I noticed that the airavata-server.properties file had a reference to airavata_credentialstore. I changed that to credential_store and restarted the server and it appears I successfully created a new token. I'm going to proceed on the assumption that this was ok to do and see if I can run the Gaussian job.
Jeff ________________________________ From: Supun Nakandala [[email protected]] Sent: Monday, June 05, 2017 7:57 AM To: [email protected] Subject: Re: Running Gaussian on Comet Can you share the airavata-server.properties file(Please mask any sensitive passwords that you have in the file)? On Mon, Jun 5, 2017 at 10:51 AM, Sale, Jeff <[email protected]<mailto:[email protected]>> wrote: Supun, Thanks. It turns out there was no CREDENTIALS table in the credential_store database to DROP (perhaps not a surprise), but I did manage to create one. Unfortunately we are still getting the "Unknown column 'DESCRIPTION' in 'field list' " error. I see there is also a database named airavata_credentialstore which also includes a CREDENTIALS table but has no DESCRIPTION field, but that's probably irrelevant. Just thought I'd mention it. I still get the "Error occurred while registering SSH Credential. More info : Error occurred while saving SSH Credentials." in the browser. Below is the error and below that are some SQL queries to confirm that the table was built and contains the DESCRIPTION field. I restarted everything including mysql just to be safe, but still no luck. Jeff [ERROR] Error persisting credentials. gateway - php_reference_gateway token id - 4eefe6f0-a9e3-4110-98c5-dc947d3268a6 com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'DESCRIPTION' in 'field list' 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:2501) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1858) at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2079) at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2013) at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(PreparedStatement.java:5104) at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1998) at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:112) at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.writeCredentials(SSHCredentialWriter.java:64) at org.apache.airavata.credential.store.server.CredentialStoreServerHandler.addSSHCredential(CredentialStoreServerHandler.java:102) at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1160) at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1144) at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39) at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39) at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) [ERROR] Error occurred while saving SSH Credentials. org.apache.airavata.credential.store.store.CredentialStoreException: Error persisting credentials. gateway - php_reference_gateway token id - 4eefe6f0-a9e3-4110-98c5-dc947d3268a6 at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:121) at org.apache.airavata.credential.store.store.impl.SSHCredentialWriter.writeCredentials(SSHCredentialWriter.java:64) at org.apache.airavata.credential.store.server.CredentialStoreServerHandler.addSSHCredential(CredentialStoreServerHandler.java:102) at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1160) at org.apache.airavata.credential.store.cpi.CredentialStoreService$Processor$addSSHCredential.getResult(CredentialStoreService.java:1144) at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39) at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39) at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Unknown column 'DESCRIPTION' in 'field list' 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:2501) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1858) at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2079) at com.mysql.jdbc.PreparedStatement.executeUpdateInternal(PreparedStatement.java:2013) at com.mysql.jdbc.PreparedStatement.executeLargeUpdate(PreparedStatement.java:5104) at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1998) at org.apache.airavata.credential.store.store.impl.db.CredentialsDAO.addCredentials(CredentialsDAO.java:112) ... 10 common frames omitted [ERROR] Error occurred while registering SSH Credential org.apache.airavata.credential.store.exception.CredentialStoreException: Error occurred while saving SSH Credentials. at org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:3719) at org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result$addSSHCredential_resultStandardScheme.read(CredentialStoreService.java:3697) at org.apache.airavata.credential.store.cpi.CredentialStoreService$addSSHCredential_result.read(CredentialStoreService.java:3639) at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:86) at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.recv_addSSHCredential(CredentialStoreService.java:210) at org.apache.airavata.credential.store.cpi.CredentialStoreService$Client.addSSHCredential(CredentialStoreService.java:197) at org.apache.airavata.api.server.handler.AiravataServerHandler.generateAndRegisterSSHKeys(AiravataServerHandler.java:528) at org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$a0d31de2.CGLIB$generateAndRegisterSSHKeys$167(<generated>) at org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$a0d31de2$$FastClassByGuice$$4a3820fa.invoke(<generated>) at com.google.inject.internal.cglib.proxy.$MethodProxy.invokeSuper(MethodProxy.java:228) at com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:75) at org.apache.airavata.api.server.security.interceptor.SecurityInterceptor.invoke(SecurityInterceptor.java:56) at com.google.inject.internal.InterceptorStackCallback$InterceptedMethodInvocation.proceed(InterceptorStackCallback.java:75) at com.google.inject.internal.InterceptorStackCallback.intercept(InterceptorStackCallback.java:55) at org.apache.airavata.api.server.handler.AiravataServerHandler$$EnhancerByGuice$$a0d31de2.generateAndRegisterSSHKeys(<generated>) at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:16585) at org.apache.airavata.api.Airavata$Processor$generateAndRegisterSSHKeys.getResult(Airavata.java:16569) at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39) at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39) at org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:286) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) mysql> show databases; +--------------------------+ | Database | +--------------------------+ | airavata_credentialstore | | app_catalog | | credential_store | | experiment_catalog | | information_schema | | mysql | | performance_schema | | replica_catalog | | sharing_catalog | | test | | workflow_catalog | +--------------------------+ 11 rows in set (0.04 sec) mysql> use credential_store; Reading table information for completion of table and column names You can turn off this feature to get a quicker startup with -A Database changed mysql> show tables; +----------------------------+ | Tables_in_credential_store | +----------------------------+ | CREDENTIALS | +----------------------------+ 1 row in set (0.00 sec) mysql> show fields from CREDENTIALS; +-----------------------+--------------+------+-----+-------------------+-------+ | Field | Type | Null | Key | Default | Extra | +-----------------------+--------------+------+-----+-------------------+-------+ | GATEWAY_ID | varchar(100) | NO | PRI | NULL | | | TOKEN_ID | varchar(100) | NO | PRI | NULL | | | CREDENTIAL | blob | NO | | NULL | | | PORTAL_USER_ID | varchar(256) | NO | | NULL | | | TIME_PERSISTED | timestamp | NO | | CURRENT_TIMESTAMP | | | DESCRIPTION | varchar(500) | YES | | NULL | | | CREDENTIAL_OWNER_TYPE | varchar(10) | NO | | GATEWAY | | +-----------------------+--------------+------+-----+-------------------+-------+ 7 rows in set (0.01 sec) -- Thank you Supun Nakandala Dept. Computer Science and Engineering University of Moratuwa
