Show Where Each Column Comes From

Review ask

As a clinical trial statistician or programmer, answer two short questions in Your review: the task and the inputs and outputs. Agreeing with both approves this benchmark; disagreeing with either needs a comment. Propose a fix with the Edit button on any source file, or add it to your comments.

We suggest spending no more than 5 minutes on a review. The other tabs beside Your review are background for assessment, not under review.

Summary

EditUnder reviewWhat this benchmark means

README.md

Public entries: Python and R. Passing coverage requires an installed inventory.

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

Edit110 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [USUBJID, VISIT, PARAMCD]6input:7  # RAWSEQ rides along in the source file but is never declared:8  # the artifact carries only the columns the specification declares.9  LB: {path: input/lb.csv, types: {VISIT: int, LBSTRESN: str}}10base: LB1112output:13  path: adlb.csv14  columns: [STUDYID, USUBJID, VISIT, PARAMCD, PARAM, AVISIT, AVAL, DTYPE, FLAG]1516columns:17  - name: STUDYID18    type: str19    label: Study Identifier20    derivation: "'YAMAA-01'"2122  - name: USUBJID23    type: str24    label: Unique Subject Identifier25    derivation: LB.USUBJID2627  - name: VISIT28    type: int29    label: Visit Number30    derivation: LB.VISIT3132  # Every row template below derives PARAMCD, PARAM, AVISIT, AVAL,33  # and DTYPE while building its rows; none of them has a34  # column-level derivation.35  - name: PARAMCD36    type: str37    label: Parameter Code3839  - name: PARAM40    type: str41    label: Parameter4243  - name: AVISIT44    type: str45    label: Analysis Visit4647  - name: AVAL48    type: float49    label: Analysis Value5051  # No row carries a derivation type: each template still gives the52  # column a value, an explicit blank, rather than leaving it without53  # one.54  - name: DTYPE55    type: str56    label: Derivation Type5758  # A working value behind FLAG: it feeds another column, it is kept59  # out of the artifact, and its own completeness check still runs.60  - name: HIGH61    type: int62    label: High Result Working Flag63    derivation:64      case:65        - when: "AVAL > 60"66          then: 167        - otherwise: 068    verifications:69      - not_missing7071  - name: FLAG72    type: str73    label: High Value Flag74    derivation:75      case:76        - when: "HIGH = 1"77          then: "'H'"78        - otherwise: "'N'"7980rows:81  # One row per record that carries a result.82  - id: components83    filter: "LB.LBSTRESN IS NOT NULL"84    derivations:85      PARAMCD: LB.LBTESTCD86      PARAM:87        case:88          - when: "LB.LBTESTCD = 'ALT'"89            then: "'Alanine Aminotransferase'"90          - otherwise: "'Aspartate Aminotransferase'"91      AVISIT:92        case:93          - when: "LB.VISIT = 1"94            then: "'WEEK 1 DAY 1'"95          - otherwise: "'WEEK 2 DAY 8'"96      AVAL: LB.LBSTRESN97      DTYPE: null9899  # One candidate row per subject-visit. The visit whose results are100  # all missing is discarded after its summary is computed.101  - id: visit_low102    group_by: [LB.USUBJID, LB.VISIT]103    filter: "AVAL IS NOT NULL"104    derivations:105      PARAMCD: "'LOW'"106      PARAM: "'Lowest Result of Visit'"107      AVISIT: "'OVERALL'"108      AVAL:109        aggregate: "MIN(LB.LBSTRESN)"110      DTYPE: "'LOWEST'"

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

Human review and assessment

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
1.7	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

R

Edit3 lines

1library(yamaa)23yamaa_spec("spec.yaml")$run()$output

Python

Edit3 lines

1import yamaa23yamaa.spec("spec.yaml").run().output

input/lb.csv

expected/adlb.csv

Your review

Mapping spec

yamaa code

R

Python