Thanks, Marcus. I guess I missed the instructions to uncomment those lines in the properties file. It is also a little unclear what lines related to derby db should be commented out. It might help to provide an example file. I found one on github but it doesn't look quite the same as the one which came with the installation.
Another problem I had pertained to using the SQL GRANT ALL command with a % rather than localhost. I am now able to connect to mysql with jdbc but I am still getting some errors. I noticed one issue related to the name of one of the databases. In the instructions it says to create a database named "credential_store" but one of the errors I was getting seemed to be looking for a database named "airavata_credentialstore". I created a database with that name and tried again and that seems to be resolved but I am still getting errors (see below): Jeffs-MacBook-Pro:bin jsale$ sh airavata-server-start.sh all ...._....................._..............._...._......................_......... .../ \..._.__...__._..___| |__...___...../ \..(_)_.__.__.___...____._|.|_.__._.. ../ _ \.| '_ \./ _` |/ __| '_ \./ _ \.../ _ \.| | '__/ _` \ \./ / _` | __/ _` |. ./ ___ \| |_) | (_| | (__| |.| | __/../ ___ \| | |.| (_| |\ V / (_| | || (_| |. /_/...\_\ .__/.\__,_|\___|_|.|_|\___|./_/...\_\_|_|..\__,_|.\_/.\__,_|\__\__,_|. ........|_|..................................................................... ................................................................................ ................,+????++~..~~++..+????????+??++.++~...~+=???+++................. ..............:???????....:::...~??????????????.~..::...=????????............... ............????????..~~..?????..??????????????.?????..~~~.~???????............. ...........?????????I,~I~~??????.+????????????.~??????~=~..?????????~........... .........?????++??????..????????:.??????????I..????????..????????+????.......... ........??.....???????....???????...???????+..+??????+.I.????????.....?,........ ........????==????????..??..?????..=???????=..?????,.=+?.?????????===??=........ ......=??????????+????..+??=.???=.~??????????,.???=,???,.????=+??????????....... ....??????????+...+I++..???,=...:??????????????.....+??..++I?+..,??????????..... ....???????=??..........??..+??.:=:.???????......??..??=..........?=???????=.... ....??????..?...........+?..???.....???????......???.??...........~=.??????=.... ....~???~.~..............?..???.~=..,??????...7..???.?.:..............~????:.... ...7....7 ...............?..????. ...??????... .????.?.?.............I ..:.:.... .....+7=,.+?................????:,I...?????..=.?????.?.............??~.=7+...... ..........????..............??????~...~??..~~??????..?...........+???,.......... ...........???............=.+???????,.?+:.?????????..+...........???+........... ............??............?,.??????.,??..??????????.,............???............ ...........??,.............=.,????.?+....????????I.I..............=?............ ..........I?..................+??.:?~.....=??????..................??........... ..........??...?...............??.:?=......??????..............?...??........... ............++?..............?.????...?....??????.+..............++I............ .............................?.??????~....???????.?............................. ............................~~.??????......??????............................... .............................=???????......???????+............................. ..........................=I??++?+++?......?+++++++?+........................... ..........................,..77..77......... .. ...7.......................... ................................................................................ SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/lib/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/lib/slf4j-simple-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. [INFO] Settings loaded from file:/Users/jsale/LocalAiravata/apache-airavata-server-0.17-SNAPSHOT/bin/airavata-server.properties [INFO] Skipping Zookeeper embedded startup ... [INFO] Airavata server instance starting... [INFO] Server Arguments: --servers=all [INFO] Starting Credential store Server on Port 8960 [INFO] Listening to Credential store clients .... [INFO] Security module reached... [INFO] connected to rabbitmq: amqp://[email protected]:5672/ for airavata_rabbitmq_exchange [INFO] setting basic.qos / prefetch count to 64 for airavata_rabbitmq_exchange [INFO] Database already created for Experiment Catalog !!! DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://localhost:3306/experiment_catalog?