Merge remote-tracking branch 'upstream/master' into demo-clickhouse-only-db

# Conflicts:
#	pom.xml
#	src/main/resources/org/cbioportal/legacy/persistence/mybatis/CosmicCountMapper.xml
#	src/test/java/org/cbioportal/legacy/persistence/mybatis/CosmicCountMyBatisRepositoryTest.java

Author: alisman

.github/workflows/integration-test.yml

@@ -49,7 +49,10 @@ jobs:
               sed 's|session.service.url=.*|session.service.url=http://cbioportal-session:5001/api/sessions/my_portal/|' | \
               sed 's|feature.study.export=.*|feature.study.export=true|' | \
               sed 's|#\?session.endpoint.publisher-api-key=.*|session.endpoint.publisher-api-key=TEST|' \
-              > application.properties
+              > application.properties && \
+          DB_VERSION=$(mvn -q -DforceStdout -Dexpression=db.version -f $PORTAL_SOURCE_DIR/pom.xml help:evaluate || true) && \
+          if [ -n "$DB_VERSION" ]; then echo "db.version=${DB_VERSION}" > maven.properties; else : > maven.properties; fi && \
+          echo "maven.properties => $(cat maven.properties | tr -d '\n' || echo '(empty)')"
       - name: 'Dump Properties'
         working-directory: ./cbioportal-docker-compose
         run: cat config/application.properties

docker/web-and-data/Dockerfile

@@ -44,7 +44,7 @@ RUN apt-get update; apt-get install -y --no-install-recommends \
 RUN mkdir -p /cbioportal
 
 #Download core files
-RUN wget https://github.com/cBioPortal/cbioportal-core/releases/download/v1.0.10/core-1.0.10.jar -P core/ ; cd core ; jar -xf core-1.0.10.jar scripts/ requirements.txt ; chmod -R a+x scripts/ ; cd ..;
+RUN wget https://github.com/cBioPortal/cbioportal-core/releases/download/v1.0.15/core-1.0.15.jar -P core/ ; cd core ; jar -xf core-1.0.15.jar scripts/ requirements.txt ; chmod -R a+x scripts/ ; cd ..;
 
 
 COPY --from=build /cbioportal/src/main/resources/db-scripts /cbioportal/db-scripts

docs/Migration-Guide.md

@@ -2,6 +2,9 @@
 
 This page describes various changes deployers will need to make as they deploy newer versions of the portal.
 
+## v6.3 -> v6.4
+- The [v6.4.0](https://github.com/cBioPortal/cbioportal/releases/tag/v6.4.0) release includes database schema changes that aren’t backward compatible. Please review the [Database Migration Guide](https://docs.cbioportal.org/updating-your-cbioportal-installation/#running-the-migration-script) before upgrading.
+
 ## v6.2 -> v6.3
 - cBioPortal Database Migration: [v6.3.0](https://github.com/cBioPortal/cbioportal/releases/tag/v6.3.0) introduces breaking changes to the cBioPortal database schema. Please see the [Database Migration Guide](https://docs.cbioportal.org/updating-your-cbioportal-installation/#running-the-migration-script) before upgrading cBioPortal to v6.3.0.
 

docs/News.md

@@ -16,6 +16,11 @@
 ## April 17, 2025
 * Released a [new about page](https://about.cbioportal.org/), which includes a roadmap and an overview of 2024 accomplishments.
 
