Release 6.4.0

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>v6.3.7</frontend.version>
     <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
-    <db.version>2.14.2</db.version>
+    <db.version>2.14.4</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/service/FrontendPropertiesServiceImpl.java

@@ -53,7 +53,6 @@ public enum FrontendProperty {
     google_tag_manager_id("google_tag_manager_id", null),
     analytics_report_url("analytics_report_url", null),
     oncoprint_hide_vus_default("oncoprint.hide_vus.default", null),
-    mycancergenome_show("mycancergenome.show", null),
     oncokb_public_api_url("oncokb.public_api.url", null),
     digitalslidearchive_iframe_url("digitalslidearchive.iframe.url", null),
     digitalslidearchive_meta_url("digitalslidearchive.meta.url", null),
@@ -78,7 +77,6 @@ public enum FrontendProperty {
     show_transcript_dropdown("show.transcript_dropdown", null),
     show_signal("show.signal", null),
     show_cbioportal("show.cbioportal", null),
-    show_cosmic("show.cosmic", null),
     show_ndex("show.ndex", null),
     survival_show_p_q_values_in_survival_type_table(
         "survival.show_p_q_values_in_survival_type_table", null),

src/main/resources/application.properties.EXAMPLE

@@ -116,8 +116,8 @@ skin.study_view.link_text=To build your own case set, try out our enhanced Study
 # skin.mutation_table.namespace_column.show_by_default=true
 
 # controls which columns from the mutation tables are immediately visible in mutation tables
-# skin.results_view.mutation_table.columns.show_on_init=Sample Id,Protein Change,Annotation,Mutation Type,Copy #,Cosmic,# Mut in Sample
-# skin.patient_view.mutation_table.columns.show_on_init=Gene,Protein Change,Annotation,Mutation Type,Copy #,Cosmic,# Mut in Sample
+# skin.results_view.mutation_table.columns.show_on_init=Sample Id,Protein Change,Annotation,Mutation Type,Copy #,# Mut in Sample
+# skin.patient_view.mutation_table.columns.show_on_init=Gene,Protein Change,Annotation,Mutation Type,Copy #,# Mut in Sample
 # skin.patient_view.copy_number_table.columns.show_on_init=Gene,CNA,Annotation,Cytoband,Cohort
 # skin.patient_view.structural_variant_table.columns.show_on_init=Gene 1,Gene2,Status,Annotation,Variant Class,Event Info,Connection Type
 
@@ -183,18 +183,13 @@ oncokb.token=
 
 # Enable "cBioPortal>=" driver annotation sources in the settings menu of Results View (true, false)
 show.cbioportal=true
-# Enable "COSMIC>=" driver annotation sources in the settings menu of Results View (true, false)
-show.cosmic=true
 
 # Enable Chang's hotspot list (true, false)
 show.hotspot=true
 
 # Enable Civic variant annotation (true, false)
 show.civic=true
 
-# Link to My Cancer Genome. Please disable (set to false) when using cBioPortal with patient identifiable data due My Cancer Genome license restrictions.
-mycancergenome.show=true
-
 # Enable transcript switch dropdown (true, false)
 # show.transcript_dropdown=false
 

src/main/resources/db-scripts/cgds.sql

@@ -51,7 +51,6 @@ DROP TABLE IF EXISTS `data_access_tokens`;
 DROP TABLE IF EXISTS `reference_genome_gene`;
 DROP TABLE IF EXISTS `clinical_event_data`;
 DROP TABLE IF EXISTS `clinical_event`;
-DROP TABLE IF EXISTS `cosmic_mutation`;
 DROP TABLE IF EXISTS `copy_number_seg_file`;
 DROP TABLE IF EXISTS `copy_number_seg`;
 DROP TABLE IF EXISTS `sample_cna_event`;
@@ -632,31 +631,13 @@ CREATE TABLE `copy_number_seg_file` (
   FOREIGN KEY (`CANCER_STUDY_ID`) REFERENCES `cancer_study` (`CANCER_STUDY_ID`) ON DELETE CASCADE
 );
 
