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Re: [Treebase-devel] Is treebase/oai-pmh_data_provider dead?

From: youjun g. <you...@gm...> - 2010-09-16 22:13:46

The code in treebase/oai-pmh_data_provide is no long used, the project was
integrated into treebase-web.

Youjun

On Thu, Sep 16, 2010 at 1:40 PM, Vladimir Gapeyev <vga...@ne...>wrote:

> As I recently found out, the hard way, the code in treebase/oai-
> pmh_data_provider is not what runs in response to OAI requests to
> Treebase. The actual OAI code is in various places under treebase/
> treebase-web.
>
> Anyone who is aware of a useful function for treebase/oai-
> pmh_data_provider, please come forward.  Otherwise, I'd like to 'svn
> rm' to avoid future confusion.
>
> --Vladimir
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>

Re: [Treebase-devel] Is treebase/oai-pmh_data_provider dead?

From: Hilmar L. <hl...@ne...> - 2010-09-16 17:45:51

Can the code that actually runs be relatively easily centralized  
under ./oai-pmh_data_provider? If not, I would agree to remove that  
directory.

	-hilmar

On Sep 16, 2010, at 1:40 PM, Vladimir Gapeyev wrote:

> As I recently found out, the hard way, the code in treebase/oai-
> pmh_data_provider is not what runs in response to OAI requests to
> Treebase. The actual OAI code is in various places under treebase/
> treebase-web.
>
> Anyone who is aware of a useful function for treebase/oai-
> pmh_data_provider, please come forward.  Otherwise, I'd like to 'svn
> rm' to avoid future confusion.
>
> --Vladimir
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

[Treebase-devel] Is treebase/oai-pmh_data_provider dead?

From: Vladimir G. <vga...@ne...> - 2010-09-16 17:40:19

As I recently found out, the hard way, the code in treebase/oai- 
pmh_data_provider is not what runs in response to OAI requests to  
Treebase. The actual OAI code is in various places under treebase/ 
treebase-web.

Anyone who is aware of a useful function for treebase/oai- 
pmh_data_provider, please come forward.  Otherwise, I'd like to 'svn  
rm' to avoid future confusion.

--Vladimir

Re: [Treebase-devel] Disk space for treebase production database

From: Jon A. <jon...@ne...> - 2010-09-15 21:29:22

Good. Vladimir and I will work on disabling login next week and I will move the database. The application will  be read only during the migration. The actual switchover should only take about a minute or so for me to restart tomcat to point to the new database.

-Jon

On Sep 14, 2010, at 6:34 AM, Rutger Vos wrote:

>> I don't think we have an easy toggle for turning off submissions -- other than temporarily commenting out the login.jsp code. Do the developers see that as an adequate measure?
>> 
> 
> That seems like the easiest way to do it, yes.
> 
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com
> 
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-------------------------------------------------------
Jon Auman
Systems Administrator
National Evolutionary Synthesis Center
Duke University
http:www.nescent.org
jon...@ne...
------------------------------------------------------

[Treebase-devel] Fwd: Disk space for treebase production database

From: Jon A. <jon...@ne...> - 2010-09-15 13:28:49

> From: Jon Auman <jon...@ne...>
> Date: September 15, 2010 9:28:10 AM EDT
> To: William Piel <wil...@ya...>
> Subject: Re: [Treebase-devel] Disk space for treebase production database
> 
> I rebooted the server. Postgresql was hung and eating all of the CPUs. I think what happens is that someone generates a query that never finishes through the application. That person then probably restarts the browser and tires again. The end result is multiple hanged queries which eats up all the CPU time. 
> 
> As fas as I see it, the solutions would be:
> 1) improve the queries (probably not going to happen until more funding is secured)
> 2) look into some kind of cacheing
> 3) bring up another database server for load balancing.
> 4) kill queries after x minutes. I thought I had that configured, but it seems that there are some instances where that doesn't happen.
> 
> I'll look into #4 some more, as that is the easiest "fix". Do you have any thoughts on this?
> 
> -Jon
> 
>  
> On Sep 15, 2010, at 9:17 AM, William Piel wrote:
> 
>> 
>> On Sep 14, 2010, at 10:53 PM, William Piel wrote:
>> 
>>> Hi Jon,
>>> 
>>> Speaking of speed issues, I'm trying to edit some submissions (Sept 14, between 9PM and 11PM EST) but I'm finding it very slow... so slow, in fact, that it's barely able to function. I don't know if there's some backup activity going on... but I just thought I'd mention it.
>>> 
>>> bp
>> 
>> This morning (9 AM EST) it back up to normal speed.
>> 
>> bp
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
> 
> -------------------------------------------------------
> Jon Auman
> Systems Administrator
> National Evolutionary Synthesis Center
> Duke University
> http:www.nescent.org
> jon...@ne...
> ------------------------------------------------------
> 
> 
> 

-------------------------------------------------------
Jon Auman
Systems Administrator
National Evolutionary Synthesis Center
Duke University
http:www.nescent.org
jon...@ne...
------------------------------------------------------

Re: [Treebase-devel] Disk space for treebase production database

From: William P. <wil...@ya...> - 2010-09-15 13:17:34

On Sep 14, 2010, at 10:53 PM, William Piel wrote:

> Hi Jon,
> 
> Speaking of speed issues, I'm trying to edit some submissions (Sept 14, between 9PM and 11PM EST) but I'm finding it very slow... so slow, in fact, that it's barely able to function. I don't know if there's some backup activity going on... but I just thought I'd mention it.
> 
> bp

This morning (9 AM EST) it back up to normal speed.

bp

Re: [Treebase-devel] Disk space for treebase production database

From: William P. <wil...@ya...> - 2010-09-15 02:54:02

Hi Jon,

Speaking of speed issues, I'm trying to edit some submissions (Sept 14, between 9PM and 11PM EST) but I'm finding it very slow... so slow, in fact, that it's barely able to function. I don't know if there's some backup activity going on... but I just thought I'd mention it.

bp

Re: [Treebase-devel] Disk space for treebase production database

From: Hilmar L. <hl...@ne...> - 2010-09-14 13:22:45

On Sep 14, 2010, at 6:34 AM, Rutger Vos wrote:

>> I don't think we have an easy toggle for turning off submissions --  
>> other than temporarily commenting out the login.jsp code. Do the  
>> developers see that as an adequate measure?
>>
>
> That seems like the easiest way to do it, yes.

And it would seem worth the (presumably moderate to little) effort to  
have TreeBASE not go entirely offline for 2 days.

	-hilmar

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] Disk space for treebase production database

From: Rutger V. <rut...@gm...> - 2010-09-14 10:34:31

> I don't think we have an easy toggle for turning off submissions -- other than temporarily commenting out the login.jsp code. Do the developers see that as an adequate measure?
>

That seems like the easiest way to do it, yes.

-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] Disk space for treebase production database

From: William P. <wil...@ya...> - 2010-09-14 00:40:06

Hi Jon,

On Sep 13, 2010, at 6:11 PM, Jon Auman wrote:

> I would like to move the database to the SAN if the performance is acceptable to Bill.

Well, I guess we don't have a lot of choice, really. This seems like the right way to go even if we take a performance hit. We'll only know the true performance hit once the move is made. 

In the event that the hit is so great that some functionality is effectively lost, can we still look into a plan b? (even if that means going down for a much longer period). 

> This move will give us:
> 
> 1) much needed space and room to grow
> 2) redundancy. Currently the database is one local disk of one of the physical servers. I can not move the database to another server if the host goes down.
> 
> Bill, if this is OK, please let me know which night in the next week or so that U can move the database. It will probably take about 12-16 hours. My plan is to put a down for maintenance message on the website. We don't want anyone submitting while we are doing a restore. Alternatively, if you have a way of disabling submissions, we do not need to disable the website.

I don't think we have an easy toggle for turning off submissions -- other than temporarily commenting out the login.jsp code. Do the developers see that as an adequate measure? 

