PlantAI-dev/docs/validation/2026-07-21-string-ppi-task1-snapshot.json

{
  "schema_version": "string_ppi_task1_snapshot_v1",
  "captured_at": "2026-07-21T04:26:31+08:00",
  "mode": "snapshot_deployment_and_validation_only",
  "deployment": {
    "ssh_host": "planai5090",
    "project_root": "/home/xzq/5090/PlantAI-dev4090-7/PlantAI-dev",
    "snapshot_path": "data/string/v12.0",
    "backend_modified": false,
    "ppi_execution_modified": false,
    "service_restarted": false
  },
  "script_audit": {
    "path": "scripts/prepare_string_species_snapshot.py",
    "changed": false,
    "conclusion": "existing implementation satisfies Task 1 requirements",
    "features_verified": [
      "fixed STRING v12.0 HTTPS source URLs",
      "temporary download followed by atomic replacement",
      "strict registry and tree parsing",
      "parent completeness and non-root cycle validation",
      "registry/tree STRING membership equality",
      "required Viridiplantae 33090 and Arabidopsis 3702 checks",
      "file sizes, SHA256, snapshot_id and source manifest"
    ]
  },
  "red_baseline": {
    "fixture_tests": {
      "command": "/home/xzq/miniconda3/envs/test4py311/bin/python -m pytest -q tests/unit/test_string_species_snapshot.py",
      "exit_code": 0,
      "result": "9 passed"
    },
    "full_snapshot_test": {
      "command": "/home/xzq/miniconda3/envs/test4py311/bin/python -m pytest -q tests/unit/test_string_species_registry.py::test_full_snapshot_supports_registry_only_species_and_second_non_ft_target",
      "exit_code": 1,
      "result": "failed as expected",
      "failure": "StringSnapshotError: STRING snapshot manifest unavailable: data/string/v12.0/source_manifest.json",
      "failure_classification": "required production snapshot missing; not syntax or fixture error"
    }
  },
  "download": {
    "command": "/home/xzq/miniconda3/envs/test4py311/bin/python scripts/prepare_string_species_snapshot.py --version 12.0 --destination data/string/v12.0",
    "exit_code": 0,
    "transfer_mode": "download",
    "string_version": "12.0",
    "downloaded_at": "2026-07-20T20:24:44.605781+00:00",
    "snapshot_id": "ede47d546d853d0ec30ee75066976a35c08fd2412e6e5fc7866bbd205fc2eeb3",
    "source_urls": {
      "species.v12.0.txt": "https://stringdb-downloads.org/download/species.v12.0.txt",
      "species.tree.v12.0.txt": "https://stringdb-downloads.org/download/species.tree.v12.0.txt"
    },
    "files": {
      "species.v12.0.txt": {
        "size": 1023159,
        "sha256": "4bb4c99c14db8d695decadf3b403a5b87ac490b468a842cbc54ec2e412400fec",
        "actual_matches_manifest": true
      },
      "species.tree.v12.0.txt": {
        "size": 97357335,
        "sha256": "54cf2e3378cbcabc38e355b044336813b7c0e76292ef34d70f8c8debc2e49ee1",
        "actual_matches_manifest": true
      }
    }
  },
  "validation": {
    "test_command": "/home/xzq/miniconda3/envs/test4py311/bin/python -m pytest -q tests/unit/test_string_species_snapshot.py tests/unit/test_string_species_registry.py",
    "test_exit_code": 0,
    "test_result": "19 passed",
    "registry_species_count": 12535,
    "tree_node_count": 2212178,
    "tree_string_species_count": 12535,
    "registry_tree_membership_equal": true,
    "parent_graph_complete": true,
    "non_root_cycle_absent": true,
    "root_taxon_id": "1",
    "required_nodes": {
      "33090": {
        "in_tree": true,
        "parent_taxon_id": "2759"
      },
      "3702": {
        "in_registry": true,
        "in_tree": true,
        "parent_taxon_id": "3701",
        "is_string_species": true
      }
    }
  },
  "setaria_viridis": {
    "scientific_name": "Setaria viridis",
    "taxon_id": "4556",
    "in_tree": true,
    "tree_parent_taxon_id": "4554",
    "in_string_registry": false,
    "is_direct_string_species": false,
    "name_resolution_source": "scientific_name",
    "taxid_resolution_source": "explicit_tree_taxon_id",
    "selection_mode": "tree_nearest",
    "requires_user_confirmation": true,
    "issue_code": "ppi_reference_confirmation_required",
    "candidates": [
      {
        "taxon_id": "4555",
        "name": "Setaria italica",
        "lca_taxon_id": "4554",
        "lca_name": "Setaria",
        "tree_distance": 2
      },
      {
        "taxon_id": "4540",
        "name": "Panicum miliaceum",
        "lca_taxon_id": "147428",
        "lca_name": "Paniceae",
        "tree_distance": 6
      },
      {
        "taxon_id": "888268",
        "name": "Dichanthelium oligosanthes",
        "lca_taxon_id": "147428",
        "lca_name": "Paniceae",
        "tree_distance": 6
      }
    ],
    "name_and_taxid_queries_agree": true
  },
  "files_changed": [
    "data/string/v12.0/species.v12.0.txt",
    "data/string/v12.0/species.tree.v12.0.txt",
    "data/string/v12.0/source_manifest.json",
    "docs/validation/2026-07-21-string-ppi-task1-snapshot.json",
    "docs/validation/2026-07-21-string-ppi-task1-snapshot.md"
  ],
  "gate_1": {
    "red_missing_snapshot_reproduced": true,
    "preexisting_script_accepted_without_change": true,
    "official_fixed_snapshot_deployed": true,
    "manifest_and_sha256_verified": true,
    "full_snapshot_and_registry_tests_pass": true,
    "setaria_file_fact_recorded": true,
    "scope_respected": true,
    "status": "pass"
  }
}