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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: attach the standardized medication name (CMDECOD) to each
collected concomitant medication by joining the coding team's output
to the WHODrug extract.
Input: collected medication verbatims (CMTRT), a coding-team
table carrying the selected WHODrug record and ATC code per
medication, plus a WHODrug extract carrying the preferred name per
record and ATC code.
Variables:
CMDECODwould be the preferred name read from the WHODrug extract matched on the coding team's record and ATC code. The coding-team table is also given a second name that selects, computes, and reshapes nothing, so the run is rejected before any data is read and no artifact is accepted.
How to fix
Drop the alias and read the coding-team table under its own name. Its
record is matched to each row by study, subject, and sequence number, so
also read its sequence number as an integer to compare with CMSEQ:
input:
CM_RAW: input/cm_raw.csv
CODING:
path: input/coding.csv
types: {CMSEQ: int}
WHODRUG: input/whodrug.csv
base: CM_RAW
columns:
- name: CMDECOD
type: str
label: Standardized Medication Name
derivation: WHODRUG_LOOKUP.PREFERRED_NAME
A named intermediate must narrow, derive, or reshape its dataset (LOOKUP-4).
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- validation
- condition
- rename_only_intermediate
- rule
- LOOKUP-4
expected/error.yaml
phase: validation
condition: rename_only_intermediate
spec_paths:
- intermediates.CODED
rule: LOOKUP-4
context:
intermediate: CODED
dataset: CODING
Inputs
Under review3 source filesinput/cm_raw.csv
Edit3 rows| STUDYID | USUBJID | CMSEQ | CMTRT |
|---|---|---|---|
| YAMAA-01 | 1 | IBUPROFEN 200MG TABLET | |
| YAMAA-01 | 2 | PARACETAMOL 500MG CAPSULE | |
| YAMAA-01 | 1 | ASPIRIN 100MG TABLET |
input/coding.csv
Edit3 rows| STUDYID | USUBJID | CMSEQ | DRUG_RECORD_NO | ATC_CODE |
|---|---|---|---|---|
| YAMAA-01 | 1 | 000001 | M01AE01 | |
| YAMAA-01 | 2 | 000002 | N02BE01 | |
| YAMAA-01 | 1 | 000003 | B01AC06 |
input/whodrug.csv
Edit3 rows| DRUG_RECORD_NO | ATC_CODE | PREFERRED_NAME |
|---|---|---|
| 000001 | M01AE01 | Ibuprofen |
| 000002 | N02BE01 | Paracetamol |
| 000003 | B01AC06 | Acetylsalicylic acid |
Unexpected Output
Under reviewNo artifact is producedNo fixture files in this directory.
Human review and assessment
| Variable Name | Variable Label | Type | Length | Controlled Terms or Format | Origin | Core | Conversion Definition | Variable Type | Variable Order | Comments for Define |
|---|---|---|---|---|---|---|---|---|---|---|
| STUDYID | Study Identifier | Char | Collected | Copy value from CM_RAW.STUDYID. | SDTM | 1 | ||||
| USUBJID | Unique Subject Identifier | Char | Collected | Copy value from CM_RAW.USUBJID. | SDTM | 2 | ||||
| CMSEQ | Sequence Number | Num | Collected | Copy value from CM_RAW.CMSEQ. | SDTM | 3 | ||||
| CMTRT | Reported Name of Drug, Med, or Therapy | Char | Collected | Copy value from CM_RAW.CMTRT. | SDTM | 4 | ||||
| CMDECOD | Standardized Medication Name | Char | Derived | Take PREFERRED_NAME from the WHODRUG record whose DRUG_RECORD_NO equals CODING.DRUG_RECORD_NO and ATC_CODE equals CODING.ATC_CODE, and a row with no match is an error. | SDTM | 5 |
| 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 |