Reject Text Read as a Whole Number from a SAS Transport File

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: carry the reported adverse event term (AETERM) and its sequence number (AESEQ) onto the adverse events domain from a SAS transport file.

Input: reported adverse events in input/ae_raw.xpt, a version 5 SAS transport file with one record per reported event. The sequence number is stored as a number and the reported term as text.

Variables:

DOMAIN is AE on every record.
AESEQ would number each subject's events in whole numbers.
AETERM would be the term as reported. The rejected file produces no output value.

Note: a SAS file stores every field either as text or as a number, and a field stored as text is never read as a number. The reported term is declared a whole number, so the file is rejected while it is read, naming the term's field, before any record is derived; no artifact is accepted.

How to fix

The reported term is verbatim text, so read it as the text it is stored as by declaring no type for it; only the sequence number needs narrowing to a whole number:

input:
  AE_RAW:
    path: input/ae_raw.xpt
    types: {AESEQ: int}
    encoding: windows-1252

When a field stored as text does hold digits meant as a number, ask the sender to store it as a number, or read it as text and convert it in the column that needs the number.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: ingest
condition: source_sas_invalid
rule: SAS-7

expected/error.yaml

phase: ingest
condition: source_sas_invalid
spec_paths:
  - input.AE_RAW.types.AETERM
rule: SAS-7
context:
  dataset: AE_RAW
  path: input/ae_raw.xpt
  cause: field_type
  field: AETERM

YAML specification

1 spec file

spec.yaml

Edit44 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: AE5keys: [STUDYID, USUBJID, AESEQ]6input:7  # Reported adverse events in a SAS transport file (version 5), written from8  # the public record layout by tools/staging/build_xport_fixtures.py. The9  # reported term is stored as character data, but the entry below declares10  # it a whole number, as the sequence number is.11  AE_RAW:12    path: input/ae_raw.xpt13    types: {AESEQ: int, AETERM: int}14    encoding: windows-12521516output:17  path: ae.csv18  columns: [DOMAIN, STUDYID, USUBJID, AESEQ, AETERM]1920columns:21  - name: DOMAIN22    type: str23    label: Domain Abbreviation24    derivation: "'AE'"2526  - name: STUDYID27    type: str28    label: Study Identifier29    derivation: AE_RAW.STUDYID3031  - name: USUBJID32    type: str33    label: Unique Subject Identifier34    derivation: AE_RAW.USUBJID3536  - name: AESEQ37    type: int38    label: Sequence Number39    derivation: AE_RAW.AESEQ4041  - name: AETERM42    type: str43    label: Reported Term for the Adverse Event44    derivation: AE_RAW.AETERM

Inputs

Under review1 source file

No preview available; inspect the fixture files in the benchmark source.

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 "AE".	SDTM	1
STUDYID	Study Identifier	Char	Collected	Copy value from AE_RAW.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	Collected	Copy value from AE_RAW.USUBJID.	SDTM	3
AESEQ	Sequence Number	Num	Collected	Copy value from AE_RAW.AESEQ.	SDTM	4
AETERM	Reported Term for the Adverse Event	Char	Collected	Copy value from AE_RAW.AETERM.	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

Your review

Mapping spec