PlantAI-rag/WORKLINE.md

WORKLINE

last_updated: 2026-07-02

Identity

• type: rag
• copy_role: cleanup baseline / maintainable RAG surface
• canonical_path: /home/xia-lab/PlantAI-rag
• source_project: related to gene-family-mas-v2, but this path is the cleaner git-tracked baseline.

Current Workline

Current workline: RAG API/runtime cleanup baseline with git-tracked local edits.

Evidence:

• git status --short --branch reports branch main with local changes:
  • M api/app.py
  • M tests/test_api_app.py
  • M tests/test_methodology_mineru_gpu_preflight.py
  • ?? nohup.out
• config/runtime_surface_manifest.json
• config/external_resources_manifest.json
• .env

Runtime Profile

• git_repo: yes
• branch: main
• mineru_api: .env contains V15_MINERU_API_URL=http://127.0.0.1:50215
• mineru_cmd: .env contains MINERU_CMD=/home/xzq/miniconda3/envs/minerupy312/bin/mineru
• neo4j_defaults: .env contains NEO4J_URI=bolt://localhost:7687, NEO4J_DATABASE=neo4j
• startup_scripts:
  • scripts/shell/start_api.sh
  • scripts/start_mineru_api_50215_20260605.sh
  • scripts/start_dual_kb_qa_api_7902.sh
  • scripts/start_taxonomy_bge_unified_7907.sh
  • scripts/start_qa_v1_0_0_7908.sh

External Dependencies

• MinerU API or local MinerU command.
• Neo4j and Qdrant depending on the selected runtime surface.
• External resources declared in config/external_resources_manifest.json.

Active Evidence

• Runtime manifest: config/runtime_surface_manifest.json
• External resource manifest: config/external_resources_manifest.json
• Environment file: .env
• Current local edits from git status --short --branch

Verification Commands

Read-only checks:

git -C /home/xia-lab/PlantAI-rag status --short --branch
rg -n 'MINERU|NEO4J|QDRANT|PORT|COLLECTION' .env config scripts -S

Run tests only when the task scope names a specific API/runtime change, for example:

pytest tests/test_api_app.py -q

Evidence Policy

When answering RAG/methodology questions, report query, index or KB version if known, chunk id or record id when available, section/source, relevance signal, and whether the result is paper evidence or generic workflow context.

Do Not Assume Duplicate Of

• Do not overwrite this cleanup baseline with experimental service wiring from gene-family-mas-v2.
• Do not treat gene-family-mas-v2 as stale just because PlantAI-rag is cleaner.
• Do not commit or delete nohup.out without a specific cleanup task.

Update Policy

Update this file when the active git branch, dirty-file scope, runtime manifest, startup script set, or evidence policy changes.