{"abstract":"Technical repeats inflate biological replicate counts.","category":"Scientific pipeline provenance","checks":6,"contract":"Rows are condition, donor, aliquot tuples; return a dictionary of distinct donor counts per condition, including donors shared across conditions independently.","contract_signature":"rows","evaluation_group":"model-7d0b3500ed1ea86b","failed_approach":"Deduplicating aliquot IDs still counts multiple aliquots from one donor.","family":"z-scientific_pipelines-biological-replicates","id":"FA-11931","implementations":{"attempt":{"sha256":"874d964738d49ccfc6795649d320eed294012e109cdf64db4b05c8cf02f48796","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(rows):\n    out={}\n    for condition,donor,aliquot in rows: out.setdefault(condition,set()).add(aliquot)\n    return {k:len(v) for k,v in out.items()}\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\nd='donor'+str(N)\ncheck('two aliquots one donor', solve([('c',d,'a'),('c',d,'b')]), {'c':1})\ncheck('repeated assay', solve([('c',d,'a'),('c',d,'a')]), {'c':1})\ncheck('two donors', solve([('c',d,'a'),('c','other','b')]), {'c':2})\ncheck('donor spans conditions', solve([('c',d,'a'),('t',d,'b')]), {'c':1,'t':1})\ncheck('empty experiment', solve([]), {})\ncheck('aliquot names local to donor', solve([('c',d,'a'),('c','other','a')]), {'c':2})\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":"64892847795abeb04cd92adadbb07924f1b0b45cf9a7da00fb67db1955f5fe0d","source":"\"\"\"Failure Map reference implementation. Python standard library only.\"\"\"\nimport json\n\nN = 1\nobservations = []\ndef solve(rows):\n    out={}\n    for condition,donor,aliquot in rows: out[condition]=out.get(condition,0)+1\n    return out\ndef check(label, actual, expected):\n    observations.append({\"check\": label, \"actual\": actual, \"expected\": expected, \"passed\": actual == expected})\nd='donor'+str(N)\ncheck('two aliquots one donor', solve([('c',d,'a'),('c',d,'b')]), {'c':1})\ncheck('repeated assay', solve([('c',d,'a'),('c',d,'a')]), {'c':1})\ncheck('two donors', solve([('c',d,'a'),('c','other','b')]), {'c':2})\ncheck('donor spans conditions', solve([('c',d,'a'),('t',d,'b')]), {'c':1,'t':1})\ncheck('empty experiment', solve([]), {})\ncheck('aliquot names local to donor', solve([('c',d,'a'),('c','other','a')]), {'c':2})\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-biological-replicates","generated_at":"2026-09-29T14:38:52.329402+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":"Measurement records are counted as independent specimens.","sha256":"3291dee57bea8cfaad539178e87a81f8b19740f6444b7bc239674a41fa19b93f","title":"Technical repeats inflate biological replicate counts · 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":40.837,"exit_code":1,"observations":[{"actual":{"c":2},"check":"two aliquots one donor","expected":{"c":1},"passed":false},{"actual":{"c":1},"check":"repeated assay","expected":{"c":1},"passed":true},{"actual":{"c":2},"check":"two donors","expected":{"c":2},"passed":true},{"actual":{"c":1,"t":1},"check":"donor spans conditions","expected":{"c":1,"t":1},"passed":true},{"actual":{},"check":"empty experiment","expected":{},"passed":true},{"actual":{"c":1},"check":"aliquot names local to donor","expected":{"c":2},"passed":false}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"two aliquots one donor\", \"actual\": {\"c\": 2}, \"expected\": {\"c\": 1}, \"passed\": false}, {\"check\": \"repeated assay\", \"actual\": {\"c\": 1}, \"expected\": {\"c\": 1}, \"passed\": true}, {\"check\": \"two donors\", \"actual\": {\"c\": 2}, \"expected\": {\"c\": 2}, \"passed\": true}, {\"check\": \"donor spans conditions\", \"actual\": {\"c\": 1, \"t\": 1}, \"expected\": {\"c\": 1, \"t\": 1}, \"passed\": true}, {\"check\": \"empty experiment\", \"actual\": {}, \"expected\": {}, \"passed\": true}, {\"check\": \"aliquot names local to donor\", \"actual\": {\"c\": 1}, \"expected\": {\"c\": 2}, \"passed\": false}], \"passed\": false}\n"},"broken":{"elapsed_ms":38.661,"exit_code":1,"observations":[{"actual":{"c":2},"check":"two aliquots one donor","expected":{"c":1},"passed":false},{"actual":{"c":2},"check":"repeated assay","expected":{"c":1},"passed":false},{"actual":{"c":2},"check":"two donors","expected":{"c":2},"passed":true},{"actual":{"c":1,"t":1},"check":"donor spans conditions","expected":{"c":1,"t":1},"passed":true},{"actual":{},"check":"empty experiment","expected":{},"passed":true},{"actual":{"c":2},"check":"aliquot names local to donor","expected":{"c":2},"passed":true}],"passed":false,"stderr":"","stdout":"{\"observations\": [{\"check\": \"two aliquots one donor\", \"actual\": {\"c\": 2}, \"expected\": {\"c\": 1}, \"passed\": false}, {\"check\": \"repeated assay\", \"actual\": {\"c\": 2}, \"expected\": {\"c\": 1}, \"passed\": false}, {\"check\": \"two donors\", \"actual\": {\"c\": 2}, \"expected\": {\"c\": 2}, \"passed\": true}, {\"check\": \"donor spans conditions\", \"actual\": {\"c\": 1, \"t\": 1}, \"expected\": {\"c\": 1, \"t\": 1}, \"passed\": true}, {\"check\": \"empty experiment\", \"actual\": {}, \"expected\": {}, \"passed\": true}, {\"check\": \"aliquot names local to donor\", \"actual\": {\"c\": 2}, \"expected\": {\"c\": 2}, \"passed\": true}], \"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."}}