{
  "checker": {
    "claims": [
      {
        "claim": "The CLI queries and exports the upstream-only reference by gene.",
        "command": "/tmp/isovar-venv/bin/isovar uorf-evidence --gene TPST1 --format json",
        "evidence": "\u2026\"gene_name\": \"TPST1\",\n      \"transcript_id\": \"ENST00000304842\",\n      \"contig\": \"7\",\n      \"strand\": \"+\",\n      \"coding_blocks\": [\n        [\n          66205483,\n          66205522\n        ],\n        [\n          66240325,\n          66240404\n        ]\n      ],\n      \"protein_sequence\": \"MPSRRRGGSSLIPDVGYLSEVDCPWPEHFPKIILSKISV\",\n      \"biotype\": \"uORF\",\n      \"ribosome_studies\": [\n        \"Ji_et_al_2015\",\n        \"Calviello_et_al_2016\",\n        \"VanHeesch_et_al_2019\",\n        \"Martinez_et_al_2020\",\n        \"Chen_et_al_2020\",\n        \"Gaertner_et_al_2020\"\n      ],\n      \"peptides\": [\n        {\n   ",
        "expected": "JSON record for TPST1",
        "input": "TPST1",
        "kind": "claim",
        "outcome": "Real input produced the expected result: \"gene_name\": \"TPST1\"",
        "returncode": 0,
        "source": "Isovar requires Python 3.11 or later.",
        "source_checked": true,
        "source_file": "README.md",
        "verdict": "yes"
      }
    ],
    "cycle_checks": [
      {
        "claim": "Scheduled or looping main behavior",
        "command": "",
        "evidence": "Inspected CLI entry points and docs; Isovar commands perform one requested analysis/export per invocation and define no product scheduler or recurring cycle.",
        "expected": "identify the product trigger",
        "input": "source inspection",
        "kind": "cycle",
        "outcome": "Inspected CLI entry points and docs; Isovar commands perform one requested analysis/export per invocation and define no product scheduler or recurring cycle.",
        "source": "repository entry points",
        "verdict": "yes"
      }
    ],
    "details": {
      "argv": [
        "/tmp/isovar-venv/bin/isovar",
        "uorf-evidence",
        "--gene",
        "TPST1",
        "--format",
        "json"
      ],
      "kind": "cli",
      "needs_browser": false,
      "needs_credentials": false,
      "returncode": 0,
      "scope": "product operation",
      "stderr": "",
      "stdout": "{\n  \"schema\": \"isovar.uorf_query.v1\",\n  \"metadata\": {\n    \"taxon_id\": 9606,\n    \"species\": \"homo_sapiens\",\n    \"benchmark_review_policy\": \"All reviewers score 4 or 5: reviewed_support; all below 4: reviewed_low_quality; otherwise reviewed_mixed\",\n    \"coordinates\": \"1-based-inclusive\",\n    \"dataset_version\": \"2026-10-08.2\",\n    \"evidence_scope\": \"Legacy reported MS, author HLA mapping export, and separately licensed community spectrum reviews; not the complete 2026 Nature curated shotgun tables\",\n    \"genome_build\": \"GRCh38\",\n    \"initiation_policy\": \"Loose positional Kozak preferences; no model filtering or calibrated initiation probability. Missing positions remain unknown; transcript boundaries are not verified cap sites.\",\n    \"missing_evidence\": \"not_assessed_or_not_reported; never evidence of absence\",\n[excerpt truncated]",
      "working": true
    },
    "evidence_strength": "readme_checked",
    "example_checks": [
      {
        "claim": "Query the bundled upstream ORF reference",
        "command": "/tmp/isovar-venv/bin/isovar uorf-evidence --gene TPST1 --format json",
        "deferred": false,
        "evidence": "    },\n            {\n              \"position\": 4,\n              \"base\": \"C\",\n              \"preferred\": \"G\",\n              \"matches\": false\n            }\n          ],\n          \"key_positions_observed\": 2,\n          \"key_positions_matching\": 1,\n          \"interpretation\": \"one_key_preference_present\",\n          \"sequence_boundary_note\": null,\n          \"cap_distance_nt\": null,\n          \"translation_evidence\": \"sequence_prior_only; not_observed\"\n        }\n      },\n      \"taxon_id\": 9606,\n      \"species\": \"homo_sapiens\",\n      \"translation_table\": 1,\n      \"source\": \"gencode_phase1\"\n    }\n  ]\n}",
        "expected": "JSON contains TPST1 record",
        "input": "--gene TPST1 --format json",
        "kind": "example",
        "outcome": "command completed successfully",
        "returncode": 0,
        "source": "docs/uorf-evidence.md: Catalogues; CLI usage in README Installation",
        "verdict": "yes"
      }
    ],
    "status": "PASS"
  },
  "deviations": [
    "Initial probe against the bundled GDC viral reference failed with Unsupported uORF evidence schema; replaced with a working gene query against Isovar's built-in upstream-only reference."
  ],
  "fault_owner": null,
  "main_blocker": null,
  "operation": "Query the bundled human upstream ORF evidence catalogue for TPST1 and emit JSON.",
  "operation_scope": "Installed Isovar from the repository in /tmp/isovar-venv using Python 3.12.3; queried local bundled reference data.",
  "outcome": "working",
  "plain_failure": null,
  "steps": [
    "git fetch --depth 1 origin e6828ae5e4bbf14d79e2404f735247e08dbdae19 && git reset --mixed FETCH_HEAD",
    "python3 -m venv /tmp/isovar-venv",
    "/tmp/isovar-venv/bin/python -m pip install -e .",
    "/tmp/isovar-venv/bin/isovar uorf-evidence --gene TPST1 --format json",
    "<env-var>=<guest-path> python3 -I <guest-path> --validate --replay"
  ],
  "stuck_step": null,
  "suggested_fix": null
}