Reject an Imputation Flag Read From Collected Text

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: one row per adverse event (AE) with an analysis start date (ASTDT) completed from the collected start, and a flag (ASTDTF) marking how much of that date was supplied.

Input: adverse event records carrying the collected start (AESTDTC): a year and month, or a full date.

Variables:

ASTDT would be the analysis start date: a full date as collected, and a year and month completed to the first of the month.
ASTDTF would be D when the day of ASTDT was supplied. The flag describes a completed date, and collected text has not been completed, so the run stops before reading any data.

How to fix

Read the flag from the completed date, which carries how much of it was collected:

imputation_flag:
  source: ASTDT
  part: date

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: incompatible_input_type
rule: TIME-18

expected/error.yaml

phase: validation
condition: incompatible_input_type
spec_paths:
  - columns.ASTDTF.derivation.imputation_flag.source
rule: TIME-18
context:
  source: AE.AESTDTC
  expected: date or datetime
  actual: str

YAML specification

1 spec file

spec.yaml

Edit48 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADAE5keys: [STUDYID, USUBJID, AESEQ]6input:7  AE: input/ae.csv8base: AE910output:11  path: adae.csv12  columns: [STUDYID, USUBJID, AESEQ, ASTDT, ASTDTF]1314columns:15  - name: STUDYID16    type: str17    label: Study Identifier18    derivation: AE.STUDYID1920  - name: USUBJID21    type: str22    label: Unique Subject Identifier23    derivation: AE.USUBJID2425  - name: AESEQ26    type: int27    label: Sequence Number28    derivation: AE.AESEQ2930  - name: ASTDT31    type: date32    label: Analysis Start Date33    derivation:34      impute:35        type: date36        source: AE.AESTDTC37        month: 138        day: first3940  # The flag reads the collected text rather than the completed date, so41  # nothing records which parts were supplied.42  - name: ASTDTF43    type: str44    label: Analysis Start Date Imputation Flag45    derivation:46      imputation_flag:47        source: AE.AESTDTC48        part: date

Inputs

Under review1 source file

input/ae.csv

Edit2 rows

input/ae.csv
STUDYID	USUBJID	AESEQ	AETERM	AESTDTC
YAMAA-01		1	HEADACHE	2025-03
YAMAA-01		2	NAUSEA	2025-03-04

Unexpected Output

Under reviewNo artifact is produced

No fixture files in this directory.

Shaded columns are derived— = missing value

Human review and assessment

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Computational Method	Origin
ADAE	STUDYID	Study Identifier	character		Copy value from AE.STUDYID.	Predecessor
ADAE	USUBJID	Unique Subject Identifier	character		Copy value from AE.USUBJID.	Predecessor
ADAE	AESEQ	Sequence Number	numeric		Copy value from AE.AESEQ.	Predecessor
ADAE	ASTDT	Analysis Start Date	numeric	ISO 8601	Impute incomplete date from AE.AESTDTC, defaulting month=1, day=first; invalid text is an error.	Derived
ADAE	ASTDTF	Analysis Start Date Imputation Flag	character		Date imputation flag for AE.AESTDTC: "Y" when the whole date was imputed, "M" when the month and day were, "D" when only the day was; blank when the date was collected in full.	Derived

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/ae.csv

Your review

Mapping spec