Spring boot upgrade 3.4 #11316
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Spring boot upgrade 3.4 #11316
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* Add Columnar SQL file to init Clickhouse DB * Refactored Mapper xml to extract StudyViewFilterMapper
* ✅ Add Unit test for StudyViewMapper Clickhouse * ✅ Update db props to include mysql and clickhouse datasources to fix tests * Address comments * Rename package to clickhouse * Update to static final * Use bean name instead of qualifier
…10803) * Create new wide table sql file and rename package * Remove genomic_event view * Add AlterationFilter to mutated_genes endpoint * Add AlterationFilter to mutated-genes endpoint * Fix unit test * Fix sonar issues * Add test for mutation types and status * remove unused imports
* add missing poc clinical data binning function
* Add sample_mv materialized view and use it in mappers
…al#10824) * Add Support for TotalProfiledCase Counts for Mutated-genes endpoint. * Create sql files to create new tables * Add unit test for totalProfiledCount * Add matching gene panel ids * Add TotalProfiledCountsWithoutPanelData * Add profileCount for genes without gene panel data * Add Comments for SQL * Update matching Gene Panel Ids * Clean up code * Fix test * Add query to get correct Gene Panels * Fix unit test * Add comments
* working poc * refactor logic into service, so clean * refactor for parameters builder, simplify min max logic, streamline service call * remove unused services and imports * remove more unused imports
* Implement molecular profile count endpoint using Clickhouse * Cleanup
* ✨ Add CNA Gene Endpoint * 🐛 Fix StudyViewFilterMapper.xml to allow ability to filter on gene and alteration * Fix merge conflict * Address comments * Fix unit tests * Fix sonar issues
* ✨ Add StructuralVariant-genes endpoint * Fix sonar issues * Update MatchingGenePanel request to return list * Create and use sample_derive * Update where sample_derived is stored to fix unit test
…Portal#10849) Co-authored-by: Bryan Lai <[email protected]>
* use clinical_data_derived instead of sample_clinical_attribute_numeric_mv and patient_clinical_attribute_numeric_mv * use clinical_attribute_meta instead of sample_clinical_attribute_numeric_mv and patient_clinical_attribute_numeric_mv * remove unused clinical data count methods and SQL * fix numericalClinicalDataCountFilter * Move CategoricalClinicalAttributeFilter to repository * remove unused columns * Add override to methods --------- Co-authored-by: haynescd <[email protected]>
…ioPortal#10857) * Add patient_id column to genomic_event_derived * Update sql to convert list of patients to list of samples
* refactor to use clickhouse * filter out empty attr values * edit comment * fix sonarcloud issues * use parallel stream, shaves off 5s * use newer mapping annotation
* simplify clinical data binning related SQL * fix numericalClinicalDataCountFilter
* Add Clinical Events Timeline counts endpoint * Add comments for StudyViewFilter
* Fix alteration count services * Only add genes that are protein coding to gene_panel_to_gene table for WES * fix test * fix sonar issues * Add documentation for filtering out WES
…y clickhouse_enabled is set (cBioPortal#11256) * Update cBioPortal to dynamically load ch Components only when property clickhouse_enabled is set * Update env var for circleCi
* Merge genomic data bins working * Workaround for clickhouse bug in numerical data parsing --------- Co-authored-by: alisman <[email protected]>
* fix CNA query for genomic data filter * rename one of the cna_query statements to cna_count_query to avoid table name clash
…#11272) * make sure study ids exist before using them in filter SQL * add involved cancer studies into StudyViewFilterHelper
…-script simplify connection checks for circleci api tests
…r-build Improve circleci api tests by removing redundant image builds
…l#11262) * add more unit tests with clickhouse service methods * fix sonar issues * fix study view service errors --------- Co-authored-by: Bryan Lai <[email protected]>
…tal#11292) Co-authored-by: Bryan Lai <[email protected]>
…tal#11274) * Use prepared statements to avoid injection attack and clickhouse native array to improve performance * Dynamically calculate sample identifiers in study view filter helper
…BioPortal#11274)" This reverts commit 7ea2fe3.
…tal#11296) * Use prepared statements to avoid injection attack and clickhouse native array to improve performance * Dynamically calculate sample identifiers in study view filter helper
* Remove CH code from legacy class and remove material_view.sql * Update CH Test container to not use material_view.sql --------- Co-authored-by: haynescd <[email protected]>
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