Show Where Each Column Comes From

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 where each column of the artifact comes from: the artifact carries exactly the columns the specification declares, and every declared column has a stated value, whether it is computed once for all rows or separately by each row template.

Input: one spec.yaml over one lab-results file. Each record carries a subject (USUBJID), a visit (VISIT), a test code (ALT or AST), and a result that arrives as text. The file also carries a sequencing field the specification never declares.

Variables:

PARAM: the test's full name (Alanine Aminotransferase for ALT, Aspartate Aminotransferase for AST), or Lowest Result of Visit on the summary rows.
AVISIT: the visit's display name (WEEK 1 DAY 1, WEEK 2 DAY 8); the summary rows replace it with OVERALL.
AVAL: the result as a number.
DTYPE: empty on the component rows; LOWEST on the summary rows.
FLAG: H when the result is above 60, else N.

Note: the undeclared sequencing field never reaches the artifact, and the working value behind FLAG is checked for completeness but stays out of the artifact.

YAML specification

1 spec file

spec.yaml

Edit113 lines

1schema_version: "1.0"2domain: ADLB3keys: [USUBJID, VISIT, PARAMCD]4input:5  # RAWSEQ rides along in the source file but is never declared:6  # the artifact carries only the columns the specification declares.7  LB: {path: input/lb.csv, types: {VISIT: int, LBSTRESN: str}}8base: LB910output:11  path: adlb.csv12  columns: [STUDYID, USUBJID, VISIT, PARAMCD, PARAM, AVISIT, AVAL, DTYPE, FLAG]1314columns:15  - name: STUDYID16    type: str17    label: Study Identifier18    derivation: {literal: YAMAA-01}1920  - name: USUBJID21    type: str22    label: Unique Subject Identifier23    derivation: LB.USUBJID2425  - name: VISIT26    type: int27    label: Visit Number28    derivation: LB.VISIT2930  # Every row template below derives PARAMCD, PARAM, AVISIT, AVAL,31  # and DTYPE while building its rows; none of them has a32  # column-level derivation.33  - name: PARAMCD34    type: str35    label: Parameter Code3637  - name: PARAM38    type: str39    label: Parameter4041  - name: AVISIT42    type: str43    label: Analysis Visit4445  - name: AVAL46    type: float47    label: Analysis Value4849  # No row carries a derivation type: each template still gives the50  # column a value, an explicit blank, rather than leaving it without51  # one.52  - name: DTYPE53    type: str54    label: Derivation Type5556  # A working value behind FLAG: it feeds another column, it is kept57  # out of the artifact, and its own completeness check still runs.58  - name: HIGH59    type: int60    label: High Result Working Flag61    derivation:62      case:63        - when: "AVAL > 60"64          then: {literal: 1}65        - otherwise: {literal: 0}66    verifications:67      - not_missing: {}6869  - name: FLAG70    type: str71    label: High Value Flag72    derivation:73      case:74        - when: "HIGH = 1"75          then: {literal: H}76        - otherwise: {literal: N}7778rows:79  # One row per record that carries a result.80  - id: components81    filter: "LB.LBSTRESN IS NOT NULL"82    derivations:83      PARAMCD: LB.LBTESTCD84      PARAM:85        case:86          - when: "LB.LBTESTCD = 'ALT'"87            then: {literal: Alanine Aminotransferase}88          - otherwise: {literal: Aspartate Aminotransferase}89      AVISIT:90        case:91          - when: "LB.VISIT = 1"92            then: {literal: WEEK 1 DAY 1}93          - otherwise: {literal: WEEK 2 DAY 8}94      AVAL: LB.LBSTRESN95      DTYPE: {literal: null}9697  # One candidate row per subject-visit. The visit whose results are98  # all missing is discarded after its summary is computed.99  - id: visit_low100    group_by: [LB.USUBJID, LB.VISIT]101    filter: "AVAL IS NOT NULL"102    derivations:103      PARAMCD: {literal: LOW}104      PARAM: {literal: Lowest Result of Visit}105      AVISIT: {literal: OVERALL}106      AVAL:107        aggregate:108          expr: "MIN(LB.LBSTRESN)"109      DTYPE: {literal: LOWEST}110111verifications:112  - unique:113      columns: [USUBJID, VISIT, PARAMCD]

