Read a Newline-Delimited Dataset-JSON File

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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 the visit number (AVISITN), the standardized result (AVAL), the collected result as written (AVALC) and the date and time of measurement (ADTM) into ADVS from a vital signs file in Dataset-JSON's newline-delimited form.

Input: one spec.yaml reading input/vs.ndjson, a Clinical Data Interchange Standards Consortium (CDISC) Dataset-JSON 1.1 file whose first line describes the dataset and whose every later line is one record. Each column states its own data type.

Variables:

AVISITN is the visit number, which the file stores as a floating-point number and the study reads as a whole number.
AVAL is the result in standard units; missing when not measured.
AVALC is the collected result exactly as the file writes it, trailing zeros included; missing when not measured.
ADTM is the date and time of the measurement; missing when not measured.

Note: a value takes the type its column states unless the study narrows it: a floating-point visit number is accepted as a whole number only when it is exactly whole, and a decimal can be kept as the text the sender wrote rather than read as a number. Dates and times are read from their ISO 8601 text, a time to the minute gaining zero seconds, and a null is missing.

YAML specification

1 spec file

spec.yaml

Edit54 lines

1yamaa: "1.0"2type: spec3model: ADaM4domain: ADVS5keys: [STUDYID, USUBJID, PARAMCD, AVISITN]6input:7  # A Dataset-JSON 1.1 file in its newline-delimited form. Each column's8  # dataType types its field, and a types entry may only narrow it: VISITNUM,9  # stored as a double, is narrowed to int, and VSORRES, a decimal, is read10  # as the text the file stores.11  VS:12    path: input/vs.ndjson13    types: {VISITNUM: int, VSORRES: str}1415output:16  path: advs.csv17  columns: [STUDYID, USUBJID, PARAMCD, AVISITN, AVAL, AVALC, ADTM]1819columns:20  - name: STUDYID21    type: str22    label: Study Identifier23    derivation: VS.STUDYID2425  - name: USUBJID26    type: str27    label: Unique Subject Identifier28    derivation: VS.USUBJID2930  - name: PARAMCD31    type: str32    label: Parameter Code33    derivation: VS.VSTESTCD3435  - name: AVISITN36    type: int37    label: Analysis Visit (N)38    derivation: VS.VISITNUM3940  - name: AVAL41    type: float42    label: Analysis Value43    derivation: VS.VSSTRESN4445  # The collected result keeps its trailing zeros.46  - name: AVALC47    type: str48    label: Analysis Value (C)49    derivation: VS.VSORRES5051  - name: ADTM52    type: datetime53    label: Analysis Datetime54    derivation: VS.VSDTC

Inputs

Under review1 source file

input/vs.ndjson

Edit

{"datasetJSONCreationDateTime": "2026-09-30T10:15:00", "datasetJSONVersion": "1.1.0", "fileOID": "www.example.org/PILOT7/VS", "sourceSystem": {"name": "Example EDC", "version": "5.1"}, "studyOID": "PILOT7", "metaDataVersionOID": "MDV.1", "itemGroupOID": "IG.VS", "records": 4, "name": "VS", "label": "Vital Signs", "columns": [{"itemOID": "IT.VS.STUDYID", "name": "STUDYID", "label": "Study Identifier", "dataType": "string", "length": 6, "keySequence": 1}, {"itemOID": "IT.VS.USUBJID", "name": "USUBJID", "label": "Unique Subject Identifier", "dataType": "string", "length": 6, "keySequence": 2}, {"itemOID": "IT.VS.VSTESTCD", "name": "VSTESTCD", "label": "Vital Signs Test Short Name", "dataType": "string", "length": 8, "keySequence": 3}, {"itemOID": "IT.VS.VISITNUM", "name": "VISITNUM", "label": "Visit Number", "dataType": "double", "keySequence": 4}, {"itemOID": "IT.VS.VSORRES", "name": "VSORRES", "label": "Result or Finding in Original Units", "dataType": "decimal"}, {"itemOID": "IT.VS.VSSTRESN", "name": "VSSTRESN", "label": "Numeric Result/Finding in Standard Units", "dataType": "double"}, {"itemOID": "IT.VS.VSDTC", "name": "VSDTC", "label": "Date/Time of Measurements", "dataType": "datetime"}]}
["PILOT7", "P7-741", "SYSBP", 1, "120.0", 120, "2025-03-04T09:20"]
["PILOT7", "P7-741", "SYSBP", 2, "118.50", 118.5, "2025-03-18T09:05:30"]
["PILOT7", "P7-742", "WEIGHT", 1, "70.00", 70, "2025-03-05T14:10"]
["PILOT7", "P7-742", "WEIGHT", 2, null, null, null]

Expected output

Under review4 expected rows

expected/advs.csv

Edit4 rows

expected/advs.csv
STUDYID	PARAMCD	AVISITN	AVAL	AVALC	ADTM
PILOT7	SYSBP	1	120	120.0	2025-03-04T09:20:00
PILOT7	SYSBP	2	118.5	118.50	2025-03-18T09:05:30
PILOT7	WEIGHT	1	70	70.00	2025-03-05T14:10:00
PILOT7	WEIGHT	2	—	—	—

Shaded columns are derived— = missing value

Human review and assessment

Dataset Name	Variable Name	Variable Label	Type	Codelist/Controlled Terms	Computational Method	Origin
ADVS	STUDYID	Study Identifier	character		Copy value from VS.STUDYID.	Predecessor
ADVS	USUBJID	Unique Subject Identifier	character		Copy value from VS.USUBJID.	Predecessor
ADVS	PARAMCD	Parameter Code	character		Copy value from VS.VSTESTCD.	Predecessor
ADVS	AVISITN	Analysis Visit (N)	numeric		Copy value from VS.VISITNUM.	Predecessor
ADVS	AVAL	Analysis Value	numeric		Copy value from VS.VSSTRESN.	Predecessor
ADVS	AVALC	Analysis Value (C)	character		Copy value from VS.VSORRES.	Predecessor
ADVS	ADTM	Analysis Datetime	numeric	ISO 8601	Copy value from VS.VSDTC.	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

R

Edit3 lines

1library(yamaa)23yamaa_spec("spec.yaml")$run()$output

Python

Edit3 lines

1import yamaa23yamaa.spec("spec.yaml").run().output

input/vs.ndjson

expected/advs.csv

Your review

Mapping spec

yamaa code

R

Python