yamaa 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 meansREADME.mdGoal: read SITEID out of the subject identifier for each
subject record.
Input: collected demographics with one record for each subject, carrying the subject identifier.
Variables:
SITEIDwould hold the site code, the text betweenCATH-and the four-digit subject number in an identifier matching^CATH-([^-]+)-[0-9]{4}$, and would be blank when the subject identifier is blank or does not fit that form.
The request asks for a second part of that match, but the match sets aside only one, the site code. The request is rejected before any data is read, and no artifact is accepted.
How to fix
Decide which part of the subject identifier names the site, then take the part the rule actually sets aside. Parts are numbered from 1 in the order their opening parentheses appear, so the site here is part 1:
str_extract:
source: USUBJID
pattern: '^CATH-([^-]+)-[0-9]{4}$'
group: 1
missing: null
no_match: null
Setting aside the subject number as well does not move the site: its opening parenthesis still comes first, so the site stays part 1 and the subject number is part 2:
str_extract:
source: USUBJID
pattern: '^CATH-([^-]+)-([0-9]{4})$'
group: 1
missing: null
no_match: null
Keep the blank results for a blank or ill-formed identifier; dropping them would stop the run on such an identifier instead.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- validation
- condition
- regex_group_out_of_range
- requirement
- REQ-0816
expected/error.yaml
phase: validation
condition: regex_group_out_of_range
spec_paths:
- columns.SITEID.derivation.str_extract.group
requirement: REQ-0816
context:
group: 2
group_count: 1
pattern: '^CATH-([^-]+)-[0-9]{4}$'
Inputs
Under review1 source fileinput/dm.csv
Edit2 rows| STUDYID | USUBJID |
|---|---|
| CATH | |
| CATH |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Comments and assessment materials
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | 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 | SITEID | Study Site Identifier | character | Extract capture group 2 matching ^CATH-([^-]+)-[0-9]{4}$ from USUBJID; a missing source → blank; no match → blank. | Derived |
| Version | Date | Author | Description | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 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 |
Comments
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