Remove backwards compatibility

cBioPortal · Aug 2, 2023 · 8ab95bb · 8ab95bb
1 parent 27b330d
commit 8ab95bb
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Showing 3 changed files with 30 additions and 55 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
@@ -18,38 +18,23 @@ public JdbcDataSource () {
         String password = dbProperties.getDbPassword();
         String mysqlDriverClassName = dbProperties.getDbDriverClassName();
         String database = dbProperties.getDbName();
-        String useSSL = (!StringUtils.isBlank(dbProperties.getDbUseSSL())) ? dbProperties.getDbUseSSL() : "false";
         String enablePooling = (!StringUtils.isBlank(dbProperties.getDbEnablePooling())) ? dbProperties.getDbEnablePooling(): "false";
         String connectionURL = dbProperties.getConnectionURL();
 
-        Assert.hasText(userName, errorMessage("username", "db.user"));
-        Assert.hasText(password, errorMessage("password", "db.password"));
-        Assert.hasText(mysqlDriverClassName, errorMessage("driver class name", "db.driver"));
-
         Assert.isTrue(
-            !((defined(host) || defined(database) || defined(dbProperties.getDbUseSSL())) && defined(connectionURL)),
-            "The portal.properties file defines both db.connection_string and (one of) db.host, " +
-             "db.portal_db_name and db.use_ssl. Please configure with either db.connection_string (preferred), " + 
-             "or db.host, db.portal_db_name and db.use_ssl."
+            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"
         );
 
-        // For backward compatibility, build connection URL from individual properties.
-        if (connectionURL == null) {
-            Assert.hasText(host, errorMessage("host", "db.host") + 
-                " Or preferably, set the 'db.connection_string' and remove 'db.host', 'db.portal_db_name' and 'db.use_ssl' (best practice).");
-            Assert.hasText(database, errorMessage("database name", "db.portal_db_name") + 
-                " Or preferably, set the 'db.connection_string' and remove 'db.host', 'db.portal_db_name' and 'db.use_ssl (best practice).");
-            System.out.println("\n----------------------------------------------------------------------------------------------------------------");
-            System.out.println("-- Deprecation warning:");
-            System.out.println("-- You are connecting to the database using the deprecated 'db.host', 'db.portal_db_name' and 'db.use_ssl' properties.");
-            System.out.println("-- Please use the 'db.connection_string' instead (see https://docs.cbioportal.org/deployment/customization/portal.properties-reference/).");
-            System.out.println("----------------------------------------------------------------------------------------------------------------\n");
-            connectionURL = String.format(
-                "jdbc:mysql://%s/%s?zeroDateTimeBehavior=convertToNull&useSSL=%s",
-                host, database, useSSL
-            );
-        }
-
+        Assert.hasText(userName, errorMessage("username", "db.user"));
+        Assert.hasText(password, errorMessage("password", "db.password"));
+        Assert.hasText(mysqlDriverClassName, errorMessage("driver class name", "db.driver"));
+
         this.setUrl(connectionURL);
 
         //  Set up poolable data source

diff --git a/core/src/main/scripts/importer/cbioportal_common.py b/core/src/main/scripts/importer/cbioportal_common.py
@@ -45,7 +45,7 @@
 PORTAL_PROPERTY_DATABASE_NAME = 'db.portal_db_name'
 PORTAL_PROPERTY_DATABASE_URL = 'db.connection_string'
 PORTAL_PROPERTY_DATABASE_USESSL = 'db.use_ssl'
-REQUIRED_DATABASE_PROPERTIES = [PORTAL_PROPERTY_DATABASE_USER, PORTAL_PROPERTY_DATABASE_PW]
+REQUIRED_DATABASE_PROPERTIES = [PORTAL_PROPERTY_DATABASE_USER, PORTAL_PROPERTY_DATABASE_PW, PORTAL_PROPERTY_DATABASE_URL]
 
 # provides a key for data types to metafile specification dict.
 class MetaFileTypes(object):
@@ -1039,33 +1039,19 @@ def get_database_properties(properties_filename: str) -> Optional[PortalProperti
             file=ERROR_FILE)
         return None
 
