Reject an ODM Export Without Collected Data

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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: an Operational Data Model (ODM) 1.3 XML file from the electronic data capture (EDC) system that describes the study's visits, forms, items and code lists but holds no collected data: an export of the study design, like a define.xml, instead of the clinical data export.

Variables:

SEX would be the subject's collected sex code.

The file has no clinical data section, so it holds no subject at all. A listing built from it would be empty and would look like a study that has enrolled no one, so the input is rejected once the whole file has been read, and no artifact is accepted.

How to fix

Export the clinical data from the EDC system: an ODM snapshot whose ClinicalData element holds the subjects' collected items. Keep the study design export for the define.xml and other metadata work, and save the clinical data export where the input reads it:

input:
  ODM: input/odm.xml

A clinical data export with no subjects yet still has its ClinicalData element, and it gives an empty listing rather than this rejection.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: ingest
condition: source_odm_no_clinical_data
rule: ODM-1

expected/error.yaml

phase: ingest
condition: source_odm_no_clinical_data
spec_paths:
  - input.ODM.path
rule: ODM-1
context:
  dataset: ODM
  path: input/odm.xml

YAML specification

1 spec file

spec.yaml

Edit33 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]6input:7  # A study-design export, which holds no collected data.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.DESIGN.20260302"
     CreationDateTime="2026-03-02T09:15:00+00:00">
  <Study OID="STUDY01">
    <GlobalVariables>
      <StudyName>STUDY01</StudyName>
      <StudyDescription>An invented study for this benchmark</StudyDescription>
      <ProtocolName>STUDY01</ProtocolName>
    </GlobalVariables>
    <MetaDataVersion OID="MDV.1" Name="Version 1">
      <Protocol>
        <StudyEventRef StudyEventOID="SE.SCREENING" Mandatory="Yes"/>
      </Protocol>
      <StudyEventDef OID="SE.SCREENING" Name="Screening" Repeating="No"
                     Type="Scheduled">
        <FormRef FormOID="F.DM" Mandatory="Yes"/>
      </StudyEventDef>
      <FormDef OID="F.DM" Name="Demographics" Repeating="No">
        <ItemGroupRef ItemGroupOID="IG.DM" Mandatory="Yes"/>
      </FormDef>
      <ItemGroupDef OID="IG.DM" Name="Demographics" Repeating="No">
        <ItemRef ItemOID="IT.DM.SEX" Mandatory="Yes"/>
      </ItemGroupDef>
      <ItemDef OID="IT.DM.SEX" Name="Sex" DataType="text" Length="1">
        <Question><TranslatedText xml:lang="en">Sex</TranslatedText></Question>
        <CodeListRef CodeListOID="CL.SEX"/>
      </ItemDef>
      <CodeList OID="CL.SEX" Name="Sex" DataType="text">
        <CodeListItem CodedValue="F">
          <Decode><TranslatedText xml:lang="en">Female</TranslatedText></Decode>
        </CodeListItem>
        <CodeListItem CodedValue="M">
          <Decode><TranslatedText xml:lang="en">Male</TranslatedText></Decode>
        </CodeListItem>
      </CodeList>
    </MetaDataVersion>
  </Study>
</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