Reject a Transactional 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, saved as a transactional file: a log of every entry, change and removal in the order they were made, instead of the current answers.

Variables:

SEX would be the subject's collected sex code, as the form holds it now.

A transactional file lists an answer once for each time it was entered or changed, and lists a removed answer as well as its removal, so its records are not the subjects' current answers. Read as if they were, a corrected answer would count twice and a removed form would still give an answer. The input is rejected while it is read, and no artifact is accepted.

How to fix

Export a snapshot from the EDC system instead: the current value of every collected item, which the export marks with FileType="Snapshot" on its root ODM element, or with no FileType at all. Applying the transactions in order is the EDC system's job, so do not edit the transactional file by hand to make it look like a snapshot:

input:
  ODM: input/odm.xml

The specification itself does not change; only the export does.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: ingest
condition: source_odm_transactional
rule: ODM-1

expected/error.yaml

phase: ingest
condition: source_odm_transactional
spec_paths:
  - input.ODM.path
rule: ODM-1
context:
  dataset: ODM
  path: input/odm.xml
  element: ODM
  attribute: FileType
  value: Transactional

YAML specification

1 spec file

spec.yaml

Edit33 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]6input:7  # A transactional export: every entry, change and removal in turn.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="Transactional"
     FileOID="STUDY01.TRANSACTIONS.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" TransactionType="Insert">
            <ItemData ItemOID="IT.DM.SEX" Value="M">
              <AuditRecord>
                <UserRef UserOID="USR.CRC"/>
                <LocationRef LocationOID="LOC.01"/>
                <DateTimeStamp>2026-02-18T09:30:00+00:00</DateTimeStamp>
              </AuditRecord>
            </ItemData>
          </ItemGroupData>
        </FormData>
      </StudyEventData>
    </SubjectData>
    <SubjectData SubjectKey="101">
      <StudyEventData StudyEventOID="SE.SCREENING">
        <FormData FormOID="F.DM">
          <ItemGroupData ItemGroupOID="IG.DM" TransactionType="Update">
            <ItemData ItemOID="IT.DM.SEX" Value="F">
              <AuditRecord>
                <UserRef UserOID="USR.CRC"/>
                <LocationRef LocationOID="LOC.01"/>
                <DateTimeStamp>2026-02-24T11:05:00+00:00</DateTimeStamp>
                <ReasonForChange>Entered in error; corrected from the source document</ReasonForChange>
              </AuditRecord>
            </ItemData>
          </ItemGroupData>
        </FormData>
      </StudyEventData>
    </SubjectData>
    <SubjectData SubjectKey="102">
      <StudyEventData StudyEventOID="SE.SCREENING">
        <FormData FormOID="F.DM">
          <ItemGroupData ItemGroupOID="IG.DM" TransactionType="Insert">
            <ItemData ItemOID="IT.DM.SEX" Value="F">
              <AuditRecord>
                <UserRef UserOID="USR.CRC"/>
                <LocationRef LocationOID="LOC.01"/>
                <DateTimeStamp>2026-02-19T14:10:00+00:00</DateTimeStamp>
              </AuditRecord>
            </ItemData>
          </ItemGroupData>
        </FormData>
      </StudyEventData>
    </SubjectData>
    <SubjectData SubjectKey="102">
      <StudyEventData StudyEventOID="SE.SCREENING">
        <FormData FormOID="F.DM">
          <ItemGroupData ItemGroupOID="IG.DM" TransactionType="Remove">
            <ItemData ItemOID="IT.DM.SEX">
              <AuditRecord>
                <UserRef UserOID="USR.CRC"/>
                <LocationRef LocationOID="LOC.01"/>
                <DateTimeStamp>2026-02-26T08:45:00+00:00</DateTimeStamp>
                <ReasonForChange>Form entered for the wrong subject</ReasonForChange>
              </AuditRecord>
            </ItemData>
          </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