Reject a Laboratory Result Without a Unit Conversion

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

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
rule: CHECK-11

expected/error.yaml

phase: verification
condition: all_or_none_failed
spec_paths:
  - verifications[0].all_or_none
rule: CHECK-11
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

Edit127 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: LB5keys: [STUDYID, USUBJID, LBSEQ]6input:7  LB_RAW:8    path: input/lb_raw.csv9    types: {LBORRES: float, LBORNRLO: float, LBORNRHI: float}10  CONV:11    path: input/conversion.csv12    types: {FACTOR: float}13base: LB_RAW1415output:16  path: lb.csv17  columns: [DOMAIN, STUDYID, USUBJID, LBSEQ, LBTESTCD, LBORRES, LBORRESU,18            LBORNRLO, LBORNRHI, LBSTRESN, LBSTRESC, LBSTRESU, LBSTNRLO,19            LBSTNRHI]2021intermediates:22  - id: CONV_LOOKUP23    dataset: CONV24    key: {TESTCD: LBTESTCD, UNIT: LBORRESU}2526columns:27  - name: DOMAIN28    type: str29    label: Domain Abbreviation30    derivation: "'LB'"3132  - name: STUDYID33    type: str34    label: Study Identifier35    derivation: LB_RAW.STUDYID3637  - name: USUBJID38    type: str39    label: Unique Subject Identifier40    derivation: LB_RAW.USUBJID4142  - name: LBSEQ43    type: int44    label: Sequence Number45    derivation: LB_RAW.LBSEQ4647  - name: LBTESTCD48    type: str49    label: Lab Test or Examination Short Name50    derivation: LB_RAW.LBTESTCD5152  - name: LBORRES53    type: str54    label: Result or Finding in Original Units55    derivation: LB_RAW.LBORRES5657  - name: LBORRESU58    type: str59    label: Original Units60    derivation: LB_RAW.LBORRESU6162  - name: LBORNRLO63    type: str64    label: Reference Range Lower Limit in Orig Unit65    derivation: LB_RAW.LBORNRLO6667  - name: LBORNRHI68    type: str69    label: Reference Range Upper Limit in Orig Unit70    derivation: LB_RAW.LBORNRHI7172  # RESN, LO_RESN and HI_RESN hold the reported result and limits as73  # numbers for the arithmetic below; the columns above keep them as text.74  - name: RESN75    type: float76    label: Numeric Result as Reported77    derivation: LB_RAW.LBORRES7879  # The factor for the record's test and reported unit; missing when the80  # conversion table has no such row, which leaves every standardized value81  # except the unit missing.82  - name: FACTOR83    type: float84    label: Conversion Factor to the Standard Unit85    derivation: CONV_LOOKUP.FACTOR8687  - name: LO_RESN88    type: float89    label: Numeric Reference Lower Limit as Reported90    derivation: LB_RAW.LBORNRLO9192  - name: HI_RESN93    type: float94    label: Numeric Reference Upper Limit as Reported95    derivation: LB_RAW.LBORNRHI9697  - name: LBSTRESN98    type: float99    label: Numeric Result/Finding in Standard Units100    derivation: "RESN * FACTOR"101102  - name: LBSTRESC103    type: str104    label: Character Result/Finding in Std Format105    derivation: LBSTRESN106107  - name: LBSTRESU108    type: str109    label: Standard Units110    derivation: "'g/dL'"111112  - name: LBSTNRLO113    type: float114    label: Reference Range Lower Limit in Standard Units115    derivation: "LO_RESN * FACTOR"116117  - name: LBSTNRHI118    type: float119    label: Reference Range Upper Limit in Standard Units120    derivation: "HI_RESN * FACTOR"121122verifications:123  # A result with no factor keeps its standard unit while its standardized124  # result and limits are missing, so this check fails for that record.125  - all_or_none:126      id: standardized-result-completeness127      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

Human review and assessment

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
1.7	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/conversion.csv

input/lb_raw.csv

expected/lb.csv

Your review

Mapping spec