Master clean arch mutation endpoint with legacy query #11750
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fuzhaoyuan
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Oct 21, 2025
| * @param fetchAllMetaMutationsInProfileUseCase | ||
| * @param fetchAllMutationsInProfileUseCase | ||
| */ | ||
| public record GetMutationUseCases( |
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Rename this and usages to MutationUseCases
fuzhaoyuan
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Oct 21, 2025
| import org.cbioportal.legacy.web.parameter.Direction; | ||
| import org.cbioportal.shared.enums.ProjectionType; | ||
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| public record MutationSearchCriteria(ProjectionType projection, |
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It's a good design to package parameters. Maybe rename to MutationQueryOptions since there's no search involved?
fuzhaoyuan
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Oct 21, 2025
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| public ClickhouseMutationRepository(ClickhouseMutationMapper clickhouseMutationMapper) { | ||
| this.mapper = clickhouseMutationMapper; | ||
| this.molecularProfileCaseIdentifierUtil = new MolecularProfileCaseIdentifierUtil(); |
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Change this from new instance to injection (include it in the parameters)
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True, High-level modules should not depend on low-level modules
…s seperate method
… for grouping profiles and removing duplicates
…e information to clickhouse for faster processing and reducing the risk of doing redundant joins
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Signed-off-by: Zhaoyuan (Ryan) Fu <[email protected]>
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Fix #11640
Migrate Mutation to Clean Architecture with ClickHouse Support
This PR refactors mutation data endpoints from legacy architecture to clean architecture with ClickHouse support, as part of the broader backend migration to ClickHouse and clean architecture patterns
ARCHITECTURAL CHANGES
Usecase Layer
FetchAllMetaMutationsInProfileUseCase- Use case for retrieving MetaMutation data
FetchAllMutationsInProfileUseCase- Use case for retrieving Mutation data
GetMutationDataUseCases- provides a centralized way to access and utilize the use cases
Repository
MutationRepository- Interface that defines the methods for retrieving data from the repository
Infrastructure
ClickhouseMutationMapper- Maps the repository methods to the ClickhouseMutationMapper.xml file
ClickhouseMutationRepository- Implements the MutationRepository methods used to communicate with the database using ClickhouseMutationMapper.
Rest Layer
ColumnMutationController- New @Profile("clickhouse") rest controller supporting retrieval of Mutation and MutationMeta data
MapStruct Integration
###Simple Flow Diagram
Limitations
In the effort to reduce the number of joins and ensure the population of all required fields needed for the Mutation object in SUMMARY and DETAILED projections, I faced a cartesian effect due to no unique combination of values in genomic_event_derived. Please take a look at this draft PR for more details #11650
Reviewer Notes
Please feel free to review the overall structure and approach. Feedback on the direction, naming, or anything architectural is welcome, especially in the use case logic, queries and dependency setup.