Reject a Choice of One Medication Beside the Pairing

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: give one row for each adverse event and medication that the related-records dataset relates to each other: the event's sequence number (AESEQ), the medication's (CMSEQ) and the relationship they share (RELID).

Input: the related-records dataset (RELREC), one record for each member of a relationship: the subject, the domain and sequence number of the related record and the relationship's identifier.

Variables:

AESEQ would be the sequence number of an adverse event that is a member of the relationship.
CMSEQ would be the sequence number of a medication of the same subject's same relationship.
RELID would be the identifier of the relationship they share.

Note: every medication of a relationship is to pair with each of its events, yet the earlier choice of the relationship's first medication is still stated beside the pairing. The two cannot both hold, so the specification is rejected before any record is read and no artifact is accepted.

How to fix

Decide whether an event takes every medication of its relationships or one of them. For one row for each event and medication, remove the order and the choice of the first record:

  - id: PAIRS
    dataset: AEMEM
    inner_join: CMMEM
    key: [USUBJID, RELID]
    derivations:
      USUBJID: {type: str, derivation: AEMEM.USUBJID}
      RELID: {type: str, derivation: AEMEM.RELID}
      AESEQ: {type: int, derivation: AEMEM.SEQ}
      CMSEQ: {type: int, derivation: CMMEM.SEQ}

For one row for each event with one chosen medication, drive the rows by the event members and read the medication through an intermediate over the medication members that declares its own key, order_by and keep, with no inner_join.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: prohibited_construct
rule: LOOKUP-27

expected/error.yaml

phase: validation
condition: prohibited_construct
spec_paths:
  - intermediates.PAIRS.order_by
  - intermediates.PAIRS.keep
  - intermediates.PAIRS.inner_join
rule: LOOKUP-27
context:
  intermediate: PAIRS
  construct: order_by

YAML specification

1 spec file

spec.yaml

Edit66 lines

1yamaa: "1.0"2type: spec3domain: AECM4keys: [USUBJID, AESEQ, CMSEQ]5input:6  RELREC: input/relrec.csv78output:9  path: aecm.csv10  columns: [USUBJID, AESEQ, CMSEQ, RELID]1112intermediates:13  # The adverse event members of each relationship, one record each.14  - id: AEMEM15    dataset: RELREC16    filter: "RELREC.RDOMAIN = 'AE' AND RELREC.IDVAR = 'AESEQ'"17    derivations:18      SEQ: {type: int, derivation: IDVARVAL}1920  # The medication members of each relationship.21  - id: CMMEM22    dataset: RELREC23    filter: "RELREC.RDOMAIN = 'CM' AND RELREC.IDVAR = 'CMSEQ'"24    derivations:25      SEQ: {type: int, derivation: IDVARVAL}2627  # One record per adverse event and medication of the same relationship,28  # yet the earlier choice of the relationship's first medication is still29  # written beside the pairing.30  - id: PAIRS31    dataset: AEMEM32    inner_join: CMMEM33    key: [USUBJID, RELID]34    order_by: [CMMEM.SEQ]35    keep: first36    derivations:37      USUBJID: {type: str, derivation: AEMEM.USUBJID}38      RELID: {type: str, derivation: AEMEM.RELID}39      AESEQ: {type: int, derivation: AEMEM.SEQ}40      CMSEQ: {type: int, derivation: CMMEM.SEQ}4142columns:43  - name: USUBJID44    type: str45    label: Unique Subject Identifier4647  - name: AESEQ48    type: int49    label: Sequence Number of the Adverse Event5051  - name: CMSEQ52    type: int53    label: Sequence Number of the Medication5455  - name: RELID56    type: str57    label: Relationship Identifier5859rows:60  - id: pairs61    dataset: PAIRS62    derivations:63      USUBJID: PAIRS.USUBJID64      AESEQ: PAIRS.AESEQ65      CMSEQ: PAIRS.CMSEQ66      RELID: PAIRS.RELID

Inputs

Under review1 source file

input/relrec.csv

Edit11 rows

input/relrec.csv
STUDYID	RDOMAIN	IDVAR	IDVARVAL	RELTYPE	RELID
TOY	AE	AESEQ	1	—	1
TOY	AE	AESEQ	2	—	1
TOY	CM	CMSEQ	1	—	1
TOY	CM	CMSEQ	2	—	1
TOY	AE	AESEQ	3	—	2
TOY	CM	CMSEQ	3	—	2
TOY	AE	AESEQ	4	—	3
TOY	CM	CMSEQ	3	—	3
TOY	AE	AESEQ	1	—	1
TOY	CM	CMSEQ	1	—	1
TOY	CM	CMSEQ	2	—	1

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
USUBJID	Unique Subject Identifier	Char	Derived	Set per constructed row; see the Row construction sheet.	SDTM	1
AESEQ	Sequence Number of the Adverse Event	Num	Derived	Set per constructed row; see the Row construction sheet.	SDTM	2
CMSEQ	Sequence Number of the Medication	Num	Derived	Set per constructed row; see the Row construction sheet.	SDTM	3
RELID	Relationship Identifier	Char	Derived	Set per constructed row; see the Row construction sheet.	SDTM	4

Template	Include when	USUBJID	AESEQ	CMSEQ	RELID
pairs		Copy USUBJID from the first AEMEM record matching on USUBJID and RELID, ordered by CMMEM.SEQ, where USUBJID is derived as {'type': 'str', 'derivation': 'AEMEM.USUBJID'}, and no match yields blank	Copy AESEQ from the first AEMEM record matching on USUBJID and RELID, ordered by CMMEM.SEQ, where AESEQ is derived as {'type': 'int', 'derivation': 'AEMEM.SEQ'}, and no match yields blank	Copy CMSEQ from the first AEMEM record matching on USUBJID and RELID, ordered by CMMEM.SEQ, where CMSEQ is derived as {'type': 'int', 'derivation': 'CMMEM.SEQ'}, and no match yields blank	Copy RELID from the first AEMEM record matching on USUBJID and RELID, ordered by CMMEM.SEQ, where RELID is derived as {'type': 'str', 'derivation': 'AEMEM.RELID'}, and no match yields blank

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/relrec.csv

Your review

Mapping spec