Merge branch 'master' into mutation-data-counts

cBioPortal · Oct 9, 2023 · 0805a70 · 0805a70
2 parents 4b9d713 + 399ca10
commit 0805a70
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Showing 2 changed files with 19 additions and 15 deletions.
diff --git a/core/src/main/java/org/mskcc/cbio/portal/dao/JdbcDataSource.java b/core/src/main/java/org/mskcc/cbio/portal/dao/JdbcDataSource.java
@@ -4,11 +4,15 @@
 import org.mskcc.cbio.portal.util.DatabaseProperties;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.util.Assert;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * Data source that self-initializes based on cBioPortal configuration.
  */
 public class JdbcDataSource extends BasicDataSource {
+
+    private static final Logger LOG = LoggerFactory.getLogger(JdbcDataSource.class);
 
     public JdbcDataSource () {
         DatabaseProperties dbProperties = DatabaseProperties.getInstance();
@@ -20,17 +24,17 @@ public JdbcDataSource () {
         String database = dbProperties.getDbName();
         String enablePooling = (!StringUtils.isBlank(dbProperties.getDbEnablePooling())) ? dbProperties.getDbEnablePooling(): "false";
         String connectionURL = dbProperties.getConnectionURL();
-        
-        Assert.isTrue(
-            !defined(host) && !defined(database) && !defined(dbProperties.getDbUseSSL()),
-            "\n----------------------------------------------------------------------------------------------------------------" +
-                "-- Connection error:\n" +
-                "-- You try to connect to the database using the deprecated 'db.host', 'db.portal_db_name' and 'db.use_ssl' properties.\n" +
-                "-- Please remove these properties and use the 'db.connection_string' property instead. See https://docs.cbioportal.org/deployment/customization/portal.properties-reference/\n" +
-                "-- for assistance on building a valid connection string.\n" +
-                "----------------------------------------------------------------------------------------------------------------\n"
-        );
-        
+
+        if (defined(host) || defined(database) || defined(dbProperties.getDbUseSSL())) {
+		LOG.warn("\n----------------------------------------------------------------------------------------------------------------" +
+			"-- Connection error:\n" +
+			"-- You try to connect to the database using the deprecated 'db.host', 'db.portal_db_name' and 'db.use_ssl' properties.\n" +
+			"-- Please remove these properties and use the 'db.connection_string' property instead. See https://docs.cbioportal.org/deployment/customization/portal.properties-reference/\n" +
+			"-- for assistance on building a valid connection string.\n" +
+			"----------------------------------------------------------------------------------------------------------------\n"
+		);
+	}
+
         Assert.hasText(userName, errorMessage("username", "db.user"));
         Assert.hasText(password, errorMessage("password", "db.password"));
         Assert.hasText(mysqlDriverClassName, errorMessage("driver class name", "db.driver"));
@@ -53,11 +57,11 @@ public JdbcDataSource () {
         this.setValidationQuery("SELECT 1");
         this.setJmxName("org.cbioportal:DataSource=" + database);
     }
-    
+
     private String errorMessage(String displayName, String propertyName) {
         return String.format("No %s provided for database connection. Please set '%s' in portal.properties.", displayName, propertyName);
     }
-    
+
     private boolean defined(String property) {
         return property != null && !property.isEmpty();
     }

diff --git a/...ava/org/cbioportal/security/spring/authentication/token/config/DataAccessTokenConfig.java b/...ava/org/cbioportal/security/spring/authentication/token/config/DataAccessTokenConfig.java
@@ -48,7 +48,7 @@ public OAuth2DataAccessTokenServiceImpl oauth2DataAccessTokenService() {
     }
 
     @Bean("dataAccessTokenService")
-    @ConditionalOnProperty(name = "dat.method", havingValue = "none")
+    @ConditionalOnProperty(name = "dat.method", havingValue = "none", matchIfMissing = true)
     public UnauthDataAccessTokenServiceImpl unauthDataAccessTokenService() {
         return new UnauthDataAccessTokenServiceImpl();
     }
@@ -65,4 +65,4 @@ public JwtDataAccessTokenServiceImpl jwtDataAccessTokenService() {
         return new JwtDataAccessTokenServiceImpl();
     }
 
-}
+}