Spec Inheritance

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: Would a real study need this derivation, specified this way? Does it follow CDISC ADaM: variable names, controlled terms, record structure? Flag any rule that is ambiguous or that a sponsor would handle differently.
Inputs: Do they look like data collected in a real trial, and do they include the situations you would expect to meet in one?
Expected output: Would independent QC programming reproduce every value from these inputs and rules?

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

Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: show how a study spec inherits from its organization and compound parents: shared levels carry the common mapping once, and the deepest study level wins on final wording.

Dataset: adlb.csv, ADLB analysis dataset. One record per subject per laboratory parameter.

Input: three spec files, read root-first:

spec_organization.yaml maps the laboratory test code, result, and unit into PARAMCD, AVAL, and AVALU;
spec_compound.yaml adds field types and retitles the AVAL result;
spec_study.yaml is the entry: it names both levels as parents, restates the AVALU unit wording, and declares the complete output.

Parents resolve depth-first, left to right, with later levels winning; the chain resolves to expected/spec_resolved.yaml, the default view in the specification dropdown.

YAML specification

4 spec files

spec_organization.yaml
Edit46 lines
1schema_version: "1.0"2input:3  LB: input/lb.csv4  UNUSED: input/not-used.csv5base: LB67intermediates:8  - id: unused_reference9    dataset: UNUSED10    key:11      - USUBJID1213columns:14  - name: USUBJID15    type: str16    label: Unique Subject Identifier17    derivation: LB.USUBJID1819  - name: PARAMCD20    type: str21    label: Parameter Code22    derivation: LB.LBTESTCD2324  - name: AVAL25    type: float26    label: Standardized Numeric Result27    derivation: LB.LBSTRESN28    metadata:29      analysis_role: analysis-value3031  - name: AVALU32    type: str33    label: Analysis Value Unit34    derivation: LB.LBSTRESU3536  - name: TEMP37    type: str38    label: Unused Intermediate Value39    derivation: {literal: unused}4041verifications:42  unique:43    columns: [USUBJID, PARAMCD]4445metadata:46  scope: organization
spec_compound.yaml
Edit16 lines
1schema_version: "1.0"2parents: spec_organization.yaml3input:4  LB:5    types:6      USUBJID: str7      LBTESTCD: str8      LBSTRESN: float9      LBSTRESU: str1011columns:12  - name: AVAL13    label: Compound Standardized Result1415metadata:16  scope: compound
spec_study.yaml
Edit18 lines
1schema_version: "1.0"2parents: [spec_organization.yaml, spec_compound.yaml]3domain: ADLB4keys: [USUBJID, PARAMCD]56output:7  path: adlb.csv8  columns: [USUBJID, PARAMCD, AVAL, AVALU]910columns:11  - name: AVAL12    label: Analysis Value1314  - name: AVALU15    label: Standardized Analysis Unit1617metadata:18  scope: study
spec_resolved.yaml
Edit60 lines
1schema_version: "1.0"2domain: ADLB3keys:4  - USUBJID5  - PARAMCD6input:7  LB:8    path: input/lb.csv9    types:10      USUBJID: str11      LBTESTCD: str12      LBSTRESN: float13      LBSTRESU: str14base: LB15output:16  path: adlb.csv17  columns:18    - USUBJID19    - PARAMCD20    - AVAL21    - AVALU22columns:23  - name: USUBJID24    type: str25    label: Unique Subject Identifier26    derivation:27      value:28        source:29          variable: LB.USUBJID30  - name: PARAMCD31    type: str32    label: Parameter Code33    derivation:34      value:35        source:36          variable: LB.LBTESTCD37  - name: AVAL38    type: float39    label: Analysis Value40    derivation:41      value:42        source:43          variable: LB.LBSTRESN44    metadata:45      analysis_role: analysis-value46  - name: AVALU47    type: str48    label: Standardized Analysis Unit49    derivation:50      value:51        source:52          variable: LB.LBSTRESU53verifications:54  - unique:55      columns:56        - USUBJID57        - PARAMCD58      severity: error59metadata:60  scope: study

Inputs

Under review1 source file

input/lb.csv

Edit2 rows

input/lb.csv
USUBJID	LBTESTCD	LBSTRESN	LBSTRESU
	ALT	12.5	U/L
	ALT	21.0	U/L

Expected output

Under review2 expected rows

expected/adlb.csv

Edit2 rows

expected/adlb.csv
USUBJID	PARAMCD	AVAL	AVALU
	ALT	12.5	U/L
	ALT	21	U/L

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Core	Computational Method	Origin
ADLB	AVAL	Analysis Value				No derivation in this specification; inherited from its parent.	Derived
ADLB	AVALU	Standardized Analysis Unit				No derivation in this specification; inherited from its parent.	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

run.R

Edit4 lines

1library(yamaa)23adlb <- yamaa_domain("spec_study.yaml")$output4adlb

run.py

Edit4 lines

1import yamaa23adlb = yamaa.yamaa_domain("spec_study.yaml").output4adlb

input/lb.csv

expected/adlb.csv

Comments

Mapping spec

yamaa code

run.R

run.py