Reject Mixed Endpoints

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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 a subject-level record carrying the moment treatment started in RFSTDTM and the calendar date of death in DTHDT and counting whole days between them in SURVDD.

Input: collected demographics carrying the treatment-start moment (RFSTDTC) and the death date (DTHDT).

Variables:

RFSTDTM would be the moment treatment started, time of day included, taken from RFSTDTC.
SURVDD would be the whole-day count from RFSTDTM to DTHDT.

Note: a day count has no meaning between a moment and a date: the hours on either side could give two different answers, so the run is rejected before any data is read and no artifact is accepted.

How to fix

Decide which calendar days the study counts, then state them as dates. When only moments are collected, take each moment's calendar date first and count from it (start: RFSTD), so the count has whole days to count:

- name: RFSTD
  type: date
  derivation:
    to_date:
      source: RFSTDTM

When the hours matter, the study needs a finer unit than days, which this vocabulary does not offer; record that gap instead of rounding it away.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: incompatible_input_type
rule: TIME-1

expected/error.yaml

phase: validation
condition: incompatible_input_type
spec_paths:
  - columns.SURVDD.derivation.diff.start
rule: TIME-1
context:
  source: RFSTDTM
  expected: date
  actual: datetime

YAML specification

1 spec file

spec.yaml

Edit44 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADSL5keys: [STUDYID, USUBJID]6input:7  DM: {path: input/dm.csv, types: {RFSTDTC: datetime, DTHDT: date}}89output:10  path: adsl.csv11  columns: [STUDYID, USUBJID, RFSTDTM, DTHDT, SURVDD]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: DM.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: DM.USUBJID2324  - name: RFSTDTM25    type: datetime26    label: Reference Start Moment27    derivation: DM.RFSTDTC2829  - name: DTHDT30    type: date31    label: Date of Death32    derivation: DM.DTHDT3334  # Counts days from a date-time to a date; a day count needs two dates, so35  # this is rejected before any data is read.36  - name: SURVDD37    type: int38    label: Survival Duration in Days39    derivation:40      diff:41        type: date42        start: RFSTDTM43        end: DTHDT44        unit: day

Inputs

Under review1 source file

input/dm.csv

Edit2 rows

input/dm.csv
STUDYID	USUBJID	RFSTDTC	DTHDT
YAMAA-01		2023-01-02T09:00:00	2023-05-14
YAMAA-01		2023-02-10T09:00:00	2023-06-01

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
ADSL	STUDYID	Study Identifier	character		Copy value from DM.STUDYID.	Predecessor
ADSL	USUBJID	Unique Subject Identifier	character		Copy value from DM.USUBJID.	Predecessor
ADSL	RFSTDTM	Reference Start Moment	numeric	ISO 8601	Copy value from DM.RFSTDTC.	Predecessor
ADSL	DTHDT	Date of Death	numeric	ISO 8601	Copy value from DM.DTHDT.	Predecessor
ADSL	SURVDD	Survival Duration in Days	numeric		Whole days from RFSTDTM to DTHDT, counting the end date but not the start.	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/dm.csv

Your review

Mapping spec