Trying to set up JIRA 7.9 with mysql 5.7.22 on ubuntu 16.04
When trying to test the connection with the setup wizard, getting the "Error connecting to database, communication link failure" message.
Mysql is up and running, jiradb and jiradbuser have been created following manual instructions.
bind-address is set to 0.0.0.0 in my.cnf
No firewall set up as far as I can tell.
Can't find helpful messages in either JIRA or mysql logs
Any idea what else could be causing this issue?
Jira does not ship with the mysql database driver needed to connect to that kind of database. I would want to make sure first that you have downloaded the jdbc file from mysql's site and then extract the .jar from that .zip file into the $JIRAINSTALL/lib/ folder. If you have not done this yet, there is no way Jira is going to be able to use that database type. This is explained in the documentation Connecting Jira to MySQL.
It is possible that you would have to restart Jira after copying that .jar file in place.
If that is not the solution here, then I would be interested to learn more about Jira's own logging on this. The $JIRAHOME/log/atlassian-jira.log might have some info, but in this case the $JIRAINSTALL/logs/catalina.out might be better since it tends to have some more verbose information in this setup phase of Jira.
Hi Andrew,
Thanks for the reply, mysql-connector-java-5.1.10.jar is in the lib dir and although I am not sure if this is the correct version, I think it is working as I've seen a different error message when the connector was missing.
The message in catalina.out looks like a generic db connection failure report, here it is, let me know if you can get anything from it:
>>
2018-05-07 00:30:57,831 http-nio-8080-exec-13 ERROR anonymous 30x521x1 zv474o 10.50.1.205 /secure/SetupDatabase!connectionCheck.jspa [c.a.config.bootstrap.DefaultAtlassianBootstrapManager] Could not successfully test your database:
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
at sun.reflect.GeneratedConstructorAccessor56.newInstance(Unknown Source)
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:406)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2214)
at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:781)
at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
... 2 filtered
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:352)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:284)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:247)
at com.atlassian.config.bootstrap.DefaultAtlassianBootstrapManager.getTestDatabaseConnection(DefaultAtlassianBootstrapManager.java:347)
at com.atlassian.jira.config.database.JdbcDatasource.getConnection(JdbcDatasource.java:211)
at com.atlassian.jira.config.database.DatabaseConfig.testConnection(DatabaseConfig.java:88)
at com.atlassian.jira.web.action.setup.SetupDatabase.testConnection(SetupDatabase.java:225)
at com.atlassian.jira.web.action.setup.SetupDatabase.doValidation(SetupDatabase.java:189)
at com.atlassian.jira.web.action.setup.SetupDatabase.doConnectionCheck(SetupDatabase.java:121)
... 2 filtered
at java.lang.reflect.Method.invoke(Method.java:498)
at webwork.util.InjectionUtils$DefaultInjectionImpl.invoke(InjectionUtils.java:70)
at webwork.util.InjectionUtils.invoke(InjectionUtils.java:56)
... 2 filtered
at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:63)
... 7 filtered
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
... 45 filtered
at com.atlassian.jira.security.JiraSecurityFilter.lambda$doFilter$0(JiraSecurityFilter.java:66)
... 1 filtered
at com.atlassian.jira.security.JiraSecurityFilter.doFilter(JiraSecurityFilter.java:64)
... 28 filtered
at com.atlassian.jira.servermetrics.CorrelationIdPopulatorFilter.doFilter(CorrelationIdPopulatorFilter.java:30)
... 24 filtered
at com.atlassian.jira.servermetrics.MetricsCollectorFilter.doFilter(MetricsCollectorFilter.java:25)
... 23 filtered
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
at sun.reflect.GeneratedConstructorAccessor56.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:343)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2137)
... 161 more
Caused by: java.net.UnknownHostException: address=(protocol=tcp)(host=10.50.1.9)(port=3306)
at java.net.InetAddress.getAllByName0(InetAddress.java:1280)
at java.net.InetAddress.getAllByName(InetAddress.java:1192)
at java.net.InetAddress.getAllByName(InetAddress.java:1126)
at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:243)
at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:292)
<<
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I recommend downloading the 5.1.46 version instead: https://dev.mysql.com/get/Downloads/Connector-J/mysql-connector-java-5.1.46.zip
There have been lots of performance improvements and known bugs that could be avoided just by using this updated version. To do this you would need to:
Try that first. My next concern is over the error you see in the stacktrace of
Caused by: java.net.UnknownHostException: address=(protocol=tcp)(host=10.50.1.9)(port=3306)
This indicates that the connection string Jira is trying to use could be incorrect. Instead of trying to connect to the database while Jira is running, I think it might help to try to manually configure the $JIRAHOME/dbconfig.xml file before Jira starts. There are a couple of ways to do this, you could create this file manually, or you can use the jira config tool to help set this up for you. I suggest that tool because it can be a good starting point to help get the file created correctly. From there, we ultimately want to see your dbconfig.xml file look very much like the sample on that exists in Connecting Jira to MySQL.
