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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: show for each adverse event the reported term (AETERM), the coded term (AEDECOD), and the two safety groupings (SMQ01NAM, SMQ01CD, SMQ02NAM, SMQ02CD).

Input: collected adverse events carrying the reported term (AETERM) and the coded term (AEDECOD), plus a query dictionary carrying each coded term (TERM) under a grouping name (GRPNAME) with code (GRPID) and place (PREFIX).

Variables:

SMQ01NAM would be the name from the dictionary entry whose place is SMQ01 and whose term matches the coded term; blank when no entry matches.
SMQ01CD would be the code from that same SMQ01 entry; missing when no entry matches.
SMQ02NAM would be the name from the dictionary entry whose place is SMQ02 and whose term matches the coded term; blank when no entry matches.
SMQ02CD would be the code from that same SMQ02 entry; missing when no entry matches.

Note: one place holds one grouping. A coded term claimed by two dictionary entries in the same place has no single answer: choosing either entry would drop the other, and which one was dropped would depend on the order the dictionary happened to be stored in. The run is therefore rejected and no artifact is accepted.

How to fix

First decide how many queries the study reports. Every query the study analyses needs a place of its own, so move the second query claiming the term, Hypersensitivity, from SMQ01 to the next free place:

PREFIX,GRPNAME,GRPID,SCOPE,TERM
SMQ03,Hypersensitivity,20000214,BROAD,STEVENS-JOHNSON SYNDROME

A new place needs its own lookup and its own SMQ03NAM and SMQ03CD, because how many groupings an artifact carries is fixed when the study rules are written and not when the dictionary is read. Do not resolve the clash by keeping whichever query is stored first: it answers with a query the study did not choose, and it stops reporting the other one at all.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: join
condition: multiple_matches
rule: LOOKUP-10

expected/error.yaml

phase: join
condition: multiple_matches
spec_paths:
  - intermediates.SMQ1
rule: LOOKUP-10
context:
  intermediate: SMQ1
  dataset: QUERY
  key:
    - TERM
  intermediate_key:
    TERM: STEVENS-JOHNSON SYNDROME
  match_count: 2
  keys:
    - STUDYID: PILOT7
      USUBJID: P7-601
      AESEQ: 2

YAML specification

1 spec file

spec.yaml

Edit81 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADAE5keys: [STUDYID, USUBJID, AESEQ]6input:7  AE: input/ae.csv8  QUERY: {path: input/queries.csv, types: {GRPID: int}}9base: AE1011output:12  path: adae.csv13  columns: [STUDYID, USUBJID, AESEQ, AETERM, AEDECOD, SMQ01NAM, SMQ01CD,14            SMQ02NAM, SMQ02CD]1516intermediates:17  # One lookup per place: the dictionary entry in place SMQ01 (or SMQ02)18  # whose term is the event's coded term; no entry gives missing values.19  # Two entries for one term in the same place stop the run.20  - id: SMQ121    dataset: QUERY22    key: {TERM: AEDECOD}23    filter: "QUERY.PREFIX = 'SMQ01'"24    require_match: true2526  - id: SMQ227    dataset: QUERY28    key: {TERM: AEDECOD}29    filter: "QUERY.PREFIX = 'SMQ02'"30    require_match: true3132columns:33  - name: STUDYID34    type: str35    label: Study Identifier36    derivation: AE.STUDYID3738  - name: USUBJID39    type: str40    label: Unique Subject Identifier41    derivation: AE.USUBJID4243  - name: AESEQ44    type: int45    label: Sequence Number46    derivation: AE.AESEQ4748  - name: AETERM49    type: str50    label: Reported Term for the Adverse Event51    derivation: AE.AETERM5253  - name: AEDECOD54    type: str55    label: Dictionary-Derived Term56    derivation: AE.AEDECOD5758  - name: SMQ01NAM59    type: str60    label: Standardized MedDRA Query 01 Name61    derivation: SMQ1.GRPNAME6263  - name: SMQ01CD64    type: int65    label: Standardized MedDRA Query 01 Code66    derivation: SMQ1.GRPID6768  - name: SMQ02NAM69    type: str70    label: Standardized MedDRA Query 02 Name71    derivation: SMQ2.GRPNAME7273  - name: SMQ02CD74    type: int75    label: Standardized MedDRA Query 02 Code76    derivation: SMQ2.GRPID7778verifications:79  - row_count:80      min: 381      max: 3

Inputs

Under review2 source files

input/ae.csv

Edit3 rows

input/ae.csv
STUDYID	AESEQ	AETERM	AEDECOD
PILOT7	1	Widespread rash	RASH
PILOT7	2	Severe skin blistering	STEVENS-JOHNSON SYNDROME
PILOT7	1	Jaundice and dark urine	HEPATITIS

input/queries.csv

Edit4 rows

input/queries.csv
PREFIX	GRPNAME	GRPID	SCOPE	TERM
SMQ01	Severe Cutaneous Adverse Reactions	20000020	BROAD	RASH
SMQ01	Severe Cutaneous Adverse Reactions	20000020	NARROW	STEVENS-JOHNSON SYNDROME
SMQ01	Hypersensitivity	20000214	BROAD	STEVENS-JOHNSON SYNDROME
SMQ02	Hepatic Disorders	20000006	NARROW	HEPATITIS

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
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	AEDECOD	Dictionary-Derived Term	character	Copy value from AE.AEDECOD.	Predecessor
ADAE	SMQ01NAM	Standardized MedDRA Query 01 Name	character	Take GRPNAME from the QUERY record whose TERM equals AEDECOD, where QUERY.PREFIX = 'SMQ01', and a row with no match is an error.	Derived
ADAE	SMQ01CD	Standardized MedDRA Query 01 Code	numeric	Take GRPID from the QUERY record whose TERM equals AEDECOD, where QUERY.PREFIX = 'SMQ01', and a row with no match is an error.	Derived
ADAE	SMQ02NAM	Standardized MedDRA Query 02 Name	character	Take GRPNAME from the QUERY record whose TERM equals AEDECOD, where QUERY.PREFIX = 'SMQ02', and a row with no match is an error.	Derived
ADAE	SMQ02CD	Standardized MedDRA Query 02 Code	numeric	Take GRPID from the QUERY record whose TERM equals AEDECOD, where QUERY.PREFIX = 'SMQ02', and a row with no match is an error.	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/ae.csv

input/queries.csv

Your review

Mapping spec