+## April 11, 2025
+*   **New Feature:** The Plots tab now has an option to draw a line connecting multiple samples from the same patient. This option is  available when data is visualized as a box plot and when there is data from multiple samples from the same patient. [Example: Mutation count in a cohort of primary grade II glioma vs patient-matched recurrences of all grades](https://www.cbioportal.org/study/plots?id=lgg_ucsf_2014&plots_horz_selection=%7B%22dataType%22%3A%22clinical_attribute%22%2C%22selectedDataSourceOption%22%3A%22SAMPLE_TYPE%22%7D&plots_vert_selection=%7B%22dataType%22%3A%22clinical_attribute%22%2C%22selectedDataSourceOption%22%3A%22MUTATION_COUNT%22%7D&plots_coloring_selection=%7B%22selectedOption%22%3A%22undefined_%7B%5C%22clinicalAttributeId%5C%22%3A%5C%22GRADE%5C%22%2C%5C%22patientAttribute%5C%22%3Afalse%2C%5C%22studyId%5C%22%3A%5C%22lgg_ucsf_2014%5C%22%7D%22%7D)
+![image](https://github.com/user-attachments/assets/c6f54905-6167-40b9-af7f-0ef07ad21fdb)
+
+
 ## January 28, 2025
 *   **Enhancement:** You can now re-order the stacked bar charts in the Plots Tab alphabetically, by the number of samples or by the data category in the plot. This enhancement allows you to create more ready-to-publish figures using cBioPortal. As usual, the plots created in the Plots Tab can be downloaded in different formats. [Example: specimen type for each cancer type in MSK-IMPACT Clinical Sequencing Cohort (MSK, Nat Med 2017](https://www.cbioportal.org/study/plots?id=msk_impact_2017&plots_horz_selection=%7B%22dataType%22%3A%22clinical_attribute%22%2C%22selectedDataSourceOption%22%3A%22CANCER_TYPE%22%2C%22mutationCountBy%22%3A%22MutationType%22%2C%22logScale%22%3A%22false%22%7D&plots_vert_selection=%7B%22selectedGeneOption%22%3A7157%2C%22dataType%22%3A%22clinical_attribute%22%2C%22selectedDataSourceOption%22%3A%22SPECIMEN_TYPE%22%2C%22mutationCountBy%22%3A%22MutationType%22%2C%22logScale%22%3A%22false%22%7D&plots_coloring_selection=%7B%7D)
 

docs/Updating-gene-and-gene_alias-tables.md

@@ -23,9 +23,6 @@ Execute these steps in case you want to reset your database to the most recent g
 
 2- If DB engine supports foreign key (FK) constraints, e.g. InnoDB, drop constraints:
 ```sql
-ALTER TABLE cosmic_mutation
-  DROP FOREIGN KEY cosmic_mutation_ibfk_1;
-
 ALTER TABLE uniprot_id_mapping
   DROP FOREIGN KEY uniprot_id_mapping_ibfk_1;
 ```
@@ -84,7 +81,6 @@ SELECT count(*) FROM cbioportal.gene_alias;
 8- Clean-up old data:
 ```sql
 SET SQL_SAFE_UPDATES = 0;
-DELETE FROM cosmic_mutation where ENTREZ_GENE_ID not in (SELECT ENTREZ_GENE_ID from gene);
 DELETE FROM sanger_cancer_census where ENTREZ_GENE_ID not in (SELECT ENTREZ_GENE_ID from gene);
 DELETE FROM uniprot_id_mapping where ENTREZ_GENE_ID not in (SELECT ENTREZ_GENE_ID from gene);
 DELETE FROM interaction where GENE_A not in (SELECT ENTREZ_GENE_ID from gene) or GENE_B not in (SELECT ENTREZ_GENE_ID from gene);
@@ -95,9 +91,6 @@ commit;
 
 9- If DB engine supports FK constraints, e.g. InnoDB, restore constraints:
 ```sql
-ALTER TABLE cosmic_mutation
-  ADD CONSTRAINT cosmic_mutation_ibfk_1 FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`);
-
 ALTER TABLE uniprot_id_mapping
   ADD CONSTRAINT uniprot_id_mapping_ibfk_1 FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`);
 ```

docs/deployment/customization/application.properties-Reference.md

@@ -389,18 +389,6 @@ A private token is required to access the OncoKB Data (for details see the secti
 oncokb.token=
 ```
 
-"cBioPortal>=" driver annotation sources in the settings menu of Results View can be hidden by turning off the following property (default: true):
-
-```
-show.cbioportal=true|false
-```
-
-"COSMIC>=" driver annotation sources in the settings menu of Results View can be hidden by turning off the following property (default: true):
-
-```
-show.cosmic=true|false
-```
-
 ## CIViC integration
 