-    if (properties.get(PORTAL_PROPERTY_DATABASE_HOST) is not None or properties.get(PORTAL_PROPERTY_DATABASE_NAME) is not None)\
-            and properties.get(PORTAL_PROPERTY_DATABASE_URL) is not None:
-        print(
-            "The portal.properties file defines both db.connection_string and (one of) db.host, db.portal_db_name and "
-            "db.use_ssl. Please configure with either db.connection_string (preferred), or "
-            "db.host, db.portal_db_name and db.use_ssl.", file=ERROR_FILE)
+    if properties.get(PORTAL_PROPERTY_DATABASE_HOST) is not None \
+        or properties.get(PORTAL_PROPERTY_DATABASE_NAME) is not None \
+        or properties.get(PORTAL_PROPERTY_DATABASE_USESSL) is not None:
+        print("""
+            ----------------------------------------------------------------------------------------------------------------
+            -- Connection error:
+            -- You try to connect to the database using the deprecated 'db.host', 'db.portal_db_name' and 'db.use_ssl' properties.
+            -- Please remove these properties and use the 'db.connection_string' property instead. See https://docs.cbioportal.org/deployment/customization/portal.properties-reference/
+            -- for assistance on building a valid connection string.
+            ------------------------------------------------------------f---------------------------------------------------
+        """, file=ERROR_FILE)
         return None
 
-    # For backward compatibility, build connection URL from individual properties
-    if properties.get(PORTAL_PROPERTY_DATABASE_URL) is None:
-        if properties.get(PORTAL_PROPERTY_DATABASE_HOST) is None or properties.get(PORTAL_PROPERTY_DATABASE_NAME) is None:
-            print("No connection information provided for database connection. Please set 'db.host' and "
-                "'db.portal_db_name' in portal.properties. Or better, use the 'db.connection_string' "
-                "(see https://docs.cbioportal.org/deployment/customization/portal.properties-reference/)",
-                file=ERROR_FILE)
-            return None
-        print("\n" + "-"*112)
-        print("-- Deprecation warning:")
-        print("-- You are connection to the database using the deprecated 'db.host', 'db.portal_db_name' and "
-            "'db.use_ssl' properties.")
-        print("-- Please use the 'db.connection_string' instead "
-            "(see https://docs.cbioportal.org/deployment/customization/portal.properties-reference/).")
-        print("-"*112 + "\n")
-        properties[PORTAL_PROPERTY_DATABASE_URL] = f"jdbc:mysql://{properties[PORTAL_PROPERTY_DATABASE_HOST]}" \
-            f"/{properties[PORTAL_PROPERTY_DATABASE_NAME]}" \
-            f"?zeroDateTimeBehavior=convertToNull&useSSL={properties[PORTAL_PROPERTY_DATABASE_USESSL]}"
-
     return PortalProperties(properties[PORTAL_PROPERTY_DATABASE_USER],
                             properties[PORTAL_PROPERTY_DATABASE_PW],
                             properties[PORTAL_PROPERTY_DATABASE_URL])

diff --git a/docker/web-and-data/docker-entrypoint.sh b/docker/web-and-data/docker-entrypoint.sh
@@ -59,10 +59,14 @@ parse_connection_string() {
 check_db_connection() {
     eval $(parse_db_params_from_config_and_command_line $@)
 
-    if ([[ -n $db_host ]] || [[ -n $db_portal_db_name ]] || [[ -n $db_use_ssl ]]) && [[ -n $db_connection_string ]]
+    if [[ -n $db_host ]] || [[ -n $db_portal_db_name ]] || [[ -n $db_use_ssl ]]
     then
-        echo "The portal.properties file defines both db.connection_string and (one of) db.host, db.portal_db_name and "
-        echo "db.use_ssl. Please configure with either db.connection_string (preferred), or db.host, db.portal_db_name and db.use_ssl."
+        echo "----------------------------------------------------------------------------------------------------------------"
+        echo "-- Connection error:"
+        echo "-- You try to connect to the database using the deprecated 'db.host', 'db.portal_db_name' and 'db.use_ssl' properties."
+        echo "-- Please remove these properties and use the 'db.connection_string' property instead. See https://docs.cbioportal.org/deployment/customization/portal.properties-reference/"
+        echo "-- for assistance on building a valid connection string."
+        echo "------------------------------------------------------------f---------------------------------------------------"
         exit 1
     fi