(Still) Problems deploying webapp

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(Still) Problems deploying webapp

Paulo Nuin
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



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Re: (Still) Problems deploying webapp

sergio contrino-2
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
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: (Still) Problems deploying webapp

Paulo Nuin
Hi

I am using branch im-269 now.

Thanks

Paulo

> On Jan 30, 2019, at 1:20 PM, sergio contrino <[hidden email]> 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
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org

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Re: (Still) Problems deploying webapp

sergio contrino-2
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 <[hidden email]> 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
>>> [hidden email]
>>> 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
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Re: (Still) Problems deploying webapp

Paulo Nuin
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 <[hidden email]> 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 <[hidden email]> 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
>>>> [hidden email]
>>>> 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

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Re: (Still) Problems deploying webapp

sergio contrino-2
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>>>>>>>> [hidden email]
>>>>>>>> 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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dev mailing list
[hidden email]
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Re: (Still) Problems deploying webapp

Paulo Nuin
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>>>>>>>>> [hidden email]
>>>>>>>>> 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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Re: (Still) Problems deploying webapp

sergio contrino-2
hi paulo!
sorry for the slow reply. you should be able to overwrite the general
layout.jsp with a file with the same name in your
wormmine/resources/webapp directory, where you could also place your
header/footer etc
if any problem, please send the link to your current github repo and i
can check it locally.
thanks!
sergio


On 19/03/2019 04:25, Paulo Nuin wrote:

> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>>>>>>>>>> [hidden email]
>>>>>>>>>> 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
>

--
sergio contrino                  InterMine, University of Cambridge
https://sergiocontrino.github.io           http://www.intermine.org
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Re: (Still) Problems deploying webapp

Paulo Nuin
Thanks, Sergio. So this would supersede the layout.jsp that comes from core?

Cheers
Paulo



> On Mar 20, 2019, at 11:22 AM, sergio contrino <[hidden email]> wrote:
>
> hi paulo!
> sorry for the slow reply. you should be able to overwrite the general layout.jsp with a file with the same name in your wormmine/resources/webapp directory, where you could also place your header/footer etc
> if any problem, please send the link to your current github repo and i can check it locally.
> thanks!
> sergio
>
>
> On 19/03/2019 04:25, Paulo Nuin wrote:
>> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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
>>>>>>>>>>> [hidden email]
>>>>>>>>>>> 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
>
> --
> sergio contrino                  InterMine, University of Cambridge
> https://sergiocontrino.github.io           http://www.intermine.org

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dev mailing list
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