yamaa 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 meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: build one analysis row for each collected laboratory
result, carrying SEX and AVAL through and adding ANRHI from
a reference table of limits by test and sex.
Input: collected laboratory results carrying the collected
result (LBSTRESN), test code (LBTESTCD), and sex (SEX),
plus the reference table of upper limits by test code and sex.
Variables:
SEXwould contain the subject's sex, carried fromSEXin the laboratory results.AVALwould contain the collected numeric result, carried fromLBSTRESN.ANRHIwould be the upper limit of normal taken from the reference row whose test code matches the collected test code and whose sex matches the subject's sex; missing when no row matches or the sex is missing.
Note: the reference table is absent from the study, so the run is rejected before any data is read and no artifact is accepted.
How to fix
Decide first whether the study should carry reference limits: add the approved table when the limits exist, and state an explicit policy only when the study genuinely has none.
Add the approved limit table to the study under the name it is read by,
input/lbref.csv, with one row per test and sex:
LBTESTCD,SEX,ANRHI
ALT,F,33
ALT,M,41
If a study genuinely has no reference limits for a test, say so explicitly by supplying a result for the unmatched case rather than by leaving the table out. A file that is simply absent cannot be told apart from one that was forgotten.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- validation
- condition
- resource_path_missing
- rule
- FILE-7
expected/error.yaml
phase: validation
condition: resource_path_missing
spec_paths:
- input.LBREF.path
rule: FILE-7
context:
dataset: LBREF
path: input/lbref.csv
Inputs
Under review1 source fileinput/lb.csv
Edit2 rows| STUDYID | USUBJID | LBTESTCD | SEX | LBSTRESN |
|---|---|---|---|---|
| PILOT7 | ALT | F | 42 | |
| PILOT7 | ALT | M | 58 |
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 |
|---|---|---|---|---|---|---|---|
| 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 |