Try these two things. If you still cannot connect, please share with us both your dbconfig.xml and any new exceptions you might find in the logs.
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Hi Andrew,
Thanks, updating the connector did it, the communication is now working.
I am now trying to import some datas from v6.4 but am getting the message that the xml is too old to be imported.
Could you let me know what is the most recent version that will accept the xml generated by v6.4 ?
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Ah, well yeah. You should first upgrade to a 7.0.x version of Jira. There is an expectation all Jira installations would need to go through one of these versions first. This is noted in Skipping major versions documentation.
Once you complete that upgrade, I would recommend that you also update any plugins that you use with Jira and make sure they work. This is important to make sure that your plugin data can also be upgraded correctly.
Next you should upgrade to a 7.2.x version and repeat the process to update your plugins as well. It's especially important if you happen to run Service Desk to make sure that this data can be maintained going forward.
Once that is complete, you can jump from a 7.2.x directly to the latest 7.9.x version. I would also recommend checking out the Upgrade guide for Jira 7.2.x. It explains in more details the caveats and gotchas with upgrading from these older versions up to the latest.
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Hi Andrew,
Thanks a lot for the detailed answer. Would it be possible for you to point me to the 7.0.x download ? I don't see those versions on the archive download site.
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The archives page only has Jira 6.4.x and earlier versions. The 7.0.x versions are still downloadable from https://www.atlassian.com/software/jira/update
However when you visit that page, you then need to click the 'View all versions' link, then in the bottom left corner of the popup click the '7.9' button and select the '7' link in order to see the other versions that are available for download.
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Hi Andrew,
Thanks, I was able to get 7.9 up and running on one of our machines.
This is an older machine running mysql 5.0.
Now I am trying to install 7.9 on a newer machine running mysql 5.7 and when importing the datas I am getting:
>>
Error importing data: org.xml.sax.SAXException: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericEntityException: while inserting:
...
(SQL Exception while executing the following:INSERT INTO jiraaction (ID, issueid, AUTHOR, actiontype, actionlevel, rolelevel, actionbody, CREATED, UPDATEAUTHOR, UPDATED, actionnum) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) (Incorrect string value: '\xEF\xBC\x9A ts...' for column 'actionbody' at row 1))
<<
I think this is probably caused by the different versions of mysql. Could you let me know if you agree and how to proceed to get around this?
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@Thomas D You are still upgrading to Jira 7.0.x first, right? Just want to confirm that this is the upgrade path you are taking before trying to go to 7.9. Also after the 7.0.x version is up and working, please then upgrade to a 7.2.x version of Jira and upgrade all your plugins again for that version. Only after you do those steps can you then upgrade to a much more current version such as 7.9.
That SQL exception error is happening because mysql can't store 4-byte characters, no idea how you backup managed to contain even one of these with your old database using mysql. This is a known limitation of mysql that is explained in the supported platforms documentation.
That said I would recommend using the KB Removing invalid characters from XML backups. It explains a process you can follow in order to strip out these invalid characters from your XML file, then repack it and use that cleaned file to import instead.
