Reject Strata Mismatch

Review ask

As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.

Task: Is this a specification error a study team could realistically make, and should the build stop on it rather than continue?
Inputs: Do they trigger the failure for the reason the summary gives?
Expected failure: Is this the right error, raised at the right point, and would it tell the programmer what to fix?

The other tabs beside Comments are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: build STRAT1R from the values recorded at randomization and STRAT1 from the matching values collected independently at entry, and require the two combined values to agree.

Input: demographics entries, disease-history entries, and the strata recorded at randomization, linked by the study and subject identifiers shared across the three files.

Variables:

METSTATR: metastatic disease status recorded at randomization, copied from input METSTAT in the randomization file.
ECOG0R: baseline performance status on the Eastern Cooperative Oncology Group (ECOG) scale recorded at randomization, copied from input ECOG0 in the randomization file.
REGIONUSR: region recorded at randomization, copied from input REGIONUS in the randomization file.
METSTAT: metastatic disease status from the disease-history entries, copied from input METSTAT there.
ECOG0: baseline ECOG performance status from the demographics entries, copied from input ECOG0 there.
REGIONUS: region from the demographics entries, copied from input REGIONUS there.
STRAT1R: combined randomization strata, joining METSTATR, ECOG0R, and REGIONUSR with |.
STRAT1: combined independently collected strata, joining METSTAT, ECOG0, and REGIONUS with | in the same order.

The two combined values must agree for every subject; a single disagreement rejects the run, and no artifact is accepted.

Note: the expected file records the completed rows as presented to the check; the disagreement still rejects the run.

How to fix

Query the disagreement and correct whichever source is wrong. If both values are valid but serve different purposes, document which one governs the analysis and replace the equality check with that reconciliation policy. Do not silently prefer the randomization value or the independently collected value.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: verification
condition: assert_failed
requirement: REQ-0384

expected/error.yaml

phase: verification
condition: assert_failed
spec_paths:
  - verifications[1].assert
requirement: REQ-0384
context:
  verification_id: randomized-strata-agree
  failure_count: 1
  keys:
    - STUDYID: PILOT7
      USUBJID: P7-103

YAML specification

1 spec file

spec.yaml

Edit82 lines

1schema_version: "1.0"2domain: ADSL3keys: [STUDYID, USUBJID]4input:5  DM: input/dm.csv6  MH: input/mh.csv7  RE: input/re.csv8base: DM910output:11  path: adsl.csv12  columns: [STUDYID, USUBJID, METSTATR, ECOG0R, REGIONUSR, METSTAT, ECOG0,13            REGIONUS, STRAT1R, STRAT1]1415columns:16  - name: STUDYID17    type: str18    label: Study Identifier19    derivation: DM.STUDYID2021  - name: USUBJID22    type: str23    label: Unique Subject Identifier24    derivation: DM.USUBJID2526  # The strata as recorded at randomization, from the subject's RE record27  # (matched on the study and subject identifiers).28  - name: METSTATR29    type: str30    label: Randomization Metastatic Disease Status31    derivation: RE.METSTAT3233  - name: ECOG0R34    type: str35    label: Randomization Baseline ECOG Performance Status36    derivation: RE.ECOG03738  - name: REGIONUSR39    type: str40    label: Randomization United States Region41    derivation: RE.REGIONUS4243  # The same strata collected independently: metastatic status from the44  # subject's MH record, performance status and region from DM.45  - name: METSTAT46    type: str47    label: Metastatic Disease Status48    derivation: MH.METSTAT4950  - name: ECOG051    type: str52    label: Baseline ECOG Performance Status53    derivation: DM.ECOG05455  - name: REGIONUS56    type: str57    label: United States Region58    derivation: DM.REGIONUS5960  # Both combined values join their three factors in the same order, so61  # the two can be compared directly.62  - name: STRAT1R63    type: str64    label: Randomization Stratification Factor 165    derivation:66      str_template: "{METSTATR}|{ECOG0R}|{REGIONUSR}"6768  - name: STRAT169    type: str70    label: Analysis Stratification Factor 171    derivation:72      str_template: "{METSTAT}|{ECOG0}|{REGIONUS}"7374verifications:75  - row_count:76      min: 377      max: 378  # The check this benchmark exists to fail: a subject whose randomization79  # strata disagree with the independently collected ones rejects the run.80  - assert:81      id: randomized-strata-agree82      require: "STRAT1R = STRAT1"

Inputs

Under review3 source files

input/dm.csv

Edit3 rows

input/dm.csv
STUDYID	ECOG0	REGIONUS
PILOT7	Y	US
PILOT7	N	NON-US
PILOT7	Y	US

input/mh.csv

Edit3 rows

input/mh.csv
STUDYID	USUBJID	METSTAT
PILOT7		M0
PILOT7		M1 NED
PILOT7		M0

input/re.csv

Edit3 rows

input/re.csv
STUDYID	METSTAT	ECOG0	REGIONUS
PILOT7	M0	Y	US
PILOT7	M1 NED	N	NON-US
PILOT7	M1 NED	Y	US

Unexpected Output

Under review3 rows presented to the failing check - not an accepted artifact

expected/adsl.csv

Edit3 rows

expected/adsl.csv
STUDYID	METSTATR	ECOG0R	REGIONUSR	METSTAT	ECOG0	REGIONUS	STRAT1R	STRAT1
PILOT7	M0	Y	US	M0	Y	US	M0\|Y\|US	M0\|Y\|US
PILOT7	M1 NED	N	NON-US	M1 NED	N	NON-US	M1 NED\|N\|NON-US	M1 NED\|N\|NON-US
PILOT7	M1 NED	Y	US	M0	Y	US	M1 NED\|Y\|US	M0\|Y\|US

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADSL	STUDYID	Study Identifier	character	Copy value from DM.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character	Copy value from DM.USUBJID.	Predecessor
ADSL	METSTATR	Randomization Metastatic Disease Status	character	Copy value from RE.METSTAT.	Predecessor
ADSL	ECOG0R	Randomization Baseline ECOG Performance Status	character	Copy value from RE.ECOG0.	Predecessor
ADSL	REGIONUSR	Randomization United States Region	character	Copy value from RE.REGIONUS.	Predecessor
ADSL	METSTAT	Metastatic Disease Status	character	Copy value from MH.METSTAT.	Predecessor
ADSL	ECOG0	Baseline ECOG Performance Status	character	Copy value from DM.ECOG0.	Predecessor
ADSL	REGIONUS	United States Region	character	Copy value from DM.REGIONUS.	Predecessor
ADSL	STRAT1R	Randomization Stratification Factor 1	character	Fill the template "{METSTATR}\|{ECOG0R}\|{REGIONUSR}".	Derived
ADSL	STRAT1	Analysis Stratification Factor 1	character	Fill the template "{METSTAT}\|{ECOG0}\|{REGIONUS}".	Derived

Version	Date	Author	Description
1.3	2026-09-29	yamaa docs build	Show study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.2	2026-09-29	yamaa docs build	Classify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.1	2026-09-29	yamaa docs build	Resolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0		yamaa docs build	Initial generation from spec.yaml

How to fix

input/dm.csv

input/mh.csv

input/re.csv

expected/adsl.csv

Comments

Mapping spec