Any night next week would be fine with me. 

bp

Re: [Treebase-devel] Disk space for treebase production database

From: Jon A. <jon...@ne...> - 2010-09-13 22:11:47

I would like to move the database to the SAN if the performance is acceptable to Bill. This move will give us:

1) much needed space and room to grow
2) redundancy. Currently the database is one local disk of one of the physical servers. I can not move the database to another server if the host goes down.

Bill, if this is OK, please let me know which night in the next week or so that U can move the database. It will probably take about 12-16 hours. My plan is to put a down for maintenance message on the website. We don't want anyone submitting while we are doing a restore. Alternatively, if you have a way of disabling submissions, we do not need to disable the website.

thanks,
Jon

On Sep 11, 2010, at 12:24 PM, Hilmar Lapp wrote:

> Jon - can you update us where we are with this? It sounds like a slow- 
> down of around 30% would be acceptable to Bill (Bill, correct me if  
> that's misinterpreting you), and it would be to me, too.
> 
> 	-hilmar
> 
> On Aug 7, 2010, at 6:09 AM, William Piel wrote:
> 
>> 
>> On Aug 6, 2010, at 3:04 PM, William Piel wrote:
>> 
>>> As a test file, I have a large NEXUS (attached) which I uploaded to  
>>> the treebase.org site, and it took me 7 minutes 51 seconds.
>> 
>> I just tested this file by uploading to http://treebase-dev.nescent.org/treebase-web/
>> 
>> Time taken: 9 minutes 22 seconds -- compared with 7 minutes 51  
>> seconds. So although one took longer, they both succeeded in  
>> uploading. It's certainly possible that some larger files will run  
>> into the 15-min timeout faster with dev than normal treebase.
>> 
>> In terms of searching, the performance is closer: going from an  
>> identical selection of taxa to a selection of studies took 27  
>> seconds on treebase and 36 seconds on treebase-dev.
>> 
>> bp
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>> 
>> Make an app they can't live without
>> Enter the BlackBerry Developer Challenge
>> http://p.sf.net/sfu/RIM-dev2dev
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
> 
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-------------------------------------------------------
Jon Auman
Systems Administrator
National Evolutionary Synthesis Center
Duke University
http:www.nescent.org
jon...@ne...
------------------------------------------------------

Re: [Treebase-devel] Disk space for treebase production database

From: Hilmar L. <hl...@ne...> - 2010-09-11 16:24:53

Jon - can you update us where we are with this? It sounds like a slow- 
down of around 30% would be acceptable to Bill (Bill, correct me if  
that's misinterpreting you), and it would be to me, too.

	-hilmar

On Aug 7, 2010, at 6:09 AM, William Piel wrote:

>
> On Aug 6, 2010, at 3:04 PM, William Piel wrote:
>
>> As a test file, I have a large NEXUS (attached) which I uploaded to  
>> the treebase.org site, and it took me 7 minutes 51 seconds.
>
> I just tested this file by uploading to http://treebase-dev.nescent.org/treebase-web/
>
> Time taken: 9 minutes 22 seconds -- compared with 7 minutes 51  
> seconds. So although one took longer, they both succeeded in  
> uploading. It's certainly possible that some larger files will run  
> into the 15-min timeout faster with dev than normal treebase.
>
> In terms of searching, the performance is closer: going from an  
> identical selection of taxa to a selection of studies took 27  
> seconds on treebase and 36 seconds on treebase-dev.
>
> bp
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] A problem running local treebase

From: youjun g. <you...@gm...> - 2010-09-09 23:45:13

Hi, Vladimir,

Looks like you got jar version conflict on xercesImpl-X.X.X.jar . See if
this link help and make sure the installation use the newer version:
http://www.mail-archive.com/cxf...@in.../msg03916.html

Youjun


On Thu, Sep 9, 2010 at 4:26 PM, Vladimir Gapeyev <vga...@ne...>wrote:

