{ "run_id": "kms2229--pmcfetch-claude-haiku-5-5-1793171962129158545", "date": "2026-10-28T07:21:51.999467+00:00", "repo": "kms2229/pmcfetch", "kind": "repo", "source": "https://github.com/kms2229/pmcfetch", "commit": "5a95f5979ffc2c521f8062a2cc6d0dc149546c12", "model": "claude-haiku-5-5", "model_version": "claude-haiku-5-5", "test_version": "readme-a0d0e27a4d0fd4c50903587087c25799260ee2578ee1953a6356df3e4fd02c35", "pass": true, "outcome": "pass", "time_to_working_s": 123.86339193900494, "total_s": 149.8702347278595, "steps": [ "cd && ls -la && git status 2>&1 | head -3; cat README.md 2>/dev/null | head -150; python3 --version", "cd && tail -c 400 README.md; echo ---; ls -la .coldpass examples tests docs; echo ---; cat pyproject.toml | head -60; echo; ls /inputs 2>&1; which pip3 pip; python3 -m pip --version", "mkdir -p && python3 -m venv 2>&1 | tail -3; ls 2>&1 | head", "cd /tmp && install --upgrade pip -q 2>&1 | tail -2; install 2>&1 | tail -5; --help 2>&1 | head -40", "cd /tmp && timeout 120 search \"burn scar\" < /dev/null; echo \"rc=$?\"", "mkdir -p && printf 'PMC10007932\\n' > && cd && timeout 300 download --corpus --out < /dev/null; echo \"rc=$?\"; ls -la 2>&1", "cd && find . -type f -exec ls -la {} \\; && find . -type f -name '*.pdf' -exec head -c 8 {} \\; ; echo; ls ; ls 2>/dev/null", "cd && install -q 'pytest>=8.0' 2>&1 | tail -2; -m pytest tests -q -p no:cacheprovider 2>&1 | tail -8; echo \"rc=${PIPESTATUS[0]}\"", "cd && grep -n -F -e \"# [pmcfetch] 20,349 open-access article(s) match 'burn scar'\" -e \"pmcfetch download --corpus ids.txt --out pdfs/\" -e \"Exit code is \\`1\\` when any article failed\" README.md; cp .coldpass/ids.txt && cat .coldpass/ids.txt", "cd && cat > claims.json <<'EOF'\n[\n {\"kind\":\"claim\",\"claim\":\"Keyword search reports how many open-access papers match before downloading\",\"source\":\"# [pmcfetch] 20,349 open-access article(s) match 'burn scar'\",\"input\":\"burn scar\",\"expected\":\"count line printed for the query\",\"probe_kind\":\"cli\",\"argv\":[\"\",\"search\",\"burn scar\"],\"expected_text\":\"open-access article(s) match 'burn scar'\",\"cwd\":\"\"},\n {\"kind\":\"claim\",\"claim\":\"Downloads the PDFs listed in a corpus id file into an output directory\",\"source\":\"pmcfetch download --corpus ids.txt --out pdfs/\",\"input\":\"ids.txt with PMC10007932\",\"expected\":\"one article downloaded, none failed\",\"probe_kind\":\"cli\",\"argv\":[\"\",\"download\",\"--corpus\",\"\",\"--out\",\"\"],\"output_directory\":\"\",\"expected_text\":\"downloaded=1 skipped=0 failed=0 total=1\",\"cwd\":\"\"}\n]\nEOF\ncat > probe.json <<'EOF'\n{\"kind\":\"cli\",\"argv\":[\"\",\"download\",\"--corpus\",\"\",\"--out\",\"\"],\"cwd\":\"\",\"output_directory\":\"\",\"expected_text\":\"downloaded=1 skipped=0 failed=0 total=1\"}\nEOF\npython3 -I -c 'import json;[json.load(open(f)) for f in [\"claims.json\",\"probe.json\"]];print(\"json ok\")'", "cd && tests -p no:cacheprovider 2>&1 | tail -3; echo \"rc=${PIPESTATUS[0]}\"; grep -rn -i \"pytest\\|cron\\|schedul\\|--once\\|--now\\|webhook\" pyproject.toml README.md .github 2>/dev/null | head; ls .github/workflows", "cd && sed -n 205,216p README.md; echo ---; grep -n \"^##\" README.md; grep -rln -i \"while true\\|sleep\\|--once\\|--now\\|cron\" src | head", "cd && grep -n -i \"while true\\|sleep\\|--once\\|--now\\|cron\\|schedule\\|webhook\" src/pmcfetch/cli.py src/pmcfetch/ratelimit.py | head -20; echo ---; grep -n -F \"\\`\\`\\`bash\" README.md | head -2 >/dev/null; grep -n -F \"pip install -e '.[dev]'\" README.md", "cd && sed -n 300,325p src/pmcfetch/cli.py", "cd && cat > examples.json <<'EOF'\n[\n {\"kind\":\"example\",\"claim\":\"The documented test suite runs and passes\",\"source\":\"README.md Tests section (## Tests)\",\"input\":\"python -m pytest tests/ -q\",\"expected\":\"all offline tests pass\",\"argv\":[\"\",\"-m\",\"pytest\",\"tests/\",\"-q\"],\"cwd\":\"\",\"env\":{},\"expected_text\":\"115 passed\"}\n]\nEOF\ncat > cycles.json <<'EOF'\n{\"detected\":false,\"checks\":[],\"reason\":\"Inspected README.md (no cron, schedule, daemon, webhook, --once or --now feature documented), pyproject.toml scripts (only pmcfetch.cli:main), and src/pmcfetch/cli.py. The only loop found is the interactive 'How many to download?' prompt in _ask_amount, which is user input retry, not a scheduled or repeating product cycle. The .github/workflows/publish.yml file is CI, not a product cycle.