Reject a Laboratory Result Without a Unit Conversion

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: convert hemoglobin results and reference limits to g/dL, and reject a result whose reported unit has no conversion factor.

Input: hemoglobin results with test code (LBTESTCD), reported units, and reference limits, plus a conversion table keyed by test code and reported unit.

Variables:

LBORRES and LBORRESU keep the reported result and unit.
LBORNRLO and LBORNRHI keep the reported reference limits.
LBSTRESN is the reported result multiplied by the matching factor; it is missing when no factor matches.
LBSTRESC is the standardized numeric result written as text, or missing with LBSTRESN.
LBSTRESU is the standard unit, g/dL.
LBSTNRLO and LBSTNRHI are the reported limits multiplied by the same factor, or missing when no factor matches.

When a reported unit is absent from the conversion table, the standard unit remains known but its result and reference limits are missing. Those standardized values must be present together, so the completed dataset is rejected and not accepted.

How to fix

Confirm the appropriate conversion for the uncovered hemoglobin unit, add its test-and-unit row with the correct factor to the conversion table, and rerun. For hemoglobin reported in mmol/L, the usual factor to g/dL is 1.611:

TESTCD,UNIT,FACTOR
HGB,g/L,0.1
HGB,mmol/L,1.611

Do not assume a factor of one for an uncovered unit.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: verification
condition: all_or_none_failed
requirement: REQ-0382

expected/error.yaml

phase: verification
condition: all_or_none_failed
spec_paths:
  - verifications[0].all_or_none
requirement: REQ-0382
context:
  verification_id: standardized-result-completeness
  failure_count: 1
  keys:
    - STUDYID: YAMAA-01
      USUBJID: YAMAA-01-001
      LBSEQ: 2

YAML specification

1 spec file

spec.yaml

Edit132 lines

1schema_version: "1.0"2domain: LB3keys: [STUDYID, USUBJID, LBSEQ]4input:5  LB_RAW:6    path: input/lb_raw.csv7    types: {LBORRES: float, LBORNRLO: float, LBORNRHI: float}8  CONV:9    path: input/conversion.csv10    types: {FACTOR: float}11base: LB_RAW1213output:14  path: lb.csv15  columns: [DOMAIN, STUDYID, USUBJID, LBSEQ, LBTESTCD, LBORRES, LBORRESU,16            LBORNRLO, LBORNRHI, LBSTRESN, LBSTRESC, LBSTRESU, LBSTNRLO,17            LBSTNRHI]1819intermediates:20  - id: CONV_LOOKUP21    dataset: CONV22    key: {TESTCD: LBTESTCD, UNIT: LBORRESU}23    no_match: null2425columns:26  - name: DOMAIN27    type: str28    label: Domain Abbreviation29    derivation: {literal: LB}3031  - name: STUDYID32    type: str33    label: Study Identifier34    derivation: LB_RAW.STUDYID3536  - name: USUBJID37    type: str38    label: Unique Subject Identifier39    derivation: LB_RAW.USUBJID4041  - name: LBSEQ42    type: int43    label: Sequence Number44    derivation: LB_RAW.LBSEQ4546  - name: LBTESTCD47    type: str48    label: Lab Test or Examination Short Name49    derivation: LB_RAW.LBTESTCD5051  - name: LBORRES52    type: str53    label: Result or Finding in Original Units54    derivation: LB_RAW.LBORRES5556  - name: LBORRESU57    type: str58    label: Original Units59    derivation: LB_RAW.LBORRESU6061  - name: LBORNRLO62    type: str63    label: Reference Range Lower Limit in Orig Unit64    derivation: LB_RAW.LBORNRLO6566  - name: LBORNRHI67    type: str68    label: Reference Range Upper Limit in Orig Unit69    derivation: LB_RAW.LBORNRHI7071  # RESN, LO_RESN and HI_RESN hold the reported result and limits as72  # numbers for the arithmetic below; the columns above keep them as text.73  - name: RESN74    type: float75    label: Numeric Result as Reported76    derivation: LB_RAW.LBORRES7778  # The factor for the record's test and reported unit; missing when the79  # conversion table has no such row, which leaves every standardized value80  # except the unit missing.81  - name: FACTOR82    type: float83    label: Conversion Factor to the Standard Unit84    derivation: CONV_LOOKUP.FACTOR8586  - name: LO_RESN87    type: float88    label: Numeric Reference Lower Limit as Reported89    derivation: LB_RAW.LBORNRLO9091  - name: HI_RESN92    type: float93    label: Numeric Reference Upper Limit as Reported94    derivation: LB_RAW.LBORNRHI9596  - name: LBSTRESN97    type: float98    label: Numeric Result/Finding in Standard Units99    derivation:100      compute:101        expr: "RESN * FACTOR"102103  - name: LBSTRESC104    type: str105    label: Character Result/Finding in Std Format106    derivation: LBSTRESN107108  - name: LBSTRESU109    type: str110    label: Standard Units111    derivation: {literal: g/dL}112113  - name: LBSTNRLO114    type: float115    label: Reference Range Lower Limit in Standard Units116    derivation:117      compute:118        expr: "LO_RESN * FACTOR"119120  - name: LBSTNRHI121    type: float122    label: Reference Range Upper Limit in Standard Units123    derivation:124      compute:125        expr: "HI_RESN * FACTOR"126127verifications:128  # A result with no factor keeps its standard unit while its standardized129  # result and limits are missing, so this check fails for that record.130  - all_or_none:131      id: standardized-result-completeness132      columns: [LBSTRESN, LBSTRESC, LBSTRESU, LBSTNRLO, LBSTNRHI]