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION objc[90332]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/bin/java and /Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined. 781 experiment_data INFO [main] openjpa.Runtime - OpenJPA dynamically loaded the class enhancer. Any classes that were not enhanced at build time will be enhanced when they are loaded by the JVM. 816 experiment_data INFO [main] openjpa.Runtime - Starting OpenJPA 2.2.0 913 experiment_data INFO [main] openjpa.jdbc.JDBC - Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary" (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5 )). 1567 experiment_data WARN [main] openjpa.jdbc.Schema - Existing column "NOTIFICATION_MESSAGE" on table "NOTIFICATION" is incompatible with the same column in the given schema definition. Existing column: Full Name: NOTIFICATION.NOTIFICATION_MESSAGE Type: varchar Size: 4096 Default: null Not Null: false Given column: Full Name: NOTIFICATION.NOTIFICATION_MESSAGE Type: varchar Size: 255 Default: null Not Null: false 1568 experiment_data WARN [main] openjpa.jdbc.Schema - Existing column "EXPERIMENT_DATA_DIR" on table "PROCESS" is incompatible with the same column in the given schema definition. Existing column: Full Name: PROCESS.EXPERIMENT_DATA_DIR Type: varchar Size: 512 Default: null Not Null: false Given column: Full Name: PROCESS.EXPERIMENT_DATA_DIR Type: varchar Size: 255 Default: null Not Null: false 1569 experiment_data WARN [main] openjpa.jdbc.Schema - Existing column "EXPERIMENT_DATA_DIR" on table "USER_CONFIGURATION_DATA" is incompatible with the same column in the given schema definition. Existing column: Full Name: USER_CONFIGURATION_DATA.EXPERIMENT_DATA_DIR Type: varchar Size: 512 Default: null Not Null: false Given column: Full Name: USER_CONFIGURATION_DATA.EXPERIMENT_DATA_DIR Type: varchar Size: 255 Default: null Not Null: false [INFO] Database already created for App Catalog !!! DriverClassName=com.mysql.jdbc.Driver,Url=jdbc:mysql://localhost:3306/app_catalog?autoReconnect=true,Username=airavata,Password=airavata,validationQuery=SELECT 1 from CONFIGURATION 1 appcatalog_data INFO [main] openjpa.Runtime - Starting OpenJPA 2.2.0 9 appcatalog_data INFO [main] openjpa.jdbc.JDBC - Using dictionary class "org.apache.openjpa.jdbc.sql.MySQLDictionary" (MySQL 5.5.5-10.1.21-MariaDB ,MySQL Connector Java mysql-connector-java-5.1.41 ( Revision: 83c6dc41b96809df81444362933043b20a1d49d5 )). 518 appcatalog_data WARN [main] openjpa.jdbc.Schema - Existing column "APPLICATION_DESCRIPTION" on table "APPLICATION_INTERFACE" is incompatible with the same column in the given schema definition. Existing column: Full Name: APPLICATION_INTERFACE.APPLICATION_DESCRIPTION Type: varchar Size: 500 Default: null Not Null: false Given column: Full Name: APPLICATION_INTERFACE.APPLICATION_DESCRIPTION Type: varchar Size: 255 Default: null Not Null: false 518 appcatalog_data WARN [main] openjpa.jdbc.Schema - Existing column "MODULE_DESC" on table "APPLICATION_MODULE" is incompatible with the same column in the given schema definition. Existing column: Full Name: APPLICATION_MODULE.MODULE_DESC Type: varchar Size: 500 Default: null Not Null: false Given column: Full Name: APPLICATION_MODULE.MODULE_DESC Type: varchar Size: 255 Default: null Not Null: false 519 appcatalog_data WARN [main] openjpa.jdbc.Schema - Existing column "GATEWAY_USAGE_MODULE_LOAD_CMD" on table "COMPUTE_RESOURCE" is incompatible with the same column in the given schema definition. Existing column: Full Name: COMPUTE_RESOURCE.GATEWAY_USAGE_MODULE_LOAD_CMD Type: varchar Size: 500 Default: null Not Null: false Given column: Full Name: COMPUTE_RESOURCE.GATEWAY_USAGE_MODULE_LOAD_CMD Type: varchar Size: 255 Default: null Not Null: false [INFO] Database already created for Workflow Catalog!!! [ERROR] Error occurred while executing : /* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. * */ CREATE TABLE COMMUNITY_USER ( GATEWAY_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_NAME VARCHAR(256) NOT NULL, TOKEN_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL, PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID) ) java.lang.Exception: Error occurred while executing : /* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. * */ CREATE TABLE COMMUNITY_USER ( GATEWAY_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_NAME VARCHAR(256) NOT NULL, TOKEN_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL, PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID) ) at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:154) at org.apache.airavata.api.server.util.DatabaseCreator.executeSQLScript(DatabaseCreator.java:299) at org.apache.airavata.api.server.util.DatabaseCreator.createDatabase(DatabaseCreator.java:238) at org.apache.airavata.api.server.util.DatabaseCreator.createRegistryDatabase(DatabaseCreator.java:66) at org.apache.airavata.api.server.util.CredentialStoreInitUtil.initializeDB(CredentialStoreInitUtil.java:70) at