\"}\nEOF\npython3 -I -c 'import json;[json.load(open(f)) for f in [\"examples.json\",\"cycles.json\"]];print(\"json ok\")'; ls -la ", "cd && = timeout 900 python3 -I --validate --replay 2>&1 | tail -60; echo \"rc=${PIPESTATUS[0]}\"", "rm -rf && cd && cat > report.json <<'EOF'\n{\"outcome\":\"working\",\"fault_owner\":null,\"operation\":\"Install pmcfetch from the pinned source and run the README's keyword search and id-list download, producing a real PDF from PubMed Central's open-access S3 bucket.\",\"operation_scope\":\"Python 3.12.3 (README requires 3.10+) in a venv at ; network access to NCBI E-utilities and the AWS S3 bucket pmc-oa-opendata; stdlib-only product. Source pinned at https://github.com/kms2229/pmcfetch @ 5a95f5979ffc2c521f8062a2cc6d0dc149546c12 (workspace supplied pre-populated; no git metadata was initialized).\",\"steps\":[\"python3 -m venv \",\" install (README says 'pip install pmcfetch'; installed the pinned local source instead, which reported pmcfetch-0.2.1)\",\" --help\",\" search \\\"burn scar\\\" (returned 20,349 open-access matches)\",\"printf PMC10007932 > ids.txt; download --corpus ids.txt --out pdfs/ (downloaded=1 failed=0; output is %PDF-1.4, 542332 bytes)\",\" -m pytest tests/ -q (README ## Tests; 115 passed)\"],\"deviations\":[\"Installed from the pinned local source with pip install rather than PyPI 'pip install pmcfetch', so the tested code matches the pin.\",\"pip install created build artifacts (src/pmcfetch.egg-info, __pycache__) inside the workspace; no product source was edited.\",\"Checker path: /inputs/coldpass-preflight.py does not exist in this VM, so was used with --validate --replay (valid=true, replay PASS).\",\"Tests were run with the README's 'python -m pytest tests/ -q' (venv python) because the pytest entrypoint was not separately documented.\",\"Replay of the search count depends on live NCBI results; claims match on the stable phrase, not the count.\",\"Cycles: none detected; the only loop is an interactive input prompt.\"],\"stuck_step\":null,\"main_blocker\":null,\"plain_failure\":null,\"suggested_fix\":\"None required for the tested operations. Optional: the README's pip install pmcfetch line should be kept in sync with the published PyPI release.\"}\nEOF\npython3 -I -c 'import json;json.load(open(\"report.json\"));print(\"report ok\")'; ls -la " ], "stuck_step": null, "error_excerpt": null, "what_it_did": "Install pmcfetch from the pinned source and run the README's keyword search and id-list download, producing a real PDF from PubMed Central's open-access S3 bucket.", "suggested_fix": null, "tokens_in": 341441, "tokens_out": 13077, "cost_usd": 0.01535861, "usage_complete": true, "checks": [ { "check": "operation", "status": "PASS", "details": { "working": true, "argv": [ "", "download", "--corpus", "", "--out", "" ], "kind": "cli", "returncode": 0, "stdout": "[pmcfetch] corpus= namespace=ALL n=1\n[1/1] ok PMC10007932\n\n[pmcfetch] ALL: downloaded=1 skipped=0 failed=0 total=1", "stderr": "", "needs_credentials": false, "needs_browser": false, "scope": "product operation" } } ], "safety": { "version": "z2x-1", "rules_version": "z2x-1", "summary": "Review signals: 1 connection review.", "expected": "Reviewed as expected for a test run: attempted writes that failed, so nothing was written.", "findings": [ { "kind": "connection-review", "count": 1, "note": "Repository processes attempted these non-loopback connections; proxies can hide the final hostname.", "location_count": 26, "process_count": 8 } ], "context": [], "limitations": [ "A