But that said, since your old version of MySQL was 5.0, and you're jumping to Mysql 5.7, there is another problem here. Jira 7.0 does not support MySQL 5.7 per https://confluence.atlassian.com/adminjiraserver070/supported-platforms-749382629.html
So, you might be able to use 5.7 with Jira 7.0.x, but it's also possible that this might not work since it's not really supported. In which case, you might need to temporarily find an supported intermediary database version, such as 5.5 or 5.6 just to complete this specific upgrade.
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Hi Andrew,
Sorry I wasn't clear:
On the machine running v6.4 and mysql 5.0 I did the 6.4->7.0->7.2->7.9 upgrades. It went well although I did see a warning about mysql 5.0 not being supported by 7.9 but I was able to bring the database up without problems so far.
Now I am trying to install 7.9 on a newer machine with mysql 5.7 and when trying to import the datas generated by 7.9 on the older machine I am getting the previously sent report.
Let me know if you have additional recommendations.
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Hi Andrew,
I tried running the xml cleaner and I am still seeing the same error message.
(Error importing data: org.xml.sax.SAXException: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericEntityException: while inserting...)
Let me know if you have other suggestions.
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Hi Thomas,
Even Jira 6.4 doesn't support mysql 5.0. Jira 6.4 supported platforms.
As such, I fear that these initial upgrades to 7.0 might not have completed 100% correctly, but without seeing logs from all of these startups, I can't say for sure. It might be best to go back to your original backup (the one from 6.4), and then migrating this database information to another supported database for back for Jira 6.4 application first and make sure that this Jira 6.4 version is using an updated jdbc driver such as 5.1.46 (that 5.1.10 driver version is from 2009, so I have no faith in using it - lots of bugs). Steps to switch databases like this are in Switching databases.
I recommend this step, because I want to understand if you are seeing this problem because of the database switch, because of the attempt to upgrade, or because the data has some other problem. And if you can complete this step, it will tell us more this problem and how to get past it now.
I suspect it's the data you have in the database, in which case the XML cleaner is expected to be able to remove these invalid characters. However when running Jira on an unsupported platform, it really adds to the confusion of what is expected of that platform.
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Hi Andrew,
I have now upgraded the machine where JIRA is currently running to mysql v.5.5.54
It is now running JIRA v7.2.13 with mysql v5.5.54, did a re-indexing as suggested.
Generated a zipped backup and ran it through the XML cleaner.
Deleted and re-created the jira database on the other machine.
Tried to import to JIRA v7.9.0 with mysql v5.7.22
I am running into the same issue:
>>
Error importing data: org.xml.sax.SAXException: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericEntityException: while inserting:
...
(SQL Exception while executing the following:INSERT INTO jiraaction (ID, issueid, AUTHOR, actiontype, actionlevel, rolelevel, actionbody, CREATED, UPDATEAUTHOR, UPDATED, actionnum) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) (Incorrect string value: '\xEF\xBC\x9A ts...' for column 'actionbody' at row 1))
<<
Could you let me know how to continue investigating this ?
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Hi Thomas,
Sorry to hear that this problem is still happening. I expected that if you extracted the entities.xml file and ran it through the cleaner jar in that KB, then repacking the cleaned file (you would have to rename this from entities-cleaned.xml back to entities.xml), along with the activeobject.xml file into a single zip file should be sufficient to remove these invalid characters from your backup.
However if that didn't help, then please see the steps in SQL Exception while updating issues or importing data in JIRA applications with MySQL due to encoding. It is possible that your destination instance of Jira is either not configured correctly from an application and/or database level and that could be causing this error you are seeing now. This KB walks you through steps to take to either correct this problem or at least identify and confirm that your destination instance is setup with the correct settings.
From that KB, please let me know the results of running these SQL commands on the mysql 5.7.x database:
SELECT DISTINCT C.collation_name, T.table_name FROM information_schema.tables AS T, information_schema.`collation_character_set_applicability` AS C WHERE C.collation_name = T.table_collation AND T.table_schema = DATABASE() AND C.collation_name != 'utf8_bin';
and
SELECT default_collation_name FROM information_schema.schemata S WHERE schema_name = (SELECT DATABASE() FROM DUAL);
The first is in regards to the table collations, and the second is the database collation. Both should be set to utf8_bin for a MySQL database. If you have some other collation here, then I would recommend creating a new database per the instructions in Connecting JIRA applications to MySQL.
