yamaa As a clinical trial statistician or programmer, answer two short questions in Your review: the task and the inputs. Agreeing with both approves this benchmark; disagreeing with either needs a comment. Propose a fix with the Edit button on any source file, or add it to your comments.
We suggest spending no more than 5 minutes on a review. The other tabs beside Your review are background for assessment, not under review.
Summary
EditUnder reviewWhat this benchmark meansREADME.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: build an administration record for each administration
in a collected exposure (EX) record, carrying the collected
record's sequence number and EXTRT, EXDOSE, EXDOSU,
ASTDT, AENDT, and NDOSE through and numbering each
administration in ADOSEN.
Input: collected exposure records with treatment, dose, unit,
start and end dates, and a count of administrations: EXTRT,
EXDOSE, EXDOSU, EXSTDTC, EXENDTC, and EXDOSCNT.
Variables:
EXDOSEis the amount given at each administration.ASTDTis the first day the collected record covers, taken fromEXSTDTC.AENDTis the last day the collected record covers, taken fromEXENDTC.ADOSENnumbers the administrations built from one collected record, from1up to its count (EXDOSCNT). Only three administrations are written out in advance, so a record standing for more loses the ones past the third, and a record with a missing or zero count builds none.NDOSEis how many administrations the collected record stands for, taken fromEXDOSCNT. A record whoseNDOSEis larger than the highestADOSENbuilt from it rejects the run, so no artifact is accepted. The expected output records the completed dataset presented to that failing check.
Note: administrations built from one collected record share
that record's treatment, dose, unit, and dates; only ADOSEN
differs between them.
How to fix
The per-administration rows belong in the input data. Expand the
aggregate record into one collected record for each administration
upstream, and read those records here one to one. For
expected-but-uncollected rows, use the long-form planning input in
adam-advs-carryforward and enrich it from collected
data.
If the analysis genuinely needs only the totals, drop the administration level and key on the collected record instead:
keys: [STUDYID, USUBJID, EXSEQ]
Do not keep the administration level and widen the written-out administrations to whatever the current extract needs. It answers correctly only for data that has already been seen, and the next extract with a longer record loses administrations again without warning.
Expected failure
Editthe run is rejected; no artifact is acceptedexpected/error.yaml- phase
- verification
- condition
- assert_failed
- rule
- CHECK-12
expected/error.yaml
phase: verification
condition: assert_failed
spec_paths:
- verifications[0].assert
rule: CHECK-12
context:
verification_id: a-record-is-expanded-into-every-administration-it-holds
failure_count: 3
keys:
- STUDYID: YAMAA-01
USUBJID: YAMAA-01-102
EXSEQ: 1
ADOSEN: 1
- STUDYID: YAMAA-01
USUBJID: YAMAA-01-102
EXSEQ: 1
ADOSEN: 2
- STUDYID: YAMAA-01
USUBJID: YAMAA-01-102
EXSEQ: 1
ADOSEN: 3
Inputs
Under review1 source fileinput/ex.csv
Edit6 rows| STUDYID | USUBJID | EXSEQ | EXTRT | EXDOSE | EXDOSU | EXDOSFRQ | EXSTDTC | EXENDTC | EXDOSCNT |
|---|---|---|---|---|---|---|---|---|---|
| YAMAA-01 | 1 | Study Drug | 10 | mg | QD | 2025-04-01 | 2025-04-01 | 1 | |
| YAMAA-01 | 2 | Study Drug | 10 | mg | QD | 2025-04-08 | 2025-04-09 | 2 | |
| YAMAA-01 | 1 | Study Drug | 20 | mg | QD | 2025-04-02 | 2025-04-06 | 5 | |
| YAMAA-01 | 1 | Study Drug | 20 | mg | QD | 2025-04-10 | 2025-04-12 | 3 | |
| YAMAA-01 | 1 | Study Drug | 10 | mg | QD | 2025-04-15 | 2025-04-15 | 0 | |
| YAMAA-01 | 1 | Study Drug | 10 | mg | QD | 2025-04-16 | 2025-04-16 | — |
Unexpected Output
Under review9 rows presented to the failing check - not an accepted artifactexpected/adex.csv
Edit9 rows| STUDYID | USUBJID | EXSEQ | EXTRT | EXDOSE | EXDOSU | ASTDT | AENDT | ADOSEN | NDOSE |
|---|---|---|---|---|---|---|---|---|---|
| YAMAA-01 | 1 | Study Drug | 10 | mg | 2025-04-01 | 2025-04-01 | 1 | 1 | |
| YAMAA-01 | 2 | Study Drug | 10 | mg | 2025-04-08 | 2025-04-09 | 1 | 2 | |
| YAMAA-01 | 1 | Study Drug | 20 | mg | 2025-04-02 | 2025-04-06 | 1 | 5 | |
| YAMAA-01 | 1 | Study Drug | 20 | mg | 2025-04-10 | 2025-04-12 | 1 | 3 | |
| YAMAA-01 | 2 | Study Drug | 10 | mg | 2025-04-08 | 2025-04-09 | 2 | 2 | |
| YAMAA-01 | 1 | Study Drug | 20 | mg | 2025-04-02 | 2025-04-06 | 2 | 5 | |
| YAMAA-01 | 1 | Study Drug | 20 | mg | 2025-04-10 | 2025-04-12 | 2 | 3 | |
| YAMAA-01 | 1 | Study Drug | 20 | mg | 2025-04-02 | 2025-04-06 | 3 | 5 | |
| YAMAA-01 | 1 | Study Drug | 20 | mg | 2025-04-10 | 2025-04-12 | 3 | 3 |
Human review and assessment
| Dataset Name | Variable Name | Variable Label | Type | Codelist/Controlled Terms | Core | Computational Method | Origin |
|---|---|---|---|---|---|---|---|
| ADEX | STUDYID | Study Identifier | character | Copy value from EX.STUDYID. | Predecessor | ||
| ADEX | USUBJID | Unique Subject Identifier | character | Copy value from EX.USUBJID. | Predecessor | ||
| ADEX | EXSEQ | Sequence Number | numeric | Copy value from EX.EXSEQ. | Predecessor | ||
| ADEX | EXTRT | Name of Treatment | character | Copy value from EX.EXTRT. | Predecessor | ||
| ADEX | EXDOSE | Dose | numeric | Copy value from EX.EXDOSE. | Predecessor | ||
| ADEX | EXDOSU | Dose Units | character | Copy value from EX.EXDOSU. | Predecessor | ||
| ADEX | ASTDT | Analysis Start Date | numeric | ISO 8601 | Copy value from EX.EXSTDTC. | Predecessor | |
| ADEX | AENDT | Analysis End Date | numeric | ISO 8601 | Copy value from EX.EXENDTC. | Predecessor | |
| ADEX | ADOSEN | Administration Sequence Number | numeric | Set per constructed row; see the Row construction sheet. | Derived | ||
| ADEX | NDOSE | Number of Administrations | numeric | Copy value from EX.EXDOSCNT. | Predecessor |
| Template | Include when | ADOSEN |
|---|---|---|
| dose_1 | EX.EXDOSCNT >= 1 | Constant "1" |
| dose_2 | EX.EXDOSCNT >= 2 | Constant "2" |
| dose_3 | EX.EXDOSCNT >= 3 | Constant "3" |
| 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 |