genetable version added to info api

docs/Updating-your-cBioPortal-installation.md

@@ -4,33 +4,37 @@ As of release **1.1.0** cBioPortal has a Database schema update mechanism which
 
 ## First time
 
-The first time you update from release **1.0.4** (or lower) to release **1.1.0** (or higher), you should get a an error banner page after restarting your webserver. The error should state something like: 
+The first time you update from release **1.0.4** (or lower) to release **1.1.0** (or higher), you should get a an error banner page after restarting your webserver. The error should state something like:
 
 ```
-Current DB schema version: xxx 
+Current DB schema version: xxx
 DB schema version expected by Portal: yyy
 ```
-where `xxx` and `yyy` will be different version numbers. 
 
-If you get `DB version expected by Portal: 0` (i.e. you are building the new release from source), you need to  add a new property to your `application.properties` file which is needed for this check. 
+where `xxx` and `yyy` will be different version numbers.
+
+If you get `DB version expected by Portal: 0` (i.e. you are building the new release from source), you need to add a new property to your `application.properties` file which is needed for this check.
 
 #### Step1
 
 In your `application.properties` file (e.g. `<your_cbioportal_dir>/src/main/resources/application.properties`) add the following property:
+
 ```
 # this is the *expected* DB version (expected by the code). Don't set it manually, it is filled by maven:
 db.version=${db.version}
+genetable.version=${genetable.version}
 ```
 
 #### Step2
 
-Compile your code again. After restarting the webserver the page should now state something like: `DB version expected by Portal: 1.1.0` (or higher), while the DB version remains as `Current DB version: -1`. 
+Compile your code again. After restarting the webserver the page should now state something like: `DB version expected by Portal: 1.1.0` (or higher), while the DB version remains as `Current DB version: -1`.
 
 ## Running the migration script
 
 First, make sure you have the DB connection properties correctly set in your application.properties file (see [DB connection settings here](/deployment/customization/application.properties-Reference.md#database-settings)).
 
 **Dependencies:** the migration script is a Python script that depends on the `mysqlclient` library. If necessary, you can install it with the following commands (example for Ubuntu):
+
 ```console
 sudo apt-get install python3-dev default-libmysqlclient-dev
 sudo python3 -m pip install mysqlclient
@@ -42,16 +46,20 @@ For macOS, try the following:
 brew install mysql-connector-c
 sudo python3 -m pip install mysqlclient
 ```
+
 and see <https://github.com/PyMySQL/mysqlclient-python/blob/master/README.md#prerequisites>
 if problems occur during installation.
 
