FA-11921 / Scientific pipeline provenance / Open access

Sorting blinded specimen IDs changes treatment assignment · case 01

Sorting blinded specimen IDs changes treatment assignment.

Verified by executionVariant 1 · 6 checks per implementationDownload source bundle ↓JSON ↗

ROOT CAUSE

Treatment is recomputed from specimen position instead of the frozen allocation manifest.

THE FAILURE

Treatment is recomputed from specimen position instead of the frozen allocation manifest.

Unsuccessful approach: Reusing manifest values in insertion order still misaligns reordered specimens.

Case contract

Return treatment labels in requested specimen order using the immutable manifest, with unassigned for missing IDs.

Why this case matters

A deterministic offline model of scientific workflow bookkeeping; the fixtures test provenance contracts without modeling instruments or biological inference.

1 / The failure

Exit 1

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(requested, manifest):
    return ['control' if i%2==0 else 'treated' for i,_ in enumerate(requested)]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
s='blind'+str(N)
check('reordered processing', solve(['b',s], {s:'control','b':'treated'}), ['treated','control'])
check('subset retains assignment', solve(['b'], {s:'control','b':'treated'}), ['treated'])
check('unknown specimen', solve(['x'], {s:'treated'}), ['unassigned'])
check('empty request', solve([], {s:'treated'}), [])
check('empty manifest', solve([s], {}), ['unassigned'])
check('repeat measurement same treatment', solve([s,s], {s:'treated'}), ['treated','treated'])
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
reordered processing	`['control', 'treated']`	`['treated', 'control']`	Failed
subset retains assignment	`['control']`	`['treated']`	Failed
unknown specimen	`['control']`	`['unassigned']`	Failed
empty request	`[]`	`[]`	Passed
empty manifest	`['control']`	`['unassigned']`	Failed
repeat measurement same treatment	`['control', 'treated']`	`['treated', 'treated']`	Failed

SHA-256 / f1faf79da9d42de2f4ea6114fc7608be9b1f299a339d34f37ae9a543949065c2

2 / The unsuccessful fix

Exit 1

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(requested, manifest):
    return (list(manifest.values())+['unassigned']*len(requested))[:len(requested)]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
s='blind'+str(N)
check('reordered processing', solve(['b',s], {s:'control','b':'treated'}), ['treated','control'])
check('subset retains assignment', solve(['b'], {s:'control','b':'treated'}), ['treated'])
check('unknown specimen', solve(['x'], {s:'treated'}), ['unassigned'])
check('empty request', solve([], {s:'treated'}), [])
check('empty manifest', solve([s], {}), ['unassigned'])
check('repeat measurement same treatment', solve([s,s], {s:'treated'}), ['treated','treated'])
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
reordered processing	`['control', 'treated']`	`['treated', 'control']`	Failed
subset retains assignment	`['control']`	`['treated']`	Failed
unknown specimen	`['treated']`	`['unassigned']`	Failed
empty request	`[]`	`[]`	Passed
empty manifest	`['unassigned']`	`['unassigned']`	Passed
repeat measurement same treatment	`['treated', 'unassigned']`	`['treated', 'treated']`	Failed

SHA-256 / ef1a67dcc266bb0c1d720e700e8f9bfd2f1bc286ee932cd8ebecf5311d29d2ee

HELD IN THE MEMBER ARCHIVE

The verified repair and its recorded checks are member-only.

This mechanism has 6 recorded checks per implementation. The open-access tier publishes the failure and the unsuccessful fix; the repaired source that passes every check, and the observations that prove it, are available to members.

Every case sharing this mechanism uses the same contract and the same repair, so this one record is held back for all of them.

Member access is invitation-based. Sign in with your invited account to inspect the repair.

Verification & scope

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.

Observations recorded using Python 3.12.14 at 2026-09-29T14:38:52.228565+00:00.

Case digest / 0c630f7820f20b26bd8737146935e83b89c681bf151a49abcc6fa5375e13f5a4