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Summary
README.mdPublic entries: Python and R. Passing coverage requires an installed inventory.
Goal: require a value only on the rows a condition selects, and allow a share of the rows to lack one: a share at its limit, a deliberately violated warning over it, and a condition that selects no row.
Input: one spec.yaml over adverse events, one row per subject and
event, each with a reported and a coded term (AETERM, AEDECOD), a
seriousness flag (AESER), a death flag (AESDTH) and start and end dates
(AESTDTC, AEENDTC).
Checks:
- A coded term is required on every event with a reported term. Events without a reported term are not checked.
- A death flag is required on every serious event. Events that are not serious, or whose seriousness is unknown, are not checked.
- At most a quarter of the events may lack a start date, and the boundary counts as held.
- At most a quarter of the events with a reported term may lack an end date. Exceeding that share produces a warning: the run still succeeds and the run report lists the affected events.
- An end date is required on every event that resulted in death. If no event is selected, the share is zero and the check holds.
The run report (ae-checks.csv) has one row per item the run handled, each
naming the dataset (ARTIFACT), the kind of item (KIND), where the spec
states it (SPEC_PATH) and the item's name (NAME, identifying an input,
row source, reported event, column, or check): the run and its outcome
(OUTCOME), the events read and built, each output column with its missing
values and longest text, then one row per check in column order. A check row
carries its label (ID), the column it covers (TARGET), the rule it
applies (RULE), its SEVERITY, and how many events failed out of every
event of the dataset (COUNT, TOTAL). A held check leaves CONDITION
and KEYS empty, reports zero failures and has empty details ({}). The
violated warning names its condition, lists the affected events in KEYS,
and reports in DETAILS its column and the number of events it checked.
Note: a check with a condition reads only the rows the condition selects; a row whose condition is false or unknown passes whatever it holds. A share is the selected rows lacking the value over the selected rows, so rows outside the condition count in neither, and a condition that selects no row has a share of zero.
Inputs
Under review1 source fileinput/ae_raw.csv
Edit8 rows| USUBJID | AESEQ | AETERM | AEDECOD | AESER | AESDTH | AESTDTC | AEENDTC |
|---|---|---|---|---|---|---|---|
| 1 | HEADACHE | Headache | N | — | 2024-01-03 | 2024-01-05 | |
| 2 | NAUSEA | Nausea | Y | N | 2024-01-10 | — | |
| 1 | RASH | Rash | N | — | — | 2024-02-09 | |
| 2 | DIZZINESS | Dizziness | — | — | 2024-02-15 | 2024-02-16 | |
| 1 | FATIGUE | Fatigue | Y | N | — | 2024-03-20 | |
| 2 | — | — | N | — | 2024-03-25 | — | |
| 1 | COUGH | Cough | N | — | 2024-04-02 | 2024-04-06 | |
| 2 | FEVER | Pyrexia | Y | N | 2024-04-10 | — |
Expected output
Under review24 expected rowsexpected/ae-checks.csv
Edit16 rows| ARTIFACT | KIND | SPEC_PATH | NAME | ID | TARGET | RULE | SEVERITY | OUTCOME | CONDITION | COUNT | TOTAL | KEYS | DETAILS |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ae.csv | run | output | — | — | — | — | — | succeeded | — | 8 | — | — | {} |
| ae.csv | input | input.AE_RAW | AE_RAW | — | — | — | — | — | — | 8 | — | — | {"bytes":364,"path":"input/ae_raw.csv","profile":"csv"} |
