Reject an ODM Export Declared in Latin-1

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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 whose first line declares the Latin-1 (ISO-8859-1) character encoding instead of UTF-8.

Variables:

SEX would be the subject's collected sex code.

The same bytes spell different accented letters in Latin-1 and in UTF-8, so a site or investigator name read in the wrong encoding comes out as a different name. Only UTF-8 is read, and the file states that it is not UTF-8, so the input is rejected while it is read, and no artifact is accepted.

How to fix

Export the file again from the EDC system as UTF-8, so that its first line reads:

<?xml version="1.0" encoding="UTF-8"?>

Do not change only that line: the bytes of every accented letter would stay in Latin-1 and be read as other letters.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: ingest
condition: source_odm_xml_unsupported
rule: ODM-1

expected/error.yaml

phase: ingest
condition: source_odm_xml_unsupported
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  # The export declares the Latin-1 (ISO-8859-1) encoding.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="ISO-8859-1"?>
<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" Value="F"/>
          </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