Reject Duplicate WBC

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

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
rule: FORMULA-20

expected/error.yaml

phase: row_construction
condition: aggregate_multiple_records
spec_paths:
  - rows.derived_lymph.derivations.WBCVAL.aggregate
rule: FORMULA-20
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

Edit99 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [STUDYID, USUBJID, VISIT, PARAMCD]6input:7  ADLB_RAW: {path: input/adlb.csv, types: {AVAL: float}}89output:10  path: adlb.csv11  columns: [STUDYID, USUBJID, PARAMCD, AVAL, PARAM, VISIT, DTYPE]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: ADLB_RAW.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: ADLB_RAW.USUBJID2324  - name: VISIT25    type: str26    label: Visit Name27    derivation: ADLB_RAW.VISIT2829  - name: PARAMCD30    type: str31    label: Parameter Code3233  - name: PARAM34    type: str35    label: Parameter3637  - name: WBCVAL38    type: float39    label: White Blood Cell Count4041  - name: LYMLEVAL42    type: float43    label: Lymphocyte Fraction4445  - name: EXISTING_ABS_COUNT46    type: int47    label: Existing Absolute Lymphocyte Record Count4849  - name: AVAL50    type: float51    label: Analysis Value5253  - name: DTYPE54    type: str55    label: Derivation Type5657rows:58  - id: collected59    derivations:60      PARAMCD: ADLB_RAW.PARAMCD61      PARAM: ADLB_RAW.PARAM62      WBCVAL: null63      LYMLEVAL: null64      EXISTING_ABS_COUNT: null65      AVAL: ADLB_RAW.AVAL66      DTYPE: null6768  # One new LYMPH record per subject and visit, kept only when both a WBC69  # count and a LYMLE fraction are present and no LYMPH record was collected.70  - id: derived_lymph71    group_by: [ADLB_RAW.STUDYID, ADLB_RAW.USUBJID, ADLB_RAW.VISIT]72    filter: >-73      WBCVAL IS NOT NULL74      AND LYMLEVAL IS NOT NULL75      AND EXISTING_ABS_COUNT IS NULL76    derivations:77      PARAMCD: "'LYMPH'"78      PARAM: "'Lymphocytes Abs (10^9/L)'"79      # ONLY takes the one WBC (or LYMLE) result at the visit; a second80      # record stops the run instead of one being picked.81      WBCVAL:82        aggregate:83          filter: "ADLB_RAW.PARAMCD = 'WBC'"84          expr: "ONLY(ADLB_RAW.AVAL)"85      LYMLEVAL:86        aggregate:87          filter: "ADLB_RAW.PARAMCD = 'LYMLE'"88          expr: "ONLY(ADLB_RAW.AVAL)"89      # A count over no records is missing rather than 0, so the filter's90      # EXISTING_ABS_COUNT IS NULL means no LYMPH record was collected.91      EXISTING_ABS_COUNT:92        aggregate:93          filter: "ADLB_RAW.PARAMCD = 'LYMPH'"94          expr: "COUNT(ADLB_RAW.*)"95      AVAL: "WBCVAL * LYMLEVAL"96      DTYPE: "'CALCULATION'"9798verifications:99  - unique: [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

Human review and assessment

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
1.7	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

How to fix

input/adlb.csv

Your review

Mapping spec