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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: build one record per subject and treatment carrying
DOSECUM, the total dose administered across the matching
exposure records.
Input: a subject-treatment inventory carrying EXTRT, plus
component exposure records carrying EXTRT, EXSEQ, and
EXDOSE, where the dose is declared numeric.
Variables:
DOSECUMwould be the total ofEXDOSEacross the matching exposure records for the same subject and treatment, and missing when no matching record carries a dose.
A stored dose that is not a plain number, such as 200 mg with
its unit attached, is rejected while the exposure records are
read, so no artifact is accepted.
How to fix
Normalize the source into separate value and unit fields before declaring the
dose numeric. For this record, the corrected input should carry EXDOSE as
200 and EXDOSU as mg; then the existing declaration is valid:
EX:
path: input/ex.csv
types:
EXDOSE: float
If the composite text must remain unchanged, ingest it as text, preserve it for traceability, and derive a validated numeric dose before attempting the aggregate. A numeric type declaration must not strip the unit implicitly.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- ingest
- condition
- field_parse_failed
- rule
- INPUT-7
expected/error.yaml
phase: ingest
condition: field_parse_failed
spec_paths:
- input.EX.types.EXDOSE
rule: INPUT-7
context:
dataset: EX
field: EXDOSE
type: float
value: "200 mg"
Inputs
Under review2 source filesinput/ex.csv
Edit5 rows| STUDYID | USUBJID | EXTRT | EXSEQ | EXDOSE |
|---|---|---|---|---|
| YAMAA-01 | Carboplatin | 1 | 100 | |
| YAMAA-01 | Carboplatin | 2 | 200 mg | |
| YAMAA-01 | Carboplatin | 3 | — | |
| YAMAA-01 | Paclitaxel | 1 | 150 | |
| YAMAA-01 | Paclitaxel | 2 | 175 |
input/subject_treatment.csv
Edit3 rows| STUDYID | USUBJID | EXTRT |
|---|---|---|
| YAMAA-01 | Carboplatin | |
| YAMAA-01 | Paclitaxel | |
| YAMAA-01 | Cisplatin |
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 |
|---|---|---|---|---|---|---|---|
| ADEX | STUDYID | Study Identifier | character | Copy value from TRT.STUDYID. | Predecessor | ||
| ADEX | USUBJID | Unique Subject Identifier | character | Copy value from TRT.USUBJID. | Predecessor | ||
| ADEX | EXTRT | Name of Treatment | character | Copy value from TRT.EXTRT. | Predecessor | ||
| ADEX | DOSECUM | Cumulative Dose | numeric | Aggregate SUM(EX.EXDOSE) over records matching on the shared output keys. | 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 |