{"abstract":"An aliquot is credited to its immediate tube instead of its specimen.","category":"Scientific pipeline provenance","checks":6,"contract":"Return the root ID for an acyclic parent mapping; return cycle if a node repeats. Missing parent means a source root.","contract_signature":"sample, parents","evaluation_group":"model-0c0843c33b7453d7","failed_approach":"Following exactly two links still truncates deeper preparation chains.","family":"z-scientific_pipelines-aliquot-root","id":"FA-11901","implementations":{"attempt":{"sha256":"689a8f320901a9fc12e0b63b418380af0d60557a2812f1ff56cde35bc841bdbd","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(sample, parents):\n    return parents.get(parents.get(sample,sample),parents.get(sample,sample))\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\nroot='specimen'+str(N)\ncheck('three preparation steps', solve('c', {'c':'b','b':'a','a':root}), root)\ncheck('source specimen', solve(root, {}), root)\ncheck('single aliquot', solve('a', {'a':root}), root)\ncheck('two aliquots', solve('b', {'b':'a','a':root}), root)\ncheck('self cycle', solve('a', {'a':'a'}), 'cycle')\ncheck('multi tube cycle', solve('a', {'a':'b','b':'a'}), 'cycle')\nprint(json.dumps({\"observations\": observations, \"passed\": all(x[\"passed\"] for x in observations)}, ensure_ascii=False))\nraise SystemExit(0 if all(x[\"passed\"] for x in observations) else 1)\n"},"broken":{"sha256":"08f1e99e1e6ce2345dd09da89cb23a18e7dcd1c751484828e4481d2624626886","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(sample, parents):\n    return parents.get(sample, sample)\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\nroot='specimen'+str(N)\ncheck('three preparation steps', solve('c', {'c':'b','b':'a','a':root}), root)\ncheck('source specimen', solve(root, {}), root)\ncheck('single aliquot', solve('a', {'a':root}), root)\ncheck('two aliquots', solve('b', {'b':'a','a':root}), root)\ncheck('self cycle', solve('a', {'a':'a'}), 'cycle')\ncheck('multi tube cycle', solve('a', {'a':'b','b':'a'}), 'cycle')\nprint(json.dumps({\"observations\": observations, \"passed\": all(x[\"passed\"] for x in observations)}, ensure_ascii=False))\nraise SystemExit(0 if all(x[\"passed\"] for x in observations) else 1)\n"}},"limitations":"In-memory symbolic records only; no instrument, assay, or production workflow validation. This reproducer isolates one failure mechanism. Results cover the supplied fixtures. Variants within a family share a test contract and should remain grouped when constructing evaluation splits. Related mechanisms with a shared evaluation_group must also remain together; these controlled models are not independent production incidents.","method":"Deterministic executable model with adversarial boundary fixtures.","provenance":{"created_by":"Failure Map","dependencies":"Python standard library","family":"z-scientific_pipelines-aliquot-root","generated_at":"2026-09-29T14:38:52.016935+00:00","license":"CC0-1.0","python":"3.12.14","seed":1,"split":"open-access"},"relevance":"A deterministic offline model of scientific workflow bookkeeping; the fixtures test provenance contracts without modeling instruments or biological inference.","root_cause":"One lineage hop is assumed sufficient.","sha256":"60cfa0fdbc0c27d634dd4eb86367a2521c01f64a9afc1fe8d9452a33083a55ef","title":"An aliquot is credited to its immediate tube instead of its specimen · case 01","variant":1,"variant_policy":"Five numbered records share a model and may reuse boundary fixtures.","verified":true,"visibility":"public","verification":{"attempt":{"elapsed_ms":41.361,"exit_code":1,"observations":[{"actual":"a","check":"three preparation steps","expected":"specimen1","passed":false},{"actual":"specimen1","check":"source specimen","expected":"specimen1","passed":true},{"actual":"specimen1","check":"single aliquot","expected":"specimen1","passed":true},{"actual":"specimen1","check":"two aliquots","expected":"specimen1","passed":true},{"actual":"a","check":"self cycle","expected":"cycle","passed":false},{"actual":"a","check":"multi tube cycle","expected":"cycle","passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"three preparation steps\", \"actual\": \"a\", \"expected\": \"specimen1\", \"passed\": false}, {\"check\": \"source specimen\", \"actual\": \"specimen1\", \"expected\": \"specimen1\", \"passed\": true}, {\"check\": \"single aliquot\", \"actual\": \"specimen1\", \"expected\": \"specimen1\", \"passed\": true}, {\"check\": \"two aliquots\", \"actual\": \"specimen1\", \"expected\": \"specimen1\", \"passed\": true}, {\"check\": \"self cycle\", \"actual\": \"a\", \"expected\": \"cycle\", \"passed\": false}, {\"check\": \"multi tube cycle\", \"actual\": \"a\", \"expected\": \"cycle\", \"passed\": false}], \"passed\": false}\n"},"broken":{"elapsed_ms":39.562,"exit_code":1,"observations":[{"actual":"b","check":"three preparation steps","expected":"specimen1","passed":false},{"actual":"specimen1","check":"source specimen","expected":"specimen1","passed":true},{"actual":"specimen1","check":"single aliquot","expected":"specimen1","passed":true},{"actual":"a","check":"two aliquots","expected":"specimen1","passed":false},{"actual":"a","check":"self cycle","expected":"cycle","passed":false},{"actual":"b","check":"multi tube cycle","expected":"cycle","passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"three preparation steps\", \"actual\": \"b\", \"expected\": \"specimen1\", \"passed\": false}, {\"check\": \"source specimen\", \"actual\": \"specimen1\", \"expected\": \"specimen1\", \"passed\": true}, {\"check\": \"single aliquot\", \"actual\": \"specimen1\", \"expected\": \"specimen1\", \"passed\": true}, {\"check\": \"two aliquots\", \"actual\": \"a\", \"expected\": \"specimen1\", \"passed\": false}, {\"check\": \"self cycle\", \"actual\": \"a\", \"expected\": \"cycle\", \"passed\": false}, {\"check\": \"multi tube cycle\", \"actual\": \"b\", \"expected\": \"cycle\", \"passed\": false}], \"passed\": false}\n"}},"member_only":{"stages":["fixed"],"fields":["implementations.fixed","verification.fixed","harness","repair"],"note":"The verified repair, its recorded checks, the repair description, and the scoring harness are available to members."}}