--- --------------------------------------------------------
-CREATE TABLE `cosmic_mutation` (
-  `COSMIC_MUTATION_ID` varchar(30) NOT NULL,
-  `CHR` varchar(5),
-  `START_POSITION` bigint(20),
-  `REFERENCE_ALLELE` varchar(255),
-  `TUMOR_SEQ_ALLELE` varchar(255),
-  `STRAND` varchar(2),
-  `CODON_CHANGE` varchar(255),
-  `ENTREZ_GENE_ID` int(11) NOT NULL,
-  `PROTEIN_CHANGE` varchar(255) NOT NULL,
-  `COUNT` int(11) NOT NULL,
-  `KEYWORD` varchar(50) DEFAULT NULL,
-  KEY (`KEYWORD`),
-  PRIMARY KEY (`COSMIC_MUTATION_ID`),
-  FOREIGN KEY (`ENTREZ_GENE_ID`) REFERENCES `gene` (`ENTREZ_GENE_ID`)
-);
-
 -- --------------------------------------------------------
 CREATE TABLE `clinical_event` (
   `CLINICAL_EVENT_ID` BIGINT NOT NULL auto_increment,
   `PATIENT_ID` int(11) NOT NULL,
   `START_DATE` int NOT NULL,
   `STOP_DATE` int,
-  `EVENT_TYPE` varchar(20) NOT NULL,
+  `EVENT_TYPE` varchar(50) NOT NULL,
   PRIMARY KEY (`CLINICAL_EVENT_ID`),
   KEY (`PATIENT_ID`,`EVENT_TYPE`),
   FOREIGN KEY (`PATIENT_ID`) REFERENCES `patient` (`INTERNAL_ID`) ON DELETE CASCADE
@@ -762,4 +743,4 @@ CREATE TABLE `resource_study` (
 
 -- DB_SCHEMA_VERSION AND DERIVED_TABLE_SCHEMA_VERSION MUST BE KEPT IN SYNC WITH THE db.version AND derived_table.version PROPERTIES IN pom.xml
 INSERT INTO `info` (`DB_SCHEMA_VERSION`, `GENESET_VERSION`, `DERIVED_TABLE_SCHEMA_VERSION`)
-  VALUES ('2.14.2', NULL, '1.0.2');
+  VALUES ('2.14.4', NULL, '1.0.2');

src/main/resources/db-scripts/migration.sql

@@ -1074,3 +1074,12 @@ UPDATE `info` SET `DB_SCHEMA_VERSION`="2.14.1";
 ALTER TABLE `resource_definition` ADD COLUMN `CUSTOM_METADATA` JSON;
 UPDATE `info` SET `DERIVED_TABLE_SCHEMA_VERSION`="1.0.2";
 UPDATE `info` SET `DB_SCHEMA_VERSION`="2.14.2";
+
+##version: 2.14.3
+DROP TABLE IF EXISTS `cosmic_mutation`;
+UPDATE `info` SET `DB_SCHEMA_VERSION`="2.14.3";
+
+##version: 2.14.4
+-- increase varchar size to accomodate larger event type names
+ALTER TABLE `clinical_event` MODIFY COLUMN `EVENT_TYPE` varchar(50) NOT NULL;
+UPDATE `info` SET `DB_SCHEMA_VERSION`="2.14.4";

src/main/resources/webapp/config_service.jsp

@@ -18,7 +18,6 @@
             "google_analytics_profile_id",
             "analytics_report_url",
             "oncoprint.hide_vus.default",
-            "mycancergenome.show",
             "oncokb.public_api.url",
             "oncokb.merge_icons_by_default",
             "digitalslidearchive.iframe.url",
@@ -35,7 +34,6 @@
             "show.hotspot",
             "show.oncokb",
             "show.cbioportal",
-            "show.cosmic",
             "show.civic",
             "show.genomenexus",
             "show.genomenexus.annotation_sources",