 To run the migration script first go to the scripts folder
-`<your_cbioportal_dir>/core/src/main/scripts` 
+`<your_cbioportal_dir>/core/src/main/scripts`
 and then run the following command:
+
 ```console
 $ python migrate_db.py
 ```
+
 This should result in the following output:
+
 ```console
 WARNING: This script will alter your database! Be sure to back up your data before running.
 Continue running DB migration? (y/n) y

pom.xml

@@ -31,7 +31,7 @@
 
         <!-- THIS SHOULD BE KEPT IN SYNC TO VERSION IN CGDS.SQL -->
 		<db.version>2.13.1</db.version>
-
+        <genetable.version>hgnc_v2023.10.1</genetable.version>
 		<!-- Version properties for dependencies that should have same version. -->
 		<!-- The rest can be set in the dependencyManagement section -->
 		<spring.social.version>1.1.6.RELEASE</spring.social.version>

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

@@ -10,6 +10,8 @@ public class Info implements Serializable {
     @NotNull
     private String dbVersion;
     @NotNull
+    private String genetableVersion;
+    @NotNull
     private String gitBranch;
     @NotNull
     private String gitCommitId;
@@ -42,6 +44,14 @@ public String getGitCommitId() {
         return this.gitCommitId;
     }
 
+    public String getGenetableVersion(){
+        return this.genetableVersion;
+    }
+
+    public void setGenetableVersion(String genetableVersion){
+        this.genetableVersion = genetableVersion;
+    }
+
     public void setGitCommitId(String gitCommitId) {
         this.gitCommitId = gitCommitId;
     }

src/main/java/org/cbioportal/web/InfoController.java

@@ -28,6 +28,9 @@ public class InfoController {
 
     @Value("${db.version}")
     private String dbVersion;
+
+    @Value("${genetable.version}")
+    private String genetableVersion;
 
     @Value("${git.branch:not set}")
     private String gitBranch;
@@ -59,15 +62,18 @@ public class InfoController {
     @Value("${git.dirty:not set}")
     private String gitDirty;
 
+
+
     @RequestMapping(value = "/api/info", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
     @Operation(description = "Get information about the running instance")
     @ApiResponse(responseCode = "200", description = "OK",
         content = @Content(schema = @Schema(implementation = Info.class)))
     public ResponseEntity<Info> getInfo() {
-
+        
         Info info = new Info();
         info.setPortalVersion(portalVersion);
         info.setDbVersion(dbVersion);
+        info.setGenetableVersion(genetableVersion);
         info.setGitBranch(gitBranch);
         info.setGitCommitId(gitCommitId);
         info.setGitCommitIdDescribe(gitCommitIdDescribe);
@@ -77,6 +83,7 @@ public ResponseEntity<Info> getInfo() {
         info.setGitCommitMessageUserEmail(gitCommitMessageUserEmail);
         info.setGitCommitMessageUserName(gitCommitMessageUserName);
         info.isGitDirty(Boolean.valueOf(gitDirty));
+
         return new ResponseEntity<>(info, HttpStatus.OK);
     }
 }

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

@@ -711,7 +711,8 @@ CREATE TABLE `allele_specific_copy_number` (
 -- --------------------------------------------------------
 CREATE TABLE `info` (
   `DB_SCHEMA_VERSION` varchar(24),
-  `GENESET_VERSION` varchar(24)
+  `GENESET_VERSION` varchar(24),
+  `GENE_TABLE_VERSION` varchar(24)
 );
 
 -- --------------------------------------------------------
@@ -755,5 +756,5 @@ CREATE TABLE `resource_study` (
 );
 
 -- THIS MUST BE KEPT IN SYNC WITH db.version PROPERTY IN pom.xml
-INSERT INTO info VALUES ('2.13.1', NULL);
+INSERT INTO info VALUES ('2.13.1','hgnc_v2023.10.1', NULL );
 

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

@@ -1027,4 +1027,6 @@ ALTER TABLE `clinical_event_data` MODIFY COLUMN `VALUE` varchar(3000) NOT NULL;
 CREATE INDEX idx_clinical_event_key ON clinical_event_data (`KEY`);
 CREATE INDEX idx_clinical_event_value ON clinical_event_data (`VALUE`);
 CREATE INDEX idx_sample_stable_id ON sample (`STABLE_ID`);
+ALTER TABLE `info` ADD COLUMN `GENE_TABLE_VERSION` varchar(24);
+UPDATE `info` SET `GENE_TABLE_VERSION`="hgnc_v2023.10.1";
 UPDATE `info` SET `DB_SCHEMA_VERSION`="2.13.1";

src/main/resources/maven.properties

@@ -1,4 +1,5 @@
 [email protected]@
 [email protected]@
 # this is the *expected* DB version (expected by the code). Don't set it manually, it is filled by maven:
-[email protected]@
+[email protected]@
