Call a Project Routine

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 standards: 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: derive an adjusted ratio (RATIO) and its variants by calling the project's own ratio routine, showing how the call fills in defaults, handles missing values, and switches the result to a percentage.

Input: spec.yaml reads a small test file (input/source.csv) carrying a numerator (NUM), a denominator (DEN), and an optional adjustment (ADJ), and calls the ratio routine from the benchmark's own Python project root (python/); the expected result is expected/test.csv.

Variables:

ID: the test record identifier, carried through unchanged.
RATIO: the numerator divided by the denominator, rounded to two places; empty when the numerator or the denominator is blank.
RATIO_DEFAULT: the same value as RATIO: leaving the rounding places out of the call uses the project's own default of two.
RATIO_PCT: the same ratio as a percentage, rounded to one place.
RATIO_ADJ_MISSING: RATIO plus the adjustment; a blank adjustment counts as zero.
RATIO_MISSING: empty on every record: the call passes no numerator at all, so the routine is never invoked.

Note: a blank value the routine does not accept skips the call entirely, so that record has no result; a blank value it accepts arrives as missing and counts as zero.

YAML specification

1 spec file

spec.yaml

Edit97 lines

1schema_version: "1.0"2domain: TEST3keys: [ID]4input:5  SOURCE:6    path: input/source.csv7    types: {NUM: float, DEN: float, ADJ: float}89output:10  path: test.csv11  columns:12    - ID13    - RATIO14    - RATIO_DEFAULT15    - RATIO_PCT16    - RATIO_ADJ_MISSING17    - RATIO_MISSING1819columns:20  - name: ID21    type: str22    label: Identifier23    derivation: SOURCE.ID2425  # The project's own ratio routine with every argument named: the26  # quotient of NUM over DEN, rounded to two places, unadjusted.27  - name: RATIO28    type: float29    label: Adjusted Ratio30    derivation:31      function:32        name: project_ratio33        args:34          numerator: SOURCE.NUM35          denominator: SOURCE.DEN36          decimals: 237          adjust: 0.038          as_percent: false3940  # The same call with the optional decimals left out: the project's41  # default of two places applies, so it matches RATIO on every row.42  - name: RATIO_DEFAULT43    type: float44    label: Adjusted Ratio With Default Decimals45    derivation:46      function:47        name: project_ratio48        args:49          numerator: SOURCE.NUM50          denominator: SOURCE.DEN51          adjust: 0.052          as_percent: false5354  # The percentage form: the quotient scaled by one hundred and rounded55  # to one place.56  - name: RATIO_PCT57    type: float58    label: Adjusted Ratio As Percentage59    derivation:60      function:61        name: project_ratio62        args:63          numerator: SOURCE.NUM64          denominator: SOURCE.DEN65          decimals: 166          adjust: 0.067          as_percent: true6869  # The adjustment is accepted missing: a blank ADJ reaches the routine70  # as missing and counts as zero, so the result matches RATIO there.71  - name: RATIO_ADJ_MISSING72    type: float73    label: Adjusted Ratio With Missing Adjustment74    derivation:75      function:76        name: project_ratio77        args:78          numerator: SOURCE.NUM79          denominator: SOURCE.DEN80          decimals: 281          adjust: SOURCE.ADJ82          as_percent: false8384  # A missing numerator skips the call entirely: the routine is never85  # invoked and the result stays empty on every row.86  - name: RATIO_MISSING87    type: float88    label: Ratio With Missing Numerator89    derivation:90      function:91        name: project_ratio92        args:93          numerator: null94          denominator: SOURCE.DEN95          decimals: 296          adjust: 0.097          as_percent: false

Inputs

Under review1 source file

input/source.csv

Edit7 rows

input/source.csv
ID	NUM	DEN	ADJ
R1	10.0	4.0	—
R2	1.0	3.0	0.5
R3	7.0	2.0	0.25
R4	0.0	5.0	—
R5	9.0	4.0	-0.5
R6	—	4.0	—
R7	10.0	—	—

Expected output

Under review7 expected rows

expected/test.csv

Edit7 rows

expected/test.csv
ID	RATIO	RATIO_DEFAULT	RATIO_PCT	RATIO_ADJ_MISSING	RATIO_MISSING
R1	2.5	2.5	250	2.5	—
R2	0.33	0.33	33.3	0.8300000000000001	—
R3	3.5	3.5	350	3.75	—
R4	0	0	0	0	—
R5	2.25	2.25	225	1.75	—
R6	—	—	—	—	—
R7	—	—	—	—	—

Shaded columns are derived— = missing value

Comments and assessment materials

Variable Name	Variable Label	Type	Origin	Conversion Definition	Variable Type	Variable Order
ID	Identifier	Char	Collected	Copy value from SOURCE.ID.	SDTM	1
RATIO	Adjusted Ratio	Num	Derived	Call project function project_ratio with numerator = SOURCE.NUM, denominator = SOURCE.DEN, decimals = 2, adjust = 0.0 and as_percent = False.	SDTM	2
RATIO_DEFAULT	Adjusted Ratio With Default Decimals	Num	Derived	Call project function project_ratio with numerator = SOURCE.NUM, denominator = SOURCE.DEN, adjust = 0.0 and as_percent = False.	SDTM	3
RATIO_PCT	Adjusted Ratio As Percentage	Num	Derived	Call project function project_ratio with numerator = SOURCE.NUM, denominator = SOURCE.DEN, decimals = 1, adjust = 0.0 and as_percent = True.	SDTM	4
RATIO_ADJ_MISSING	Adjusted Ratio With Missing Adjustment	Num	Derived	Call project function project_ratio with numerator = SOURCE.NUM, denominator = SOURCE.DEN, decimals = 2, adjust = SOURCE.ADJ and as_percent = False.	SDTM	5
RATIO_MISSING	Ratio With Missing Numerator	Num	Derived	Call project function project_ratio with numerator = None, denominator = SOURCE.DEN, decimals = 2, adjust = 0.0 and as_percent = False.	SDTM	6

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)23test <- yamaa_domain("spec.yaml", environment = "r/environment.yaml")$output4test

run.py

Edit4 lines

1import yamaa23test = yamaa.domain("spec.yaml", environment="python/environment.yaml").output4test

input/source.csv

expected/test.csv

Comments

Mapping spec

yamaa code

run.R

run.py