FA-11891 / Scientific pipeline provenance / Open access

Sorting measurements separately reassigns sample values · case 01

Sorting measurements separately reassigns sample values.

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

ROOT CAUSE

Independent ordering is mistaken for a shared sample axis.

VERIFIED REPAIR

Index measurements by unique specimen ID and emit requested order.

Unsuccessful approach: Sorting both lists still emits sorted order instead of the requested axis.

Case contract

For unique measurement IDs, return values in requested ID order, with None 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(axis, rows):
    return [r[1] for r in rows][:len(axis)]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('reversed specimen axis', solve(['b','a'], [('a',N),('b',N+4)]), [N+4,N])
check('missing specimen', solve(['x','a'], [('a',N)]), [None,N])
check('empty axis', solve([], [('a',N)]), [])
check('empty measurements', solve(['a'], []), [None])
check('repeated requested specimen', solve(['a','a'], [('a',N)]), [N,N])
check('irrelevant measurement', solve(['a'], [('z',0),('a',N)]), [N])
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
reversed specimen axis	`[1, 5]`	`[5, 1]`	Failed
missing specimen	`[1]`	`[None, 1]`	Failed
empty axis	`[]`	`[]`	Passed
empty measurements	`[]`	`[None]`	Failed
repeated requested specimen	`[1]`	`[1, 1]`	Failed
irrelevant measurement	`[0]`	`[1]`	Failed

SHA-256 / 4ddae0ec4c508a0b28138912c046857bcce6b35d1f87ab0240f02215eca769f3

2 / The unsuccessful fix

Exit 1

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

N = 1
observations = []
def solve(axis, rows):
    d = dict(rows)
    return [d.get(k) for k in sorted(axis)]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('reversed specimen axis', solve(['b','a'], [('a',N),('b',N+4)]), [N+4,N])
check('missing specimen', solve(['x','a'], [('a',N)]), [None,N])
check('empty axis', solve([], [('a',N)]), [])
check('empty measurements', solve(['a'], []), [None])
check('repeated requested specimen', solve(['a','a'], [('a',N)]), [N,N])
check('irrelevant measurement', solve(['a'], [('z',0),('a',N)]), [N])
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
reversed specimen axis	`[1, 5]`	`[5, 1]`	Failed
missing specimen	`[1, None]`	`[None, 1]`	Failed
empty axis	`[]`	`[]`	Passed
empty measurements	`[None]`	`[None]`	Passed
repeated requested specimen	`[1, 1]`	`[1, 1]`	Passed
irrelevant measurement	`[1]`	`[1]`	Passed

SHA-256 / 5878f63837d2e4ea3bcf3fa8d35c260a62254192d1406fe0f4280af5963c479f

3 / The verified repair

Exit 0

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

N = 1
observations = []
def solve(axis, rows):
    d = dict(rows)
    return [d.get(k) for k in axis]
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
check('reversed specimen axis', solve(['b','a'], [('a',N),('b',N+4)]), [N+4,N])
check('missing specimen', solve(['x','a'], [('a',N)]), [None,N])
check('empty axis', solve([], [('a',N)]), [])
check('empty measurements', solve(['a'], []), [None])
check('repeated requested specimen', solve(['a','a'], [('a',N)]), [N,N])
check('irrelevant measurement', solve(['a'], [('z',0),('a',N)]), [N])
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
reversed specimen axis	`[5, 1]`	`[5, 1]`	Passed
missing specimen	`[None, 1]`	`[None, 1]`	Passed
empty axis	`[]`	`[]`	Passed
empty measurements	`[None]`	`[None]`	Passed
repeated requested specimen	`[1, 1]`	`[1, 1]`	Passed
irrelevant measurement	`[1]`	`[1]`	Passed

SHA-256 / 8fdab310b7a20881f5d12eddddcb53a0a2a567d49d1b91ac40b8edbe01408381

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 2026-09-29T14:38:51.847188+00:00.

Case digest / 6c3ac24bc67d2230c7bdd2a3ec6fa3ab469a5d5e05e2bdade37c4b4125660b70