| ae.csv | rows | base | AE_RAW | — | — | — | — | — | — | 8 | 8 | — | {} |
| ae.csv | column | columns.USUBJID | USUBJID | — | — | — | — | — | — | 0 | 8 | — | {"max_length":3} |
| ae.csv | column | columns.AESEQ | AESEQ | — | — | — | — | — | — | 0 | 8 | — | {} |
| ae.csv | column | columns.AETERM | AETERM | — | — | — | — | — | — | 1 | 8 | — | {"max_length":9} |
| ae.csv | column | columns.AEDECOD | AEDECOD | — | — | — | — | — | — | 1 | 8 | — | {"max_length":9} |
| ae.csv | column | columns.AESER | AESER | — | — | — | — | — | — | 1 | 8 | — | {"max_length":1} |
| ae.csv | column | columns.AESDTH | AESDTH | — | — | — | — | — | — | 5 | 8 | — | {"max_length":1} |
| ae.csv | column | columns.AESTDTC | AESTDTC | — | — | — | — | — | — | 2 | 8 | — | {"max_length":10} |
| ae.csv | column | columns.AEENDTC | AEENDTC | — | — | — | — | — | — | 3 | 8 | — | {"max_length":10} |
| ae.csv | check | columns.AEDECOD.verifications[0].not_missing | not_missing | coded-when-reported | AEDECOD | CHECK-5 | error | held | — | 0 | 8 | — | {} |
| ae.csv | check | columns.AESDTH.verifications[0].not_missing | not_missing | death-when-serious | AESDTH | CHECK-5 | error | held | — | 0 | 8 | — | {} |
| ae.csv | check | columns.AESTDTC.verifications[0].not_missing | not_missing | start-mostly-present | AESTDTC | CHECK-5 | error | held | — | 0 | 8 | — | {} |
| ae.csv | check | columns.AEENDTC.verifications[0].not_missing | not_missing | end-mostly-present | AEENDTC | CHECK-5 | warning | violated | not_missing_failed | 2 | 8 | [{"AESEQ":2,"USUBJID":"S-1"},{"AESEQ":2,"USUBJID":"S-4"}] | {"column":"AEENDTC","denominator":7} |
| ae.csv | check | columns.AEENDTC.verifications[1].not_missing | not_missing | end-when-fatal | AEENDTC | CHECK-5 | error | held | — | 0 | 8 | — | {} |
expected/ae.csv
Edit8 rows| USUBJID | AESEQ | AETERM | AEDECOD | AESER | AESDTH | AESTDTC | AEENDTC |
|---|---|---|---|---|---|---|---|
| 1 | HEADACHE | Headache | N | — | 2024-01-03 | 2024-01-05 | |
| 2 | NAUSEA | Nausea | Y | N | 2024-01-10 | — | |
| 1 | RASH | Rash | N | — | — | 2024-02-09 | |
| 2 | DIZZINESS | Dizziness | — | — | 2024-02-15 | 2024-02-16 | |
| 1 | FATIGUE | Fatigue | Y | N | — | 2024-03-20 | |
| 2 | — | — | N | — | 2024-03-25 | — | |
| 1 | COUGH | Cough | N | — | 2024-04-02 | 2024-04-06 | |
| 2 | FEVER | Pyrexia | Y | N | 2024-04-10 | — |
Human review and assessment
| Variable Name | Variable Label | Type | Length | Controlled Terms or Format | Origin | Core | Conversion Definition | Variable Type | Variable Order | Comments for Define |
|---|---|---|---|---|---|---|---|---|---|---|
| USUBJID | Unique Subject Identifier | Char | Collected | Copy value from AE_RAW.USUBJID. | SDTM | 1 | ||||
| AESEQ | Sequence Number | Num | Collected | Copy value from AE_RAW.AESEQ. | SDTM | 2 | ||||
| AETERM | Reported Term for the Adverse Event | Char | Collected | Copy value from AE_RAW.AETERM. | SDTM | 3 | ||||
| AEDECOD | Dictionary-Derived Term | Char | Collected | Copy value from AE_RAW.AEDECOD. | SDTM | 4 | ||||
| AESER | Serious Event | Char | Collected | Copy value from AE_RAW.AESER. | SDTM | 5 | ||||
| AESDTH | Results in Death | Char | Collected | Copy value from AE_RAW.AESDTH. | SDTM | 6 | ||||
| AESTDTC | Start Date/Time of Adverse Event | Char | Collected | Copy value from AE_RAW.AESTDTC. | SDTM | 7 | ||||
| AEENDTC | End Date/Time of Adverse Event | Char | Collected | Copy value from AE_RAW.AEENDTC. | SDTM | 8 |
| 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 |
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