I have the openspecimen.war built from source code. I have a mysql docker container running with the database for openspecimen. Now I am trying to connect the openspecimen running in a separate docker container (which contains tomcat/java also) to the aforementioned database container. I can get the tomcat running and also see the openspecimen.war deployed (see attached). However when I start the application from the tomcat manager, I get some error
Message: FAIL - Application at context path /openspecimen could not be started and then navigating to openspecimen results in 404 not found.
In the database container, I see 4 tables being created (see attached).
Also in the tomcat/logs I see errors which is attached here.
I have also set lower_case_table_names = 1 in my.cnf but it did not help.
localhost.2016-07-04.log (17.3 KB)
Hi @suyesh,
The log file shows two errors:
- Invalid plugin directory: /opt/openspecimen/os-plugins, Please cross check the plugin directory and specify a valid directory.
- Case sensitivity flag is not set for MySQL. For the steps to configure the MySQL case sensitivity flag please visit: https://openspecimen.atlassian.net/wiki/x/fAYR
Please note that after changing the MySQL configuration, you need to restart the MySQL service.
~Nitesh
Hi Nitesh,
The plugin directory is correct and valid. I had already for the case sensitivity issue set [quote=“suyesh, post:1, topic:731”]
lower_case_table_names = 1 in my.cnf
[/quote]
and restarted the MySQL server but still did not work.
The my.cnf file that I worked was in etc/mysql/.
Hi Nitesh,
The metioned errors have been fixed now. And in the log files I don’t see any errors. I can also start the openspecimen from the tomcat manager without any error. Now I see there are more tables (278) created in the database. However I only see a blank page in the browser when I navigate to the application page. The logs in the tomcat shows:
Jul 08, 2016 8:05:43 AM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Jul 08, 2016 8:05:44 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Jul 08, 2016 8:06:12 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring FrameworkServlet 'pluginUiResources'
Jul 08, 2016 8:06:12 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring FrameworkServlet 'restApi'
Jul 08, 2016 8:07:38 AM org.apache.catalina.core.ApplicationContext log
INFO: Destroying Spring FrameworkServlet 'pluginUiResources'
Jul 08, 2016 8:07:38 AM org.apache.catalina.core.ApplicationContext log
INFO: Destroying Spring FrameworkServlet 'restApi'
Jul 08, 2016 8:07:38 AM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Jul 08, 2016 8:07:47 AM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
Jul 08, 2016 8:07:47 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Jul 08, 2016 8:08:08 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring FrameworkServlet 'pluginUiResources'
Jul 08, 2016 8:08:08 AM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring FrameworkServlet 'restApi'Hi @suyesh,
Can you please send us the tomcat log files and the browser error. Please follow below steps to get the log:
- Tomcat log: Should be present under ${TOMCAT_HOME}/logs directory. Please zip the log and share.
- Browser error:
a. Open the browser and press f12.
b. It will open the developer tools section.
c. Now try to open the OpenSpecimen page(https://:/openspecimen).
d. There must be some errors in the console and network section of the browser developer tools.
e. Please take the screenshot of console errors and network errors and share.
~Nitesh
Hi Nitesh. I was away for couple of weeks so could not reply. Please find attached the logs. Also the browser error.logs.zip (6.7 KB)
I have managed to resolve the problem.