Reject Uncaptured Group

Review ask

As a clinical trial statistician or programmer, answer two short questions in Your review: the task and the inputs. Agreeing with both approves this benchmark; disagreeing with either needs a comment. Propose a fix with the Edit button on any source file, or add it to your comments.

We suggest spending no more than 5 minutes on a review. The other tabs beside Your review are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

Goal: 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:

SITEID would hold the site code, the text between CATH- 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
  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
  no_match: null

Keep the blank result for an ill-formed identifier; dropping no_match: null would stop the run on such an identifier instead. A blank identifier gives a blank site either way.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: regex_group_out_of_range
rule: TEXT-10

expected/error.yaml

phase: validation
condition: regex_group_out_of_range
spec_paths:
  - columns.SITEID.derivation.str_extract.group
rule: TEXT-10
context:
  group: 2
  group_count: 1
  pattern: '^CATH-([^-]+)-[0-9]{4}$'

YAML specification

1 spec file

spec.yaml

Edit34 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  DM: input/dm.csv89output:10  path: adsl.csv11  columns: [STUDYID, USUBJID, SITEID]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: DM.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: DM.USUBJID2324  # The defect: the pattern sets aside one part (the site code), so there25  # is no part 2 to return and the spec is rejected before any data is read.26  - name: SITEID27    type: str28    label: Study Site Identifier29    derivation:30      str_extract:31        source: USUBJID32        pattern: '^CATH-([^-]+)-[0-9]{4}$'33        group: 234        no_match: null

Inputs

Under review1 source file

input/dm.csv

Edit2 rows

input/dm.csv
STUDYID	USUBJID
CATH
CATH

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

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	SITEID	Study Site Identifier	character	Extract capture group 2 matching ^CATH-([^-]+)-[0-9]{4}$ from USUBJID; no match → blank.	Derived

Version	Date	Author	Description
1.7	2026-10-20	yamaa docs build	Read a specification in the 1.0 surface as its 0.5 counterpart; state that missing values stay missing where a mapping declares no missing handler, and leave out a declared missing answer that restates a handler's default
1.6	2026-10-17	yamaa docs build	Describe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.5	2026-10-17	yamaa docs build	Name collected precision in words instead of letter codes; state imputation fallbacks, minimum source precision, bounds ignored outside the collected period, and invalid text with no handler as an error; describe date and datetime shifts, imputation flag codes, and partial text giving no date part
1.4	2026-10-15	yamaa docs build	State datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
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

Your review

Mapping spec