms the file does not exist anywhere in the repository — it only appears as a referenced path in documentation. Anyone following the docs will get a "file not found" error.

Additional Locations (1)

• docs/JSON_JSONLD_CONVERSION_CLI.md#L1-L461