Inputs

Under review2 source files

input/conversion.csv

Edit1 row

input/conversion.csv
TESTCD	UNIT	FACTOR
HGB	g/L	0.1

input/lb_raw.csv

Edit2 rows

input/lb_raw.csv
STUDYID	USUBJID	LBSEQ	LBTESTCD	LBORRES	LBORRESU	LBORNRLO	LBORNRHI
YAMAA-01		1	HGB	138	g/L	120	160
YAMAA-01		2	HGB	8.5	mmol/L	7.5	10

Unexpected Output

Under review2 rows presented to the failing check - not an accepted artifact

expected/lb.csv

Edit2 rows

expected/lb.csv
DOMAIN	STUDYID	USUBJID	LBSEQ	LBTESTCD	LBORRES	LBORRESU	LBORNRLO	LBORNRHI	LBSTRESN	LBSTRESC	LBSTRESU	LBSTNRLO	LBSTNRHI
LB	YAMAA-01		1	HGB	138	g/L	120	160	13.8	13.8	g/dL	12	16
LB	YAMAA-01		2	HGB	8.5	mmol/L	7.5	10	—	—	g/dL	—	—

Shaded columns are derived— = missing value

Comments and assessment materials

Variable Name	Variable Label	Type	Origin	Conversion Definition	Variable Type	Variable Order
DOMAIN	Domain Abbreviation	Char	Assigned	Set constant value "LB".	SDTM	1
STUDYID	Study Identifier	Char	Collected	Copy value from LB_RAW.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	Collected	Copy value from LB_RAW.USUBJID.	SDTM	3
LBSEQ	Sequence Number	Num	Collected	Copy value from LB_RAW.LBSEQ.	SDTM	4
LBTESTCD	Lab Test or Examination Short Name	Char	Collected	Copy value from LB_RAW.LBTESTCD.	SDTM	5
LBORRES	Result or Finding in Original Units	Char	Collected	Copy value from LB_RAW.LBORRES.	SDTM	6
LBORRESU	Original Units	Char	Collected	Copy value from LB_RAW.LBORRESU.	SDTM	7
LBORNRLO	Reference Range Lower Limit in Orig Unit	Char	Collected	Copy value from LB_RAW.LBORNRLO.	SDTM	8
LBORNRHI	Reference Range Upper Limit in Orig Unit	Char	Collected	Copy value from LB_RAW.LBORNRHI.	SDTM	9
LBSTRESN	Numeric Result/Finding in Standard Units	Num	Derived	Compute RESN * FACTOR.	SDTM	10
LBSTRESC	Character Result/Finding in Std Format	Char	Derived	Copy value from LBSTRESN.	SDTM	11
LBSTRESU	Standard Units	Char	Assigned	Set constant value "g/dL".	SDTM	12
LBSTNRLO	Reference Range Lower Limit in Standard Units	Num	Derived	Compute LO_RESN * FACTOR.	SDTM	13
LBSTNRHI	Reference Range Upper Limit in Standard Units	Num	Derived	Compute HI_RESN * FACTOR.	SDTM	14

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/conversion.csv

input/lb_raw.csv

expected/lb.csv

Comments

Mapping spec