Please let me know the results.
Andy
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Hi Andy,
Thanks, I am now running into a different problem when trying to import the datas, I get the following report: "JIRA has already been set up. "
I have tried reinstalling v7.9 a couple of times but keep getting this message, do you know what might be causing it ?
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I'm not sure exactly where you are seeing that message. However if you see that it tends to indicate that Jira is not using a truly empty database. I would recommend that you
By doing this, you can be sure that you are taken to the setup wizard of Jira. For the sake of upgrading Jira, this is what you want. You would need to use the link in the setup wizard called 'import existing data'.
This way makes sure that you are actually upgrading the Jira data when it is imported.
Otherwise, if you are actually already logged into Jira and trying to use the system administration menu's "Restore data", I do not have the same confidence that Jira will upgrade that data. That restore data option in the system administration side of Jira is intended for restoring backups created on the same version of Jira.
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Thanks for the suggestion,
I am unfortunately hitting that problem again.
I deleted JIRA by removing the /opt/atlassian /var/atlassian directories
Created a new database/user with never used before names.
Went through the JIRA install wizard, connection to the db was successful.
Started importing datas, browser switched briefly to the data import progress bar before reporting again "JIRA has already been set up", here's a screenshot.
Could you let me know what could be causing this ?
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Here a partial catalina.out content if it can help.
>>
2018-05-16 17:11:13,605 JiraImportTaskExecutionThread-1 INFO anonymous 1030x37x1 1ms9iml 10.50.1.200 /secure/SetupImport.jspa [c.a.j.bc.dataimport.DefaultDataImportService] Importing data is 90% complete...
2018-05-16 17:11:13,997 JiraImportTaskExecutionThread-1 INFO anonymous 1030x37x1 1ms9iml 10.50.1.200 /secure/SetupImport.jspa [c.a.j.bc.dataimport.DefaultDataImportService] Finished storing Generic Values.
2018-05-16 17:11:14,078 JiraImportTaskExecutionThread-1 DEBUG anonymous 1030x37x1 1ms9iml 10.50.1.200 /secure/SetupImport.jspa [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] startCleaning
2018-05-16 17:11:14,080 JiraImportTaskExecutionThread-1 DEBUG anonymous 1030x37x1 1ms9iml 10.50.1.200 /secure/SetupImport.jspa [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] stopCleaning
2018-05-16 17:11:16,428 JiraImportTaskExecutionThread-1 ERROR anonymous 1030x37x1 1ms9iml 10.50.1.200 /secure/SetupImport.jspa [c.a.j.bc.dataimport.DefaultDataImportService] Error during ActiveObjects restore
com.atlassian.activeobjects.spi.ActiveObjectsImportExportException: There was an error during import/export with <unknown plugin>:Error executing update for SQL statement 'ALTER TABLE AO_563AEE_ACTIVITY_ENTITY ADD CONSTRAINT fk_ao_563aee_activity_entity_actor_id FOREIGN KEY (ACTOR_ID) REFERENCES AO_563AEE_ACTOR_ENTITY(ID)'
at com.atlassian.activeobjects.backup.ImportExportErrorServiceImpl.newImportExportSqlException(ImportExportErrorServiceImpl.java:26)
at com.atlassian.activeobjects.backup.SqlUtils.onSqlException(SqlUtils.java:46)
at com.atlassian.activeobjects.backup.SqlUtils.executeUpdate(SqlUtils.java:37)
at com.atlassian.activeobjects.backup.ActiveObjectsForeignKeyCreator.create(ActiveObjectsForeignKeyCreator.java:43)
at com.atlassian.activeobjects.backup.ForeignKeyAroundImporter.after(ForeignKeyAroundImporter.java:26)
at com.atlassian.dbexporter.importer.AbstractImporter.importNode(AbstractImporter.java:47)
at com.atlassian.dbexporter.DbImporter.importData(DbImporter.java:69)
at com.atlassian.activeobjects.backup.ActiveObjectsBackup.restore(ActiveObjectsBackup.java:151)
