Reject URL Path

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Summary

EditUnder reviewWhat this benchmark means

README.md

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

Goal: attempt one record per subject and laboratory test carrying the collected result in AVAL and the upper limit of normal for that test and the subject's sex in ANRHI.

Input: collected laboratory results carrying the collected result (LBSTRESN), test code (LBTESTCD), and sex (SEX), plus a reference table of upper limits by test code and sex.

Variables:

SEX would be the collected sex, taken from SEX in the collected records, and also chooses the limit.
AVAL would be the collected numeric result, taken from LBSTRESN.
ANRHI would be the upper limit of normal from the reference table for the record's test code and sex; missing when the table has no limit for that pair or the sex is missing.

Note: the reference table is named by a web address, https://reference.example.org/limits/lbref.csv, whose contents depend on when it is fetched and on who fetches it, so two runs of one study could read different limits while recording the same request. A run opens only stored files, never a web address, so the run is rejected before any data is read and no artifact is accepted.

How to fix

Fetch the governed limits once, record which version was received, and store that copy with the study:

input:
  LBREF: input/lbref.csv

Retrieval belongs to the step that assembles study data, where the received version can be recorded and reviewed. It is not part of building the analysis dataset.

Expected failure

Editthe run is rejected; no artifact is accepted

expected/error.yaml

phase: validation
condition: resource_path_uri_scheme
rule: FILE-5

expected/error.yaml

phase: validation
condition: resource_path_uri_scheme
spec_paths:
  - input.LBREF.path
rule: FILE-5
context:
  dataset: LBREF
  path: https://reference.example.org/limits/lbref.csv

YAML specification

1 spec file

spec.yaml

Edit53 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADLB5keys: [STUDYID, USUBJID, PARAMCD]6input:7  LB: input/lb.csv8  # A web address, not a stored file: rejected before any data is read.9  LBREF: https://reference.example.org/limits/lbref.csv10base: LB1112output:13  path: adlb.csv14  columns: [STUDYID, USUBJID, PARAMCD, SEX, AVAL, ANRHI]1516intermediates:17  - id: LBREF_LOOKUP18    dataset: LBREF19    key: {LBTESTCD: PARAMCD, SEX: SEX}20    require_match: true2122columns:23  - name: STUDYID24    type: str25    label: Study Identifier26    derivation: LB.STUDYID2728  - name: USUBJID29    type: str30    label: Unique Subject Identifier31    derivation: LB.USUBJID3233  - name: PARAMCD34    type: str35    label: Parameter Code36    derivation: LB.LBTESTCD3738  - name: SEX39    type: str40    label: Sex41    derivation: LB.SEX4243  - name: AVAL44    type: float45    label: Analysis Value46    derivation: LB.LBSTRESN4748  - name: ANRHI49    type: float50    label: Analysis Normal Range Upper Limit51    # The reference limit for the record's test code and sex; missing when52    # the table has no row for that pair or the sex is missing.53    derivation: LBREF_LOOKUP.ANRHI

Inputs

Under review1 source file

input/lb.csv

Edit2 rows

input/lb.csv
STUDYID	USUBJID	LBTESTCD	SEX	LBSTRESN
PILOT7		ALT	F	42
PILOT7		ALT	M	58

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	PARAMCD	Parameter Code	character	Copy value from LB.LBTESTCD.	Predecessor
ADLB	SEX	Sex	character	Copy value from LB.SEX.	Predecessor
ADLB	AVAL	Analysis Value	numeric	Copy value from LB.LBSTRESN.	Predecessor
ADLB	ANRHI	Analysis Normal Range Upper Limit	numeric	Take ANRHI from the LBREF record whose LBTESTCD equals PARAMCD and SEX equals SEX, 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/lb.csv

Your review

Mapping spec