PlantAI-rag/config/external_resources_manifest.json

{
  "schema_version": 1,
  "description": "Env-managed external resources for PlantAI-rag. This file documents required local inputs without storing real paths, credentials, or host-specific defaults.",
  "resources": [
    {
      "env_key": "PLANTAI_SOURCE_ROOT",
      "category": "source_project",
      "required_for": [
        "migration_parity_audit"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Read-only original gene-family-mas-v2 project root used for parity checks."
    },
    {
      "env_key": "PC_DATA_ROOT",
      "category": "external_data",
      "required_for": [
        "plantconnectome_matching",
        "strict_validation"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "required_files": [
        "scientific_chunks.json",
        "gene_alias.json",
        "all_dic.json",
        "relationships_by_category_final.json"
      ],
      "description": "PlantConnectome-compatible data root. Kept separate from split user data."
    },
    {
      "env_key": "PLANTAI_SPLIT_DATA_ROOT",
      "category": "external_data",
      "required_for": [
        "optional_split_data_validation"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "User-split data root. The cleanup workflow must not deduplicate, merge, clean, or rewrite it."
    },
    {
      "env_key": "BGE_RERANKER_ROOT",
      "category": "external_model",
      "required_for": [
        "reranking"
      ],
      "repo_policy": "env_or_symlink",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Local BGE reranker model root or symlink target."
    },
    {
      "env_key": "BBAV5_ROOT",
      "category": "integration_project",
      "required_for": [
        "bbav5_integration"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Read-only bbav5 integration project root."
    },
    {
      "env_key": "BBAV5_CAPABILITY_CATALOG",
      "category": "integration_input",
      "required_for": [
        "bbav5_methodology_alignment"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Generated bbav5 capability catalog JSON used by methodology alignment validation."
    },
    {
      "env_key": "BBAV5_REAL_INPUT_DIR",
      "category": "integration_input",
      "required_for": [
        "bbav5_real_run_validation"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Existing bbav5 real input directory used for validation."
    },
    {
      "env_key": "BBAV5_REAL_WORKSPACE_DIR",
      "category": "integration_workspace",
      "required_for": [
        "bbav5_real_run_validation"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Existing bbav5 workspace directory used for validation."
    },
    {
      "env_key": "BBAV5_PRIMARY_PAPER",
      "category": "validation_input",
      "required_for": [
        "bbav5_real_run_validation"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Primary local paper path used by integration validation."
    },
    {
      "env_key": "BBAV5_RNASEQ_PAPER",
      "category": "validation_input",
      "required_for": [
        "bbav5_rnaseq_validation"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "RNA-seq evidence paper path used by integration validation."
    },
    {
      "env_key": "FT_SPL_V15_RESULT",
      "category": "validation_input",
      "required_for": [
        "v15_result_comparison"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Existing V15 result JSON used for comparison-only validation."
    },
    {
      "env_key": "PLANTAI_CONDA_ROOT",
      "category": "runtime_tooling",
      "required_for": [
        "local_runtime"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Local conda installation root. Environment names remain unchanged for now."
    },
    {
      "env_key": "PLANTAI_CONDA_PROFILE",
      "category": "runtime_tooling",
      "required_for": [
        "local_runtime"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Local conda shell profile path."
    },
    {
      "env_key": "PLANTAI_PYTHON",
      "category": "runtime_tooling",
      "required_for": [
        "local_runtime"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Optional Python executable path for PlantAI-rag commands."
    },
    {
      "env_key": "GF_PYTHON",
      "category": "runtime_tooling",
      "required_for": [
        "local_runtime",
        "validation"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Python executable for the current gfpy312 environment."
    },
    {
      "env_key": "MINERU_CMD",
      "category": "runtime_tooling",
      "required_for": [
        "mineru_validation"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "MinerU command path for the existing minerupy312 environment."
    },
    {
      "env_key": "PLANTAI_TEST_PDF",
      "category": "validation_input",
      "required_for": [
        "baseline_validation"
      ],
      "repo_policy": "env_only",
      "read_only": true,
      "tracked_in_repo": false,
      "description": "Local PDF path used by baseline validation wrappers."
    }
  ]
}