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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: one record for each subject and collected parameter,
carrying the numeric analysis result (AVAL).
Input: collected laboratory results carrying the test code
(LBTESTCD) and the reported character result (LBSTRESC).
Variables:
AVALwould hold the reported number read fromLBSTRESCfor the collected parameter, and is missing when no result is reported. A result reported as a limit (such as<50) instead of a number cannot be read as the limit, as zero, or as missing without a stated rule, so the run fails and no artifact is accepted.
How to fix
Retain the reported text in a string column and state what the numeric analysis
value should be. If a result such as <50 is intentionally represented as a
missing numeric value, handle the failed conversion explicitly:
derivation:
value: LB.LBSTRESC
unconvertible: null
If the study uses a numeric substitution for values below the assay limit, derive that documented value instead and keep the original character result for traceability.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- convert
- condition
- conversion_failed
- rule
- VALUE-3
expected/error.yaml
phase: convert
condition: conversion_failed
spec_paths:
- columns.AVAL
rule: VALUE-3
context:
from: str
to: float
value: "<50"
keys:
- STUDYID: PILOT7
USUBJID: P7-942
PARAMCD: HIVRNA
Inputs
Under review1 source fileinput/lb.csv
Edit2 rows| STUDYID | USUBJID | LBTESTCD | LBSTRESC |
|---|---|---|---|
| PILOT7 | HIVRNA | 12000 | |
| PILOT7 | HIVRNA | <50 |
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 | AVAL | Analysis Value | numeric | Copy value from LB.LBSTRESC. | Predecessor |
| 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 |