> Hi, Youjun,
>
> I cannot start a local TB instance in Tomcat, for any of the recent
> versions: the application breaks on startup. The catalina.out error
> log for the tomcat startup sequence is appended below.
>
> I tracked the problem down to SVN#731 that you committed on 7/13:
> versions up to 730 start up and run just fine, while 731 and the later
> ones, up to the head (#748) break at startup with the same error.
> Inexplicably, rebuild on treebase-dev works just fine.
>
> Looking at the error log below and the SVN log for 731 that I am
> resending separately, do you have any idea what has changed in #731
> that made things go wrong?
>
> Thanks,
>
> --Vladimir
>
>
>
> -----------------------------------------------------------------------------------------------
>  Thursday, September 9, 2010 4:20:30 PM US/Eastern
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.AprLifecycleListener
> lifecycleEvent
> INFO: The Apache Tomcat Native library which allows optimal
> performance in production environments was not found on the
> java.library.path: .:/Library/Java/Extensions:/System/Library/Java/
> Extensions:/usr/lib/java
> Sep 9, 2010 4:20:33 PM org.apache.coyote.http11.Http11BaseProtocol init
> INFO: Initializing Coyote HTTP/1.1 on http-8080
> Sep 9, 2010 4:20:33 PM org.apache.catalina.startup.Catalina load
> INFO: Initialization processed in 479 ms
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardService start
> INFO: Starting service Catalina
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardEngine start
> INFO: Starting Servlet Engine: Apache Tomcat/5.5.28
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardHost start
> INFO: XML validation disabled
> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader
> validateJarFile
> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache-
> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/geronimo-
> servlet_2.5_spec-1.2.jar) - jar not loaded. See Servlet Spec 2.3,
> section 9.7.2. Offending class: javax/servlet/Servlet.class
> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader
> validateJarFile
> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache-
> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/servlet-api-2.4.jar) -
> jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class:
> javax/servlet/Servlet.class
> [main] DEBUG org.cipres.treebase.web.listeners.StartupListener -
> contextInitialized(ServletContextEvent) -
> FORMAT_DELIMITER_MSG= :FORMAT_RETURN_VALUE_NAME=return valuestart
> [main] WARN org.hibernate.cache.CacheFactory - read-only cache
> configured for mutable class: staticCache
> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find
> configuration [org.hibernate.cache.UpdateTimestampsCache]; using
> defaults.
> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find
> configuration [org.hibernate.cache.StandardQueryCache]; using defaults.
> [main] INFO org.cipres.treebase.service.nexus.NexusServiceMesquite -
> Setting mesquite folder location from JNDI: /Users/vgapeyev/Work/
> TreeBase/mytomcat/mesquite-2.01.tb
> Sep 9, 2010 4:20:40 PM
> org.apache.cxf.service.factory.ReflectionServiceFactoryBean
> buildServiceFromClass
> INFO: Creating Service {http://
> webservices.web.treebase.cipres.org/}StudiesContainingKeyword<http://webservices.web.treebase.cipres.org/%7DStudiesContainingKeyword>from
> class org.cipres.treebase.web.webservices.StudyServiceByKeyword
> [main] ERROR org.springframework.web.context.ContextLoader - Context
> initialization failed
> org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'searchStudiesByKeyword': Invocation of init
> method failed; nested exception is java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
> Caused by:
> java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at
> org
> .apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java:
> 602)
>        at
> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java:84)
>        at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 424)
>        at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 418)
>        at
> org
> .apache
> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
>        at
> org
> .apache
> .cxf
> .databinding
> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
>        at
> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java:345)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
>        at
> org
> .apache
> .cxf
> .jaxws
> .support
> .JaxWsServiceFactoryBean
> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .initializeServiceModel(ReflectionServiceFactoryBean.java:396)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean.create(ReflectionServiceFactoryBean.java:
> 181)
>        at
> org
> .apache
> .cxf
> .jaxws
> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java:
> 163)
>        at
> org
> .apache
> .cxf
> .frontend
> .AbstractWSDLBasedEndpointFactory
> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
>        at
> org
> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java:
> 114)
>        at
> org
> .apache
> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java:
> 164)
>        at
> org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
>        at
> org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
>        at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
>        at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .createBean(AbstractAutowireCapableBeanFactory.java:427)
>        at org.springframework.beans.factory.support.AbstractBeanFactory
> $1.getObject(AbstractBeanFactory.java:249)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultSingletonBeanRegistry
> .getSingleton(DefaultSingletonBeanRegistry.java:155)
>        at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 246)
>        at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 160)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultListableBeanFactory
> .preInstantiateSingletons(DefaultListableBeanFactory.java:291)
>        at
> org
> .springframework
> .context
> .support
> .AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
>        at
> org.springframework.web.context.ContextLoader.createWebApplicationContext
> (ContextLoader.java:245)
>        at
> org.springframework.web.context.ContextLoader.initWebApplicationContext
> (ContextLoader.java:188)
>        at
> org.springframework.web.context.ContextLoaderListener.contextInitialized
> (ContextLoaderListener.java:49)
>        at
> org
> .cipres
> .treebase
> .web.listeners.StartupListener.contextInitialized(StartupListener.java:
> 45)
>        at
> org
> .apache
> .catalina.core.StandardContext.listenerStart(StandardContext.java:3795)
>        at
> org.apache.catalina.core.StandardContext.start(StandardContext.java:
> 4252)
>        at
> org
> .apache
> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
>        at
> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
> 740)
>        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:
> 544)
>        at
> org
> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:
> 626)
>        at
> org
> .apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:
> 553)
>        at
> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:
> 488)
>        at
> org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
>        at
> org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
> 311)
>        at
> org
> .apache
> .catalina
> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
>        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1022)
>        at
> org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
>        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1014)
>        at
> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:
> 443)
>        at
> org.apache.catalina.core.StandardService.start(StandardService.java:448)
>        at
> org.apache.catalina.core.StandardServer.start(StandardServer.java:
> 700)
>        at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
>        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
> [main] ERROR org.apache.catalina.core.ContainerBase.[Catalina].
> [localhost].[/treebase-web] - Exception sending context initialized
> event to listener instance of class
> org.cipres.treebase.web.listeners.StartupListener
> org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'searchStudiesByKeyword': Invocation of init
> method failed; nested exception is java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
> Caused by:
> java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at
> org
> .apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java:
> 602)
>        at
> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java:84)
>        at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 424)
>        at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 418)
>        at
> org
> .apache
> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
>        at
> org
> .apache
> .cxf
> .databinding
> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
>        at
> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java:345)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
>        at
> org
> .apache
> .cxf
> .jaxws
> .support
> .JaxWsServiceFactoryBean
> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .initializeServiceModel(ReflectionServiceFactoryBean.java:396)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean.create(ReflectionServiceFactoryBean.java:
> 181)
>        at
> org
> .apache
> .cxf
> .jaxws
> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java:
> 163)
>        at
> org
> .apache
> .cxf
> .frontend
> .AbstractWSDLBasedEndpointFactory
> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
>        at
> org
> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java:
> 114)
>        at
> org
> .apache
> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java:
> 164)
>        at
> org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
>        at
> org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
>        at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
>        at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .createBean(AbstractAutowireCapableBeanFactory.java:427)
>        at org.springframework.beans.factory.support.AbstractBeanFactory
> $1.getObject(AbstractBeanFactory.java:249)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultSingletonBeanRegistry
> .getSingleton(DefaultSingletonBeanRegistry.java:155)
>        at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 246)
>        at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 160)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultListableBeanFactory
> .preInstantiateSingletons(DefaultListableBeanFactory.java:291)
>        at
> org
> .springframework
> .context
> .support
> .AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
>        at
> org.springframework.web.context.ContextLoader.createWebApplicationContext
> (ContextLoader.java:245)
>        at
> org.springframework.web.context.ContextLoader.initWebApplicationContext
> (ContextLoader.java:188)
>        at
> org.springframework.web.context.ContextLoaderListener.contextInitialized
> (ContextLoaderListener.java:49)
>        at
> org
> .cipres
> .treebase
> .web.listeners.StartupListener.contextInitialized(StartupListener.java:
> 45)
>        at
> org
> .apache
> .catalina.core.StandardContext.listenerStart(StandardContext.java:3795)
>        at
> org.apache.catalina.core.StandardContext.start(StandardContext.java:
> 4252)
>        at
> org
> .apache
> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
>        at
> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
> 740)
>        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:
> 544)
>        at
> org
> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:
> 626)
>        at
> org
> .apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:
> 553)
>        at
> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:
> 488)
>        at
> org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
>        at
> org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
> 311)
>        at
> org
> .apache
> .catalina
> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
>        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1022)
>        at
> org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
>        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1014)
>        at
> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:
> 443)
>        at
> org.apache.catalina.core.StandardService.start(StandardService.java:448)
>        at
> org.apache.catalina.core.StandardServer.start(StandardServer.java:
> 700)
>        at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
>        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Error listenerStart
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Context [/treebase-web] startup failed due to previous errors
> WARN: The method class
> org.apache.commons.logging.impl.SLF4JLogFactory#release() was invoked.
> WARN: Please see http://www.slf4j.org/codes.html for an explanation.
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Error filterStart
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Context [/balancer] startup failed due to previous errors
> Sep 9, 2010 4:20:41 PM org.apache.coyote.http11.Http11BaseProtocol start
> INFO: Starting Coyote HTTP/1.1 on http-8080
> Sep 9, 2010 4:20:41 PM org.apache.jk.common.ChannelSocket init
> INFO: JK: ajp13 listening on /0.0.0.0:8009
> Sep 9, 2010 4:20:41 PM org.apache.jk.server.JkMain start
> INFO: Jk running ID=0 time=0/16  config=null
> Sep 9, 2010 4:20:41 PM org.apache.catalina.storeconfig.StoreLoader load
> INFO: Find registry server-registry.xml at classpath resource
> Sep 9, 2010 4:20:42 PM org.apache.catalina.startup.Catalina start
> INFO: Server startup in 8433 ms
>
>
>

Re: [Treebase-devel] Fwd: A problem running local treebase

From: Vladimir G. <vla...@du...> - 2010-09-09 22:18:56

Shouldn't trouble like this be fixable by a complete rebuild? I do  
'mvn clean' all the time.

My only next guess along this line of thought is that Maven update  
magic went wrong in my account and I should try nixing the Maven  
repository and rebuilding treebase from a fresh SVN checkout.

In either case, this does not enlighten me what goes wrong between SVN  
versions 730 and 731 -- the startup error seems to come from deep  
inside Spring, so I have no clue how updates in #731 could have  
affected that behavior.  A feeble guess is that something is fishy  
with pom.xml changes that did occur in #731.

I'll try to get hold of the WAR built by Hudson for treebase-dev and  
see if it runs on my tomcat...

--VG


On Sep 9, 2010, at 4:45 PM, Hilmar Lapp wrote:

