Column Composition

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: demonstrate a study level changing details inside inherited columns - AVAL, ANRIND, and PARCAT1.

Input: three spec files, read root-first:

spec_organization.yaml turns the laboratory test code, result, and reference range indicator into PARAMCD, AVAL, ANRIND, and PARCAT1, reading the indicator without regard to letter case; it marks AVAL as the analysis value and checks that it is not negative;
spec_compound.yaml adds the low reference range wording the organization does not list, and notes that AVAL comes from the central laboratory;
spec_study.yaml is the entry: it applies one corrected result, marks AVAL as adjudicated and checks that it is never missing, leaves an unrecognized indicator empty, states PARCAT1 as the one category this study collects, 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.

Note: a later level composes a column detail by detail. The added reference range wording joins the two the organization already lists, the three annotations on AVAL accumulate, and the case-insensitive reading survives a level that never mentions it. A level naming a different way to produce a value replaces it whole instead, which is why PARCAT1 stops reading the test code. Lists never accumulate: the study's own check on AVAL replaces the organization's.

YAML specification

4 spec files

spec_organization.yaml
Edit60 lines
1schema_version: "1.0"2input:3  LB:4    path: input/lb.csv5    types:6      USUBJID: str7      LBTESTCD: str8      LBSTRESN: float9      LBNRIND: str10base: LB1112columns:13  - name: USUBJID14    type: str15    label: Unique Subject Identifier16    derivation: LB.USUBJID1718  - name: PARAMCD19    type: str20    label: Parameter Code21    derivation: LB.LBTESTCD2223  # The compound and study levels each add a metadata entry; the study24  # level also replaces the derivation and the whole verification list.25  - name: AVAL26    type: float27    label: Analysis Value28    derivation: LB.LBSTRESN29    verifications:30      - range:31          min: 032    metadata:33      analysis_role: analysis-value3435  # Later levels add an entry to dict and the mapping handlers; source and36  # case_sensitive are inherited from here unchanged.37  - name: ANRIND38    type: str39    label: Analysis Reference Range Indicator40    derivation:41      mapping:42        source: LB.LBNRIND43        dict:44          N: NORMAL45          H: HIGH46        case_sensitive: false4748  # The study level replaces this mapping with a literal.49  - name: PARCAT150    type: str51    label: Parameter Category52    derivation:53      mapping:54        source: LB.LBTESTCD55        dict:56          ALT: HEPATIC57          AST: HEPATIC5859metadata:60  scope: organization
spec_compound.yaml
Edit19 lines
1schema_version: "1.0"2parents: spec_organization.yaml34columns:5  # Merged into the organization's AVAL: this entry joins analysis_role.6  - name: AVAL7    metadata:8      source_system: central-laboratory910  # Merged into the organization's mapping: L joins N and H, and the11  # source and case_sensitive setting carry over.12  - name: ANRIND13    derivation:14      mapping:15        dict:16          L: LOW1718metadata:19  scope: compound
spec_study.yaml
Edit38 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, ANRIND, PARCAT1]910columns:11  # A case is a different operation from the inherited plain source, so it12  # replaces it whole. The verification list replaces the organization's13  # range check (lists never merge); the metadata entry joins the other two.14  - name: AVAL15    derivation:16      case:17        - when: "USUBJID = '01' AND PARAMCD = 'AST'"18          then: {literal: 31.0}19        - otherwise: LB.LBSTRESN20    verifications:21      - not_missing: {}22    metadata:23      review_status: adjudicated2425  # Adds only the handlers to the inherited mapping: an absent indicator26  # and one with no dict entry (such as x) both come out missing.27  - name: ANRIND28    derivation:29      mapping:30        missing: null31        unmapped: null3233  # A literal replaces the inherited mapping whole.34  - name: PARCAT135    derivation: {literal: CHEMISTRY}3637metadata:38  scope: study
spec_resolved.yaml
Edit76 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      LBNRIND: str14base: LB15output:16  path: adlb.csv17  columns:18    - USUBJID19    - PARAMCD20    - AVAL21    - ANRIND22    - PARCAT123columns:24  - name: USUBJID25    type: str26    label: Unique Subject Identifier27    derivation:28      value:29        source:30          variable: LB.USUBJID31  - name: PARAMCD32    type: str33    label: Parameter Code34    derivation:35      value:36        source:37          variable: LB.LBTESTCD38  - name: AVAL39    type: float40    label: Analysis Value41    derivation:42      value:43        case:44          - when: USUBJID = '01' AND PARAMCD = 'AST'45            then: {literal: 31.0}46          - otherwise:47              source:48                variable: LB.LBSTRESN49    verifications:50      - not_missing:51          severity: error52    metadata:53      analysis_role: analysis-value54      source_system: central-laboratory55      review_status: adjudicated56  - name: ANRIND57    type: str58    label: Analysis Reference Range Indicator59    derivation:60      value:61        mapping:62          source: LB.LBNRIND63          dict:64            N: NORMAL65            H: HIGH66            L: LOW67          case_sensitive: false68          missing: null69          unmapped: null70  - name: PARCAT171    type: str72    label: Parameter Category73    derivation:74      value: {literal: CHEMISTRY}75metadata:76  scope: study

Inputs

Under review1 source file

input/lb.csv

Edit4 rows

input/lb.csv
LBTESTCD	LBSTRESN	LBSTRESU	LBNRIND
ALT	12.5	U/L	n
AST	-1.0	U/L	h
ALT	21.0	U/L	l
AST	30.0	U/L	x

Expected output

Under review4 expected rows

expected/adlb.csv

Edit4 rows

expected/adlb.csv
PARAMCD	AVAL	ANRIND	PARCAT1
ALT	12.5	NORMAL	CHEMISTRY
AST	31	HIGH	CHEMISTRY
ALT	21	LOW	CHEMISTRY
AST	30	—	CHEMISTRY

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Computational Method	Origin
ADLB	AVAL	If USUBJID = '01' AND PARAMCD = 'AST' then "31.0"; otherwise "LB.LBSTRESN".	Derived
ADLB	ANRIND	Recode None: ; missing or unlisted values stay missing.	Derived
ADLB	PARCAT1	Set constant value "CHEMISTRY".	Assigned

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