org.apache.airavata.api.server.AiravataAPIServer.startAiravataServer(AiravataAPIServer.java:74) at org.apache.airavata.api.server.AiravataAPIServer.start(AiravataAPIServer.java:202) at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320) at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169) at org.apache.airavata.server.ServerMain.main(ServerMain.java:152) Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Specified key was too long; max key length is 767 bytes at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at com.mysql.jdbc.Util.handleNewInstance(Util.java:425) at com.mysql.jdbc.Util.getInstance(Util.java:408) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2497) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2455) at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:839) at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:739) at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:126) ... 9 more [ERROR] Server Start Error: java.lang.RuntimeException: Database failure at org.apache.airavata.api.server.util.CredentialStoreInitUtil.initializeDB(CredentialStoreInitUtil.java:77) at org.apache.airavata.api.server.AiravataAPIServer.startAiravataServer(AiravataAPIServer.java:74) at org.apache.airavata.api.server.AiravataAPIServer.start(AiravataAPIServer.java:202) at org.apache.airavata.server.ServerMain.startAllServers(ServerMain.java:320) at org.apache.airavata.server.ServerMain.performServerStart(ServerMain.java:169) at org.apache.airavata.server.ServerMain.main(ServerMain.java:152) Caused by: java.lang.Exception: Error occurred while executing : /* * * Licensed to the Apache Software Foundation (ASF) under one * or more contributor license agreements. See the NOTICE file * distributed with this work for additional information * regarding copyright ownership. The ASF licenses this file * to you under the Apache License, Version 2.0 (the * "License"); you may not use this file except in compliance * with the License. You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, * software distributed under the License is distributed on an * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY * KIND, either express or implied. See the License for the * specific language governing permissions and limitations * under the License. * */ CREATE TABLE COMMUNITY_USER ( GATEWAY_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_NAME VARCHAR(256) NOT NULL, TOKEN_ID VARCHAR(256) NOT NULL, COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL, PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID) ) at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:154) at org.apache.airavata.api.server.util.DatabaseCreator.executeSQLScript(DatabaseCreator.java:299) at org.apache.airavata.api.server.util.DatabaseCreator.createDatabase(DatabaseCreator.java:238) at org.apache.airavata.api.server.util.DatabaseCreator.createRegistryDatabase(DatabaseCreator.java:66) at org.apache.airavata.api.server.util.CredentialStoreInitUtil.initializeDB(CredentialStoreInitUtil.java:70) ... 5 more Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Specified key was too long; max key length is 767 bytes at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at com.mysql.jdbc.Util.handleNewInstance(Util.java:425) at com.mysql.jdbc.Util.getInstance(Util.java:408) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:943) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3973) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3909) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2527) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2680) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2497) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2455) at com.mysql.jdbc.StatementImpl.executeInternal(StatementImpl.java:839) at com.mysql.jdbc.StatementImpl.execute(StatementImpl.java:739) at org.apache.airavata.api.server.util.DatabaseCreator.executeSQL(DatabaseCreator.java:126) ... 9 more [INFO] connected to rabbitmq: amqp://[email protected]:5672/ for airavata_rabbitmq_exchange [INFO] setting basic.qos / prefetch count to 64 for airavata_rabbitmq_exchange [INFO] connected to rabbitmq: amqp://[email protected]:5672/ for null [INFO] setting basic.qos / prefetch count to 64 for null [INFO] connected to rabbitmq: amqp://[email protected]:5672/ for airavata_rabbitmq_exchange [INFO] Starting [INFO] Started Orchestrator Server on Port 8940 ... [INFO] State change: CONNECTED [INFO] Starting [INFO] State change: CONNECTED [INFO] connected to rabbitmq: amqp://[email protected]:5672/ for airavata_task_launch_rabbitmq_exchange [INFO] connected to rabbitmq: amqp://[email protected]:5672/ for airavata_rabbitmq_exchange [INFO] setting basic.qos / prefetch count to 64 for airavata_rabbitmq_exchange [INFO] Started Gfac Server on Port 8950 ...
