* 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

…rtal#10833)

* Implement molecular profile count endpoint using Clickhouse

* Cleanup

…rtal#10846)

* ✨ 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

…ase64) (cBioPortal#10898)

* 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

…11007)

…ompare them properly (cBioPortal#11021)

cBioPortal#11026)

* Merge Alteration Counts that have conflicting HugoSymbols for Study View Page

* Add comments

* add clickhouse custom data endpoints

* move custom data binning logic to binner and util class

* address review comments

* remove wildcards

* use basicDataBinner for custom data binning

* split custom and clinical data binning case

* make custom and clinical binning switch case more readable

---------

Co-authored-by: Bryan Lai <[email protected]>

… session (cBioPortal#10998)

* add samples field and handling to custom filters

---------

Co-authored-by: Bryan Lai <[email protected]>
Co-authored-by: Zhaoyuan (Ryan) Fu <[email protected]>

* Add NA for genomic-data-bin-counts

* Filtering with NA for genomic-data-bin-counts

* Fix when subqueries return empty for NA counts

* Refinement and comments

* Address comments

* Fix intersection with parens (cBioPortal#11032)

* Fix intersection with parens

* Demo rfc80 poc genomic data filter tests (cBioPortal#11036)

* add genomic data filter tests testing for missing NAs
* add NA genomic data filter tests


---------

Co-authored-by: Zhaoyuan (Ryan) Fu <[email protected]>

* Update to add QValue for Alteration Count Services

* Update to return List instead of Set

* Update to only add mut_sig to mutated_genes

* Remove unneeded Exception

* Add Qvalue for Structural Variant and CNA

* Update logic to add gistic to map

* Add NA for generic-assay-bin-counts

* Filtering with NA for generic-assay-data-bin-counts

* Parens precautions

* unskip generic assay api tests

---------

Co-authored-by: alisman <[email protected]>

…1037)

* Add Categorical Clinical Attribute NA filtering

* add api tests

---------

Co-authored-by: alisman <[email protected]>

* Add generic-assay-data-counts endpoint

* Update GenericAssayFilter to support NA's

* Add tests for generic assay data counts endpoint (categorical)

---------

Co-authored-by: alisman <[email protected]>

…BioPortal#11071)

…1076)

…ngle study (cBioPortal#11093)

* add separate property for clickhouse cache enabling


---------

Co-authored-by: Bryan Lai <[email protected]>
Co-authored-by: alisman <[email protected]>

* Fix trim trailing error

* reduce substr logic using negative end index

* Update clickhouse.sql

---------

Co-authored-by: Robert Sheridan <[email protected]>

…l#11120)

* add singleStudyUnfiltered condition to cacheable clickhouse methods

* add condition for density and violin plot data methods

* change singleStudyUnfiltered to just unfiltered

---------

Co-authored-by: Bryan Lai <[email protected]>

* use samples filtered without numerical clinical data filter when converting patient clinical data to sample clinical data
* make clinical data sample/patient ids match legacy ids, and use stable ids to count samples when internal id is null

…11132)

* Fix errant genetic profile matches due to overlapping type suffix

* fix legacy broken profile counts

* Fix clinical event availability grouping (broken for multi study where stable sampleids are repeated)

…1139)

…g for sample acquisition and specimen (cBioPortal#11143)

…ceptions (cBioPortal#11135)

Co-authored-by: alisman <[email protected]>