Row Templates

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: build output rows from input records and groups with the three row-template shapes: record-driven templates with input filters, a case split across several templates, and a grouped template whose own filter decides each candidate row.

Input: one spec.yaml over LB, which carries one record per lab test per visit: subject, visit number, test code, and result, with the tests interleaved in the file. A result may be missing.

Templates:

alt makes one ALT row per ALT record that has a result, writing the result as the analysis value (AVAL) and leaving DTYPE blank. Its filter reads the input record, so a record with a missing result is dropped before any row is built.
ast does the same for AST. Every ALT row comes before every AST row even though the input interleaves the tests: templates are sections of the output and concatenate in specification order.
visit_total builds one candidate TOTAL row per subject and visit, in the order each pair first appears in the input, with AVAL the sum of that visit's results, skipping missing ones. Its filter reads the finished candidate and keeps it only when the total exceeds 100, with DTYPE set to CALCULATION. A visit whose results are all missing sums to missing, which is neither above 100 nor not, so its candidate is dropped too.

Shared columns: the study identifier, subject, and visit number are the same for every template, so they are stated once at column level. The subject and visit read the input record on the record-driven templates and the group keys on the grouped template.

YAML specification

1 spec file

spec.yaml

Edit87 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [USUBJID, VISIT, PARAMCD]6input:7  LB: {path: input/lb.csv, types: {LBSTRESN: float}}8base: LB910output:11  path: adlb.csv12  columns: [STUDYID, USUBJID, VISIT, PARAMCD, PARAM, AVAL, DTYPE]1314columns:15  # Uniform derivations shared by every row template live at column16  # level. USUBJID and VISIT are group keys of the grouped template, so17  # the qualified source reads resolve from the group; on the18  # record-driven templates they read the retained input record.19  - name: STUDYID20    type: str21    label: Study Identifier22    derivation: "'YAMAA-01'"2324  - name: USUBJID25    type: str26    label: Unique Subject Identifier27    derivation: LB.USUBJID2829  - name: VISIT30    type: int31    label: Visit Number32    derivation: LB.VISIT3334  - name: PARAMCD35    type: str36    label: Parameter Code3738  - name: PARAM39    type: str40    label: Parameter4142  - name: AVAL43    type: float44    label: Analysis Value4546  - name: DTYPE47    type: str48    label: Derivation Type4950rows:51  # Case split, first section: every collected ALT record becomes one52  # row. The filter reads the input record before any row derivation,53  # so a record with a missing result is dropped here, never derived.54  - id: alt55    filter: "LB.LBTESTCD = 'ALT' AND LB.LBSTRESN IS NOT NULL"56    derivations:57      PARAMCD: "'ALT'"58      PARAM: "'Alanine Aminotransferase'"59      AVAL: LB.LBSTRESN60      DTYPE: null6162  # Case split, second section: the AST records follow all ALT rows in63  # the output, even though the input interleaves the two tests. Row64  # templates concatenate in specification order.65  - id: ast66    filter: "LB.LBTESTCD = 'AST' AND LB.LBSTRESN IS NOT NULL"67    derivations:68      PARAMCD: "'AST'"69      PARAM: "'Aspartate Aminotransferase'"70      AVAL: LB.LBSTRESN71      DTYPE: null7273  # Grouped template: one candidate row per subject-visit in first74  # appearance order, totaling every test of the visit (SUM skips missing75  # results). The filter reads the completed candidate's unqualified76  # columns after the group reduction: a total failing the comparison is77  # FALSE and suppressed, while a visit whose results are all missing78  # reduces to missing, which is UNKNOWN and suppressed.79  - id: visit_total80    group_by: [LB.USUBJID, LB.VISIT]81    filter: "AVAL > 100"82    derivations:83      PARAMCD: "'TOTAL'"84      PARAM: "'Total of Components'"85      AVAL:86        aggregate: "SUM(LB.LBSTRESN)"87      DTYPE: "'CALCULATION'"

Inputs

Under review1 source file

input/lb.csv

Edit9 rows

input/lb.csv
VISIT	LBTESTCD	LBSTRESN
1	ALT	40
1	AST	30
2	ALT	50
2	AST	45
1	ALT	60
1	AST	55
2	ALT	—
2	AST	—
1	ALT	30

Expected output

Under review8 expected rows

expected/adlb.csv

Edit8 rows

expected/adlb.csv
STUDYID	VISIT	PARAMCD	PARAM	AVAL	DTYPE
YAMAA-01	1	ALT	Alanine Aminotransferase	40	—
YAMAA-01	2	ALT	Alanine Aminotransferase	50	—
YAMAA-01	1	ALT	Alanine Aminotransferase	60	—
YAMAA-01	1	ALT	Alanine Aminotransferase	30	—
YAMAA-01	1	AST	Aspartate Aminotransferase	30	—
YAMAA-01	2	AST	Aspartate Aminotransferase	45	—
YAMAA-01	1	AST	Aspartate Aminotransferase	55	—
YAMAA-01	1	TOTAL	Total of Components	115	CALCULATION

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	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

Template	Include when	PARAMCD	PARAM	AVAL	DTYPE
alt	LB.LBTESTCD = 'ALT' AND LB.LBSTRESN IS NOT NULL	Constant "ALT"	Constant "Alanine Aminotransferase"	Copy LB.LBSTRESN	Constant "None"
ast	LB.LBTESTCD = 'AST' AND LB.LBSTRESN IS NOT NULL	Constant "AST"	Constant "Aspartate Aminotransferase"	Copy LB.LBSTRESN	Constant "None"
visit_total	AVAL > 100	Constant "TOTAL"	Constant "Total of Components"	Aggregate SUM(LB.LBSTRESN) over records matching on the shared output keys	Constant "CALCULATION"

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