Reject a Missing Output Key

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: carry an analysis date (ADT), study day (ADY), and measured value (AVAL) into analysis visits (AVISIT).

Input: pre-derived vital signs records, one per measurement, with a study day that can be missing.

Variables:

AVISIT would be SCREENING before day 0, BASELINE on days 0 and 1, WEEK 2 on days 2 to 21, WEEK 4 on days 22 to 42, and POST-TREATMENT from day 43. It is blank when the study day is missing.

Note: analysis visit is part of each record's identity. A record with no study day has no analysis visit, so the completed dataset fails its identity check and no artifact is accepted.

How to fix

Decide whether the record belongs in an analysis visit. If a governed source supplies the missing study day, correct that source. Otherwise, exclude the record before constructing the output rows:

rows:
  - id: windowed
    filter: "ADVS_RAW.ADY IS NOT NULL"
    derivations: {}

If the dataset must retain measurements without a visit, identify rows by the collected record instead, for example with VSSEQ in keys.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: output
condition: missing_key
requirement: REQ-0240

expected/error.yaml

phase: output
condition: missing_key
spec_paths:
  - keys[3]
requirement: REQ-0240
context:
  column: AVISIT
  missing_count: 1
  keys:
    - STUDYID: CATH
      USUBJID: CATH-UCSD-0002
      PARAMCD: SYSBP
      AVISIT: null

YAML specification

1 spec file

spec.yaml

Edit59 lines

1schema_version: "1.0"2domain: ADVS3keys: [STUDYID, USUBJID, PARAMCD, AVISIT]4input:5  ADVS_RAW: {path: input/advs_raw.csv, types: {ADY: int, ADT: date}}67output:8  path: advs.csv9  columns: [STUDYID, USUBJID, PARAMCD, VSSEQ, ADT, ADY, AVAL, AVISIT]1011columns:12  - name: STUDYID13    type: str14    label: Study Identifier15    derivation: ADVS_RAW.STUDYID1617  - name: USUBJID18    type: str19    label: Unique Subject Identifier20    derivation: ADVS_RAW.USUBJID2122  - name: PARAMCD23    type: str24    label: Parameter Code25    derivation: ADVS_RAW.PARAMCD2627  - name: VSSEQ28    type: int29    label: Sequence Number30    derivation: ADVS_RAW.VSSEQ3132  - name: ADT33    type: date34    label: Analysis Date35    derivation: ADVS_RAW.ADT3637  - name: ADY38    type: int39    label: Analysis Relative Day40    derivation: ADVS_RAW.ADY4142  - name: AVAL43    type: float44    label: Analysis Value45    derivation: ADVS_RAW.AVAL4647  # Reading the input's typed ADY directly avoids the key dependency error.48  # The last record has no ADY, so its AVISIT is missing when the completed49  # dataset reaches the output key check.50  - name: AVISIT51    type: str52    label: Analysis Visit53    derivation:54      cut:55        source: ADVS_RAW.ADY56        breaks: [0, 2, 22, 43]57        labels: [SCREENING, BASELINE, WEEK 2, WEEK 4, POST-TREATMENT]58        right: false59        missing: null

Inputs

Under review1 source file

input/advs_raw.csv

Edit6 rows

input/advs_raw.csv
STUDYID	PARAMCD	VSSEQ	ADT	ADY	AVAL
CATH	SYSBP	1	2025-01-08	1	132
CATH	SYSBP	2	2025-01-22	15	138
CATH	SYSBP	3	2025-02-05	29	130
CATH	SYSBP	1	2025-02-08	1	118
CATH	SYSBP	2	2025-02-21	14	122
CATH	SYSBP	3	—	—	120

Unexpected Output

Under review6 rows presented to the failing check - not an accepted artifact

expected/advs.csv

Edit6 rows

expected/advs.csv
STUDYID	PARAMCD	VSSEQ	ADT	ADY	AVAL	AVISIT
CATH	SYSBP	1	2025-01-08	1	132	BASELINE
CATH	SYSBP	2	2025-01-22	15	138	WEEK 2
CATH	SYSBP	3	2025-02-05	29	130	WEEK 4
CATH	SYSBP	1	2025-02-08	1	118	BASELINE
CATH	SYSBP	2	2025-02-21	14	122	WEEK 2
CATH	SYSBP	3	—	—	120	—

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Computational Method	Origin
ADVS	STUDYID	Study Identifier	character		Copy value from ADVS_RAW.STUDYID.	Predecessor
ADVS	USUBJID	Unique Subject Identifier	character		Copy value from ADVS_RAW.USUBJID.	Predecessor
ADVS	PARAMCD	Parameter Code	character		Copy value from ADVS_RAW.PARAMCD.	Predecessor
ADVS	VSSEQ	Sequence Number	numeric		Copy value from ADVS_RAW.VSSEQ.	Predecessor
ADVS	ADT	Analysis Date	numeric	ISO 8601	Copy value from ADVS_RAW.ADT.	Predecessor
ADVS	ADY	Analysis Relative Day	numeric		Copy value from ADVS_RAW.ADY.	Predecessor
ADVS	AVAL	Analysis Value	numeric		Copy value from ADVS_RAW.AVAL.	Predecessor
ADVS	AVISIT	Analysis Visit	character		Band ADVS_RAW.ADY at 0, 2, 22, 43 into "SCREENING", "BASELINE", "WEEK 2", "WEEK 4" and "POST-TREATMENT", intervals closed on the left; a missing source → blank.	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/advs_raw.csv

expected/advs.csv

Comments

Mapping spec