short run cannot establish that code is safe.", "Connections show IP addresses; proxies can hide the final hostname.", "Tracing covers dispatched commands and their children, not the whole OS; guest root can interfere with tracing." ], "static": { "dependency_note": "OSV scanned supported lockfiles; unpinned dependencies and unsupported formats are outside this check." }, "evidence_url": "/safety/?run=kms2229--pmcfetch-claude-haiku-5-5-1793171962129158545", "evidence_file": "/data/safety/kms2229--pmcfetch-claude-haiku-5-5-1793171962129158545.json.gz" }, "agent_execution": "native_agent", "agent_runtime": "claude-code", "agent_runtime_version": "2.1.310 (Claude Code)", "tool_transport": "mcp-assigned-vm", "platform": "linux", "reasoning": "low", "service_tier": null, "resources": { "cpus": 2, "memory_mib": 4096, "disk_mib": 32768 }, "native_tool_calls": 17, "native_bundle": null, "architecture": null, "backend": "hyperv", "platform_details": { "backend": "hyperv", "os": "linux" }, "platform_conflicts": null, "sandbox_source": null, "source_pin": { "commit": "5a95f5979ffc2c521f8062a2cc6d0dc149546c12", "url": "https://github.com/kms2229/pmcfetch" }, "purpose": "initial", "profile": { "model": "claude-haiku-5-5", "reasoning": "low" }, "fault": { "owner": null, "status": "resolved", "reason": null }, "fix_id": null, "verifies_run_id": null, "hosting": null, "operation_scope": "product operation", "tool_calls": 17, "guest_setup": null, "runtime": null, "runtime_version": null, "runtime_revision": null, "source_revision": null, "evidence_version": null, "failure_origin": null, "evidence_strength": "readme_checked", "works": "yes", "install_s": null, "first_use_s": null, "mcp": "none", "needs": [], "needs_which": null, "agent_interface": [ "cli" ], "license": "MIT", "repo_url": "https://github.com/kms2229/pmcfetch", "cost_to_try": "free", "hardware": null, "what_failed": null, "local_or_hosted": "local", "cycle_checks": [ { "kind": "cycle", "claim": "Scheduled or looping main behavior", "source": "repository entry points", "input": "source inspection", "expected": "identify the product trigger", "verdict": "yes", "outcome": "Inspected README.md (no cron, schedule, daemon, webhook, --once or --now feature documented), pyproject.toml scripts (only pmcfetch.cli:main), and src/pmcfetch/cli.py. The only loop found is the interactive 'How many to download?' prompt in _ask_amount, which is user input retry, not a scheduled or repeating product cycle. The .github/workflows/publish.yml file is CI, not a product cycle.", "evidence": "Inspected README.md (no cron, schedule, daemon, webhook, --once or --now feature documented), pyproject.toml scripts (only pmcfetch.cli:main), and src/pmcfetch/cli.py. The only loop found is the interactive 'How many to download?' prompt in _ask_amount, which is user input retry, not a scheduled or repeating product cycle. The .github/workflows/publish.yml file is CI, not a product cycle.", "command": "" } ], "claims": [ { "kind": "claim", "claim": "Keyword search reports how many open-access papers match before downloading", "source": "# [pmcfetch] 20,349 open-access article(s) match 'burn scar'", "input": "burn scar", "expected": "count line printed for the query", "command": " search 'burn scar'", "verdict": "yes", "outcome": "Real input produced the expected result: open-access article(s) match 'burn scar'", "evidence": "\u2026open-access article(s) match 'burn scar'\n[pmcfetch] NCBI searched: (\"burns\"[MeSH Terms] OR \"burns\"[All Fields] OR \"burn\"[All Fields]) AND (\"cicatrix\"[MeSH Terms] OR \"cicatrix\"[All Fields] OR \"scar\"[All Fields]) AND \"open access\"[Filter]\n[pmcfetch] to download, rerun with --download N or --download all (saves to pdfs/)\n", "returncode": 0, "source_checked": true, "source_file": "README.md" }, { "kind": "claim", "claim": "Downloads the PDFs listed in a corpus id file into an output directory", "source": "pmcfetch download --corpus ids.txt --out pdfs/", "input": "ids.txt