Reject Duplicate WBC

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: Is this a specification error a study team could realistically make, and should the build stop on it rather than continue?
Inputs: Do they trigger the failure for the reason the summary gives?
Expected failure: Is this the right error, raised at the right point, and would it tell the programmer what to fix?

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Summary

EditUnder reviewWhat this benchmark means

README.md

Goal: add an absolute lymphocyte (LYMPH) record carrying AVAL and DTYPE.

Input: collected laboratory records carrying the collected result in AVAL, identified by subject, visit, and parameter code, including white blood cell (WBC) counts and lymphocyte fractions (LYMLE).

Variables:

AVAL: the collected result on collected records. On the new LYMPH record it is the WBC count multiplied by the LYMLE fraction from the same subject and visit; that record is added only when both values are present and no LYMPH result was collected at the visit.
DTYPE: CALCULATION on the new LYMPH record, empty on collected records.

Note: each contributing parameter may occur at most once within a subject and visit. A repeated WBC or LYMLE result leaves no single value to multiply, so the run stops with no artifact rather than choosing one record by amount or position or adding both values.

How to fix

Resolve the duplicate WBC records according to the study's data conventions before calculating the absolute differential. The run then sees one WBC record per subject and visit, for example:

STUDYID,USUBJID,PARAMCD,AVAL,PARAM,VISIT
YAMAA-01,YAMAA-01-101,WBC,34,Leukocyte Count (10^9/L),CYCLE 1 DAY 1
YAMAA-01,YAMAA-01-101,LYMLE,0.90,Lymphocytes (fraction of 1),CYCLE 1 DAY 1

Do not replace ONLY with MIN, MAX, or file-order selection unless that choice is a documented clinical rule; those alternatives answer a different question.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: row_construction
condition: aggregate_multiple_records
requirement: REQ-0501

expected/error.yaml

phase: row_construction
condition: aggregate_multiple_records
spec_paths:
  - rows[1].derivations.WBCVAL.aggregate
requirement: REQ-0501
context:
  expr: ONLY(ADLB_RAW.AVAL)
  reducer: ONLY
  row: derived_lymph
  group:
    STUDYID: YAMAA-01
    USUBJID: YAMAA-01-101
    VISIT: CYCLE 1 DAY 1
  record_count: 2

YAML specification

1 spec file

spec.yaml

Edit100 lines

1schema_version: "1.0"2domain: ADLB3keys: [STUDYID, USUBJID, VISIT, PARAMCD]4input:5  ADLB_RAW: {path: input/adlb.csv, types: {AVAL: float}}67output:8  path: adlb.csv9  columns: [STUDYID, USUBJID, PARAMCD, AVAL, PARAM, VISIT, DTYPE]1011columns:12  - name: STUDYID13    type: str14    label: Study Identifier15    derivation: ADLB_RAW.STUDYID1617  - name: USUBJID18    type: str19    label: Unique Subject Identifier20    derivation: ADLB_RAW.USUBJID2122  - name: VISIT23    type: str24    label: Visit Name25    derivation: ADLB_RAW.VISIT2627  - name: PARAMCD28    type: str29    label: Parameter Code3031  - name: PARAM32    type: str33    label: Parameter3435  - name: WBCVAL36    type: float37    label: White Blood Cell Count3839  - name: LYMLEVAL40    type: float41    label: Lymphocyte Fraction4243  - name: EXISTING_ABS_COUNT44    type: int45    label: Existing Absolute Lymphocyte Record Count4647  - name: AVAL48    type: float49    label: Analysis Value5051  - name: DTYPE52    type: str53    label: Derivation Type5455rows:56  - id: collected57    derivations:58      PARAMCD: ADLB_RAW.PARAMCD59      PARAM: ADLB_RAW.PARAM60      WBCVAL: {literal: null}61      LYMLEVAL: {literal: null}62      EXISTING_ABS_COUNT: {literal: null}63      AVAL: ADLB_RAW.AVAL64      DTYPE: {literal: null}6566  # One new LYMPH record per subject and visit, kept only when both a WBC67  # count and a LYMLE fraction are present and no LYMPH record was collected.68  - id: derived_lymph69    group_by: [ADLB_RAW.STUDYID, ADLB_RAW.USUBJID, ADLB_RAW.VISIT]70    filter: >-71      WBCVAL IS NOT NULL72      AND LYMLEVAL IS NOT NULL73      AND EXISTING_ABS_COUNT IS NULL74    derivations:75      PARAMCD: {literal: LYMPH}76      PARAM: {literal: Lymphocytes Abs (10^9/L)}77      # ONLY takes the one WBC (or LYMLE) result at the visit; a second78      # record stops the run instead of one being picked.79      WBCVAL:80        aggregate:81          filter: "ADLB_RAW.PARAMCD = 'WBC'"82          expr: "ONLY(ADLB_RAW.AVAL)"83      LYMLEVAL:84        aggregate:85          filter: "ADLB_RAW.PARAMCD = 'LYMLE'"86          expr: "ONLY(ADLB_RAW.AVAL)"87      # A count over no records is missing rather than 0, so the filter's88      # EXISTING_ABS_COUNT IS NULL means no LYMPH record was collected.89      EXISTING_ABS_COUNT:90        aggregate:91          filter: "ADLB_RAW.PARAMCD = 'LYMPH'"92          expr: "COUNT(ADLB_RAW.*)"93      AVAL:94        compute:95          expr: "WBCVAL * LYMLEVAL"96      DTYPE: {literal: CALCULATION}9798verifications:99  - unique:100      columns: [USUBJID, VISIT, PARAMCD]

Inputs

Under review1 source file

input/adlb.csv

Edit3 rows

input/adlb.csv
STUDYID	PARAMCD	AVAL	PARAM	VISIT
YAMAA-01	WBC	33	Leukocyte Count (10^9/L)	CYCLE 1 DAY 1
YAMAA-01	WBC	34	Leukocyte Count (10^9/L)	CYCLE 1 DAY 1
YAMAA-01	LYMLE	0.90	Lymphocytes (fraction of 1)	CYCLE 1 DAY 1

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

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	Copy value from ADLB_RAW.STUDYID.	Predecessor
ADLB	USUBJID	Unique Subject Identifier	character	Copy value from ADLB_RAW.USUBJID.	Predecessor
ADLB	VISIT	Visit Name	character	Copy value from ADLB_RAW.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	WBCVAL	LYMLEVAL	EXISTING_ABS_COUNT	AVAL	DTYPE
collected		Copy ADLB_RAW.PARAMCD	Copy ADLB_RAW.PARAM	Constant "None"	Constant "None"	Constant "None"	Copy ADLB_RAW.AVAL	Constant "None"
derived_lymph	WBCVAL IS NOT NULL AND LYMLEVAL IS NOT NULL AND EXISTING_ABS_COUNT IS NULL	Constant "LYMPH"	Constant "Lymphocytes Abs (10^9/L)"	Aggregate ONLY(ADLB_RAW.AVAL) over records matching on the shared output keys, where ADLB_RAW.PARAMCD = 'WBC'	Aggregate ONLY(ADLB_RAW.AVAL) over records matching on the shared output keys, where ADLB_RAW.PARAMCD = 'LYMLE'	Aggregate COUNT(ADLB_RAW.*) over records matching on the shared output keys, where ADLB_RAW.PARAMCD = 'LYMPH'	Compute WBCVAL * LYMLEVAL	Constant "CALCULATION"

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

How to fix

input/adlb.csv

Comments

Mapping spec