+[email protected]@

src/test/java/org/cbioportal/web/InfoControllerTest.java

@@ -19,7 +19,8 @@
 @ContextConfiguration(classes = {InfoController.class, TestConfig.class})
 @TestPropertySource(properties = {
     "portal.version=test_portal_version",
-    "db.version=test_db_version"
+    "db.version=test_db_version",
+    "genetable.version=test_genetable_version"
 })
 public class InfoControllerTest {
 
@@ -35,6 +36,7 @@ public void getInfo() throws Exception {
             .andExpect(MockMvcResultMatchers.status().isOk())
             .andExpect(MockMvcResultMatchers.content().contentTypeCompatibleWith(MediaType.APPLICATION_JSON))
             .andExpect(MockMvcResultMatchers.jsonPath("$.portalVersion").value("test_portal_version"))
-            .andExpect(MockMvcResultMatchers.jsonPath("$.dbVersion").value("test_db_version"));
+            .andExpect(MockMvcResultMatchers.jsonPath("$.dbVersion").value("test_db_version"))
+            .andExpect(MockMvcResultMatchers.jsonPath("$.genetableVersion").value("test_genetable_version"));
     }
 }

src/test/resources/maven.properties

@@ -1,3 +1,4 @@
 portal.version=test_portal_version
 db.version=test_db_version
 app.version=test_app_version
+genetable.version=test_genetable_version

test/test_db_version.sh

@@ -1,30 +1,54 @@
 #!/usr/bin/env bash
-# halt on error
+# Halt on error
 set -e
-# script dir
+
+# Script directory
 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
-#colors
+
+# Colors for output
 RED='\033[0;31m'
 GREEN='\033[0;32m'
 YELLOW='\033[1;33m'
 NC='\033[0m'
 
-echo "Making sure all db versions are the same in cgds.sql, pom.xml and migration.sql"
+echo "Checking db and genetable versions in pom.xml, cgds.sql, and migration.sql"
+
+# Fetch db version from pom.xml
+POM_DB_VERSION=$(grep '<db.version>' ${DIR}/../pom.xml | cut -d'>' -f2 | cut -d'<' -f1)
+echo "pom.xml db version is $POM_DB_VERSION"
+
+# Fetch geneTable version from pom.xml
+POM_GENE_TABLE_VERSION=$(grep '<genetable.version>' ${DIR}/../pom.xml | cut -d'>' -f2 | cut -d'<' -f1)
+echo "pom.xml genetable version is $POM_GENE_TABLE_VERSION"
 
-POM_DB_VERSION=$(grep db.version ${DIR}/../pom.xml | cut -d'>' -f2 | cut -d'<' -f1)
-echo pom.xml db version is $POM_DB_VERSION
+# Fetch db version from cgds.sql
+CGDS_DB_SQL_VERSION=$(grep "INSERT INTO info" ${DIR}/../src/main/resources/db-scripts/cgds.sql | cut -d"'" -f2 | cut -d"'" -f1)
+echo "src/main/resources/db-scripts/cgds.sql db version is $CGDS_DB_SQL_VERSION"
 
-CGDS_DB_SQL_VERSION=$(grep 'INSERT INTO info' ${DIR}/../src/main/resources/db-scripts/cgds.sql | cut -d"'" -f2 | cut -d"'" -f1)
-echo src/main/resources/db-scripts/cgds.sql db version is $CGDS_DB_SQL_VERSION
+# Fetch geneTable version from cgds.sql
+CGDS_GENE_TABLE_VERSION=$(grep "INSERT INTO info" ${DIR}/../src/main/resources/db-scripts/cgds.sql | grep "genetable" | cut -d"'" -f4)
+echo "src/main/resources/db-scripts/cgds.sql genetable version is $CGDS_GENE_TABLE_VERSION"
 
+# Fetch db version from migration.sql
 MIGRATION_DB_VERSION=$(grep 'UPDATE `info`' ${DIR}/../src/main/resources/db-scripts/migration.sql | tail -1 | cut -d '"' -f2 | cut -d'"' -f1)
-echo src/main/resources/db-scripts/migration.sql db version is $MIGRATION_DB_VERSION
+echo "src/main/resources/db-scripts/migration.sql db version is $MIGRATION_DB_VERSION"
+
+# Fetch geneTable version from migration.sql
+MIGRATION_GENE_TABLE_VERSION=$(grep 'UPDATE `info`' ${DIR}/../src/main/resources/db-scripts/migration.sql | tail -1 | cut -d '"' -f4 | cut -d'"' -f1)
+echo "src/main/resources/db-scripts/migration.sql genetable version is $MIGRATION_GENE_TABLE_VERSION"
+
+# Verify db versions match
+if [ "$POM_DB_VERSION" == "$CGDS_DB_SQL_VERSION" ] && [ "$CGDS_DB_SQL_VERSION" == "$MIGRATION_DB_VERSION" ]; then
+    echo -e "${GREEN}db versions match${NC}"
+else
+    echo -e "${RED}db versions mismatch${NC}"
+    exit 1
+fi
 
-if [ "$POM_DB_VERSION" == "$CGDS_DB_SQL_VERSION" ] && [ "$CGDS_DB_SQL_VERSION" == "$MIGRATION_DB_VERSION" ]
-then
-    echo -e "${GREEN}db versions match${NC}";
-    exit 0;
+# Verify geneTable versions match
+if [ "$POM_GENE_TABLE_VERSION" == "$CGDS_GENE_TABLE_VERSION" ] && [ "$CGDS_GENE_TABLE_VERSION" == "$MIGRATION_GENE_TABLE_VERSION" ]; then
+    echo -e "${GREEN}genetable versions match${NC}"
 else
-    echo -e "${RED}db versions mismatch${NC}";
-    exit 1;
+    echo -e "${RED}genetable versions mismatch${NC}"
+    exit 1
 fi