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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: take each subject's site number (SITEID) from the collected site
description.
Input: collected demographics whose SITE text gives the site number
and the city, such as Site 701 - Copenhagen; one subject's site was
entered by its name alone.
Variables:
SITEIDwould be the three-digit site number taken fromSITE.
Karolinska Stockholm holds no site number, and nothing in the study says
which number that site has, so the subject's site cannot be told. Leaving
the site empty would lose a collected fact. The run is rejected, and no
artifact is accepted.
How to fix
Correct the entry at the source so that it gives the site number:
STUDYID,USUBJID,SITE
CTX,CTX-73,Site 703 - Stockholm
If some sites are known only by name, state how the study numbers them, for example by looking each name up in a list of sites, rather than leaving their site empty.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- mapping
- condition
- unmatched_pattern
- rule
- COLUMN-10
expected/error.yaml
phase: mapping
condition: unmatched_pattern
spec_paths:
- columns.SITEID.derivation.str_extract
rule: COLUMN-10
context:
value: Karolinska Stockholm
pattern: 'Site ([0-9]{3})'
Inputs
Under review1 source fileinput/dm.csv
Edit3 rows| STUDYID | USUBJID | SITE |
|---|---|---|
| CTX | Site 701 - Copenhagen | |
| CTX | Site 702 - Lund | |
| CTX | Karolinska Stockholm |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Human review and assessment
| 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 1 matching Site ([0-9]{3}) from DM.SITE. | Derived |
| Version | Date | Author | Description | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 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 |