 CIViC integration can be turned on or off with the following property (default: true):

pom.xml

@@ -12,7 +12,7 @@
 
   <groupId>io.github.cbioportal</groupId>
   <artifactId>cbioportal</artifactId>
-  <version>v6.3.7-SNAPSHOT</version>
+  <version>v6.4.1</version>
   <packaging>jar</packaging>
   <description>cBioPortal for Cancer Genomics</description>
 
@@ -28,9 +28,9 @@
     <!-- TODO replace with version of cbioportal frontend with compatible login url-->
     <frontend.groupId>io.github.cbioportal</frontend.groupId>
     <frontend.artifactId>frontend-cbioportal</frontend.artifactId>
-    <frontend.version>v6.3.6</frontend.version>
+    <frontend.version>v6.4.1</frontend.version>
     <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
-    <db.version>2.14.2</db.version>
+    <db.version>2.14.5</db.version>
     <derived_table.version>1.0.3</derived_table.version>
 
     <!-- Version properties for dependencies that should have same version. -->

src/e2e/java/org/cbioportal/ColumnStoreMutationControllerE2ETest.java

@@ -0,0 +1,132 @@
+package org.cbioportal;
+
+
+import org.cbioportal.application.rest.response.MutationDTO;
+import org.cbioportal.shared.enums.ProjectionType;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.web.client.TestRestTemplate;
+import org.springframework.boot.test.web.server.LocalServerPort;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.http.HttpMethod;
+import org.springframework.test.context.junit.jupiter.SpringExtension;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+@ExtendWith(SpringExtension.class)
+public class ColumnStoreMutationControllerE2ETest extends AbstractE2ETest{
+    
+    @Autowired
+    private TestRestTemplate restTemplate;
+
+    @LocalServerPort
+    private int port;
+
+    private static final com.fasterxml.jackson.databind.ObjectMapper OBJECT_MAPPER = new com.fasterxml.jackson.databind.ObjectMapper();
+
+
+    private MutationDTO[] callFetchMutationEndPoint(String testDataJson, ProjectionType projectionType)throws Exception{
+        HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.APPLICATION_JSON);
+        HttpEntity<String> requestEntity = new HttpEntity<>(testDataJson, headers);
+
+        ResponseEntity<String> response = restTemplate.exchange(
+            "http://localhost:" + port + "/api/column-store/mutations/fetch?projection=" 
+                    + projectionType.name(),
+            HttpMethod.POST,
+            requestEntity,
+            String.class
+        );
+
+        assertEquals(HttpStatus.OK, response.getStatusCode());
+        assertNotNull(response.getBody());
+        
+        return OBJECT_MAPPER.readValue(response.getBody(), MutationDTO[].class);
+
+    }
+
+    private String loadTestData(String filename) throws Exception {
+        return new String(java.nio.file.Files.readAllBytes(
+            java.nio.file.Paths.get("src/e2e/java/org/cbioportal/ColumnStoreMutationControllerE2ETest/" + filename)));
+    }
+    
+    @Test
+    void testFetchMutationEndPointWithDataJson_IdProjection() throws Exception {
+        // The json has two molecularProfileId and a sampleId and entrezGeneIds to restrict search  
+        // Two profiles meet this criteria 
+
+        String testDataJson = loadTestData("mutation_filter.json");
+        MutationDTO[] mutationResultID = callFetchMutationEndPoint(testDataJson, ProjectionType.ID);
+       
+        assertNotNull(mutationResultID, "Response should have mutation DTO");
+        assertEquals(2, mutationResultID.length, "Two mutations meet the search criteria of the json file");
+
+
+        //Compare the fields that should be equal
+        //MolecularProfile id should be identical
+        assertEquals(mutationResultID[0].molecularProfileId(), mutationResultID[1].molecularProfileId(), "molecularProfile IDs should match");
+        //study id should be identical; 
+        assertEquals(mutationResultID[0].studyId(), mutationResultID[1].studyId(), "study IDs should match");
+
+
+    }
+    @Test
+    void testFetchMutationEndPointWithDataJson_SummaryProjection() throws Exception {
+        // The json has two molecularProfileId and a sampleId and entrezGeneIds to restrict search  
+        // Two profiles meet this criteria 
+
+        String testDataJson = loadTestData("mutation_filter.json");
+        MutationDTO[] mutationResultSummary = callFetchMutationEndPoint(testDataJson,ProjectionType.SUMMARY);
+
+        assertNotNull(mutationResultSummary, "Response should have mutation DTO");
+        assertEquals(2, mutationResultSummary.length, "SUMMARY projection should not add or remove records");
+
+
+        //Compare the fields that should be equal
+        //MolecularProfile id should be identical
+        assertEquals(mutationResultSummary[0].molecularProfileId(), mutationResultSummary[1].molecularProfileId(), "molecularProfile IDs should match");
+
+        //study id should be identical; 
+        assertEquals(mutationResultSummary[0].studyId(), mutationResultSummary[1].studyId(), "study IDs should match");
+
+        // Testing different projection expose different fields 
+        // SUMMARY projection should not have gene present or any AlleleSpecificCopyNumber. AlleleSpecificCopyNumber is null for this mutation profile
+        for (MutationDTO mutationDTO : mutationResultSummary) {
+            assertNull(mutationDTO.gene(), "Response should not have gene present");
+            assertNull(mutationDTO.alleleSpecificCopyNumber(), "Response should not have AlleleSpecificCopyNumber present");
+        }
+
+    }
+
+    @Test
+    void testFetchMutationEndPointWithDataJson_DetailedProjection() throws Exception {
+        // The json has two molecularProfileId and a sampleId and entrezGeneIds to restrict search  
+        // Two profiles meet this criteria 
+
+        String testDataJson = loadTestData("mutation_filter.json");
+        MutationDTO[] mutationResultDetailed = callFetchMutationEndPoint(testDataJson,ProjectionType.DETAILED);
+
+        assertNotNull(mutationResultDetailed, "Response should have mutation DTO");
+        assertEquals(2, mutationResultDetailed.length, "DETAILED projection should not add or remove records");
+
+
+        //Compare the fields that should be equal 
+
+        //MolecularProfile id should be identical
+        assertEquals(mutationResultDetailed[0].molecularProfileId(), mutationResultDetailed[1].molecularProfileId(), "molecularProfile IDs should match");
+        //study id should be identical; 
+        assertEquals(mutationResultDetailed[0].studyId(), mutationResultDetailed[1].studyId(), "study IDs should match");
+
+        // Testing different projection expose different fields 
+        // Detailed projection should have gene present or any AlleleSpecificCopyNumber. AlleleSpecificCopyNumber is null for this mutation profile
+        for (MutationDTO mutationDTO : mutationResultDetailed) {
+            assertNotNull(mutationDTO.gene(), "Response should have gene present");
+            assertNull(mutationDTO.alleleSpecificCopyNumber(), "Response should not have AlleleSpecificCopyNumber present ");
+        }
+    }
+}

