Reject Non-Numeric Sum

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.

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

The other tabs beside Comments are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: build one analysis record per collected adverse event, carrying ASEV and adding SEVTOT.

Input: collected adverse events with the severity word recorded in AESEV.

Variables:

ASEV would contain the severity word reported for the event, carried unchanged from the collected severity.
SEVTOT would be the subject's total severity burden, totalling the severity across all of their reported events and repeated on each of their event records.

Note: severity is recorded as words, and words have no total. Ordering the words and totalling their positions would be a real rule, but it is a different one, and the request never states the numbers it would use. The run is rejected before any data is read, so no artifact is accepted.

How to fix

Declare the study's numeric severity scale first, then total that numeric column:

- name: ASEVN
  type: int
  derivation:
    mapping:
      source: ASEV
      dict:
        MILD: 1
        MODERATE: 2
        SEVERE: 3

- name: SEVTOT
  type: int
  derivation:
    aggregate:
      group_by: [STUDYID, USUBJID]
      expr: "SUM(ASEVN)"

Keep the intermediate numeric column out of the artifact by leaving it off the artifact column list. The numeric assignments are analysis policy and must be confirmed rather than inferred from the order of the words.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: incompatible_input_type
requirement: REQ-0510

expected/error.yaml

phase: validation
condition: incompatible_input_type
spec_paths:
  - columns.SEVTOT.derivation.aggregate.expr
requirement: REQ-0510
context:
  source: ASEV
  expected: numeric
  actual: str

YAML specification

1 spec file

spec.yaml

Edit41 lines

1schema_version: "1.0"2domain: ADAE3keys: [STUDYID, USUBJID, AESEQ]4input:5  AE: input/ae.csv67output:8  path: adae.csv9  columns: [STUDYID, USUBJID, AESEQ, ASEV, SEVTOT]1011columns:12  - name: STUDYID13    type: str14    label: Study Identifier15    derivation: AE.STUDYID1617  - name: USUBJID18    type: str19    label: Unique Subject Identifier20    derivation: AE.USUBJID2122  - name: AESEQ23    type: int24    label: Sequence Number25    derivation: AE.AESEQ2627  - name: ASEV28    type: str29    label: Analysis Severity/Intensity30    derivation: AE.AESEV3132  # One total per subject, repeated on each of their event rows. ASEV33  # holds severity words (MILD, SEVERE), and SUM needs numbers, so the34  # run is rejected before any data is read.35  - name: SEVTOT36    type: float37    label: Total Severity Score38    derivation:39      aggregate:40        group_by: [STUDYID, USUBJID]41        expr: "SUM(ASEV)"

Inputs

Under review1 source file

input/ae.csv

Edit2 rows

input/ae.csv
STUDYID	USUBJID	AESEQ	AETERM	AESEV
PILOT7		1	Nausea	MILD
PILOT7		2	Fatigue	SEVERE

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADAE	STUDYID	Study Identifier	character	Copy value from AE.STUDYID.	Predecessor
ADAE	USUBJID	Unique Subject Identifier	character	Copy value from AE.USUBJID.	Predecessor
ADAE	AESEQ	Sequence Number	numeric	Copy value from AE.AESEQ.	Predecessor
ADAE	ASEV	Analysis Severity/Intensity	character	Copy value from AE.AESEV.	Predecessor
ADAE	SEVTOT	Total Severity Score	numeric	Aggregate SUM(ASEV) over records grouped by STUDYID, USUBJID, matching on the shared output keys.	Derived

Version	Date	Author	Description
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

How to fix

input/ae.csv

Comments

Mapping spec