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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: carry sex and the numeric result into the output and
choose the upper limit of normal (ANRHI) from a reference table
by test and sex.
Input: collected laboratory records carrying test code
(LBTESTCD), sex (SEX), and numeric result (LBSTRESN), plus a
reference table carrying test code, sex, and upper limit
(ANRHI).
Variables:
ANRHIwould be the upper limit of normal for that test and sex, taken from the reference table row matching the collected test code and sex.
Note: a result whose test and sex match more than one line of the reference table has no single line to take its limit from. Taking either line, or the first the file happens to list, would make the result depend on file order rather than on the study's reference ranges, so the run is rejected with no artifact accepted, even when the lines agree.
How to fix
Make the lookup table unique on [LBTESTCD, SEX] by resolving the
conflicting ALT/F reference limits under the study's governed
reference-range rules. A lookup cannot choose one duplicate by file order.
If both rows are valid for different conditions, such as different assay methods, carry that condition on both the collected records and the table, and add it to the key, pairing the table column with the collected value. A collected field that is not an output column is named with its dataset prefix:
intermediates:
- id: LBREF_LOOKUP
dataset: LBREF
key: {LBTESTCD: PARAMCD, SEX: SEX, METHOD: LB.METHOD}
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- join
- condition
- multiple_matches
- rule
- LOOKUP-10
expected/error.yaml
phase: join
condition: multiple_matches
spec_paths:
- intermediates.LBREF_LOOKUP
rule: LOOKUP-10
context:
intermediate: LBREF_LOOKUP
dataset: LBREF
key:
- LBTESTCD
- SEX
intermediate_key:
LBTESTCD: ALT
SEX: F
match_count: 2
keys:
- STUDYID: PILOT7
USUBJID: P7-831
PARAMCD: ALT
Inputs
Under review2 source filesUnexpected 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 |
|---|---|---|---|---|---|---|---|
| ADLB | STUDYID | Study Identifier | character | Copy value from LB.STUDYID. | Predecessor | ||
| ADLB | USUBJID | Unique Subject Identifier | character | Copy value from LB.USUBJID. | Predecessor | ||
| ADLB | PARAMCD | Parameter Code | character | Copy value from LB.LBTESTCD. | Predecessor | ||
| ADLB | SEX | Sex | character | Copy value from LB.SEX. | Predecessor | ||
| ADLB | AVAL | Analysis Value | numeric | Copy value from LB.LBSTRESN. | Predecessor | ||
| ADLB | ANRHI | Analysis Normal Range Upper Limit | numeric | Take ANRHI from the LBREF record whose LBTESTCD equals PARAMCD and SEX equals SEX, and a row with no match is an error. | 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 |