Reject a Visit Name Read From Text Codes by a Visit Number

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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 analysis visit (AVISIT) of each laboratory result from its visit number (AVISITN), as the study's visit terminology names the visit.

Input: collected laboratory results with the study and subject identifiers, the test code and the visit number.

Variables:

AVISITN is the analysis visit number, the collected visit number.
AVISIT would be the name the study's visit terminology gives the visit number, such as Week 2 for 2.

Note: the visit terminology writes its codes as text, while the visit number is a number, and a number never equals text, so no visit could be named. The request is rejected before any record is read and no artifact is accepted.

How to fix

Declare the visit codes as the integers they are, in the project file's codelist:

- id: VISIT
  name: Analysis Visit
  data_type: integer
  items:
    - {value: 1, decode: Baseline}
    - {value: 2, decode: Week 2}

Keep text codes only when the visit is identified by text, and then read it from a text column.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: incompatible_input_type
rule: EXPR-15

expected/error.yaml

phase: validation
condition: incompatible_input_type
spec_paths:
  - columns.AVISIT.derivation.decode.source
rule: EXPR-15
context:
  source: AVISITN
  expected: str
  actual: int

YAML specification

1 spec file

spec.yaml

Edit45 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [STUDYID, USUBJID, PARAMCD, AVISITN]6input:7  LB:8    path: input/lb.csv9    types: {VISITNUM: int}1011output:12  path: adlb.csv13  columns: [STUDYID, USUBJID, PARAMCD, AVISITN, AVISIT]1415columns:16  - name: STUDYID17    type: str18    label: Study Identifier19    derivation: LB.STUDYID2021  - name: USUBJID22    type: str23    label: Unique Subject Identifier24    derivation: LB.USUBJID2526  - name: PARAMCD27    type: str28    label: Parameter Code29    derivation: LB.LBTESTCD3031  - name: AVISITN32    type: int33    label: Analysis Visit (N)34    derivation: LB.VISITNUM3536  # The defect: the visit codelist's codes are text, while the visit number37  # is an integer, so no visit number could ever equal a code and the spec38  # is rejected before any data is read.39  - name: AVISIT40    type: str41    label: Analysis Visit42    derivation:43      decode:44        source: AVISITN45        codelist: VISIT

Inputs

Under review1 source file

input/lb.csv

Edit2 rows

input/lb.csv
STUDYID	USUBJID	LBTESTCD	VISITNUM
YAMAA-01		ALT	1
YAMAA-01		ALT	2

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADLB	STUDYID	Study Identifier	character	Copy value from LB.STUDYID.	Predecessor
ADLB	USUBJID	Unique Subject Identifier	character	Copy value from LB.USUBJID.	Predecessor
ADLB	PARAMCD	Parameter Code	character	Copy value from LB.LBTESTCD.	Predecessor
ADLB	AVISITN	Analysis Visit (N)	numeric	Copy value from LB.VISITNUM.	Predecessor
ADLB	AVISIT	Analysis Visit	character	Decode AVISITN through codelist VISIT; missing values stay missing; unlisted values are errors.	Derived

Codelist ID	Name	Value	Decode	Codelist NCI alias	Value NCI alias	Extensible	Extended value	SAS format	Dictionary	Version
VISIT	Analysis Visit	1	Baseline			No
VISIT	Analysis Visit	2	Week 2			No

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/lb.csv

Your review

Mapping spec