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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: carry an analysis date (ADT), study day (ADY), and measured
value (AVAL) into analysis visits (AVISIT).
Input: pre-derived vital signs records, one per measurement, with a study day that can be missing.
Variables:
AVISITwould beSCREENINGbefore day 0,BASELINEon days 0 and 1,WEEK 2on days 2 to 21,WEEK 4on days 22 to 42, andPOST-TREATMENTfrom day 43. It is blank when the study day is missing.
Note: analysis visit is part of each record's identity. A record with no study day has no analysis visit, so the completed dataset fails its identity check and no artifact is accepted.
How to fix
Decide whether the record belongs in an analysis visit. If a governed source supplies the missing study day, correct that source. Otherwise, exclude the record before constructing the output rows:
rows:
- id: windowed
filter: "ADVS_RAW.ADY IS NOT NULL"
If the dataset must retain measurements without a visit, identify rows
by the collected record instead, for example with VSSEQ in keys.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- output
- condition
- missing_key
- rule
- OUTPUT-3
expected/error.yaml
phase: output
condition: missing_key
spec_paths:
- keys[3]
rule: OUTPUT-3
context:
column: AVISIT
missing_count: 1
keys:
- STUDYID: CATH
USUBJID: CATH-UCSD-0002
PARAMCD: SYSBP
AVISIT: null
Inputs
Under review1 source fileinput/advs_raw.csv
Edit6 rows| STUDYID | USUBJID | PARAMCD | VSSEQ | ADT | ADY | AVAL |
|---|---|---|---|---|---|---|
| CATH | SYSBP | 1 | 2025-01-08 | 1 | 132 | |
| CATH | SYSBP | 2 | 2025-01-22 | 15 | 138 | |
| CATH | SYSBP | 3 | 2025-02-05 | 29 | 130 | |
| CATH | SYSBP | 1 | 2025-02-08 | 1 | 118 | |
| CATH | SYSBP | 2 | 2025-02-21 | 14 | 122 | |
| CATH | SYSBP | 3 | — | — | 120 |
Unexpected Output
Under review6 rows presented to the failing check - not an accepted artifactexpected/advs.csv
Edit6 rows| STUDYID | USUBJID | PARAMCD | VSSEQ | ADT | ADY | AVAL | AVISIT |
|---|---|---|---|---|---|---|---|
| CATH | SYSBP | 1 | 2025-01-08 | 1 | 132 | BASELINE | |
| CATH | SYSBP | 2 | 2025-01-22 | 15 | 138 | WEEK 2 | |
| CATH | SYSBP | 3 | 2025-02-05 | 29 | 130 | WEEK 4 | |
| CATH | SYSBP | 1 | 2025-02-08 | 1 | 118 | BASELINE | |
| CATH | SYSBP | 2 | 2025-02-21 | 14 | 122 | WEEK 2 | |
| CATH | SYSBP | 3 | — | — | 120 | — |
Human review and assessment
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADVS | STUDYID | Study Identifier | character | Copy value from ADVS_RAW.STUDYID. | Predecessor | ||
| ADVS | USUBJID | Unique Subject Identifier | character | Copy value from ADVS_RAW.USUBJID. | Predecessor | ||
| ADVS | PARAMCD | Parameter Code | character | Copy value from ADVS_RAW.PARAMCD. | Predecessor | ||
| ADVS | VSSEQ | Sequence Number | numeric | Copy value from ADVS_RAW.VSSEQ. | Predecessor | ||
| ADVS | ADT | Analysis Date | numeric | ISO 8601 | Copy value from ADVS_RAW.ADT. | Predecessor | |
| ADVS | ADY | Analysis Relative Day | numeric | Copy value from ADVS_RAW.ADY. | Predecessor | ||
| ADVS | AVAL | Analysis Value | numeric | Copy value from ADVS_RAW.AVAL. | Predecessor | ||
| ADVS | AVISIT | Analysis Visit | character | Band ADVS_RAW.ADY at 0, 2, 22, 43 into "SCREENING", "BASELINE", "WEEK 2", "WEEK 4" and "POST-TREATMENT", intervals closed on the left. | Derived |
| Version | Date | Author | Description | Reviewer | Sign-off |
|---|---|---|---|---|---|
| 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 |