> This sounds like a class with an abstract method is being  
> instantiated.
>
> This can happen in Java for example if a different version of an  
> external library changes the definition (signature) of an abstract  
> method in a (therefore abstract) class so that the inheriting class  
> in your own code that previously implemented the abstract method now  
> no longer does so, or if it adds a new abstract method to the class  
> that your implementing class wasn't aware of at the time it was  
> implemented.
>
> In other words, this smells like a version incompatibility with an  
> external library, likely the Xerces parser given the error message.
>
> Does this ring a bell or give you a target for trying to fix the  
> issue?
>
> 	-hilmar
>
> On Sep 9, 2010, at 4:31 PM, Vladimir Gapeyev wrote:
>
>>
>> Hi, Youjun,
>>
>> I cannot start a local TB instance in Tomcat, for any of the recent
>> versions: the application breaks on startup. The catalina.out error
>> log for the tomcat startup sequence is appended below.
>>
>> I tracked the problem down to SVN#731 that you committed on 7/13:
>> versions up to 730 start up and run just fine, while 731 and the  
>> later
>> ones, up to the head (#748) break at startup with the same error.
>> Inexplicably, rebuild on treebase-dev works just fine.
>>
>> Looking at the error log below and the SVN log for 731 that I am
>> resending separately, do you have any idea what has changed in #731
>> that made things go wrong?
>>
>> Thanks,
>>
>> --Vladimir
>>
>>
>> -----------------------------------------------------------------------------------------------
>> Thursday, September 9, 2010 4:20:30 PM US/Eastern
>> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.AprLifecycleListener
>> lifecycleEvent
>> INFO: The Apache Tomcat Native library which allows optimal
>> performance in production environments was not found on the
>> java.library.path: .:/Library/Java/Extensions:/System/Library/Java/
>> Extensions:/usr/lib/java
>> Sep 9, 2010 4:20:33 PM org.apache.coyote.http11.Http11BaseProtocol  
>> init
>> INFO: Initializing Coyote HTTP/1.1 on http-8080
>> Sep 9, 2010 4:20:33 PM org.apache.catalina.startup.Catalina load
>> INFO: Initialization processed in 479 ms
>> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardService start
>> INFO: Starting service Catalina
>> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardEngine start
>> INFO: Starting Servlet Engine: Apache Tomcat/5.5.28
>> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardHost start
>> INFO: XML validation disabled
>> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader
>> validateJarFile
>> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache-
>> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/geronimo-
>> servlet_2.5_spec-1.2.jar) - jar not loaded. See Servlet Spec 2.3,
>> section 9.7.2. Offending class: javax/servlet/Servlet.class
>> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader
>> validateJarFile
>> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache-
>> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/servlet-api-2.4.jar) -
>> jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class:
>> javax/servlet/Servlet.class
>> [main] DEBUG org.cipres.treebase.web.listeners.StartupListener -
>> contextInitialized(ServletContextEvent) -
>> FORMAT_DELIMITER_MSG= :FORMAT_RETURN_VALUE_NAME=return valuestart
>> [main] WARN org.hibernate.cache.CacheFactory - read-only cache
>> configured for mutable class: staticCache
>> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find
>> configuration [org.hibernate.cache.UpdateTimestampsCache]; using
>> defaults.
>> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find
>> configuration [org.hibernate.cache.StandardQueryCache]; using  
>> defaults.
>> [main] INFO org.cipres.treebase.service.nexus.NexusServiceMesquite -
>> Setting mesquite folder location from JNDI: /Users/vgapeyev/Work/
>> TreeBase/mytomcat/mesquite-2.01.tb
>> Sep 9, 2010 4:20:40 PM
>> org.apache.cxf.service.factory.ReflectionServiceFactoryBean
>> buildServiceFromClass
>> INFO: Creating Service {http://
>> webservices.web.treebase.cipres.org/}StudiesContainingKeyword from
>> class org.cipres.treebase.web.webservices.StudyServiceByKeyword
>> [main] ERROR org.springframework.web.context.ContextLoader - Context
>> initialization failed
>> org.springframework.beans.factory.BeanCreationException: Error
>> creating bean with name 'searchStudiesByKeyword': Invocation of init
>> method failed; nested exception is java.lang.AbstractMethodError:
>> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ 
>> String;
>> Caused by:
>> java.lang.AbstractMethodError:
>> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ 
>> String;
>> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> 	at
>> sun
>> .reflect 
>> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
>> 39)
>> 	at
>> sun
>> .reflect
>> .DelegatingMethodAccessorImpl 
>> .invoke(DelegatingMethodAccessorImpl.java:
>> 25)
>> 	at java.lang.reflect.Method.invoke(Method.java:592)
>> 	at
>> org
>> .apache 
>> .ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java:
>> 602)
>> 	at
>> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java: 
>> 84)
>> 	at
>> org
>> .apache
>> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
>> 424)
>> 	at
>> org
>> .apache
>> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
>> 418)
>> 	at
>> org
>> .apache
>> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java: 
>> 142)
>> 	at
>> org
>> .apache
>> .cxf
>> .databinding
>> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
>> 	at
>> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java: 
>> 345)
>> 	at
>> org
>> .apache
>> .cxf
>> .service
>> .factory
>> .ReflectionServiceFactoryBean
>> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
>> 	at
>> org
>> .apache
>> .cxf
>> .jaxws
>> .support
>> .JaxWsServiceFactoryBean
>> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
>> 	at
>> org
>> .apache
>> .cxf
>> .service
>> .factory
>> .ReflectionServiceFactoryBean
>> .initializeServiceModel(ReflectionServiceFactoryBean.java:396)
>> 	at
>> org
>> .apache
>> .cxf
>> .service
>> .factory
>> .ReflectionServiceFactoryBean 
>> .create(ReflectionServiceFactoryBean.java:
>> 181)
>> 	at
>> org
>> .apache
>> .cxf
>> .jaxws
>> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java:
>> 163)
>> 	at
>> org
>> .apache
>> .cxf
>> .frontend
>> .AbstractWSDLBasedEndpointFactory
>> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
>> 	at
>> org
>> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java:
>> 114)
>> 	at
>> org
>> .apache
>> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java:
>> 164)
>> 	at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java: 
>> 334)
>> 	at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java: 
>> 251)
>> 	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
>> 	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
>> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> 	at
>> sun
>> .reflect 
>> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
>> 39)
>> 	at
>> sun
>> .reflect
>> .DelegatingMethodAccessorImpl 
>> .invoke(DelegatingMethodAccessorImpl.java:
>> 25)
>> 	at java.lang.reflect.Method.invoke(Method.java:592)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .AbstractAutowireCapableBeanFactory
>> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .AbstractAutowireCapableBeanFactory
>> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .AbstractAutowireCapableBeanFactory
>> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .AbstractAutowireCapableBeanFactory
>> .createBean(AbstractAutowireCapableBeanFactory.java:427)
>> 	at org.springframework.beans.factory.support.AbstractBeanFactory
>> $1.getObject(AbstractBeanFactory.java:249)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .DefaultSingletonBeanRegistry
>> .getSingleton(DefaultSingletonBeanRegistry.java:155)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory 
>> .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
>> 246)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory 
>> .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
>> 160)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .DefaultListableBeanFactory
>> .preInstantiateSingletons(DefaultListableBeanFactory.java:291)
>> 	at
>> org
>> .springframework
>> .context
>> .support
>> .AbstractApplicationContext.refresh(AbstractApplicationContext.java: 
>> 352)
>> 	at org.springframework.web.context.ContextLoader.createWebApplicationContext
>> (ContextLoader.java:245)
>> 	at org.springframework.web.context.ContextLoader.initWebApplicationContext
>> (ContextLoader.java:188)
>> 	at org.springframework.web.context.ContextLoaderListener.contextInitialized
>> (ContextLoaderListener.java:49)
>> 	at
>> org
>> .cipres
>> .treebase
>> .web 
>> .listeners.StartupListener.contextInitialized(StartupListener.java:
>> 45)
>> 	at
>> org
>> .apache
>> .catalina.core.StandardContext.listenerStart(StandardContext.java: 
>> 3795)
>> 	at
>> org.apache.catalina.core.StandardContext.start(StandardContext.java:
>> 4252)
>> 	at
>> org
>> .apache
>> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
>> 	at  
>> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
>> 740)
>> 	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:
>> 544)
>> 	at
>> org
>> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:
>> 626)
>> 	at
>> org
>> .apache 
>> .catalina.startup.HostConfig.deployDescriptors(HostConfig.java:
>> 553)
>> 	at  
>> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:
>> 488)
>> 	at org.apache.catalina.startup.HostConfig.start(HostConfig.java: 
>> 1150)
>> 	at
>> org 
>> .apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
>> 311)
>> 	at
>> org
>> .apache
>> .catalina
>> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
>> 	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
>> 1022)
>> 	at org.apache.catalina.core.StandardHost.start(StandardHost.java: 
>> 736)
>> 	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
>> 1014)
>> 	at  
>> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:
>> 443)
>> 	at
>> org.apache.catalina.core.StandardService.start(StandardService.java: 
>> 448)
>> 	at  
>> org.apache.catalina.core.StandardServer.start(StandardServer.java:
>> 700)
>> 	at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
>> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> 	at
>> sun
>> .reflect 
>> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
>> 39)
>> 	at
>> sun
>> .reflect
>> .DelegatingMethodAccessorImpl 
>> .invoke(DelegatingMethodAccessorImpl.java:
>> 25)
>> 	at java.lang.reflect.Method.invoke(Method.java:592)
>> 	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
>> 	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
>> [main] ERROR org.apache.catalina.core.ContainerBase.[Catalina].
>> [localhost].[/treebase-web] - Exception sending context initialized
>> event to listener instance of class org.cipres.treebase.web.listeners.StartupListener
>> org.springframework.beans.factory.BeanCreationException: Error
>> creating bean with name 'searchStudiesByKeyword': Invocation of init
>> method failed; nested exception is java.lang.AbstractMethodError:
>> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ 
>> String;
>> Caused by:
>> java.lang.AbstractMethodError:
>> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ 
>> String;
>> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> 	at
>> sun
>> .reflect 
>> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
>> 39)
>> 	at
>> sun
>> .reflect
>> .DelegatingMethodAccessorImpl 
>> .invoke(DelegatingMethodAccessorImpl.java:
>> 25)
>> 	at java.lang.reflect.Method.invoke(Method.java:592)
>> 	at
>> org
>> .apache 
>> .ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java:
>> 602)
>> 	at
>> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java: 
>> 84)
>> 	at
>> org
>> .apache
>> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
>> 424)
>> 	at
>> org
>> .apache
>> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
>> 418)
>> 	at
>> org
>> .apache
>> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java: 
>> 142)
>> 	at
>> org
>> .apache
>> .cxf
>> .databinding
>> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
>> 	at
>> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java: 
>> 345)
>> 	at
>> org
>> .apache
>> .cxf
>> .service
>> .factory
>> .ReflectionServiceFactoryBean
>> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
>> 	at
>> org
>> .apache
>> .cxf
>> .jaxws
>> .support
>> .JaxWsServiceFactoryBean
>> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
>> 	at
>> org
>> .apache
>> .cxf
>> .service
>> .factory
>> .ReflectionServiceFactoryBean
>> .initializeServiceModel(ReflectionServiceFactoryBean.java:396)
>> 	at
>> org
>> .apache
>> .cxf
>> .service
>> .factory
>> .ReflectionServiceFactoryBean 
>> .create(ReflectionServiceFactoryBean.java:
>> 181)
>> 	at
>> org
>> .apache
>> .cxf
>> .jaxws
>> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java:
>> 163)
>> 	at
>> org
>> .apache
>> .cxf
>> .frontend
>> .AbstractWSDLBasedEndpointFactory
>> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
>> 	at
>> org
>> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java:
>> 114)
>> 	at
>> org
>> .apache
>> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java:
>> 164)
>> 	at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java: 
>> 334)
>> 	at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java: 
>> 251)
>> 	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
>> 	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
>> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> 	at
>> sun
>> .reflect 
>> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
>> 39)
>> 	at
>> sun
>> .reflect
>> .DelegatingMethodAccessorImpl 
>> .invoke(DelegatingMethodAccessorImpl.java:
>> 25)
>> 	at java.lang.reflect.Method.invoke(Method.java:592)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .AbstractAutowireCapableBeanFactory
>> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .AbstractAutowireCapableBeanFactory
>> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .AbstractAutowireCapableBeanFactory
>> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .AbstractAutowireCapableBeanFactory
>> .createBean(AbstractAutowireCapableBeanFactory.java:427)
>> 	at org.springframework.beans.factory.support.AbstractBeanFactory
>> $1.getObject(AbstractBeanFactory.java:249)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .DefaultSingletonBeanRegistry
>> .getSingleton(DefaultSingletonBeanRegistry.java:155)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory 
>> .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
>> 246)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory 
>> .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
>> 160)
>> 	at
>> org
>> .springframework
>> .beans
>> .factory
>> .support
>> .DefaultListableBeanFactory
>> .preInstantiateSingletons(DefaultListableBeanFactory.java:291)
>> 	at
>> org
>> .springframework
>> .context
>> .support
>> .AbstractApplicationContext.refresh(AbstractApplicationContext.java: 
>> 352)
>> 	at org.springframework.web.context.ContextLoader.createWebApplicationContext
>> (ContextLoader.java:245)
>> 	at org.springframework.web.context.ContextLoader.initWebApplicationContext
>> (ContextLoader.java:188)
>> 	at org.springframework.web.context.ContextLoaderListener.contextInitialized
>> (ContextLoaderListener.java:49)
>> 	at
>> org
>> .cipres
>> .treebase
>> .web 
>> .listeners.StartupListener.contextInitialized(StartupListener.java:
>> 45)
>> 	at
>> org
>> .apache
>> .catalina.core.StandardContext.listenerStart(StandardContext.java: 
>> 3795)
>> 	at
>> org.apache.catalina.core.StandardContext.start(StandardContext.java:
>> 4252)
>> 	at
>> org
>> .apache
>> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
>> 	at  
>> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
>> 740)
>> 	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:
>> 544)
>> 	at
>> org
>> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:
>> 626)
>> 	at
>> org
>> .apache 
>> .catalina.startup.HostConfig.deployDescriptors(HostConfig.java:
>> 553)
>> 	at  
>> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:
>> 488)
>> 	at org.apache.catalina.startup.HostConfig.start(HostConfig.java: 
>> 1150)
>> 	at
>> org 
>> .apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
>> 311)
>> 	at
>> org
>> .apache
>> .catalina
>> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
>> 	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
>> 1022)
>> 	at org.apache.catalina.core.StandardHost.start(StandardHost.java: 
>> 736)
>> 	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
>> 1014)
>> 	at  
>> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:
>> 443)
>> 	at
>> org.apache.catalina.core.StandardService.start(StandardService.java: 
>> 448)
>> 	at  
>> org.apache.catalina.core.StandardServer.start(StandardServer.java:
>> 700)
>> 	at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
>> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>> 	at
>> sun
>> .reflect 
>> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
>> 39)
>> 	at
>> sun
>> .reflect
>> .DelegatingMethodAccessorImpl 
>> .invoke(DelegatingMethodAccessorImpl.java:
>> 25)
>> 	at java.lang.reflect.Method.invoke(Method.java:592)
>> 	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
>> 	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
>> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
>> SEVERE: Error listenerStart
>> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
>> SEVERE: Context [/treebase-web] startup failed due to previous errors
>> WARN: The method class
>> org.apache.commons.logging.impl.SLF4JLogFactory#release() was  
>> invoked.
>> WARN: Please see http://www.slf4j.org/codes.html for an explanation.
>> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
>> SEVERE: Error filterStart
>> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
>> SEVERE: Context [/balancer] startup failed due to previous errors
>> Sep 9, 2010 4:20:41 PM org.apache.coyote.http11.Http11BaseProtocol  
>> start
>> INFO: Starting Coyote HTTP/1.1 on http-8080
>> Sep 9, 2010 4:20:41 PM org.apache.jk.common.ChannelSocket init
>> INFO: JK: ajp13 listening on /0.0.0.0:8009
>> Sep 9, 2010 4:20:41 PM org.apache.jk.server.JkMain start
>> INFO: Jk running ID=0 time=0/16  config=null
>> Sep 9, 2010 4:20:41 PM org.apache.catalina.storeconfig.StoreLoader  
>> load
>> INFO: Find registry server-registry.xml at classpath resource
>> Sep 9, 2010 4:20:42 PM org.apache.catalina.startup.Catalina start
>> INFO: Server startup in 8433 ms
>>
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net Dev2Dev email is sponsored by:
>>
>> Show off your parallel programming skills.
>> Enter the Intel(R) Threading Challenge 2010.
>> http://p.sf.net/sfu/intel-thread-sfd
>> _______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>

Re: [Treebase-devel] Fwd: A problem running local treebase

From: Hilmar L. <hl...@ne...> - 2010-09-09 20:45:59

This sounds like a class with an abstract method is being instantiated.

This can happen in Java for example if a different version of an  
external library changes the definition (signature) of an abstract  
method in a (therefore abstract) class so that the inheriting class in  
your own code that previously implemented the abstract method now no  
longer does so, or if it adds a new abstract method to the class that  
your implementing class wasn't aware of at the time it was implemented.

In other words, this smells like a version incompatibility with an  
external library, likely the Xerces parser given the error message.

Does this ring a bell or give you a target for trying to fix the issue?

	-hilmar

On Sep 9, 2010, at 4:31 PM, Vladimir Gapeyev wrote:

>
> Hi, Youjun,
>
> I cannot start a local TB instance in Tomcat, for any of the recent
> versions: the application breaks on startup. The catalina.out error
> log for the tomcat startup sequence is appended below.
>
> I tracked the problem down to SVN#731 that you committed on 7/13:
> versions up to 730 start up and run just fine, while 731 and the later
> ones, up to the head (#748) break at startup with the same error.
> Inexplicably, rebuild on treebase-dev works just fine.
>
> Looking at the error log below and the SVN log for 731 that I am
> resending separately, do you have any idea what has changed in #731
> that made things go wrong?
>
> Thanks,
>
> --Vladimir
>
>
> -----------------------------------------------------------------------------------------------
> Thursday, September 9, 2010 4:20:30 PM US/Eastern
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.AprLifecycleListener
> lifecycleEvent
> INFO: The Apache Tomcat Native library which allows optimal
> performance in production environments was not found on the
> java.library.path: .:/Library/Java/Extensions:/System/Library/Java/
> Extensions:/usr/lib/java
> Sep 9, 2010 4:20:33 PM org.apache.coyote.http11.Http11BaseProtocol  
> init
> INFO: Initializing Coyote HTTP/1.1 on http-8080
> Sep 9, 2010 4:20:33 PM org.apache.catalina.startup.Catalina load
> INFO: Initialization processed in 479 ms
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardService start
> INFO: Starting service Catalina
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardEngine start
> INFO: Starting Servlet Engine: Apache Tomcat/5.5.28
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardHost start
> INFO: XML validation disabled
> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader
> validateJarFile
> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache-
> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/geronimo-
> servlet_2.5_spec-1.2.jar) - jar not loaded. See Servlet Spec 2.3,
> section 9.7.2. Offending class: javax/servlet/Servlet.class
> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader
> validateJarFile
> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache-
> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/servlet-api-2.4.jar) -
> jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class:
> javax/servlet/Servlet.class
> [main] DEBUG org.cipres.treebase.web.listeners.StartupListener -
> contextInitialized(ServletContextEvent) -
> FORMAT_DELIMITER_MSG= :FORMAT_RETURN_VALUE_NAME=return valuestart
> [main] WARN org.hibernate.cache.CacheFactory - read-only cache
> configured for mutable class: staticCache
> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find
> configuration [org.hibernate.cache.UpdateTimestampsCache]; using
> defaults.
> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find
> configuration [org.hibernate.cache.StandardQueryCache]; using  
> defaults.
> [main] INFO org.cipres.treebase.service.nexus.NexusServiceMesquite -
> Setting mesquite folder location from JNDI: /Users/vgapeyev/Work/
> TreeBase/mytomcat/mesquite-2.01.tb
> Sep 9, 2010 4:20:40 PM
> org.apache.cxf.service.factory.ReflectionServiceFactoryBean
> buildServiceFromClass
> INFO: Creating Service {http://
> webservices.web.treebase.cipres.org/}StudiesContainingKeyword from
> class org.cipres.treebase.web.webservices.StudyServiceByKeyword
> [main] ERROR org.springframework.web.context.ContextLoader - Context
> initialization failed
> org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'searchStudiesByKeyword': Invocation of init
> method failed; nested exception is java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ 
> String;
> Caused by:
> java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ 
> String;
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at
> sun
> .reflect 
> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> 	at
> sun
> .reflect
> .DelegatingMethodAccessorImpl 
> .invoke(DelegatingMethodAccessorImpl.java:
> 25)
> 	at java.lang.reflect.Method.invoke(Method.java:592)
> 	at
> org
> .apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java:
> 602)
> 	at
> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java: 
> 84)
> 	at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 424)
> 	at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 418)
> 	at
> org
> .apache
> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
> 	at
> org
> .apache
> .cxf
> .databinding
> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
> 	at
> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java: 
> 345)
> 	at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
> 	at
> org
> .apache
> .cxf
> .jaxws
> .support
> .JaxWsServiceFactoryBean
> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
> 	at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .initializeServiceModel(ReflectionServiceFactoryBean.java:396)
> 	at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean 
> .create(ReflectionServiceFactoryBean.java:
> 181)
> 	at
> org
> .apache
> .cxf
> .jaxws
> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java:
> 163)
> 	at
> org
> .apache
> .cxf
> .frontend
> .AbstractWSDLBasedEndpointFactory
> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
> 	at
> org
> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java:
> 114)
> 	at
> org
> .apache
> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java:
> 164)
> 	at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
> 	at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
> 	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
> 	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at
> sun
> .reflect 
> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> 	at
> sun
> .reflect
> .DelegatingMethodAccessorImpl 
> .invoke(DelegatingMethodAccessorImpl.java:
> 25)
> 	at java.lang.reflect.Method.invoke(Method.java:592)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .createBean(AbstractAutowireCapableBeanFactory.java:427)
> 	at org.springframework.beans.factory.support.AbstractBeanFactory
> $1.getObject(AbstractBeanFactory.java:249)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultSingletonBeanRegistry
> .getSingleton(DefaultSingletonBeanRegistry.java:155)
> 	at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 246)
> 	at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 160)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultListableBeanFactory
> .preInstantiateSingletons(DefaultListableBeanFactory.java:291)
> 	at
> org
> .springframework
> .context
> .support
> .AbstractApplicationContext.refresh(AbstractApplicationContext.java: 
> 352)
> 	at org.springframework.web.context.ContextLoader.createWebApplicationContext
> (ContextLoader.java:245)
> 	at org.springframework.web.context.ContextLoader.initWebApplicationContext
> (ContextLoader.java:188)
> 	at org.springframework.web.context.ContextLoaderListener.contextInitialized
> (ContextLoaderListener.java:49)
> 	at
> org
> .cipres
> .treebase
> .web 
> .listeners.StartupListener.contextInitialized(StartupListener.java:
> 45)
> 	at
> org
> .apache
> .catalina.core.StandardContext.listenerStart(StandardContext.java: 
> 3795)
> 	at
> org.apache.catalina.core.StandardContext.start(StandardContext.java:
> 4252)
> 	at
> org
> .apache
> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
> 	at  
> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
