* 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

* 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

* 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

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]>

…0857)

* 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) (#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

* Create new endpoint treatment/patient-counts/fetch

* Create StudyViewFilterHelper class

* ⬆️ Upgrade CH client Version

* Fix Merge Conflict issue

* Update Treatment event name

* Update to handle patient treatment filtering

* Fix sonar issues

* Fix sonar comments 2

…ent) (#10919)

* Add Sample Count Report Endpoint

* Push counting logic to sql

* Remove unused methods

* Update PatientTreatments to pass int from db for totalPatientTreatmentCount

* Fix tests

* Add unit test for sample Treatments

* Remove unused import

* Fix indentation

* Fix Sample Treatment Endpoint

* Fix Sample ID only StudyView Filter

* add unit tests for molecular-profile-counts-service
* fix multiple-study scenario

Update method name getGenomicDataCounts -> getMolecularProfileSampleCounts

Clickhouse implementations of mutation data counts & genomic data counts services

---------

Co-authored-by: Qi-Xuan Lu <[email protected]>

* Add tests for case list sample counts endpoint and fix merge of lists across studies

* Implement custom-data-bin-counts associated filter
* Create StudyViewFilterContext and Helper



---------

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

#10959)

* Update Treatment Endpoint to handle event_type TREATMENT, previously only searched on Treatment

* Handle all variations of Treatment

…#10974)

* Genomic and Generic Assay bin counts endpoints

fix clinical data NA counts for multiple studies
---------

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

* Fix CNA table definition

Fix rfc80 build

…10986)

* 🐛 Fix Mutated Genes Filter bug with Or logic

* ✅ Add Tests for Mutated-genes,Cna-genes, and structural-variant filters