Reject a Day Count from 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: count the exposure start (EXSTDY) in days since 1970-01-01, for exposure records with sequence number 1.

Input: exposure records, each identified by study, subject, and sequence, carrying the start date as collected text (EXSTDT).

Variables:

EXSTDY would hold the number of days from 1970-01-01 to the exposure start, negative for an earlier date. Only a date can be counted, and the start is still text that nothing has read as a date, so the run is rejected before any data is read and no artifact is accepted.

How to fix

Read the collected start as a date before counting days. The simplest correction declares the field's type on the input, so the text becomes a date as it is read and a start that is not a complete date is rejected there:

input:
  EX: {path: input/ex.csv, types: {EXSEQ: int, EXSTDT: date}}

If a start that is not a complete date should leave the day count empty instead, bind the text to an internal date column that answers the failed conversion, and count from that column:

- name: ASTDT
  type: date
  derivation:
    value: EX.EXSTDT
    unconvertible: null

- name: EXSTDY
  type: int
  derivation:
    to_epoch_day:
      source: ASTDT

to_epoch_day takes a variable as its source, so a to_date nested inside it is itself rejected.

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.EXSTDY.derivation.to_epoch_day.source
rule: TIME-1
context:
  source: EX.EXSTDT
  expected: date
  actual: str

YAML specification

1 spec file

spec.yaml

Edit42 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADEX5keys: [STUDYID, USUBJID, EXSEQ]6input:7  EX: {path: input/ex.csv, types: {EXSEQ: int}}89output:10  path: adex.csv11  columns: [STUDYID, USUBJID, EXSEQ, EXSTDY]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: EX.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: EX.USUBJID2324  - name: EXSEQ25    type: int26    label: Sequence Number27    derivation: EX.EXSEQ2829  # EX.EXSTDT has no declared input type, so it is text, and to_epoch_day30  # counts days only from a date: the specification is rejected before any31  # data is read.32  - name: EXSTDY33    type: int34    label: Epoch Day of Exposure Start35    derivation:36      to_epoch_day:37        source: EX.EXSTDT3839# One row for each exposure record with sequence number 1.40rows:41  - id: exposure42    filter: "EX.EXSEQ = 1"

Inputs

Under review1 source file

input/ex.csv

Edit1 row

input/ex.csv
STUDYID	USUBJID	EXSEQ	EXSTDT
YAMAA-01		1	2024-01-15

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	Computational Method	Origin
ADEX	STUDYID	Study Identifier	character	Copy value from EX.STUDYID.	Predecessor
ADEX	USUBJID	Unique Subject Identifier	character	Copy value from EX.USUBJID.	Predecessor
ADEX	EXSEQ	Sequence Number	numeric	Copy value from EX.EXSEQ.	Predecessor
ADEX	EXSTDY	Epoch Day of Exposure Start	numeric	Days since 1970-01-01 for EX.EXSTDT.	Derived

Template	Include when
exposure	EX.EXSEQ = 1

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/ex.csv

Your review

Mapping spec