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 analysis records for laboratory tests carrying
SEX, AVAL, and ANRHI, with the upper limit chosen for each
test and sex.
Input: collected laboratory results carrying the collected
result (LBSTRESN), test code (LBTESTCD), and sex (SEX),
plus a reference table of upper limits by test code and sex.
Variables:
SEXwould hold the sex the limit is chosen by, copied from the collected record.AVALwould hold the collected result, copied fromLBSTRESN.ANRHIwould hold the upper limit of normal for that test and sex, taken from the reference table for the matching test code andSEX; missing when no row matches or the sex is missing.
Note: the name the study reads for the reference table,
input/lbref.csv, is a symbolic link: a stand-in that points at
another file. Where it points can be changed without changing the
study, so the limits that were reviewed and the limits that are
read need not be the same. The run is rejected before any data is
read and no artifact is accepted.
How to fix
Read the limits under the name that holds them:
input:
LBREF: input/reference/lbref.csv
Storing the file itself where the study reads it works equally well. Either way one name reaches one file, and reviewing the study is reviewing what it reads.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- validation
- condition
- resource_path_symlink
- rule
- FILE-8
expected/error.yaml
phase: validation
condition: resource_path_symlink
spec_paths:
- input.LBREF.path
rule: FILE-8
context:
dataset: LBREF
path: input/lbref.csv
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 |