Review ask

As a clinical trial statistician or programmer, answer two short questions in Your review: the task and the inputs and outputs. 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

Lifecycle: finalizedEditUnder review
What this benchmark means
README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

Goal: show how a study spec inherits through its compound level from its organization level: shared levels carry the common mapping once, and the study level wins on final wording.

Dataset: adlb.csv, ADLB analysis dataset. One record per subject per laboratory parameter.

Input: three spec files, read root-first:

  • spec_organization.yaml maps the laboratory test code, result, and unit into PARAMCD, AVAL, and AVALU;
  • spec_compound.yaml adds field types and retitles the AVAL result;
  • spec_study.yaml is the entry: it names the compound level as its parent, restates the AVALU unit wording, and declares the complete output.

Each level names the one level above it, so the chain reads organization, then compound, then study, and a later level wins where two levels state the same detail.

Inputs

Under review
1 source file

input/lb.csv

Edit
2 rows
input/lb.csv
USUBJIDLBTESTCDLBSTRESNLBSTRESU
ALT12.5U/L
ALT21.0U/L

Expected output

Under review
2 expected rows

expected/adlb.csv

Edit
2 rows
expected/adlb.csv
USUBJIDPARAMCDAVALAVALU
ALT12.5U/L
ALT21U/L
Shaded columns are derived— = missing value

Human review and assessment

Your review

2 questions and your comments · View benchmark discussions

Mapping spec

Generated from the benchmark YAML; do not edit by hand

Dataset NameVariable NameVariable LabelTypeCodelist/Controlled TermsCoreComputational MethodOrigin
ADLBAVALAnalysis ValueNo derivation in this specification; inherited from its parent.Derived
ADLBAVALUStandardized Analysis UnitNo derivation in this specification; inherited from its parent.Derived
VersionDateAuthorDescriptionReviewerSign-off
1.72026-10-20yamaa docs buildRead 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
1.62026-10-17yamaa docs buildDescribe collected date parts written as ISO 8601 date text and times of day counted in seconds since midnight
1.52026-10-17yamaa docs buildName 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
1.42026-10-15yamaa docs buildState datetime precision codes through the hour and minute, and complete only the time parts a collected datetime lacks
1.32026-09-29yamaa docs buildShow study codelist names, external dictionaries, and ISO 8601 formats in variable rows; list the document's codelist values and metadata
1.22026-09-29yamaa docs buildClassify ADaM copies from a declared input as Predecessor and recodes as Derived, and SDTM recodes of locally derived columns as Derived
1.12026-09-29yamaa docs buildResolve lookups into the donor record they select, and give every derivation shape a plain-language rule instead of its raw YAML
1.0yamaa docs buildInitial generation from spec.yaml

yamaa code

Public calls generated from benchmark.yaml; results must match the expected output

R

Edit
3 lines
library(yamaa)yamaa_spec("spec_study.yaml")$run()$output

Python

Edit
3 lines
import yamaayamaa.spec("spec_study.yaml").run().output