Allow Java system properties to override config

This re-enables the Heroku setup now that the maven system properties
can no longer override the database credentials. To be documented later,
as tracked on GitHub.

Co-Authored-By: Ino de Bruijn <[email protected]>

app.json

@@ -17,12 +17,11 @@
     },
     "MAVEN_CUSTOM_OPTS": {
         "description":"set heroku profile for mvn",
-        "value":"-Pheroku,public -DskipTests -Dfinal.war.name=cbioportal -Ddb.user=cbio_user -Ddb.password=cbio_pass -Ddb.portal_db_name=public_test_small -Dtomcat.catalina.scope=runtime -Ddb.connection_string=jdbc:mysql://sm4sa6ozhn5ya6.cuooweljyhix.us-east-1.rds.amazonaws.com:3306/ -Ddb.host=sm4sa6ozhn5ya6.cuooweljyhix.us-east-1.rds.amazonaws.com"
+        "value":"-Pheroku,public -DskipTests -Dtomcat.catalina.scope=runtime -Dfinal.war.name=cbioportal"
     },
-    "FRONTEND_URL": {
-        "description":"set frontend URL to use (default: empty string, uses frontend inside war)",
-        "value":"",
-        "required":false
+    "SPRING_OPTS": {
+        "description":"set spring properties with e.g. -Dshow.civic=true (TODO: not all props work atm)",
+        "value":"-Dtomcat.catalina.scope=runtime -Ddb.user=cbio_user -Ddb.password=cbio_pass -Ddb.portal_db_name=public_test_small -Ddb.connection_string=jdbc:mysql://devdb.cbioportal.org:3306/ -Ddb.host=devdb.cbioportal.org -Dshow.civic=true -Ddbconnector=dbcp -Dsuppress_schema_version_mismatch_errors=true"
     }
   },
   "buildpacks": [

core/src/main/java/org/mskcc/cbio/portal/util/GlobalProperties.java

@@ -32,12 +32,9 @@
 
 package org.mskcc.cbio.portal.util;
 
-import org.mskcc.cbio.portal.servlet.QueryBuilder;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Value;
-import org.springframework.core.io.ClassPathResource;
 import org.springframework.security.core.Authentication;
 import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.stereotype.Component;
@@ -308,9 +305,49 @@ public static String parseUrl(String url)
     public void setFrontendUrlRuntime(String property) { frontendUrlRuntime = property; }
 
     private static Log LOG = LogFactory.getLog(GlobalProperties.class);
-    private static Properties portalProperties = initializeProperties(PORTAL_PROPERTIES_FILE_NAME);
+    private static ConfigPropertyResolver portalProperties = new ConfigPropertyResolver();
     private static Properties mavenProperties = initializeProperties(MAVEN_PROPERTIES_FILE_NAME);
 
+    /**
+     * Minimal portal property resolver that takes system property overrides.
+     *
+     * Provides properties from runtime or the baked-in
+     * portal.properties config file, but takes overrides from <code>-D</code>
+     * system properties.
+     */
+    private static class ConfigPropertyResolver {
+        private Properties configFileProperties;
+        /**
+         * Finds the config file for properties not overridden by system props.
+         *
+         * Either the runtime or buildtime portal.properties file.
+         */
+        public ConfigPropertyResolver() {
+            configFileProperties = initializeProperties(PORTAL_PROPERTIES_FILE_NAME);
+        }
+        /**
+         * Finds the property with the specified key, or returns the default.
+         */
+        public String getProperty(String key, String defaultValue) {
+            String propertyValue = configFileProperties.getProperty(key, defaultValue);
+            return System.getProperty(key, propertyValue);
+        }
+        /**
+         * Finds the property with the specified key, or returns null.
+         */
+        public String getProperty(String key) {
+            return getProperty(key, null);
+        }
+        /**
+        * Tests if a property has been specified for this key.
+        *
+        * @return true iff the property was specified, even if blank.
+        */
+        public boolean containsKey(String key) {
+            return getProperty(key) != null;
+        }
+    }
+
     private static Properties initializeProperties(String propertiesFileName)
     {
         return loadProperties(getResourceStream(propertiesFileName));

heroku/Procfile

@@ -1 +1 @@
-web: java $JAVA_OPTS -Dfrontend.url=$FRONTEND_URL -Dshow.civic=true -Ddb.suppress_schema_version_mismatch_errors=true -Dsession.service.url=https://cbioportal-session-service.herokuapp.com/api/sessions/heroku_portal/ -Ddbconnector=dbcp -jar portal/target/dependency/webapp-runner.jar --enable-compression --expand-war --port $PORT portal/target/cbioportal.war
+web: java $JAVA_OPTS $SPRING_OPTS -jar portal/target/dependency/webapp-runner.jar --enable-compression --expand-war --port $PORT portal/target/cbioportal.war