Reject a Parameter Decoded Through a Format Name

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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 parameter name (PARAM) of each laboratory result from its parameter code (PARAMCD), as the study's parameter terminology decodes the code.

Input: collected laboratory results with the study and subject identifiers and the test code, which is the parameter code.

Variables:

PARAM would be the name the study's parameter terminology gives the code, such as Alanine Aminotransferase (U/L) for ALT.

Note: the study declares its parameter terminology once, under a name a specification refers to it by. $PARAMCD is the SAS format a reader of the submission applies to the codes, not that name, and no terminology name begins with a dollar sign, so the request is rejected before any record is read and no artifact is accepted.

How to fix

Refer to the terminology by the id the study's project file declares it under, PARAMCD, rather than by its format_name, and build the dataset from that project file, which declares the codes and their decodes once:

yamaa: "1.0"
type: project
codelists:
  - codelists:
      - id: PARAMCD
        name: Parameter Code
        format_name: $PARAMCD
        items:
          - {value: ALT, decode: Alanine Aminotransferase (U/L)}
          - {value: AST, decode: Aspartate Aminotransferase (U/L)}
adam:
  specs: [spec.yaml]

derivation:
  decode:
    source: PARAMCD
    codelist: PARAMCD

Each code then takes the decode its item declares, and a code the terminology does not list stops the run unless an unmapped answer is declared.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: pattern_mismatch
rule: SCHEMA-12

expected/error.yaml

phase: validation
condition: pattern_mismatch
spec_paths:
  - columns.PARAM.derivation.decode.codelist
rule: SCHEMA-12
context:
  value: $PARAMCD
  pattern: '^[A-Za-z_][A-Za-z0-9_]*$'

YAML specification

1 spec file

spec.yaml

Edit39 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [STUDYID, USUBJID, PARAMCD]6input:7  LB: input/lb.csv89output:10  path: adlb.csv11  columns: [STUDYID, USUBJID, PARAMCD, PARAM]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: LB.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: LB.USUBJID2324  - name: PARAMCD25    type: str26    label: Parameter Code27    derivation: LB.LBTESTCD2829  # The defect: $PARAMCD is the format name a parameter codelist carries for30  # a reader, not the id a project file declares the codelist under, and no31  # codelist id begins with a dollar sign, so the spec is rejected before any32  # data is read.33  - name: PARAM34    type: str35    label: Parameter36    derivation:37      decode:38        source: PARAMCD39        codelist: $PARAMCD

Inputs

Under review1 source file

input/lb.csv

Edit3 rows

input/lb.csv
STUDYID	USUBJID	LBTESTCD
YAMAA-01		ALT
YAMAA-01		AST
YAMAA-01		ALT

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	PARAM	Parameter	character	Decode PARAMCD through codelist $PARAMCD; missing values stay missing; unlisted values are errors.	Derived

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