at com.atlassian.jira.bc.dataimport.DefaultDataImportService.restoreActiveObjects(DefaultDataImportService.java:577)
at com.atlassian.jira.bc.dataimport.DefaultDataImportService.performImport(DefaultDataImportService.java:751)
at com.atlassian.jira.bc.dataimport.DefaultDataImportService.doImport(DefaultDataImportService.java:324)
at com.atlassian.jira.web.action.setup.DataImportAsyncCommand.call(DataImportAsyncCommand.java:60)
at com.atlassian.jira.web.action.setup.DataImportAsyncCommand.call(DataImportAsyncCommand.java:28)
at com.atlassian.jira.task.ImportTaskManagerImpl$TaskCallableDecorator.call(ImportTaskManagerImpl.java:157)
at com.atlassian.jira.task.ImportTaskManagerImpl$TaskCallableDecorator.call(ImportTaskManagerImpl.java:133)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
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: REFERENCES command denied to user 'jiradbuser1'@'10.50.1.9' for table 'AO_563AEE_ACTOR_ENTITY'
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.SQLError.createSQLException(SQLError.java:944)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3976)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3912)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2530)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2683)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2482)
at com.mysql.jdbc.StatementImpl.executeUpdateInternal(StatementImpl.java:1552)
at com.mysql.jdbc.StatementImpl.executeLargeUpdate(StatementImpl.java:2607)
at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1480)
at org.apache.commons.dbcp2.DelegatingStatement.executeUpdate(DelegatingStatement.java:234)
at org.apache.commons.dbcp2.DelegatingStatement.executeUpdate(DelegatingStatement.java:234)
at com.atlassian.activeobjects.backup.SqlUtils.executeUpdate(SqlUtils.java:34)
... 18 more
2018-05-16 17:11:16,437 JiraImportTaskExecutionThread-1 WARN anonymous 1030x37x1 1ms9iml 10.50.1.200 /secure/SetupImport.jspa [c.a.j.p.d.dao.impl.CachingOrganizationDaoImpl] onImportCompleted - clearing cache !!
2018-05-16 17:11:16,438 JiraImportTaskExecutionThread-1 INFO anonymous 1030x37x1 1ms9iml 10.50.1.200 /secure/SetupImport.jspa [c.a.j.bc.dataimport.DefaultDataImportService] Importing data is 100% complete...
2018-05-16 17:11:16,438 JiraImportTaskExecutionThread-1 INFO anonymous 1030x37x1 1ms9iml 10.50.1.200 /secure/SetupImport.jspa [c.a.j.bc.dataimport.DefaultDataImportService] JIRA Data Import has finished.
2018-05-16 17:12:24,151 hipchat-plugin-tasks-executor-0 DEBUG anonymous 1029x31x1 1ms9iml 10.50.1.200 /secure/SetupDatabase.jspa [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.plugins.base-hipchat-integration-plugin-api]
<<
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I researched that error message and was able to identify the cause which is that the REFERENCES attribute has to be added when creating the mysql user with v5.7
I have now been able to import the datas successfully and finish the install, thanks again for all your help.
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YAY, thanks for letting us know. Once I saw that last stack trace I knew what the problem was here. Glad things are working now.
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Hi @Thomas D,
You need to change your my.cnf and comment this lines:
#skip-networking
#bind-address = 0.0.0.0
for more information, you can see this post: https://serverfault.com/questions/139323/how-to-bind-mysql-server-to-more-than-one-ip-address
Cheers,
Adrián.
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Thanks Adrian but there is no skip-networking line in my.cnf and it makes no difference whether bind-address is commented or not, still can't connect.
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Hi @Thomas D,
When you comment the line
#bind-address
execute this command:
service mysql restart
And try to connect do you get the same message?
Cheers,
Adrián.
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Then I don't know sorry @Thomas D
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