Reject Unreadable Pattern

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: record SEX for each subject, accepting only M, F, and U.

Input: collected demographics carrying subject sex (SEX).

Variables:

SEX would be the subject's sex, copied from the collected records, holding M, F, or U.

Note: the text pattern the codes are checked against names a group in a spelling ((?P<code>...)) that only some pattern readers accept, so the run is rejected before any data is read and no artifact is accepted.

How to fix

Decide which codes the study collects, then write the check in the one notation every reader uses. A named group is spelled (?<name>...) rather than (?P<name>...), and a check that must describe the whole value anchors itself:

- matches:
    pattern: '^[MFU]$'

When the permitted set is small and fixed, list it instead. The list needs no text rule at all and cannot drift from the codes it names:

- allowed_values:
    values: [M, F, U]

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: invalid_regex
requirement: REQ-0827

expected/error.yaml

phase: validation
condition: invalid_regex
spec_paths:
  - columns.SEX.verifications[0].matches.pattern
requirement: REQ-0827
context:
  pattern: '(?P<code>[MFU])'

YAML specification

1 spec file

spec.yaml

Edit31 lines

1schema_version: "1.0"2domain: ADSL3keys: [STUDYID, USUBJID]4input:5  DM: input/dm.csv67output:8  path: adsl.csv9  columns: [STUDYID, USUBJID, SEX]1011columns:12  - name: STUDYID13    type: str14    label: Study Identifier15    derivation: DM.STUDYID1617  - name: USUBJID18    type: str19    label: Unique Subject Identifier20    derivation: DM.USUBJID2122  - name: SEX23    type: str24    label: Sex25    derivation: DM.SEX26    verifications:27      - matches:28          # (?P<name>...) is a Python-only named group; the portable29          # spelling is (?<name>...), so this pattern is rejected before30          # any data is read.31          pattern: '(?P<code>[MFU])'

Inputs

Under review1 source file

input/dm.csv

Edit2 rows

input/dm.csv
STUDYID	USUBJID	SEX
CATH		M
CATH		F

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

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	SEX	Sex	character	Copy value from DM.SEX.	Predecessor

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

Comments

Mapping spec