src/e2e/java/org/cbioportal/ColumnStoreMutationControllerE2ETest/mutation_filter.json

@@ -0,0 +1,7 @@
+ {
+   "sampleMolecularIdentifiers": [
+     {"sampleId": "P01_Pri", "molecularProfileId": "lgg_ucsf_2014_mutations"},
+     {"sampleId": "P05_Rec", "molecularProfileId": "lgg_ucsf_2014_mutations"}
+   ],
+   "entrezGeneIds": [287,2]
+ }

src/main/java/org/cbioportal/application/rest/mapper/AlleleSpecificCopyNumberMapper.java

@@ -0,0 +1,14 @@
+package org.cbioportal.application.rest.mapper;
+
+import org.cbioportal.application.rest.response.AlleleSpecificCopyNumberDTO;
+import org.cbioportal.legacy.model.AlleleSpecificCopyNumber;
+import org.mapstruct.Mapper;
+import org.mapstruct.factory.Mappers;
+
+@Mapper
+public interface AlleleSpecificCopyNumberMapper {
+  AlleleSpecificCopyNumberMapper INSTANCE = Mappers.getMapper(AlleleSpecificCopyNumberMapper.class);
+
+  AlleleSpecificCopyNumberDTO toAlleleSpecificCopyNumberDTO(
+      AlleleSpecificCopyNumber alleleSpecificCopyNumber);
+}