Reject Source Domains Checked Without the Study's Dataset List

Review ask

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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 each adverse event's source domain (SRCDOM) and source sequence number (SRCSEQ) onto the analysis dataset.

Input: reported adverse events with the study and subject identifiers, the domain they belong to, a sequence number and the reported term.

Variables:

SRCDOM would be the name of the dataset each record comes from, which must be a dataset the study defines.
SRCSEQ would be the record's sequence number in that dataset.

Note: the datasets a study defines are listed once, in the study's own file, beside the specifications that build them. Built on its own, the analysis dataset has no list to check its source domains against, so the run is refused before any record is read instead of accepting source domains that nobody checked.

How to fix

Build the dataset as part of its study: open it from the study's project file, which lists the SDTM dataset the source domains name, for example yamaa_project("project.yaml")$spec("ADAE")$run() in R, yamaa.project("project.yaml").spec("ADAE").run() in Python, or yamaa run project.yaml --spec ADAE on the command line:

yamaa: "1.0"
type: project
sdtm:
  specs: [../sdtm/ae.yaml]
adam:
  specs: [spec.yaml]

Every SRCDOM value must then be the domain of a specification the project lists, here AE.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: project_binding_missing
rule: CT-13

expected/error.yaml

phase: validation
condition: project_binding_missing
spec_paths:
  - columns.SRCDOM.submission.inventory_vocabulary
rule: CT-13
context:
  binding: inventory_vocabulary
  column: SRCDOM

YAML specification

1 spec file

spec.yaml

Edit53 lines

1yamaa: "1.0"23type: spec45model: ADaM6domain: ADAE7keys: [STUDYID, USUBJID, AESEQ]8input:9  AE: input/ae.csv1011output:12  path: adae.csv13  columns: [STUDYID, USUBJID, AESEQ, AETERM, SRCDOM, SRCSEQ]1415columns:16  - name: STUDYID17    type: str18    label: Study Identifier19    derivation: AE.STUDYID2021  - name: USUBJID22    type: str23    label: Unique Subject Identifier24    derivation: AE.USUBJID2526  - name: AESEQ27    type: int28    label: Sequence Number29    derivation: AE.AESEQ3031  - name: AETERM32    type: str33    label: Reported Term for the Adverse Event34    derivation: AE.AETERM3536  # A source domain must name a dataset of the study, which the study's37  # project file lists.38  - name: SRCDOM39    type: str40    label: Source Data41    derivation: AE.DOMAIN42    submission:43      core: Perm44      length: 245      inventory_vocabulary: true46      origins:47        - type: Predecessor48          description: AE.DOMAIN4950  - name: SRCSEQ51    type: int52    label: Source Sequence Number53    derivation: AE.AESEQ

Inputs

Under review1 source file

input/ae.csv

Edit3 rows

input/ae.csv
STUDYID	DOMAIN	AESEQ	AETERM
STUDY01	AE	1	HEADACHE
STUDY01	AE	2	NAUSEA
STUDY01	AE	1	RASH

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	Core	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	AETERM	Reported Term for the Adverse Event	character		Copy value from AE.AETERM.	Predecessor
ADAE	SRCDOM	Source Data	character	Perm	Copy value from AE.DOMAIN.	Predecessor
ADAE	SRCSEQ	Source Sequence Number	numeric		Copy value from AE.AESEQ.	Predecessor

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