Inputs

Under review1 source file

input/lb.csv

Edit7 rows

input/lb.csv
VISIT	LBTESTCD	LBSTRESN	RAWSEQ
1	ALT	32	r1
1	AST	45	r2
2	ALT	28	r3
2	AST	60	r4
1	ALT	90	r5
1	AST	70	r6
2	ALT	—	r7

Expected output

Under review9 expected rows

expected/adlb.csv

Edit9 rows

expected/adlb.csv
STUDYID	VISIT	PARAMCD	PARAM	AVISIT	AVAL	DTYPE	FLAG
YAMAA-01	1	ALT	Alanine Aminotransferase	WEEK 1 DAY 1	32	—	N
YAMAA-01	1	AST	Aspartate Aminotransferase	WEEK 1 DAY 1	45	—	N
YAMAA-01	2	ALT	Alanine Aminotransferase	WEEK 2 DAY 8	28	—	N
YAMAA-01	2	AST	Aspartate Aminotransferase	WEEK 2 DAY 8	60	—	N
YAMAA-01	1	ALT	Alanine Aminotransferase	WEEK 1 DAY 1	90	—	H
YAMAA-01	1	AST	Aspartate Aminotransferase	WEEK 1 DAY 1	70	—	H
YAMAA-01	1	LOW	Lowest Result of Visit	OVERALL	32	LOWEST	N
YAMAA-01	2	LOW	Lowest Result of Visit	OVERALL	28	LOWEST	N
YAMAA-01	1	LOW	Lowest Result of Visit	OVERALL	70	LOWEST	H

Shaded columns are derived— = missing value

Comments and assessment materials

Dataset Name	Variable Name	Variable Label	Type	Computational Method	Origin
ADLB	STUDYID	Study Identifier	character	Set constant value "YAMAA-01".	Assigned
ADLB	USUBJID	Unique Subject Identifier	character	Copy value from LB.USUBJID.	Predecessor
ADLB	VISIT	Visit Number	numeric	Copy value from LB.VISIT.	Predecessor
ADLB	PARAMCD	Parameter Code	character	Set per constructed row; see the Row construction sheet.	Derived
ADLB	PARAM	Parameter	character	Set per constructed row; see the Row construction sheet.	Derived
ADLB	AVISIT	Analysis Visit	character	Set per constructed row; see the Row construction sheet.	Derived
ADLB	AVAL	Analysis Value	numeric	Set per constructed row; see the Row construction sheet.	Derived
ADLB	DTYPE	Derivation Type	character	Set per constructed row; see the Row construction sheet.	Derived
ADLB	FLAG	High Value Flag	character	If HIGH = 1 then "H"; otherwise "N".	Derived

Template	Include when	PARAMCD	PARAM	AVISIT	AVAL	DTYPE
components	LB.LBSTRESN IS NOT NULL	Copy LB.LBTESTCD	If LB.LBTESTCD = 'ALT' then "Alanine Aminotransferase"; otherwise "Aspartate Aminotransferase"	If LB.VISIT = 1 then "WEEK 1 DAY 1"; otherwise "WEEK 2 DAY 8"	Copy LB.LBSTRESN	Constant "None"
visit_low	AVAL IS NOT NULL	Constant "LOW"	Constant "Lowest Result of Visit"	Constant "OVERALL"	Aggregate MIN(LB.LBSTRESN) over records matching on the shared output keys	Constant "LOWEST"

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.yaml")$output4adlb

run.py

Edit4 lines

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

input/lb.csv

expected/adlb.csv

Comments

Mapping spec

yamaa code

run.R

run.py