[BI-2134] Append Experimental Dataset Workflow#359
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…eeding-Insight/bi-api into experiment-processor-refactor
davedrp
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Jul 8, 2024
...ter/services/processors/experiment/appendoverwrite/middleware/commit/BrAPIDatasetCommit.java
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davedrp
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...services/processors/experiment/appendoverwrite/middleware/commit/BrAPIObservationCommit.java
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all tests passing
davedrp
approved these changes
Jul 11, 2024
| private WorkflowUpdate<BrAPIObservation> brAPIObservationUpdate; | ||
| private Optional<WorkflowCreation.BrAPICreationState> createdBrAPIObservations; | ||
| private Optional<WorkflowUpdate.BrAPIUpdateState> priorBrAPIObservations; | ||
| private Optional<WorkflowUpdate.BrAPIUpdateState> updatedObservations; |
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this field gets initialized, but is never used.
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| public abstract class Middleware<T> { | ||
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| Middleware next; |
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Use type arguments (see suggestions below)
Suggested change
| Middleware next; | |
| Middleware<T> next; |
| public abstract class Middleware<T> { | ||
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| Middleware next; | ||
| Middleware prior; |
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Suggested change
| Middleware prior; | |
| Middleware<T> prior; |
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Other change in this file may also need to be modified for this to work
| return this.next == null ? this : this.next.getLastLink(); | ||
| } | ||
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| private Middleware getFirstLink() { |
| * @return A PendingImportObject containing the dataset with the existing list and reference ID | ||
| * @throws IllegalStateException if external references weren't found for the list | ||
| */ | ||
| public PendingImportObject<BrAPIListDetails> constructPIOFromDataset(BrAPIListDetails dataset, Program program) { |
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the parameter program is not used
| * @return An Optional containing a ValidationError if validation fails, or Optional.empty() if validation passes. | ||
| */ | ||
| @Override | ||
| public Optional<ValidationError> validateField(String fieldName, String value, Trait variable) { |
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| * @return Optional<ValidationError> Optional containing the first validation error encountered, if any | ||
| */ | ||
| @Override | ||
| public Optional<ValidationError> validateField(String fieldName, String value, Trait variable) { |
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| * @return an Optional containing a ValidationError if validation fails, otherwise an empty Optional | ||
| */ | ||
| @Override | ||
| public Optional<ValidationError> validateField(String fieldName, String value, Trait variable) { |
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| * @return Optional containing a ValidationError if validation fails, or Optional.empty() if successful. | ||
| */ | ||
| @Override | ||
| public Optional<ValidationError> validateField(String fieldName, String value, Trait variable) { |
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| * @return an Optional containing a ValidationError if validation fails, empty otherwise | ||
| */ | ||
| @Override | ||
| public Optional<ValidationError> validateField(String fieldName, String value, Trait variable) { |
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This was referenced Aug 13, 2024
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Description
Story: BI-2134
Workflow selection code (BI-2122) will be shown as changes in here until it is merged into develop
Updated experiment import integration tests for appending or overwriting observations
Features and fixes merged into develop since the refactor started are not included
BI-2128 has been addressed in the refactor---blank values will not overwrite existing observation values
When exceptions are caught in the workflow, any compensating steps to restore the initial state are executed before re-throwing the exception at the ExperimentFileImportService level.
Workflow Overview
Main entrypoint is AppendOverwritePhenotypesWorkflow
Middleware class is used to break down the workflow into composable steps that are joined as a linked list
Factories are used to encapsulate the entity, actions, and processed data
Common methods are saved into various service and injected as dependencies to the factories
FieldValidator is a @FunctionalInterface used to validate observation data against trait properties
Dependencies
Testing
some variations to check
Checklist: