Error on web app deployment

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Error on web app deployment

Paulo Nuin
Hi everyone

I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment

31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
 javax.servlet.UnavailableException

I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.

Any help appreciated.

Paulo
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Re: Error on web app deployment

Paulo Nuin
Hi

I have found a typo on my gradle.properties file, but I am still having an error:

31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
 java.lang.NullPointerException
….
31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable

I am rebuilding without the typo in order to check. The typo was on the line

systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl

Thanks

Paulo


> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>
> Hi everyone
>
> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>
> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
> javax.servlet.UnavailableException
>
> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>
> Any help appreciated.
>
> Paulo

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Re: Error on web app deployment

Paulo Nuin
Hi everyone

Updated the Gradle file and rebuilt the DB, on deploement I see the same error:

31-Oct-2019 20:12:33.570 SEVERE [http-nio-8080-exec-87] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [ws-version] in context with path [/tools/wormmine] threw exception
 org.intermine.web.context.ContextNotInitialisedException: Attempt to access InterMineContext before it has  been initialised


Any help appreciated.

Cheers

Paulo

> On Oct 31, 2019, at 6:46 AM, Paulo Nuin <[hidden email]> wrote:
>
> Hi
>
> I have found a typo on my gradle.properties file, but I am still having an error:
>
> 31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
> java.lang.NullPointerException
> ….
> 31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>
> I am rebuilding without the typo in order to check. The typo was on the line
>
> systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
>
> Thanks
>
> Paulo
>
>
>> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>>
>> Hi everyone
>>
>> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>>
>> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
>> javax.servlet.UnavailableException
>>
>> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>>
>> Any help appreciated.
>>
>> Paulo
>

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Re: Error on web app deployment

Daniela Butano-2
Ciao Paulo,

I'm sorry you have this issue.

I don't remember we have ever had a similar one before, I have checked
in github too.

The exception is thrown when you try to call one of the following
methods (getInterMineAPI, getKeyStore, getWebConfig, getWebProperties,
shutdown) before initializing the InteMineContext ( which is executed in
the InitializerPlugin)

Maybe the log file can help to identify which of the methods above has
been called....

Cheers,

Daniela

On 31/10/2019 20:17, Paulo Nuin wrote:

> Hi everyone
>
> Updated the Gradle file and rebuilt the DB, on deploement I see the same error:
>
> 31-Oct-2019 20:12:33.570 SEVERE [http-nio-8080-exec-87] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [ws-version] in context with path [/tools/wormmine] threw exception
>   org.intermine.web.context.ContextNotInitialisedException: Attempt to access InterMineContext before it has  been initialised
>
>
> Any help appreciated.
>
> Cheers
>
> Paulo
>
>> On Oct 31, 2019, at 6:46 AM, Paulo Nuin <[hidden email]> wrote:
>>
>> Hi
>>
>> I have found a typo on my gradle.properties file, but I am still having an error:
>>
>> 31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>> java.lang.NullPointerException
>> ….
>> 31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>
>> I am rebuilding without the typo in order to check. The typo was on the line
>>
>> systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
>>
>> Thanks
>>
>> Paulo
>>
>>
>>> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>>>
>>> Hi everyone
>>>
>>> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>>>
>>> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>>> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
>>> javax.servlet.UnavailableException
>>>
>>> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>>>
>>> Any help appreciated.
>>>
>>> Paulo
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
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Re: Error on web app deployment

Paulo Nuin
Hi Daniela

Which log file? Is there any InterMine log file that would show that? I am trying all Tomcat ones.

Thanks

Paulo

> On Nov 1, 2019, at 3:50 AM, Daniela Butano <[hidden email]> wrote:
>
> Ciao Paulo,
>
> I'm sorry you have this issue.
>
> I don't remember we have ever had a similar one before, I have checked in github too.
>
> The exception is thrown when you try to call one of the following methods (getInterMineAPI, getKeyStore, getWebConfig, getWebProperties, shutdown) before initializing the InteMineContext ( which is executed in the InitializerPlugin)
>
> Maybe the log file can help to identify which of the methods above has been called....
>
> Cheers,
>
> Daniela
>
> On 31/10/2019 20:17, Paulo Nuin wrote:
>> Hi everyone
>>
>> Updated the Gradle file and rebuilt the DB, on deploement I see the same error:
>>
>> 31-Oct-2019 20:12:33.570 SEVERE [http-nio-8080-exec-87] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [ws-version] in context with path [/tools/wormmine] threw exception
>>  org.intermine.web.context.ContextNotInitialisedException: Attempt to access InterMineContext before it has  been initialised
>>
>>
>> Any help appreciated.
>>
>> Cheers
>>
>> Paulo
>>
>>> On Oct 31, 2019, at 6:46 AM, Paulo Nuin <[hidden email]> wrote:
>>>
>>> Hi
>>>
>>> I have found a typo on my gradle.properties file, but I am still having an error:
>>>
>>> 31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>>> java.lang.NullPointerException
>>> ….
>>> 31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>>
>>> I am rebuilding without the typo in order to check. The typo was on the line
>>>
>>> systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
>>>
>>> Thanks
>>>
>>> Paulo
>>>
>>>
>>>> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>>>>
>>>> Hi everyone
>>>>
>>>> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>>>>
>>>> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>>>> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
>>>> javax.servlet.UnavailableException
>>>>
>>>> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>>>>
>>>> Any help appreciated.
>>>>
>>>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: Error on web app deployment

Paulo Nuin
Also, does updating gradle or some configurations file fix the problem? Build worked fine with 3.1, no errors and everything on 2.0 works fine, deployment, build etc

Thanks

Paulo



> On Nov 1, 2019, at 5:48 AM, Paulo Nuin <[hidden email]> wrote:
>
> Hi Daniela
>
> Which log file? Is there any InterMine log file that would show that? I am trying all Tomcat ones.
>
> Thanks
>
> Paulo
>
>> On Nov 1, 2019, at 3:50 AM, Daniela Butano <[hidden email]> wrote:
>>
>> Ciao Paulo,
>>
>> I'm sorry you have this issue.
>>
>> I don't remember we have ever had a similar one before, I have checked in github too.
>>
>> The exception is thrown when you try to call one of the following methods (getInterMineAPI, getKeyStore, getWebConfig, getWebProperties, shutdown) before initializing the InteMineContext ( which is executed in the InitializerPlugin)
>>
>> Maybe the log file can help to identify which of the methods above has been called....
>>
>> Cheers,
>>
>> Daniela
>>
>> On 31/10/2019 20:17, Paulo Nuin wrote:
>>> Hi everyone
>>>
>>> Updated the Gradle file and rebuilt the DB, on deploement I see the same error:
>>>
>>> 31-Oct-2019 20:12:33.570 SEVERE [http-nio-8080-exec-87] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [ws-version] in context with path [/tools/wormmine] threw exception
>>> org.intermine.web.context.ContextNotInitialisedException: Attempt to access InterMineContext before it has  been initialised
>>>
>>>
>>> Any help appreciated.
>>>
>>> Cheers
>>>
>>> Paulo
>>>
>>>> On Oct 31, 2019, at 6:46 AM, Paulo Nuin <[hidden email]> wrote:
>>>>
>>>> Hi
>>>>
>>>> I have found a typo on my gradle.properties file, but I am still having an error:
>>>>
>>>> 31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>>>> java.lang.NullPointerException
>>>> ….
>>>> 31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>>>
>>>> I am rebuilding without the typo in order to check. The typo was on the line
>>>>
>>>> systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
>>>>
>>>> Thanks
>>>>
>>>> Paulo
>>>>
>>>>
>>>>> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>
>>>>> Hi everyone
>>>>>
>>>>> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>>>>>
>>>>> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>>>>> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
>>>>> javax.servlet.UnavailableException
>>>>>
>>>>> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>>>>>
>>>>> Any help appreciated.
>>>>>
>>>>> Paulo
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>

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Re: Error on web app deployment

Daniela Butano-2
You should find the intermine.log file in the wormine directory.

On 01/11/2019 13:50, Paulo Nuin wrote:

> Also, does updating gradle or some configurations file fix the problem? Build worked fine with 3.1, no errors and everything on 2.0 works fine, deployment, build etc
>
> Thanks
>
> Paulo
>
>
>
>> On Nov 1, 2019, at 5:48 AM, Paulo Nuin <[hidden email]> wrote:
>>
>> Hi Daniela
>>
>> Which log file? Is there any InterMine log file that would show that? I am trying all Tomcat ones.
>>
>> Thanks
>>
>> Paulo
>>
>>> On Nov 1, 2019, at 3:50 AM, Daniela Butano <[hidden email]> wrote:
>>>
>>> Ciao Paulo,
>>>
>>> I'm sorry you have this issue.
>>>
>>> I don't remember we have ever had a similar one before, I have checked in github too.
>>>
>>> The exception is thrown when you try to call one of the following methods (getInterMineAPI, getKeyStore, getWebConfig, getWebProperties, shutdown) before initializing the InteMineContext ( which is executed in the InitializerPlugin)
>>>
>>> Maybe the log file can help to identify which of the methods above has been called....
>>>
>>> Cheers,
>>>
>>> Daniela
>>>
>>> On 31/10/2019 20:17, Paulo Nuin wrote:
>>>> Hi everyone
>>>>
>>>> Updated the Gradle file and rebuilt the DB, on deploement I see the same error:
>>>>
>>>> 31-Oct-2019 20:12:33.570 SEVERE [http-nio-8080-exec-87] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [ws-version] in context with path [/tools/wormmine] threw exception
>>>> org.intermine.web.context.ContextNotInitialisedException: Attempt to access InterMineContext before it has  been initialised
>>>>
>>>>
>>>> Any help appreciated.
>>>>
>>>> Cheers
>>>>
>>>> Paulo
>>>>
>>>>> On Oct 31, 2019, at 6:46 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>
>>>>> Hi
>>>>>
>>>>> I have found a typo on my gradle.properties file, but I am still having an error:
>>>>>
>>>>> 31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>>>>> java.lang.NullPointerException
>>>>> ….
>>>>> 31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>>>>
>>>>> I am rebuilding without the typo in order to check. The typo was on the line
>>>>>
>>>>> systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
>>>>>
>>>>> Thanks
>>>>>
>>>>> Paulo
>>>>>
>>>>>
>>>>>> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>
>>>>>> Hi everyone
>>>>>>
>>>>>> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>>>>>>
>>>>>> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>>>>>> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
>>>>>> javax.servlet.UnavailableException
>>>>>>
>>>>>> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>>>>>>
>>>>>> Any help appreciated.
>>>>>>
>>>>>> Paulo
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
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Re: Error on web app deployment

Paulo Nuin
Hi Daniela

I don’t see errors on the intermine.log, and after redeploying a couple of times I get the same errors on Tomcat


This is on intermine.log just after redeploying the webapp


2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Finding global properties file default.intermine.properties
2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Loading properties from file:/mnt/data2/3.0/WormMine/webapp/build/resources/main/default.intermine.properties
2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Finding global properties file intermine.properties
2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Loading properties from file:/mnt/data2/3.0/WormMine/webapp/build/resources/main/intermine.properties
2019-11-01 17:18:16 INFO             org.intermine.sql.Database  [] - Creating new Database jdbc:postgresql://localhost/intermine_test({platform=PostgreSQL, datasource.dataSourceClassName=org.postgresql.ds.PGSimpleDataSource, datasource.dataSourceName=d$
2019-11-01 17:18:17 INFO  org.intermine.objectstore.ObjectStoreAbstractImpl  [] - Creating new org.intermine.objectstore.intermine.ObjectStoreInterMineImpl with sequence = {}, model = "genomic"


And on localhost log just after (InterMine related line highlighted)

01-Nov-2019 17:20:23.241 WARNING [http-nio-8080-exec-121] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
01-Nov-2019 17:20:24.741 WARNING [http-nio-8080-exec-122] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
01-Nov-2019 17:20:25.960 WARNING [http-nio-8080-exec-123] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
01-Nov-2019 17:23:29.405 SEVERE [http-nio-8080-exec-124] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
 java.lang.NullPointerException
        at org.intermine.web.logic.session.SessionMethods.initSession(SessionMethods.java:458)
        at org.intermine.web.logic.session.SessionListener.sessionCreated(SessionListener.java:31)
        at org.apache.catalina.session.StandardSession.tellNew(StandardSession.java:396)
        at org.apache.catalina.session.StandardSession.setId(StandardSession.java:368)
        at org.apache.catalina.session.StandardSession.setId(StandardSession.java:349)
        at org.apache.catalina.session.ManagerBase.createSession(ManagerBase.java:663)
        at org.apache.catalina.connector.Request.doGetSession(Request.java:3044)
        at org.apache.catalina.connector.Request.getSession(Request.java:2434)
        at org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:896)
        at org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:908)
        at org.apache.jasper.runtime.PageContextImpl.initialize(PageContextImpl.java:137)
        at org.apache.jasper.runtime.JspFactoryImpl.internalGetPageContext(JspFactoryImpl.java:109)
        at org.apache.jasper.runtime.JspFactoryImpl.getPageContext(JspFactoryImpl.java:60)
        at org.apache.jsp.index_jsp._jspService(index_jsp.java:100)
        at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
        at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:443)
        at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
        at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139) <----------
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:496)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
        at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:677)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803)
        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)
        at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Thread.java:748)

Thanks

Paulo


> On Nov 1, 2019, at 8:05 AM, Daniela Butano <[hidden email]> wrote:
>
> You should find the intermine.log file in the wormine directory.
>
> On 01/11/2019 13:50, Paulo Nuin wrote:
>> Also, does updating gradle or some configurations file fix the problem? Build worked fine with 3.1, no errors and everything on 2.0 works fine, deployment, build etc
>>
>> Thanks
>>
>> Paulo
>>
>>
>>
>>> On Nov 1, 2019, at 5:48 AM, Paulo Nuin <[hidden email]> wrote:
>>>
>>> Hi Daniela
>>>
>>> Which log file? Is there any InterMine log file that would show that? I am trying all Tomcat ones.
>>>
>>> Thanks
>>>
>>> Paulo
>>>
>>>> On Nov 1, 2019, at 3:50 AM, Daniela Butano <[hidden email]> wrote:
>>>>
>>>> Ciao Paulo,
>>>>
>>>> I'm sorry you have this issue.
>>>>
>>>> I don't remember we have ever had a similar one before, I have checked in github too.
>>>>
>>>> The exception is thrown when you try to call one of the following methods (getInterMineAPI, getKeyStore, getWebConfig, getWebProperties, shutdown) before initializing the InteMineContext ( which is executed in the InitializerPlugin)
>>>>
>>>> Maybe the log file can help to identify which of the methods above has been called....
>>>>
>>>> Cheers,
>>>>
>>>> Daniela
>>>>
>>>> On 31/10/2019 20:17, Paulo Nuin wrote:
>>>>> Hi everyone
>>>>>
>>>>> Updated the Gradle file and rebuilt the DB, on deploement I see the same error:
>>>>>
>>>>> 31-Oct-2019 20:12:33.570 SEVERE [http-nio-8080-exec-87] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [ws-version] in context with path [/tools/wormmine] threw exception
>>>>> org.intermine.web.context.ContextNotInitialisedException: Attempt to access InterMineContext before it has  been initialised
>>>>>
>>>>>
>>>>> Any help appreciated.
>>>>>
>>>>> Cheers
>>>>>
>>>>> Paulo
>>>>>
>>>>>> On Oct 31, 2019, at 6:46 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>
>>>>>> Hi
>>>>>>
>>>>>> I have found a typo on my gradle.properties file, but I am still having an error:
>>>>>>
>>>>>> 31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>>>>>> java.lang.NullPointerException
>>>>>> ….
>>>>>> 31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>>>>>
>>>>>> I am rebuilding without the typo in order to check. The typo was on the line
>>>>>>
>>>>>> systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Paulo
>>>>>>
>>>>>>
>>>>>>> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>>
>>>>>>> Hi everyone
>>>>>>>
>>>>>>> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>>>>>>>
>>>>>>> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>>>>>>> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
>>>>>>> javax.servlet.UnavailableException
>>>>>>>
>>>>>>> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>>>>>>>
>>>>>>> Any help appreciated.
>>>>>>>
>>>>>>> Paulo
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev

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Re: Error on web app deployment

Paulo Nuin
Hi Daniela

Any idea on the error(s) below?

Upgrading Tomcat might work?

Thanks

Paulo

> On Nov 1, 2019, at 11:58 AM, Paulo Nuin <[hidden email]> wrote:
>
> Hi Daniela
>
> I don’t see errors on the intermine.log, and after redeploying a couple of times I get the same errors on Tomcat
>
>
> This is on intermine.log just after redeploying the webapp
>
>
> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Finding global properties file default.intermine.properties
> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Loading properties from file:/mnt/data2/3.0/WormMine/webapp/build/resources/main/default.intermine.properties
> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Finding global properties file intermine.properties
> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Loading properties from file:/mnt/data2/3.0/WormMine/webapp/build/resources/main/intermine.properties
> 2019-11-01 17:18:16 INFO             org.intermine.sql.Database  [] - Creating new Database jdbc:postgresql://localhost/intermine_test({platform=PostgreSQL, datasource.dataSourceClassName=org.postgresql.ds.PGSimpleDataSource, datasource.dataSourceName=d$
> 2019-11-01 17:18:17 INFO  org.intermine.objectstore.ObjectStoreAbstractImpl  [] - Creating new org.intermine.objectstore.intermine.ObjectStoreInterMineImpl with sequence = {}, model = "genomic"
>
>
> And on localhost log just after (InterMine related line highlighted)
>
> 01-Nov-2019 17:20:23.241 WARNING [http-nio-8080-exec-121] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
> 01-Nov-2019 17:20:24.741 WARNING [http-nio-8080-exec-122] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
> 01-Nov-2019 17:20:25.960 WARNING [http-nio-8080-exec-123] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
> 01-Nov-2019 17:23:29.405 SEVERE [http-nio-8080-exec-124] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
> java.lang.NullPointerException
>        at org.intermine.web.logic.session.SessionMethods.initSession(SessionMethods.java:458)
>        at org.intermine.web.logic.session.SessionListener.sessionCreated(SessionListener.java:31)
>        at org.apache.catalina.session.StandardSession.tellNew(StandardSession.java:396)
>        at org.apache.catalina.session.StandardSession.setId(StandardSession.java:368)
>        at org.apache.catalina.session.StandardSession.setId(StandardSession.java:349)
>        at org.apache.catalina.session.ManagerBase.createSession(ManagerBase.java:663)
>        at org.apache.catalina.connector.Request.doGetSession(Request.java:3044)
>        at org.apache.catalina.connector.Request.getSession(Request.java:2434)
>        at org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:896)
>        at org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:908)
>        at org.apache.jasper.runtime.PageContextImpl.initialize(PageContextImpl.java:137)
>        at org.apache.jasper.runtime.JspFactoryImpl.internalGetPageContext(JspFactoryImpl.java:109)
>        at org.apache.jasper.runtime.JspFactoryImpl.getPageContext(JspFactoryImpl.java:60)
>        at org.apache.jsp.index_jsp._jspService(index_jsp.java:100)
>        at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
>        at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:443)
>        at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
>        at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
>        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
>        at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139) <----------
>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
>        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
>        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
>        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:496)
>        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
>        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
>        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
>        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
>        at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:677)
>        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
>        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803)
>        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
>        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
>        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)
>        at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
>        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>        at java.lang.Thread.run(Thread.java:748)
>
> Thanks
>
> Paulo
>
>
>> On Nov 1, 2019, at 8:05 AM, Daniela Butano <[hidden email]> wrote:
>>
>> You should find the intermine.log file in the wormine directory.
>>
>> On 01/11/2019 13:50, Paulo Nuin wrote:
>>> Also, does updating gradle or some configurations file fix the problem? Build worked fine with 3.1, no errors and everything on 2.0 works fine, deployment, build etc
>>>
>>> Thanks
>>>
>>> Paulo
>>>
>>>
>>>
>>>> On Nov 1, 2019, at 5:48 AM, Paulo Nuin <[hidden email]> wrote:
>>>>
>>>> Hi Daniela
>>>>
>>>> Which log file? Is there any InterMine log file that would show that? I am trying all Tomcat ones.
>>>>
>>>> Thanks
>>>>
>>>> Paulo
>>>>
>>>>> On Nov 1, 2019, at 3:50 AM, Daniela Butano <[hidden email]> wrote:
>>>>>
>>>>> Ciao Paulo,
>>>>>
>>>>> I'm sorry you have this issue.
>>>>>
>>>>> I don't remember we have ever had a similar one before, I have checked in github too.
>>>>>
>>>>> The exception is thrown when you try to call one of the following methods (getInterMineAPI, getKeyStore, getWebConfig, getWebProperties, shutdown) before initializing the InteMineContext ( which is executed in the InitializerPlugin)
>>>>>
>>>>> Maybe the log file can help to identify which of the methods above has been called....
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Daniela
>>>>>
>>>>> On 31/10/2019 20:17, Paulo Nuin wrote:
>>>>>> Hi everyone
>>>>>>
>>>>>> Updated the Gradle file and rebuilt the DB, on deploement I see the same error:
>>>>>>
>>>>>> 31-Oct-2019 20:12:33.570 SEVERE [http-nio-8080-exec-87] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [ws-version] in context with path [/tools/wormmine] threw exception
>>>>>> org.intermine.web.context.ContextNotInitialisedException: Attempt to access InterMineContext before it has  been initialised
>>>>>>
>>>>>>
>>>>>> Any help appreciated.
>>>>>>
>>>>>> Cheers
>>>>>>
>>>>>> Paulo
>>>>>>
>>>>>>> On Oct 31, 2019, at 6:46 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>>
>>>>>>> Hi
>>>>>>>
>>>>>>> I have found a typo on my gradle.properties file, but I am still having an error:
>>>>>>>
>>>>>>> 31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>>>>>>> java.lang.NullPointerException
>>>>>>> ….
>>>>>>> 31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>>>>>>
>>>>>>> I am rebuilding without the typo in order to check. The typo was on the line
>>>>>>>
>>>>>>> systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Paulo
>>>>>>>
>>>>>>>
>>>>>>>> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>>>
>>>>>>>> Hi everyone
>>>>>>>>
>>>>>>>> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>>>>>>>>
>>>>>>>> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>>>>>>>> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
>>>>>>>> javax.servlet.UnavailableException
>>>>>>>>
>>>>>>>> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>>>>>>>>
>>>>>>>> Any help appreciated.
>>>>>>>>
>>>>>>>> Paulo
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email]
>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>

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Re: Error on web app deployment

Daniela Butano-2
I would have liked to try to reproduce your issue, but I haven't had
time yet.

First. The tomcat where you are running the webapp with the session
issue is the same tomcat where you have run the working webapp before?

(I want to exclude any wrong tomcat configuration)

Second. before calling cargodeployremote, have you tried

1. ./gradlew --stop

2. delete any cache in your browse (maybe try in an incognito mode)

Daniela

On 04/11/2019 13:33, Paulo Nuin wrote:

> Hi Daniela
>
> Any idea on the error(s) below?
>
> Upgrading Tomcat might work?
>
> Thanks
>
> Paulo
>
>> On Nov 1, 2019, at 11:58 AM, Paulo Nuin <[hidden email]> wrote:
>>
>> Hi Daniela
>>
>> I don’t see errors on the intermine.log, and after redeploying a couple of times I get the same errors on Tomcat
>>
>>
>> This is on intermine.log just after redeploying the webapp
>>
>>
>> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Finding global properties file default.intermine.properties
>> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Loading properties from file:/mnt/data2/3.0/WormMine/webapp/build/resources/main/default.intermine.properties
>> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Finding global properties file intermine.properties
>> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Loading properties from file:/mnt/data2/3.0/WormMine/webapp/build/resources/main/intermine.properties
>> 2019-11-01 17:18:16 INFO             org.intermine.sql.Database  [] - Creating new Database jdbc:postgresql://localhost/intermine_test({platform=PostgreSQL, datasource.dataSourceClassName=org.postgresql.ds.PGSimpleDataSource, datasource.dataSourceName=d$
>> 2019-11-01 17:18:17 INFO  org.intermine.objectstore.ObjectStoreAbstractImpl  [] - Creating new org.intermine.objectstore.intermine.ObjectStoreInterMineImpl with sequence = {}, model = "genomic"
>>
>>
>> And on localhost log just after (InterMine related line highlighted)
>>
>> 01-Nov-2019 17:20:23.241 WARNING [http-nio-8080-exec-121] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>> 01-Nov-2019 17:20:24.741 WARNING [http-nio-8080-exec-122] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>> 01-Nov-2019 17:20:25.960 WARNING [http-nio-8080-exec-123] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>> 01-Nov-2019 17:23:29.405 SEVERE [http-nio-8080-exec-124] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>> java.lang.NullPointerException
>>         at org.intermine.web.logic.session.SessionMethods.initSession(SessionMethods.java:458)
>>         at org.intermine.web.logic.session.SessionListener.sessionCreated(SessionListener.java:31)
>>         at org.apache.catalina.session.StandardSession.tellNew(StandardSession.java:396)
>>         at org.apache.catalina.session.StandardSession.setId(StandardSession.java:368)
>>         at org.apache.catalina.session.StandardSession.setId(StandardSession.java:349)
>>         at org.apache.catalina.session.ManagerBase.createSession(ManagerBase.java:663)
>>         at org.apache.catalina.connector.Request.doGetSession(Request.java:3044)
>>         at org.apache.catalina.connector.Request.getSession(Request.java:2434)
>>         at org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:896)
>>         at org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:908)
>>         at org.apache.jasper.runtime.PageContextImpl.initialize(PageContextImpl.java:137)
>>         at org.apache.jasper.runtime.JspFactoryImpl.internalGetPageContext(JspFactoryImpl.java:109)
>>         at org.apache.jasper.runtime.JspFactoryImpl.getPageContext(JspFactoryImpl.java:60)
>>         at org.apache.jsp.index_jsp._jspService(index_jsp.java:100)
>>         at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
>>         at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:443)
>>         at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
>>         at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
>>         at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
>>         at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
>>         at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>         at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
>>         at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
>>         at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139) <----------
>>         at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
>>         at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
>>         at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
>>         at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
>>         at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:496)
>>         at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
>>         at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
>>         at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
>>         at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
>>         at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:677)
>>         at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
>>         at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803)
>>         at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
>>         at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
>>         at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)
>>         at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
>>         at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>         at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>         at java.lang.Thread.run(Thread.java:748)
>>
>> Thanks
>>
>> Paulo
>>
>>
>>> On Nov 1, 2019, at 8:05 AM, Daniela Butano <[hidden email]> wrote:
>>>
>>> You should find the intermine.log file in the wormine directory.
>>>
>>> On 01/11/2019 13:50, Paulo Nuin wrote:
>>>> Also, does updating gradle or some configurations file fix the problem? Build worked fine with 3.1, no errors and everything on 2.0 works fine, deployment, build etc
>>>>
>>>> Thanks
>>>>
>>>> Paulo
>>>>
>>>>
>>>>
>>>>> On Nov 1, 2019, at 5:48 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>
>>>>> Hi Daniela
>>>>>
>>>>> Which log file? Is there any InterMine log file that would show that? I am trying all Tomcat ones.
>>>>>
>>>>> Thanks
>>>>>
>>>>> Paulo
>>>>>
>>>>>> On Nov 1, 2019, at 3:50 AM, Daniela Butano <[hidden email]> wrote:
>>>>>>
>>>>>> Ciao Paulo,
>>>>>>
>>>>>> I'm sorry you have this issue.
>>>>>>
>>>>>> I don't remember we have ever had a similar one before, I have checked in github too.
>>>>>>
>>>>>> The exception is thrown when you try to call one of the following methods (getInterMineAPI, getKeyStore, getWebConfig, getWebProperties, shutdown) before initializing the InteMineContext ( which is executed in the InitializerPlugin)
>>>>>>
>>>>>> Maybe the log file can help to identify which of the methods above has been called....
>>>>>>
>>>>>> Cheers,
>>>>>>
>>>>>> Daniela
>>>>>>
>>>>>> On 31/10/2019 20:17, Paulo Nuin wrote:
>>>>>>> Hi everyone
>>>>>>>
>>>>>>> Updated the Gradle file and rebuilt the DB, on deploement I see the same error:
>>>>>>>
>>>>>>> 31-Oct-2019 20:12:33.570 SEVERE [http-nio-8080-exec-87] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [ws-version] in context with path [/tools/wormmine] threw exception
>>>>>>> org.intermine.web.context.ContextNotInitialisedException: Attempt to access InterMineContext before it has  been initialised
>>>>>>>
>>>>>>>
>>>>>>> Any help appreciated.
>>>>>>>
>>>>>>> Cheers
>>>>>>>
>>>>>>> Paulo
>>>>>>>
>>>>>>>> On Oct 31, 2019, at 6:46 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>>>
>>>>>>>> Hi
>>>>>>>>
>>>>>>>> I have found a typo on my gradle.properties file, but I am still having an error:
>>>>>>>>
>>>>>>>> 31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>>>>>>>> java.lang.NullPointerException
>>>>>>>> ….
>>>>>>>> 31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>>>>>>>
>>>>>>>> I am rebuilding without the typo in order to check. The typo was on the line
>>>>>>>>
>>>>>>>> systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Paulo
>>>>>>>>
>>>>>>>>
>>>>>>>>> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> Hi everyone
>>>>>>>>>
>>>>>>>>> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>>>>>>>>>
>>>>>>>>> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>>>>>>>>> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
>>>>>>>>> javax.servlet.UnavailableException
>>>>>>>>>
>>>>>>>>> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>>>>>>>>>
>>>>>>>>> Any help appreciated.
>>>>>>>>>
>>>>>>>>> Paulo
>>>>>>> _______________________________________________
>>>>>>> dev mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>> _______________________________________________
>>>>>> dev mailing list
>>>>>> [hidden email]
>>>>>> https://lists.intermine.org/mailman/listinfo/dev
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Re: Error on web app deployment

Paulo Nuin
Hi Daniela



> On Nov 4, 2019, at 6:41 AM, Daniela Butano <[hidden email]> wrote:
>
> I would have liked to try to reproduce your issue, but I haven't had time yet.
>

I can send you the DB too, it’s quite small.



> First. The tomcat where you are running the webapp with the session issue is the same tomcat where you have run the working webapp before?
>

Yes, same one, if deployed with 2.0 works fine.


> (I want to exclude any wrong tomcat configuration)
>
> Second. before calling cargodeployremote, have you tried
>
> 1. ./gradlew —stop
>
> 2. delete any cache in your browse (maybe try in an incognito mode)
>

I will try that.

Thanks a lot

Paulo





> Daniela
>
> On 04/11/2019 13:33, Paulo Nuin wrote:
>> Hi Daniela
>>
>> Any idea on the error(s) below?
>>
>> Upgrading Tomcat might work?
>>
>> Thanks
>>
>> Paulo
>>
>>> On Nov 1, 2019, at 11:58 AM, Paulo Nuin <[hidden email]> wrote:
>>>
>>> Hi Daniela
>>>
>>> I don’t see errors on the intermine.log, and after redeploying a couple of times I get the same errors on Tomcat
>>>
>>>
>>> This is on intermine.log just after redeploying the webapp
>>>
>>>
>>> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Finding global properties file default.intermine.properties
>>> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Loading properties from file:/mnt/data2/3.0/WormMine/webapp/build/resources/main/default.intermine.properties
>>> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Finding global properties file intermine.properties
>>> 2019-11-01 17:18:16 INFO      org.intermine.util.PropertiesUtil  [] - Loading properties from file:/mnt/data2/3.0/WormMine/webapp/build/resources/main/intermine.properties
>>> 2019-11-01 17:18:16 INFO             org.intermine.sql.Database  [] - Creating new Database jdbc:postgresql://localhost/intermine_test({platform=PostgreSQL, datasource.dataSourceClassName=org.postgresql.ds.PGSimpleDataSource, datasource.dataSourceName=d$
>>> 2019-11-01 17:18:17 INFO  org.intermine.objectstore.ObjectStoreAbstractImpl  [] - Creating new org.intermine.objectstore.intermine.ObjectStoreInterMineImpl with sequence = {}, model = "genomic"
>>>
>>>
>>> And on localhost log just after (InterMine related line highlighted)
>>>
>>> 01-Nov-2019 17:20:23.241 WARNING [http-nio-8080-exec-121] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>> 01-Nov-2019 17:20:24.741 WARNING [http-nio-8080-exec-122] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>> 01-Nov-2019 17:20:25.960 WARNING [http-nio-8080-exec-123] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>> 01-Nov-2019 17:23:29.405 SEVERE [http-nio-8080-exec-124] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>>> java.lang.NullPointerException
>>>        at org.intermine.web.logic.session.SessionMethods.initSession(SessionMethods.java:458)
>>>        at org.intermine.web.logic.session.SessionListener.sessionCreated(SessionListener.java:31)
>>>        at org.apache.catalina.session.StandardSession.tellNew(StandardSession.java:396)
>>>        at org.apache.catalina.session.StandardSession.setId(StandardSession.java:368)
>>>        at org.apache.catalina.session.StandardSession.setId(StandardSession.java:349)
>>>        at org.apache.catalina.session.ManagerBase.createSession(ManagerBase.java:663)
>>>        at org.apache.catalina.connector.Request.doGetSession(Request.java:3044)
>>>        at org.apache.catalina.connector.Request.getSession(Request.java:2434)
>>>        at org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:896)
>>>        at org.apache.catalina.connector.RequestFacade.getSession(RequestFacade.java:908)
>>>        at org.apache.jasper.runtime.PageContextImpl.initialize(PageContextImpl.java:137)
>>>        at org.apache.jasper.runtime.JspFactoryImpl.internalGetPageContext(JspFactoryImpl.java:109)
>>>        at org.apache.jasper.runtime.JspFactoryImpl.getPageContext(JspFactoryImpl.java:60)
>>>        at org.apache.jsp.index_jsp._jspService(index_jsp.java:100)
>>>        at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
>>>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
>>>        at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:443)
>>>        at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:386)
>>>        at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:330)
>>>        at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
>>>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
>>>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
>>>        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
>>>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
>>>        at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139) <----------
>>>        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
>>>        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
>>>        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
>>>        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
>>>        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:496)
>>>        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
>>>        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
>>>        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
>>>        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
>>>        at org.apache.catalina.valves.RemoteIpValve.invoke(RemoteIpValve.java:677)
>>>        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
>>>        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:803)
>>>        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
>>>        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:790)
>>>        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1459)
>>>        at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
>>>        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>>        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>>        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>>        at java.lang.Thread.run(Thread.java:748)
>>>
>>> Thanks
>>>
>>> Paulo
>>>
>>>
>>>> On Nov 1, 2019, at 8:05 AM, Daniela Butano <[hidden email]> wrote:
>>>>
>>>> You should find the intermine.log file in the wormine directory.
>>>>
>>>> On 01/11/2019 13:50, Paulo Nuin wrote:
>>>>> Also, does updating gradle or some configurations file fix the problem? Build worked fine with 3.1, no errors and everything on 2.0 works fine, deployment, build etc
>>>>>
>>>>> Thanks
>>>>>
>>>>> Paulo
>>>>>
>>>>>
>>>>>
>>>>>> On Nov 1, 2019, at 5:48 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>
>>>>>> Hi Daniela
>>>>>>
>>>>>> Which log file? Is there any InterMine log file that would show that? I am trying all Tomcat ones.
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Paulo
>>>>>>
>>>>>>> On Nov 1, 2019, at 3:50 AM, Daniela Butano <[hidden email]> wrote:
>>>>>>>
>>>>>>> Ciao Paulo,
>>>>>>>
>>>>>>> I'm sorry you have this issue.
>>>>>>>
>>>>>>> I don't remember we have ever had a similar one before, I have checked in github too.
>>>>>>>
>>>>>>> The exception is thrown when you try to call one of the following methods (getInterMineAPI, getKeyStore, getWebConfig, getWebProperties, shutdown) before initializing the InteMineContext ( which is executed in the InitializerPlugin)
>>>>>>>
>>>>>>> Maybe the log file can help to identify which of the methods above has been called....
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Daniela
>>>>>>>
>>>>>>> On 31/10/2019 20:17, Paulo Nuin wrote:
>>>>>>>> Hi everyone
>>>>>>>>
>>>>>>>> Updated the Gradle file and rebuilt the DB, on deploement I see the same error:
>>>>>>>>
>>>>>>>> 31-Oct-2019 20:12:33.570 SEVERE [http-nio-8080-exec-87] org.apache.catalina.core.StandardWrapperValve.invoke Servlet.service() for servlet [ws-version] in context with path [/tools/wormmine] threw exception
>>>>>>>> org.intermine.web.context.ContextNotInitialisedException: Attempt to access InterMineContext before it has  been initialised
>>>>>>>>
>>>>>>>>
>>>>>>>> Any help appreciated.
>>>>>>>>
>>>>>>>> Cheers
>>>>>>>>
>>>>>>>> Paulo
>>>>>>>>
>>>>>>>>> On Oct 31, 2019, at 6:46 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> Hi
>>>>>>>>>
>>>>>>>>> I have found a typo on my gradle.properties file, but I am still having an error:
>>>>>>>>>
>>>>>>>>> 31-Oct-2019 12:37:32.505 SEVERE [http-nio-8080-exec-56] org.apache.catalina.session.StandardSession.tellNew Session event listener threw exception
>>>>>>>>> java.lang.NullPointerException
>>>>>>>>> ….
>>>>>>>>> 31-Oct-2019 12:37:32.845 WARNING [http-nio-8080-exec-54] org.apache.catalina.core.ApplicationDispatcher.invoke Servlet [action] is currently unavailable
>>>>>>>>>
>>>>>>>>> I am rebuilding without the typo in order to check. The typo was on the line
>>>>>>>>>
>>>>>>>>> systemProp.javax.xml.stream.XMLOutputFactory = com.sun.xml.internal.stream.XMLOutputFactoryImpl
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> Paulo
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> On Oct 31, 2019, at 6:20 AM, Paulo Nuin <[hidden email]> wrote:
>>>>>>>>>>
>>>>>>>>>> Hi everyone
>>>>>>>>>>
>>>>>>>>>> I am trying to upgrade our Mine to 3.1 and beyond, but I am having an error after web app deployment
>>>>>>>>>>
>>>>>>>>>> 31-Oct-2019 12:14:40.339 INFO [http-nio-8080-exec-49] org.apache.catalina.core.ApplicationContext.log Marking servlet [action] as unavailable
>>>>>>>>>> 31-Oct-2019 12:14:40.339 SEVERE [http-nio-8080-exec-49] org.apache.catalina.core.StandardContext.loadOnStartup Servlet [action] in web application [/tools/wormmine] threw load() excepti$
>>>>>>>>>> javax.servlet.UnavailableException
>>>>>>>>>>
>>>>>>>>>> I had this error before on a local test (not on AWS) and found some reference from Yo where she needed Tomcat and grade to be in the same disk. This is impossible in the AWS as / is pretty small and we rely on extra mounts for larger data.
>>>>>>>>>>
>>>>>>>>>> Any help appreciated.
>>>>>>>>>>
>>>>>>>>>> Paulo
>>>>>>>> _______________________________________________
>>>>>>>> dev mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>>>>> _______________________________________________
>>>>>>> dev mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.intermine.org/mailman/listinfo/dev

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Re: Error on web app deployment

Paulo Nuin
Hi

Tried the steps bellow, same results. 

Cheers

Paulo

On Nov 4, 2019, at 7:01 AM, Paulo Nuin <[hidden email]> wrote:

Second. before calling cargodeployremote, have you tried

1. ./gradlew —stop

2. delete any cache in your browse (maybe try in an incognito mode)


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Re: Error on web app deployment

Daniela Butano-2

Hi Paulo,

Tomorrow I will try to reproduce locally your issue using my Tomcat (8.5.32)

I will deploy biotestmine using intermine 2.0 and gradle wrapper 4.1

Then I will deploy biotestmine using intermine 4.1.1 and gradle wrapper 4.9.

Daniela


On 04/11/2019 15:05, Paulo Nuin wrote:
Hi

Tried the steps bellow, same results. 

Cheers

Paulo

On Nov 4, 2019, at 7:01 AM, Paulo Nuin <[hidden email]> wrote:

Second. before calling cargodeployremote, have you tried

1. ./gradlew —stop

2. delete any cache in your browse (maybe try in an incognito mode)


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Re: Error on web app deployment

Paulo Nuin
Hi

Thanks, I can provide versions on different things on my end if you need.

I am trying with 3.0, should I try 4.1.1? 

Cheers
Paulo

On Nov 4, 2019, at 8:33 AM, Daniela Butano <[hidden email]> wrote:

Hi Paulo,

Tomorrow I will try to reproduce locally your issue using my Tomcat (8.5.32)

I will deploy biotestmine using intermine 2.0 and gradle wrapper 4.1

Then I will deploy biotestmine using intermine 4.1.1 and gradle wrapper 4.9.

Daniela


On 04/11/2019 15:05, Paulo Nuin wrote:
Hi

Tried the steps bellow, same results. 

Cheers

Paulo

On Nov 4, 2019, at 7:01 AM, Paulo Nuin <[hidden email]> wrote:

Second. before calling cargodeployremote, have you tried

1. ./gradlew —stop

2. delete any cache in your browse (maybe try in an incognito mode)



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Re: Error on web app deployment

Daniela Butano-2

So it's the 3.0 which does not work to you?

On 04/11/2019 15:36, Paulo Nuin wrote:
Hi

Thanks, I can provide versions on different things on my end if you need.

I am trying with 3.0, should I try 4.1.1? 

Cheers
Paulo

On Nov 4, 2019, at 8:33 AM, Daniela Butano <[hidden email]> wrote:

Hi Paulo,

Tomorrow I will try to reproduce locally your issue using my Tomcat (8.5.32)

I will deploy biotestmine using intermine 2.0 and gradle wrapper 4.1

Then I will deploy biotestmine using intermine 4.1.1 and gradle wrapper 4.9.

Daniela


On 04/11/2019 15:05, Paulo Nuin wrote:
Hi

Tried the steps bellow, same results. 

Cheers

Paulo

On Nov 4, 2019, at 7:01 AM, Paulo Nuin <[hidden email]> wrote:

Second. before calling cargodeployremote, have you tried

1. ./gradlew —stop

2. delete any cache in your browse (maybe try in an incognito mode)



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Re: Error on web app deployment

Paulo Nuin
Yes, currently we are testing 3.0 with SOLR, I can upgrade to 4.1.1 and try


Cheers
Paulo

On Nov 4, 2019, at 8:37 AM, Daniela Butano <[hidden email]> wrote:

So it's the 3.0 which does not work to you?

On 04/11/2019 15:36, Paulo Nuin wrote:
Hi

Thanks, I can provide versions on different things on my end if you need.

I am trying with 3.0, should I try 4.1.1? 

Cheers
Paulo

On Nov 4, 2019, at 8:33 AM, Daniela Butano <[hidden email]> wrote:

Hi Paulo,

Tomorrow I will try to reproduce locally your issue using my Tomcat (8.5.32)

I will deploy biotestmine using intermine 2.0 and gradle wrapper 4.1

Then I will deploy biotestmine using intermine 4.1.1 and gradle wrapper 4.9.

Daniela


On 04/11/2019 15:05, Paulo Nuin wrote:
Hi

Tried the steps bellow, same results. 

Cheers

Paulo

On Nov 4, 2019, at 7:01 AM, Paulo Nuin <[hidden email]> wrote:

Second. before calling cargodeployremote, have you tried

1. ./gradlew —stop

2. delete any cache in your browse (maybe try in an incognito mode)




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Re: Error on web app deployment

Daniela Butano-2

Paulo,

please send me the db, the mine properties file and the wormine.war  generated.

I will try to run locally


On 04/11/2019 15:38, Paulo Nuin wrote:
Yes, currently we are testing 3.0 with SOLR, I can upgrade to 4.1.1 and try


Cheers
Paulo

On Nov 4, 2019, at 8:37 AM, Daniela Butano <[hidden email]> wrote:

So it's the 3.0 which does not work to you?

On 04/11/2019 15:36, Paulo Nuin wrote:
Hi

Thanks, I can provide versions on different things on my end if you need.

I am trying with 3.0, should I try 4.1.1? 

Cheers
Paulo

On Nov 4, 2019, at 8:33 AM, Daniela Butano <[hidden email]> wrote:

Hi Paulo,

Tomorrow I will try to reproduce locally your issue using my Tomcat (8.5.32)

I will deploy biotestmine using intermine 2.0 and gradle wrapper 4.1

Then I will deploy biotestmine using intermine 4.1.1 and gradle wrapper 4.9.

Daniela


On 04/11/2019 15:05, Paulo Nuin wrote:
Hi

Tried the steps bellow, same results. 

Cheers

Paulo

On Nov 4, 2019, at 7:01 AM, Paulo Nuin <[hidden email]> wrote:

Second. before calling cargodeployremote, have you tried

1. ./gradlew —stop

2. delete any cache in your browse (maybe try in an incognito mode)




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Re: Error on web app deployment

Daniela Butano-2

The issues has been resolved.

The problem was a missing line at the end of the WEB-INF/global.web.properties file

# needed for SOLR dep conflict. See #1889
javax.xml.stream.XMLOutputFactory=com.sun.xml.internal.stream.XMLOutputFactoryImpl

The global.web.properties file should NOT be in the mine webapp, it's provided by  the intermine-webapp module.
In general, if you you want to  add mine specific properties or override the properties defined in the global.web.properties file, please use the web.properties file in the mine
Here a few more details.
Thanks!
Daniela

On 04/11/2019 15:46, Daniela Butano wrote:

Paulo,

please send me the db, the mine properties file and the wormine.war  generated.

I will try to run locally


On 04/11/2019 15:38, Paulo Nuin wrote:
Yes, currently we are testing 3.0 with SOLR, I can upgrade to 4.1.1 and try


Cheers
Paulo

On Nov 4, 2019, at 8:37 AM, Daniela Butano <[hidden email]> wrote:

So it's the 3.0 which does not work to you?

On 04/11/2019 15:36, Paulo Nuin wrote:
Hi

Thanks, I can provide versions on different things on my end if you need.

I am trying with 3.0, should I try 4.1.1? 

Cheers
Paulo

On Nov 4, 2019, at 8:33 AM, Daniela Butano <[hidden email]> wrote:

Hi Paulo,

Tomorrow I will try to reproduce locally your issue using my Tomcat (8.5.32)

I will deploy biotestmine using intermine 2.0 and gradle wrapper 4.1

Then I will deploy biotestmine using intermine 4.1.1 and gradle wrapper 4.9.

Daniela


On 04/11/2019 15:05, Paulo Nuin wrote:
Hi

Tried the steps bellow, same results. 

Cheers

Paulo

On Nov 4, 2019, at 7:01 AM, Paulo Nuin <[hidden email]> wrote:

Second. before calling cargodeployremote, have you tried

1. ./gradlew —stop

2. delete any cache in your browse (maybe try in an incognito mode)




_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev