Merge pull request #11748 from cBioPortal/release-6.4.0

Release 6.4.0

Author: dippindots

.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/v1.0.11/core-1.0.11.jar -P core/ ; cd core ; jar -xf core-1.0.11.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/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

@@ -30,7 +30,7 @@
     <frontend.artifactId>frontend-cbioportal</frontend.artifactId>
     <frontend.version>v6.4.0</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>1.0.2</derived_table.version>
 
     <!-- Version properties for dependencies that should have same version. -->

src/main/java/org/cbioportal/legacy/model/CosmicMutation.java

@@ -7,6 +7,8 @@ public class Info implements Serializable {
   @NotNull private String portalVersion;
   @NotNull private String dbVersion;
   @NotNull private String derivedTableVersion;
+  @NotNull private String genesetVersion;
+  @NotNull private String geneTableVersion;
   @NotNull private String gitBranch;
   @NotNull private String gitCommitId;
   @NotNull private String gitCommitIdAbbrev;
@@ -121,4 +123,20 @@ public String getDerivedTableVersion() {
   public void setDerivedTableVersion(String derivedTableVersion) {
     this.derivedTableVersion = derivedTableVersion;
   }
+
+  public String getGenesetVersion() {
+    return genesetVersion;
+  }
+
+  public void setGenesetVersion(String genesetVersion) {
+    this.genesetVersion = genesetVersion;
+  }
+
+  public String getGeneTableVersion() {
+    return geneTableVersion;
+  }
+
+  public void setGeneTableVersion(String geneTableVersion) {
+    this.geneTableVersion = geneTableVersion;
+  }
 }

src/main/java/org/cbioportal/legacy/model/Info.java

@@ -0,0 +1,43 @@
+package org.cbioportal.legacy.model;
+
+import java.io.Serializable;
+
+public class InfoDb implements Serializable {
+
+  private String dbSchemaVersion;
+  private String genesetVersion;
+  private String derivedTableSchemaVersion;
+  private String geneTableVersion;
+
+  public String getDbSchemaVersion() {
+    return dbSchemaVersion;
+  }
+
+  public void setDbSchemaVersion(String dbSchemaVersion) {
+    this.dbSchemaVersion = dbSchemaVersion;
+  }
+
+  public String getGenesetVersion() {
+    return genesetVersion;
+  }
+
+  public void setGenesetVersion(String genesetVersion) {
+    this.genesetVersion = genesetVersion;
+  }
+
+  public String getDerivedTableSchemaVersion() {
+    return derivedTableSchemaVersion;
+  }
+
+  public void setDerivedTableSchemaVersion(String derivedTableSchemaVersion) {
+    this.derivedTableSchemaVersion = derivedTableSchemaVersion;
+  }
+
+  public String getGeneTableVersion() {
+    return geneTableVersion;
+  }
+
+  public void setGeneTableVersion(String geneTableVersion) {
+    this.geneTableVersion = geneTableVersion;
+  }
+}