Reject an Unknown Null Marker in an ODM Export

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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 with the sex (SEX) collected on the demographics form.

Input: the electronic data capture (EDC) system's export as an Operational Data Model (ODM) 1.3 XML file, in which the second subject's sex is marked as not collected with IsNull="Y".

Variables:

SEX would be the subject's collected sex code.

ODM marks an item that holds no answer with IsNull="Yes". The reader admits yes, true or 1 for a null item and no, false or 0 for an answered one, in any letter case, and Y is none of them. Reading it either way would decide on the export's behalf whether the answer is missing, so the input is rejected while it is read, and no artifact is accepted.

How to fix

Have the EDC system write the null marker as ODM defines it:

<ItemData ItemOID="IT.DM.SEX" IsNull="Yes"/>

If the system cannot be changed, ask its vendor which value Y stands for before the export is used.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: ingest
condition: source_odm_attribute_invalid
rule: ODM-1

expected/error.yaml

phase: ingest
condition: source_odm_attribute_invalid
spec_paths:
  - input.ODM.path
rule: ODM-1
context:
  dataset: ODM
  path: input/odm.xml
  element: ItemData
  attribute: IsNull
  value: "Y"

YAML specification

1 spec file

spec.yaml

Edit33 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]6input:7  # One item marks its missing answer with IsNull="Y".8  ODM: input/odm.xml910output:11  path: dm.csv12  columns: [DOMAIN, STUDYID, USUBJID, SEX]1314columns:15  - name: DOMAIN16    type: str17    label: Domain Abbreviation18    derivation: "'DM'"1920  - name: STUDYID21    type: str22    label: Study Identifier23    derivation: ODM.StudyOID2425  - name: USUBJID26    type: str27    label: Unique Subject Identifier28    derivation: {str_template: "{ODM.StudyOID}-{ODM.SubjectKey}"}2930  - name: SEX31    type: str32    label: Sex33    derivation: {odm: ODM.IT.DM.SEX}

Inputs

Under review1 source file

input/odm.xml

Edit

<?xml version="1.0" encoding="UTF-8"?>
<ODM xmlns="http://www.cdisc.org/ns/odm/v1.3"
     ODMVersion="1.3.2"
     FileType="Snapshot"
     FileOID="STUDY01.SNAPSHOT.20260302"
     CreationDateTime="2026-03-02T09:15:00+00:00">
  <ClinicalData StudyOID="STUDY01" MetaDataVersionOID="MDV.1">
    <SubjectData SubjectKey="101">
      <StudyEventData StudyEventOID="SE.SCREENING">
        <FormData FormOID="F.DM">
          <ItemGroupData ItemGroupOID="IG.DM">
            <ItemData ItemOID="IT.DM.SEX" Value="M"/>
          </ItemGroupData>
        </FormData>
      </StudyEventData>
    </SubjectData>
    <SubjectData SubjectKey="102">
      <StudyEventData StudyEventOID="SE.SCREENING">
        <FormData FormOID="F.DM">
          <ItemGroupData ItemGroupOID="IG.DM">
            <ItemData ItemOID="IT.DM.SEX" IsNull="Y"/>
          </ItemGroupData>
        </FormData>
      </StudyEventData>
    </SubjectData>
  </ClinicalData>
</ODM>

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	Derived	Fill the template "{ODM.StudyOID}-{ODM.SubjectKey}".	SDTM	3
SEX	Sex	Char	Collected	Read collected ODM item IT.DM.SEX; no identified record yields blank.	SDTM	4

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.xml

Your review

Mapping spec