Reject Empty Text Kept as a Value in a Comma-Separated 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 collected free-text race (RACEOTH) onto the demographics domain, keeping an empty entry as collected text.

Input: collected demographics in a comma-separated file, one record per subject.

Variables:

DOMAIN is DM on every record.
RACEOTH would be the free-text race as collected.

Note: the input is declared to keep an empty text entry as a collected value, distinct from a value that was never collected. A comma-separated file writes both as an empty field, so it cannot carry that distinction, and the run is rejected before any data is read; no artifact is accepted.

How to fix

Treat an empty field as not collected, which is what a comma-separated file can express, by removing empty_string: present (the default is missing):

input:
  RAW: input/dm_raw.csv

When the study does need to tell collected empty text from a value never collected, export the source as Parquet, which stores the two differently, and keep empty_string: present on that input.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: empty_string_present_unsupported
rule: INPUT-9

expected/error.yaml

phase: validation
condition: empty_string_present_unsupported
spec_paths:
  - input.RAW.empty_string
rule: INPUT-9
context:
  dataset: RAW

YAML specification

1 spec file

spec.yaml

Edit35 lines

1yamaa: "1.0"2type: spec3model: SDTM4domain: DM5keys: [STUDYID, USUBJID]6input:7  # An empty race text is meant to be kept as collected text, distinct from8  # a value that was never collected. A comma-separated file cannot tell9  # the two apart.10  RAW: {path: input/dm_raw.csv, empty_string: present}1112output:13  path: dm.csv14  columns: [DOMAIN, STUDYID, USUBJID, RACEOTH]1516columns:17  - name: DOMAIN18    type: str19    label: Domain Abbreviation20    derivation: "'DM'"2122  - name: STUDYID23    type: str24    label: Study Identifier25    derivation: RAW.STUDYID2627  - name: USUBJID28    type: str29    label: Unique Subject Identifier30    derivation: RAW.USUBJID3132  - name: RACEOTH33    type: str34    label: Race, Other35    derivation: RAW.RACEOTH

Inputs

Under review1 source file

input/dm_raw.csv

Edit2 rows

input/dm_raw.csv
STUDYID	USUBJID	RACEOTH
YAMAA-01		—
YAMAA-01		MAORI

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 RAW.STUDYID.	SDTM	2
USUBJID	Unique Subject Identifier	Char	Collected	Copy value from RAW.USUBJID.	SDTM	3
RACEOTH	Race, Other	Char	Collected	Copy value from RAW.RACEOTH.	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/dm_raw.csv

Your review

Mapping spec