Reject Numeric Filter

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: number collected laboratory results within each subject, with VISITSEQ giving the collection sequence for each result.

Input: collected laboratory results carrying the numeric result (LBSTRESN) and the collection sequence.

Variables:

VISITSEQ would number each result within its subject in collection-sequence order, counting only the results a stated condition selects; the other results would keep their rows with a missing number. The condition arrives as a bare number (7) instead of a comparison, so which results it selects is undefined, and the run is rejected before any data is read and no artifact is accepted.

How to fix

Decide which rows the study numbers, then state the rule as a comparison. When every collected result counts, leave the filter out entirely:

- name: VISITSEQ
  type: int
  derivation:
    row_number:
      window:
        group_by: [STUDYID, USUBJID]
        order_by: [LBSEQ]

When only some results count, write the condition they satisfy under window, for example filter: "LBSTRESN > 5.5", rather than numbering the rows by hand. The results it excludes keep their rows with a missing number.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: invalid_field_type
rule: SCHEMA-12

expected/error.yaml

phase: validation
condition: invalid_field_type
spec_paths:
  - columns.VISITSEQ.derivation.row_number.window.filter
rule: SCHEMA-12
context:
  expected: predicate
  actual: int

YAML specification

1 spec file

spec.yaml

Edit44 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [STUDYID, USUBJID, LBSEQ]6input:7  LB: input/lb.csv89output:10  path: adlb.csv11  columns: [STUDYID, USUBJID, LBSEQ, LBSTRESN, VISITSEQ]1213columns:14  - name: STUDYID15    type: str16    label: Study Identifier17    derivation: LB.STUDYID1819  - name: USUBJID20    type: str21    label: Unique Subject Identifier22    derivation: LB.USUBJID2324  - name: LBSEQ25    type: int26    label: Sequence Number27    derivation: LB.LBSEQ2829  - name: LBSTRESN30    type: float31    label: Numeric Result32    derivation: LB.LBSTRESN3334  # The defect: the window filter is the number 7 rather than a condition,35  # so the specification is rejected before any data is read.36  - name: VISITSEQ37    type: int38    label: Visit Sequence39    derivation:40      row_number:41        window:42          group_by: [STUDYID, USUBJID]43          order_by: [LBSEQ]44          filter: 7

Inputs

Under review1 source file

input/lb.csv

Edit2 rows

input/lb.csv
STUDYID	USUBJID	LBSEQ	LBSTRESN
PILOT7		1	5.2
PILOT7		2	5.8

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
ADLB	STUDYID	Study Identifier	character	Copy value from LB.STUDYID.	Predecessor
ADLB	USUBJID	Unique Subject Identifier	character	Copy value from LB.USUBJID.	Predecessor
ADLB	LBSEQ	Sequence Number	numeric	Copy value from LB.LBSEQ.	Predecessor
ADLB	LBSTRESN	Numeric Result	numeric	Copy value from LB.LBSTRESN.	Predecessor
ADLB	VISITSEQ	Visit Sequence	numeric	Row number within each group of STUDYID, USUBJID, ordered by LBSEQ.	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/lb.csv

Your review

Mapping spec