> 740)
> 	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:
> 544)
> 	at
> org
> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:
> 626)
> 	at
> org
> .apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:
> 553)
> 	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:
> 488)
> 	at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
> 	at
> org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
> 311)
> 	at
> org
> .apache
> .catalina
> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
> 	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1022)
> 	at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
> 	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1014)
> 	at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:
> 443)
> 	at
> org.apache.catalina.core.StandardService.start(StandardService.java: 
> 448)
> 	at org.apache.catalina.core.StandardServer.start(StandardServer.java:
> 700)
> 	at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at
> sun
> .reflect 
> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> 	at
> sun
> .reflect
> .DelegatingMethodAccessorImpl 
> .invoke(DelegatingMethodAccessorImpl.java:
> 25)
> 	at java.lang.reflect.Method.invoke(Method.java:592)
> 	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
> 	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
> [main] ERROR org.apache.catalina.core.ContainerBase.[Catalina].
> [localhost].[/treebase-web] - Exception sending context initialized
> event to listener instance of class org.cipres.treebase.web.listeners.StartupListener
> org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'searchStudiesByKeyword': Invocation of init
> method failed; nested exception is java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ 
> String;
> Caused by:
> java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/ 
> String;
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at
> sun
> .reflect 
> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> 	at
> sun
> .reflect
> .DelegatingMethodAccessorImpl 
> .invoke(DelegatingMethodAccessorImpl.java:
> 25)
> 	at java.lang.reflect.Method.invoke(Method.java:592)
> 	at
> org
> .apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java:
> 602)
> 	at
> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java: 
> 84)
> 	at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 424)
> 	at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 418)
> 	at
> org
> .apache
> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
> 	at
> org
> .apache
> .cxf
> .databinding
> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
> 	at
> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java: 
> 345)
> 	at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
> 	at
> org
> .apache
> .cxf
> .jaxws
> .support
> .JaxWsServiceFactoryBean
> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
> 	at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .initializeServiceModel(ReflectionServiceFactoryBean.java:396)
> 	at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean 
> .create(ReflectionServiceFactoryBean.java:
> 181)
> 	at
> org
> .apache
> .cxf
> .jaxws
> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java:
> 163)
> 	at
> org
> .apache
> .cxf
> .frontend
> .AbstractWSDLBasedEndpointFactory
> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
> 	at
> org
> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java:
> 114)
> 	at
> org
> .apache
> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java:
> 164)
> 	at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
> 	at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
> 	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
> 	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at
> sun
> .reflect 
> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> 	at
> sun
> .reflect
> .DelegatingMethodAccessorImpl 
> .invoke(DelegatingMethodAccessorImpl.java:
> 25)
> 	at java.lang.reflect.Method.invoke(Method.java:592)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .createBean(AbstractAutowireCapableBeanFactory.java:427)
> 	at org.springframework.beans.factory.support.AbstractBeanFactory
> $1.getObject(AbstractBeanFactory.java:249)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultSingletonBeanRegistry
> .getSingleton(DefaultSingletonBeanRegistry.java:155)
> 	at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 246)
> 	at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 160)
> 	at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultListableBeanFactory
> .preInstantiateSingletons(DefaultListableBeanFactory.java:291)
> 	at
> org
> .springframework
> .context
> .support
> .AbstractApplicationContext.refresh(AbstractApplicationContext.java: 
> 352)
> 	at org.springframework.web.context.ContextLoader.createWebApplicationContext
> (ContextLoader.java:245)
> 	at org.springframework.web.context.ContextLoader.initWebApplicationContext
> (ContextLoader.java:188)
> 	at org.springframework.web.context.ContextLoaderListener.contextInitialized
> (ContextLoaderListener.java:49)
> 	at
> org
> .cipres
> .treebase
> .web 
> .listeners.StartupListener.contextInitialized(StartupListener.java:
> 45)
> 	at
> org
> .apache
> .catalina.core.StandardContext.listenerStart(StandardContext.java: 
> 3795)
> 	at
> org.apache.catalina.core.StandardContext.start(StandardContext.java:
> 4252)
> 	at
> org
> .apache
> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
> 	at  
> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
> 740)
> 	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:
> 544)
> 	at
> org
> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:
> 626)
> 	at
> org
> .apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:
> 553)
> 	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:
> 488)
> 	at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
> 	at
> org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
> 311)
> 	at
> org
> .apache
> .catalina
> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
> 	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1022)
> 	at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
> 	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1014)
> 	at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:
> 443)
> 	at
> org.apache.catalina.core.StandardService.start(StandardService.java: 
> 448)
> 	at org.apache.catalina.core.StandardServer.start(StandardServer.java:
> 700)
> 	at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at
> sun
> .reflect 
> .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> 	at
> sun
> .reflect
> .DelegatingMethodAccessorImpl 
> .invoke(DelegatingMethodAccessorImpl.java:
> 25)
> 	at java.lang.reflect.Method.invoke(Method.java:592)
> 	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
> 	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Error listenerStart
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Context [/treebase-web] startup failed due to previous errors
> WARN: The method class
> org.apache.commons.logging.impl.SLF4JLogFactory#release() was invoked.
> WARN: Please see http://www.slf4j.org/codes.html for an explanation.
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Error filterStart
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Context [/balancer] startup failed due to previous errors
> Sep 9, 2010 4:20:41 PM org.apache.coyote.http11.Http11BaseProtocol  
> start
> INFO: Starting Coyote HTTP/1.1 on http-8080
> Sep 9, 2010 4:20:41 PM org.apache.jk.common.ChannelSocket init
> INFO: JK: ajp13 listening on /0.0.0.0:8009
> Sep 9, 2010 4:20:41 PM org.apache.jk.server.JkMain start
> INFO: Jk running ID=0 time=0/16  config=null
> Sep 9, 2010 4:20:41 PM org.apache.catalina.storeconfig.StoreLoader  
> load
> INFO: Find registry server-registry.xml at classpath resource
> Sep 9, 2010 4:20:42 PM org.apache.catalina.startup.Catalina start
> INFO: Server startup in 8433 ms
>
>
>
> ------------------------------------------------------------------------------
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
> http://p.sf.net/sfu/intel-thread-sfd
> _______________________________________________
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> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

