Reject Duplicate Sex

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: build one Demographics (DM) record per subject carrying sex (SEX) and age (AGE).

Input: EDC output in long form, one row per collected item. A visit entered more than once repeats its items under a new visit repeat key (StudyEventRepeatKey), so one question can carry two answers.

Variables:

SEX would be the recorded sex coded M (Male) or F (Female), and U when no answer, a blank answer, or any other answer was collected. The same answer entered twice is still one answer, but a subject with two different answers has no single recorded sex and one record cannot carry both, so the run is rejected and no artifact is accepted.
AGE: age in whole years as collected; blank when missing.

How to fix

Decide which answer stands for the subject. Two different sexes for one subject is usually a data issue to query and correct at the source, and correcting it there leaves one answer and needs nothing here.

When both entries are legitimate and the later one corrects the earlier, say so: order the answers as they were collected and keep the last, in a working column the coded value then reads.

- name: SEXCOLL
  type: str
  derivation:
    source:
      filter: ODM.ItemOID = 'IT.DM.SEX'
      variable: ODM.Value
      order_by: [ODM.StudyEventRepeatKey]
      keep: last

- name: SEX
  type: str
  derivation:
    mapping:
      source: SEXCOLL
      dict:
        Male: M
        Female: F
      missing: U

When one entry is the record of the visit and the other is a duplicate to be ignored, name the entry the record reports instead, for example with ODM.ItemOID = 'IT.DM.SEX' AND ODM.StudyEventRepeatKey = 1.

Do not widen the keys to keep both answers: a subject whose visit was entered twice is still one demographics record.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: derivation
condition: multiple_values_per_key
rule: COLUMN-2

expected/error.yaml

phase: derivation
condition: multiple_values_per_key
spec_paths:
  - columns.SEX.derivation.mapping
rule: COLUMN-2
context:
  identifier: ODM.Value
  value_count: 2
  keys:
    - STUDYID: STUDY01
      USUBJID: "002"

YAML specification

1 spec file

spec.yaml

Edit55 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]67input:8  ODM:9    path: input/odm.csv10    types:11      StudyEventRepeatKey: int1213output:14  path: dm.csv15  columns: [DOMAIN, STUDYID, USUBJID, SEX, AGE]1617columns:18  - name: DOMAIN19    type: str20    label: Domain Abbreviation21    derivation: "'DM'"2223  - name: STUDYID24    type: str25    label: Study Identifier26    derivation: ODM.StudyOID2728  - name: USUBJID29    type: str30    label: Unique Subject Identifier31    derivation: ODM.SubjectKey3233  # No answer, a blank answer or any other answer gives U. The defect: a34  # subject whose sex was answered differently in two entries of the visit35  # gives one record two values, which stops the run.36  - name: SEX37    type: str38    label: Sex39    derivation:40      mapping:41        source:42          filter: ODM.ItemOID = 'IT.DM.SEX'43          variable: ODM.Value44        dict:45          Male: M46          Female: F47        missing: U4849  - name: AGE50    type: int51    label: Age52    derivation:53      source:54        filter: ODM.ItemOID = 'IT.DM.AGE'55        variable: ODM.Value

Inputs

Under review1 source file

input/odm.csv

Edit5 rows

input/odm.csv
StudyOID	MetaDataVersionOID	SubjectKey	StudyEventOID	StudyEventRepeatKey	ItemGroupOID	ItemGroupRepeatKey	ItemOID	Value
STUDY01	MDV.1	001	SCREENING	1	IG.DM	1	IT.DM.SEX	Male
STUDY01	MDV.1	001	SCREENING	1	IG.DM	1	IT.DM.AGE	34
STUDY01	MDV.1	002	SCREENING	1	IG.DM	1	IT.DM.SEX	Female
STUDY01	MDV.1	002	SCREENING	2	IG.DM	1	IT.DM.SEX	Male
STUDY01	MDV.1	002	SCREENING	1	IG.DM	1	IT.DM.AGE	28

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

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 "DM".	SDTM	1
STUDYID	Study Identifier	Char	Collected	Copy value from ODM.StudyOID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	Collected	Copy value from ODM.SubjectKey.	SDTM	3
SEX	Sex	Char	Collected	Recode ODM.Value where ODM.ItemOID = 'IT.DM.SEX': "Male" → "M", "Female" → "F"; missing values → "U"; unlisted values are errors.	SDTM	4
AGE	Age	Num	Collected	Copy value from ODM.Value where ODM.ItemOID = 'IT.DM.AGE'.	SDTM	5

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/odm.csv

Your review

Mapping spec