# 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:

```bash
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:

```bash
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.