Review ask

As a clinical trial statistician or programmer, challenge anything in this benchmark: describe a problem in Comments, or propose a fix with the Edit button on any source file.

  1. Task: Is this a specification error a study team could realistically make, and should the build stop on it rather than continue?
  2. Inputs: Do they trigger the failure for the reason the summary gives?
  3. Expected failure: Is this the right error, raised at the right point, and would it tell the programmer what to fix?

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Summary

Lifecycle: reviewedEditUnder review
What this benchmark means
README.md

Goal: fill SEVAL, the severity recorded at the visit, from the collected severity when present, otherwise from SEVAL itself, defaulting to 0 when neither gives a value.

Input: vital-sign records carrying study, subject, and sequence entries plus the collected severity (SEVAL), which is missing when no severity was recorded.

Variables:

  • SEVAL: the collected severity when one was recorded at the visit, otherwise the value of SEVAL itself, otherwise 0. Because SEVAL reads its own value, there is no earlier value to carry and the definition loops back on itself, so the run is rejected before any data is read and no artifact is accepted.

How to fix

Carry forward from the collected source instead of the column being derived. Search the subject's earlier collected values in a separate column, and fall back to it, then to 0, only when the current record has no severity:

- name: SEVPREV
  type: int
  derivation:
    previous_non_missing:
      source: VS.SEVAL
      window:
        group_by: [STUDYID, USUBJID]
        order_by: [VSSEQ]

- name: SEVAL
  type: int
  derivation:
    first_available:
      sources: [VS.SEVAL, SEVPREV]
      missing: 0

Keep SEVPREV internal by omitting it from output.columns. A subject whose first record has no severity gets 0 there, because no earlier value exists.

Expected failure

Edit
the run is rejected; no artifact is accepted
expected/error.yaml
phase
validation
condition
dependency_cycle
requirement
REQ-0072
expected/error.yaml
phase: validation
condition: dependency_cycle
spec_paths:
  - columns.SEVAL.derivation.first_available
requirement: REQ-0072
context:
  cycle: [SEVAL, SEVAL]

Inputs

Under review
1 source file

input/vs.csv

Edit
2 rows
input/vs.csv
STUDYIDUSUBJIDVSSEQSEVAL
YAMAA-011—
YAMAA-0122

Unexpected Output

Under review
No artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Comments and assessment materials

Comments

Signed in with GitHub; saved in repository Discussions

Mapping spec

Generated from the benchmark YAML; do not edit by hand

Dataset NameVariable NameVariable LabelTypeCodelist/Controlled TermsCoreComputational MethodOrigin
ADVSSTUDYIDStudy IdentifiercharacterCopy value from VS.STUDYID.Predecessor
ADVSUSUBJIDUnique Subject IdentifiercharacterCopy value from VS.USUBJID.Predecessor
ADVSVSSEQSequence NumbernumericCopy value from VS.VSSEQ.Predecessor
ADVSSEVALSeverity ValuenumericFirst non-missing of VS.SEVAL and SEVAL; all missing → "0".Derived
VersionDateAuthorDescriptionReviewerSign-off
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