[InterMine Dev] (Still) Problems deploying webapp

Paulo Nuin paulo.nuin at gmail.com
Tue Mar 19 04:25:32 GMT 2019


Hi

I was able to set a theme, albeit is not complete, we are missing our header, footer, and some styling. Is there a way to modify the layout.jsp to use our previous setup?

Thanks

Paulo




> On Feb 5, 2019, at 3:15 AM, sergio contrino <contrino at intermine.org> wrote:
> 
> great paulo. for the theme, please check docs here
> https://intermine.readthedocs.io/en/latest/webapp/layout/
> bottom of the page.
> let us know if any issue. i cc dev so we record solution.
> thanks!
> sergio
> 
> On 04/02/2019 16:41, Paulo Nuin wrote:
>> Hi Sergio
>> Removing the files did the trick, and I guess I have to setup the theme now, as most of our changes are gone. Is there any documentation on how to setup that in the new version?
>> Thanks a lot
>> Paulo
>>> On Feb 1, 2019, at 5:10 AM, sergio contrino <contrino at intermine.org> wrote:
>>> 
>>> hi paulo,
>>> you have a few files in
>>> 
>>> webapp/src/main/webapp/
>>> 
>>> that you should remove. i have checked a few of them and it seems fine just to get rid of them. it is possible that you have a couple of links to adjust, but we can discuss this after the cleanup.
>>> so please remove
>>> 
>>> begin.jsp
>>> errorMessages.jsp
>>> footer.jsp
>>> headMenu.jsp
>>> historyBagView.jsp
>>> historyQueryView.jsp
>>> layout.jsp
>>> 
>>> from your webapp/src/main/webapp/
>>> directory
>>> thanks
>>> sergio
>>> 
>>> 
>>> 
>>> On 31/01/2019 16:19, Paulo Nuin wrote:
>>>> Hi Sergio
>>>> DB is on
>>>> https://www.dropbox.com/s/3jfsq7v5cjeac13/intermine_dev_268_7.sql.gz?dl=0
>>>> Cheers
>>>> Paulo
>>>>> On Jan 31, 2019, at 9:09 AM, Paulo Nuin <paulo.nuin at gmail.com> wrote:
>>>>> 
>>>>> Hi
>>>>> 
>>>>> I have only a regular DB build with 2.+. I will share it with you, about 1.3 Gb compressed.
>>>>> 
>>>>> Cheers
>>>>> Paulo
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Jan 31, 2019, at 7:34 AM, sergio contrino <contrino at intermine.org> wrote:
>>>>>> 
>>>>>> hi paulo,
>>>>>> could you send me (a link to) a dump of your test database? i did not find one here...
>>>>>> webapp seems broadly fine (i can deploy and i don't get the blank page) but i would like to test it with your data.
>>>>>> thanks
>>>>>> sergio
>>>>>> 
>>>>>> 
>>>>>> On 30/01/2019 20:21, Paulo Nuin wrote:
>>>>>>> Hi
>>>>>>> I am using branch im-269 now.
>>>>>>> Thanks
>>>>>>> Paulo
>>>>>>>> On Jan 30, 2019, at 1:20 PM, sergio contrino <contrino at intermine.org> wrote:
>>>>>>>> 
>>>>>>>> hi paulo,
>>>>>>>> sorry you have still problems.
>>>>>>>> i'll try to deploy here, using your wormmine branch im-266 (correct?). i think i have a database you shared some time ago, but if not i'll do a test with a dummy.
>>>>>>>> thanks
>>>>>>>> sergio
>>>>>>>> 
>>>>>>>> On 30/01/2019 17:54, Paulo Nuin wrote:
>>>>>>>>> Hi everyone
>>>>>>>>> I am still having problems deploying the webapp, with errors varying from not deploying it at all to successfully deploying with access errors. I have there test instances set, 2 on Mac computers and one on AWS, and on each one I have a different error:
>>>>>>>>> 1 - Mac 1 - deployment is fine but when trying to access I get this on Tomcat’s localhost log:
>>>>>>>>> 30-Jan-2019 10:27:50.433 INFO [http-nio-8080-exec-14] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>>>>>>>>> 30-Jan-2019 10:27:50.434 SEVERE [http-nio-8080-exec-14] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() exception
>>>>>>>>> javax.servlet.UnavailableException: Production object store is null
>>>>>>>>> Which is similar to https://github.com/intermine/intermine/issues/1903, but in this case all files are in the same disk. Tomcat is on /opt/tomcat and InterMine/WormMine is under /Users/****/WormMine
>>>>>>>>> 2- Mac 2 - deployment fails with
>>>>>>>>> org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:cargoRedeployLocal'.
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:100)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:70)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.SkipUpToDateTaskExecuter.execute(SkipUpToDateTaskExecuter.java:63)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.ResolveTaskOutputCachingStateExecuter.execute(ResolveTaskOutputCachingStateExecuter.java:54)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.ValidatingTaskExecuter.execute(ValidatingTaskExecuter.java:58)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.SkipEmptySourceFilesTaskExecuter.execute(SkipEmptySourceFilesTaskExecuter.java:88)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.ResolveTaskArtifactStateTaskExecuter.execute(ResolveTaskArtifactStateTaskExecuter.java:52)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:52)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:54)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.ExecuteAtMostOnceTaskExecuter.execute(ExecuteAtMostOnceTaskExecuter.java:43)
>>>>>>>>>        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:34)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker$1.run(DefaultTaskGraphExecuter.java:248)
>>>>>>>>>        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
>>>>>>>>>        at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
>>>>>>>>>        at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:197)
>>>>>>>>>        at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:107)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:241)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskGraphExecuter$EventFiringTaskWorker.execute(DefaultTaskGraphExecuter.java:230)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.processTask(DefaultTaskPlanExecutor.java:124)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.access$200(DefaultTaskPlanExecutor.java:80)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:105)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker$1.execute(DefaultTaskPlanExecutor.java:99)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.execute(DefaultTaskExecutionPlan.java:625)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskExecutionPlan.executeWithTask(DefaultTaskExecutionPlan.java:580)
>>>>>>>>>        at org.gradle.execution.taskgraph.DefaultTaskPlanExecutor$TaskExecutorWorker.run(DefaultTaskPlanExecutor.java:99)
>>>>>>>>>        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63)
>>>>>>>>>        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46)
>>>>>>>>>        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55)
>>>>>>>>> Caused by: java.lang.NullPointerException: Cannot get property 'canonicalPath' on null object
>>>>>>>>> Both machines, and AWS, have the same code, maybe a different DB name or so, but identical in almost every other detail.
>>>>>>>>> 3 - AWS, deployment is fine but when accessing the page I get this over and over on Catalina.out
>>>>>>>>> 25386 [http-nio-8080-exec-67] ERROR org.apache.struts.tiles.taglib.InsertTag  - Can't insert page 'hints.tile' : The requested resource [/tools/wormmine/hints.tile] is not available
>>>>>>>>> java.io.FileNotFoundException: The requested resource [/tools/wormmine/hints.tile] is not available
>>>>>>>>>        at org.apache.catalina.servlets.DefaultServlet.serveResource(DefaultServlet.java:770)
>>>>>>>>>        at org.apache.catalina.servlets.DefaultServlet.doGet(DefaultServlet.java:438)
>>>>>>>>>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:635)
>>>>>>>>>        at org.apache.catalina.servlets.DefaultServlet.service(DefaultServlet.java:418)
>>>>>>>>> I did all the suggested steps from Sergio, but I still get the same thing after a couple of times when I was able to see the header of the page (theme problem) which reverted to the hints.page problem.
>>>>>>>>> Any help appreciated.
>>>>>>>>> Cheers
>>>>>>>>> Paulo
>>>>>>>>> _______________________________________________
>>>>>>>>> dev mailing list
>>>>>>>>> dev at lists.intermine.org
>>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>>> 
>>>>>>>> -- 
>>>>>>>> sergio contrino                  InterMine, University of Cambridge
>>>>>>>> https://sergiocontrino.github.io           http://www.intermine.org
>>>>>> 
>>>>>> -- 
>>>>>> sergio contrino                  InterMine, University of Cambridge
>>>>>> https://sergiocontrino.github.io           http://www.intermine.org
>>>>> 
>>> 
>>> -- 
>>> sergio contrino                  InterMine, University of Cambridge
>>> https://sergiocontrino.github.io           http://www.intermine.org
> 
> -- 
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org



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