with PMC10007932", "expected": "one article downloaded, none failed", "command": " download --corpus --out ", "verdict": "yes", "outcome": "Real input produced the expected result: downloaded=1 skipped=0 failed=0 total=1", "evidence": "\u2026downloaded=1 skipped=0 failed=0 total=1\n", "returncode": 0, "source_checked": true, "source_file": "README.md" } ], "claims_note": null, "example_checks": [ { "kind": "example", "claim": "The documented test suite runs and passes", "source": "README.md Tests section (## Tests)", "input": "python -m pytest tests/ -q", "command": " -m pytest tests/ -q", "evidence": "........................................................................ [ 62%]\n........................................... [100%]", "deferred": false, "expected": "all offline tests pass", "returncode": 0, "verdict": "yes", "outcome": "command completed successfully" } ], "does_what_it_says": "yes", "maintenance": { "last_commit_at": "2026-10-28T05:04:52Z", "commits_90d": 8, "merged_prs_90d": 0, "open_issues": 0, "open_prs": 0, "reply_share": null, "reply_threads": 0, "median_reply_hours": null, "last_release_at": "2026-10-28T05:07:11Z", "archived": false, "verdict": "maintained", "note": "actively maintained: last commit 0 days ago; 8 commits and 0 merged PRs in 90 days; 0 open issues, 0 open PRs; latest release 2026-10-28" }, "maintenance_verdict": "maintained", "maintenance_note": "actively maintained: last commit 0 days ago; 8 commits and 0 merged PRs in 90 days; 0 open issues, 0 open PRs; latest release 2026-10-28", "maintained": "active", "maintained_note": "last commit 0 days ago", "last_commit_at": "2026-10-28T05:07:11Z", "last_release_at": "2026-10-28T05:07:11Z", "open_issues": null, "answered_issues": null, "platforms_claimed": [ "linux" ], "topic": "coding", "agent_interfaces": [ { "interface": "cli", "evidence": "independent checker", "observed": true, "operation_checked": true } ], "agent_interfaces_note": "README metadata is a discovery hint, not pinned documentation proof. Observed interfaces were exercised in this run. An empty list means unknown.", "mcp_context": null, "tested_at": "2026-10-28T07:21:51.999467+00:00", "tested_commit": "5a95f5979ffc2c521f8062a2cc6d0dc149546c12", "tested_with": { "agent": "claude-code", "agent_version": "2.1.310 (Claude Code)", "model": "claude-haiku-5-5", "model_route": "claude-haiku-5-5", "reasoning": "low", "os": "linux", "backend": "hyperv", "transport": "mcp-assigned-vm" }, "setup_identity": { "repo": "kms2229/pmcfetch", "source": "https://github.com/kms2229/pmcfetch", "commit": "5a95f5979ffc2c521f8062a2cc6d0dc149546c12", "source_revision": null, "os": "linux", "architecture": null, "backend": "hyperv", "model": "claude-haiku-5-5", "model_version": "claude-haiku-5-5", "agent_execution": "native_agent", "agent_runtime": "claude-code", "agent_runtime_version": "2.1.310 (Claude Code)", "tool_transport": "mcp-assigned-vm", "runtime": null, "runtime_version": null, "runtime_revision": null, "sandbox_source": null, "guest_setup": null, "source_pin": { "commit": "5a95f5979ffc2c521f8062a2cc6d0dc149546c12", "url": "https://github.com/kms2229/pmcfetch" }, "platform_details": { "os": "linux", "backend": "hyperv" }, "platform_conflicts": null, "reasoning": "low", "service_tier": null, "resources": { "cpus": 2, "memory_mib": 4096, "disk_mib": 32768 }, "operation": "Install pmcfetch from the pinned source and run the README's keyword search and id-list download, producing a real PDF from PubMed Central's open-access S3 bucket.", "operation_scope": "product operation", "hosting": null, "kind": "repo", "test_version": "readme-a0d0e27a4d0fd4c50903587087c25799260ee2578ee1953a6356df3e4fd02c35", "evidence_version": null }, "other_model": null, "other_run_id": null, "models_agree": null, "furthest_model": null, "transcript_url": "/transcripts/kms2229--pmcfetch-claude-haiku-5-5-1793171962129158545.txt", "report_url": "/reports/kms2229--pmcfetch-claude-haiku-5-5-1793171962129158545.json" }