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Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: show the order a specification runs in: rows are built first, then columns are added on top of the finished rows, and rows discarded along the way never reach the final checks.
Input: one spec.yaml over one lab-results file. Each record carries
a subject (USUBJID), a visit (VISIT), a test code (ALT or AST),
and a result that arrives as text.
Behavior:
- A record with no result never becomes a row: it is dropped before any
row is built. Each surviving record becomes one component row carrying
its test code, the test's full name (
PARAM), and its result (AVAL). - One summary row per subject-visit carries that visit's lowest result.
The visit whose results are all missing is discarded after its summary
is computed, so the final completeness check on
AVALpasses: it never sees the discarded row. - Text results become numbers while the rows are built, so the two
columns added afterwards read numbers, never text:
DOUBLEholds twice the result, andFLAGmarks results above 50 withH. - Every row carries the study identifier
YAMAA-01inSTUDYID.
Note: building rows may change the row count while adding columns may
not: each finished row gets exactly one DOUBLE and one FLAG.
Inputs
Under review1 source fileinput/lb.csv
Edit8 rows| USUBJID | VISIT | LBTESTCD | LBSTRESN |
|---|---|---|---|
| 1 | ALT | 32 | |
| 1 | AST | 45 | |
| 2 | ALT | 28 | |
| 2 | AST | — | |
| 3 | ALT | — | |
| 3 | AST | — | |
| 1 | ALT | 60 | |
| 1 | AST | 70 |
Expected output
Under review8 expected rowsexpected/adlb.csv
Edit8 rows| STUDYID | USUBJID | VISIT | PARAMCD | PARAM | AVAL | DOUBLE | FLAG |
|---|---|---|---|---|---|---|---|
| YAMAA-01 | 1 | ALT | Alanine Aminotransferase | 32 | 64 | N | |
| YAMAA-01 | 1 | AST | Aspartate Aminotransferase | 45 | 90 | N | |
| YAMAA-01 | 2 | ALT | Alanine Aminotransferase | 28 | 56 | N | |
| YAMAA-01 | 1 | ALT | Alanine Aminotransferase | 60 | 120 | H | |
| YAMAA-01 | 1 | AST | Aspartate Aminotransferase | 70 | 140 | H | |
| YAMAA-01 | 1 | LOW | Lowest Result of Visit | 32 | 64 | N | |
| YAMAA-01 | 2 | LOW | Lowest Result of Visit | 28 | 56 | N | |
| YAMAA-01 | 1 | LOW | Lowest Result of Visit | 60 | 120 | H |
Human review and assessment
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADLB | STUDYID | Study Identifier | character | Set constant value "YAMAA-01". | Assigned | ||
| ADLB | USUBJID | Unique Subject Identifier | character | Copy value from LB.USUBJID. | Predecessor | ||
| ADLB | VISIT | Visit Number | numeric | Copy value from LB.VISIT. | Predecessor | ||
| ADLB | PARAMCD | Parameter Code | character | Set per constructed row; see the Row construction sheet. | Derived | ||
| ADLB | PARAM | Parameter | character | Set per constructed row; see the Row construction sheet. | Derived | ||
| ADLB | AVAL | Analysis Value | numeric | Set per constructed row; see the Row construction sheet. | Derived | ||
| ADLB | DOUBLE | Twice the Analysis Value | numeric | Compute 2 * AVAL. | Derived | ||
| ADLB | FLAG | High Value Flag | character | If AVAL > 50 then "H"; otherwise "N". | Derived |
| Template | Include when | PARAMCD | PARAM | AVAL |
|---|---|---|---|---|
| components | LB.LBSTRESN IS NOT NULL | Copy LB.LBTESTCD | If LB.LBTESTCD = 'ALT' then "Alanine Aminotransferase"; otherwise "Aspartate Aminotransferase" | Copy LB.LBSTRESN |
| visit_low | AVAL IS NOT NULL | Constant "LOW" | Constant "Lowest Result of Visit" | Aggregate MIN(LB.LBSTRESN) over records matching on the shared output keys |
| 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 |