Reject Unknown Column

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: derive the measurement code (VSTESTCD) and the numeric result in standard units (VSSTRESN) for each collected vital-signs measurement, presented by subject and then by visit number.

Input: each input record is one collected vital-signs measurement carrying the measurement code (VSTESTCD), the numeric result (VSSTRESN), and the visit number (VISITNUM).

Variables:

VSTESTCD would name the measurement (for example SYSBP), taken from the collected code.
VSSTRESN would hold the numeric result in standard units, taken from the collected result.

Note: the requested order rests on the visit number, but no variable of the requested dataset carries it, so a completed record has no value to be ordered by. The run is rejected before any data is read and no artifact is accepted.

How to fix

Decide whether the visit number belongs in the dataset. When the order must rest on it, declare it as a variable and order by that variable; place it in the artifact columns only when the artifact should carry it:

output:
  path: vs.csv
  columns: [STUDYID, USUBJID, VSSEQ, VSTESTCD, VSSTRESN]
  order_by: [USUBJID, VISITNUM]

columns:
  # ... the existing columns, then:
  - name: VISITNUM
    type: float
    label: Visit Number
    derivation: VS_RAW.VISITNUM

An unplanned visit takes a sponsor-assigned decimal number (for example 2.01 after the planned visit it follows), which would fail int conversion, so the declared type is float.

When the visit number is not wanted at all, order by a variable the dataset already declares, such as the sequence number.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: undeclared_column
rule: OUTPUT-12

expected/error.yaml

phase: validation
condition: undeclared_column
spec_paths:
  - output.order_by[1]
rule: OUTPUT-12
context:
  column: VISITNUM

YAML specification

1 spec file

spec.yaml

Edit40 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: VS5keys: [STUDYID, USUBJID, VSSEQ]6input:7  VS_RAW: {path: input/vs.csv, types: {VSSEQ: int, VSSTRESN: float}}89output:10  path: vs.csv11  columns: [STUDYID, USUBJID, VSSEQ, VSTESTCD, VSSTRESN]12  # VISITNUM is an input field, not a declared column, so it cannot13  # order the output rows.14  order_by: [USUBJID, VISITNUM]1516columns:17  - name: STUDYID18    type: str19    label: Study Identifier20    derivation: VS_RAW.STUDYID2122  - name: USUBJID23    type: str24    label: Unique Subject Identifier25    derivation: VS_RAW.USUBJID2627  - name: VSSEQ28    type: int29    label: Sequence Number30    derivation: VS_RAW.VSSEQ3132  - name: VSTESTCD33    type: str34    label: Vital Signs Test Short Name35    derivation: VS_RAW.VSTESTCD3637  - name: VSSTRESN38    type: float39    label: Numeric Result/Finding in Standard Units40    derivation: VS_RAW.VSSTRESN

Inputs

Under review1 source file

input/vs.csv

Edit3 rows

input/vs.csv
STUDYID	VSSEQ	VISITNUM	VSTESTCD	VSSTRESN
CATH	1	1	SYSBP	128
CATH	2	2	SYSBP	132
CATH	1	1	SYSBP	119

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Variable Name	Variable Label	Type	Origin	Conversion Definition	Variable Type	Variable Order
STUDYID	Study Identifier	Char	Collected	Copy value from VS_RAW.STUDYID.	SDTM	1
USUBJID	Unique Subject Identifier	Char	Collected	Copy value from VS_RAW.USUBJID.	SDTM	2
VSSEQ	Sequence Number	Num	Collected	Copy value from VS_RAW.VSSEQ.	SDTM	3
VSTESTCD	Vital Signs Test Short Name	Char	Collected	Copy value from VS_RAW.VSTESTCD.	SDTM	4
VSSTRESN	Numeric Result/Finding in Standard Units	Num	Collected	Copy value from VS_RAW.VSSTRESN.	SDTM	5

Version	Date	Author	Description
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

How to fix

input/vs.csv

Your review

Mapping spec