[Treebase-devel] A problem running local treebase

From: Vladimir G. <vga...@ne...> - 2010-09-09 20:41:30

Hi, Youjun,

I cannot start a local TB instance in Tomcat, for any of the recent  
versions: the application breaks on startup. The catalina.out error  
log for the tomcat startup sequence is appended below.

I tracked the problem down to SVN#731 that you committed on 7/13:  
versions up to 730 start up and run just fine, while 731 and the later  
ones, up to the head (#748) break at startup with the same error.   
Inexplicably, rebuild on treebase-dev works just fine.

Looking at the error log below and the SVN log for 731 that I am  
resending separately, do you have any idea what has changed in #731  
that made things go wrong?

Thanks,

--Vladimir


-----------------------------------------------------------------------------------------------
  Thursday, September 9, 2010 4:20:30 PM US/Eastern
Sep 9, 2010 4:20:33 PM org.apache.catalina.core.AprLifecycleListener  
lifecycleEvent
INFO: The Apache Tomcat Native library which allows optimal  
performance in production environments was not found on the  
java.library.path: .:/Library/Java/Extensions:/System/Library/Java/ 
Extensions:/usr/lib/java
Sep 9, 2010 4:20:33 PM org.apache.coyote.http11.Http11BaseProtocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Sep 9, 2010 4:20:33 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 479 ms
Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/5.5.28
Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardHost start
INFO: XML validation disabled
Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader  
validateJarFile
INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache- 
tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/geronimo- 
servlet_2.5_spec-1.2.jar) - jar not loaded. See Servlet Spec 2.3,  
section 9.7.2. Offending class: javax/servlet/Servlet.class
Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader  
validateJarFile
INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache- 
tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/servlet-api-2.4.jar) -  
jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class:  
javax/servlet/Servlet.class
[main] DEBUG org.cipres.treebase.web.listeners.StartupListener -  
contextInitialized(ServletContextEvent) - 
FORMAT_DELIMITER_MSG= :FORMAT_RETURN_VALUE_NAME=return valuestart
[main] WARN org.hibernate.cache.CacheFactory - read-only cache  
configured for mutable class: staticCache
[main] WARN org.hibernate.cache.EhCacheProvider - Could not find  
configuration [org.hibernate.cache.UpdateTimestampsCache]; using  
defaults.
[main] WARN org.hibernate.cache.EhCacheProvider - Could not find  
configuration [org.hibernate.cache.StandardQueryCache]; using defaults.
[main] INFO org.cipres.treebase.service.nexus.NexusServiceMesquite -  
Setting mesquite folder location from JNDI: /Users/vgapeyev/Work/ 
TreeBase/mytomcat/mesquite-2.01.tb
Sep 9, 2010 4:20:40 PM  
org.apache.cxf.service.factory.ReflectionServiceFactoryBean  
buildServiceFromClass
INFO: Creating Service {http:// 
webservices.web.treebase.cipres.org/}StudiesContainingKeyword from  
class org.cipres.treebase.web.webservices.StudyServiceByKeyword
[main] ERROR org.springframework.web.context.ContextLoader - Context  
initialization failed
org.springframework.beans.factory.BeanCreationException: Error  
creating bean with name 'searchStudiesByKeyword': Invocation of init  
method failed; nested exception is java.lang.AbstractMethodError:  
org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
Caused by:
java.lang.AbstractMethodError:  
org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at  
org 
.apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java: 
602)
	at  
org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java:84)
	at  
org 
.apache 
.ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: 
424)
	at  
org 
.apache 
.ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: 
418)
	at  
org 
.apache 
.cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
	at  
org 
.apache 
.cxf 
.databinding 
.AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
	at  
org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java:345)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean 
.buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
	at  
org 
.apache 
.cxf 
.jaxws 
.support 
.JaxWsServiceFactoryBean 
.buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean 
.initializeServiceModel(ReflectionServiceFactoryBean.java:396)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean.create(ReflectionServiceFactoryBean.java: 
181)
	at  
org 
.apache 
.cxf 
.jaxws 
.support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java: 
163)
	at  
org 
.apache 
.cxf 
.frontend 
.AbstractWSDLBasedEndpointFactory 
.createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
	at  
org 
.apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java: 
114)
	at  
org 
.apache 
.cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java: 
164)
	at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
	at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.createBean(AbstractAutowireCapableBeanFactory.java:427)
	at org.springframework.beans.factory.support.AbstractBeanFactory 
$1.getObject(AbstractBeanFactory.java:249)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.DefaultSingletonBeanRegistry 
.getSingleton(DefaultSingletonBeanRegistry.java:155)
	at  
org 
.springframework 
.beans 
.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 
246)
	at  
org 
.springframework 
.beans 
.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 
160)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.DefaultListableBeanFactory 
.preInstantiateSingletons(DefaultListableBeanFactory.java:291)
	at  
org 
.springframework 
.context 
.support 
.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
	at org.springframework.web.context.ContextLoader.createWebApplicationContext 
(ContextLoader.java:245)
	at org.springframework.web.context.ContextLoader.initWebApplicationContext 
(ContextLoader.java:188)
	at org.springframework.web.context.ContextLoaderListener.contextInitialized 
(ContextLoaderListener.java:49)
	at  
org 
.cipres 
.treebase 
.web.listeners.StartupListener.contextInitialized(StartupListener.java: 
45)
	at  
org 
.apache 
.catalina.core.StandardContext.listenerStart(StandardContext.java:3795)
	at  
org.apache.catalina.core.StandardContext.start(StandardContext.java: 
4252)
	at  
org 
.apache 
.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: 
740)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java: 
544)
	at  
org 
.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java: 
626)
	at  
org 
.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java: 
553)
	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java: 
488)
	at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
	at  
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: 
311)
	at  
org 
.apache 
.catalina 
.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 
1022)
	at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 
1014)
	at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 
443)
	at  
org.apache.catalina.core.StandardService.start(StandardService.java:448)
	at org.apache.catalina.core.StandardServer.start(StandardServer.java: 
700)
	at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
[main] ERROR org.apache.catalina.core.ContainerBase.[Catalina]. 
[localhost].[/treebase-web] - Exception sending context initialized  
event to listener instance of class org.cipres.treebase.web.listeners.StartupListener
org.springframework.beans.factory.BeanCreationException: Error  
creating bean with name 'searchStudiesByKeyword': Invocation of init  
method failed; nested exception is java.lang.AbstractMethodError:  
org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
Caused by:
java.lang.AbstractMethodError:  
org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at  
org 
.apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java: 
602)
	at  
org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java:84)
	at  
org 
.apache 
.ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: 
424)
	at  
org 
.apache 
.ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: 
418)
	at  
org 
.apache 
.cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
	at  
org 
.apache 
.cxf 
.databinding 
.AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
	at  
org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java:345)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean 
.buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
	at  
org 
.apache 
.cxf 
.jaxws 
.support 
.JaxWsServiceFactoryBean 
.buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean 
.initializeServiceModel(ReflectionServiceFactoryBean.java:396)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean.create(ReflectionServiceFactoryBean.java: 
181)
	at  
org 
.apache 
.cxf 
.jaxws 
.support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java: 
163)
	at  
org 
.apache 
.cxf 
.frontend 
.AbstractWSDLBasedEndpointFactory 
.createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
	at  
org 
.apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java: 
114)
	at  
org 
.apache 
.cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java: 
164)
	at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
	at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.createBean(AbstractAutowireCapableBeanFactory.java:427)
	at org.springframework.beans.factory.support.AbstractBeanFactory 
$1.getObject(AbstractBeanFactory.java:249)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.DefaultSingletonBeanRegistry 
.getSingleton(DefaultSingletonBeanRegistry.java:155)
	at  
org 
.springframework 
.beans 
.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 
246)
	at  
org 
.springframework 
.beans 
.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 
160)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.DefaultListableBeanFactory 
.preInstantiateSingletons(DefaultListableBeanFactory.java:291)
	at  
org 
.springframework 
.context 
.support 
.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
	at org.springframework.web.context.ContextLoader.createWebApplicationContext 
(ContextLoader.java:245)
	at org.springframework.web.context.ContextLoader.initWebApplicationContext 
(ContextLoader.java:188)
	at org.springframework.web.context.ContextLoaderListener.contextInitialized 
(ContextLoaderListener.java:49)
	at  
org 
.cipres 
.treebase 
.web.listeners.StartupListener.contextInitialized(StartupListener.java: 
45)
	at  
org 
.apache 
.catalina.core.StandardContext.listenerStart(StandardContext.java:3795)
	at  
org.apache.catalina.core.StandardContext.start(StandardContext.java: 
4252)
	at  
org 
.apache 
.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: 
740)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java: 
544)
	at  
org 
.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java: 
626)
	at  
org 
.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java: 
553)
	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java: 
488)
	at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
	at  
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: 
311)
	at  
org 
.apache 
.catalina 
.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 
1022)
	at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 
1014)
	at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 
443)
	at  
org.apache.catalina.core.StandardService.start(StandardService.java:448)
	at org.apache.catalina.core.StandardServer.start(StandardServer.java: 
700)
	at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Error listenerStart
Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Context [/treebase-web] startup failed due to previous errors
WARN: The method class  
org.apache.commons.logging.impl.SLF4JLogFactory#release() was invoked.
WARN: Please see http://www.slf4j.org/codes.html for an explanation.
Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Error filterStart
Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Context [/balancer] startup failed due to previous errors
Sep 9, 2010 4:20:41 PM org.apache.coyote.http11.Http11BaseProtocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Sep 9, 2010 4:20:41 PM org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
Sep 9, 2010 4:20:41 PM org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/16  config=null
Sep 9, 2010 4:20:41 PM org.apache.catalina.storeconfig.StoreLoader load
INFO: Find registry server-registry.xml at classpath resource
Sep 9, 2010 4:20:42 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 8433 ms

[Treebase-devel] Fwd: A problem running local treebase

From: Vladimir G. <vla...@du...> - 2010-09-09 20:31:53

Hi, Youjun,

I cannot start a local TB instance in Tomcat, for any of the recent  
versions: the application breaks on startup. The catalina.out error  
log for the tomcat startup sequence is appended below.

I tracked the problem down to SVN#731 that you committed on 7/13:  
versions up to 730 start up and run just fine, while 731 and the later  
ones, up to the head (#748) break at startup with the same error.   
Inexplicably, rebuild on treebase-dev works just fine.

Looking at the error log below and the SVN log for 731 that I am  
resending separately, do you have any idea what has changed in #731  
that made things go wrong?

Thanks,

--Vladimir


-----------------------------------------------------------------------------------------------
Thursday, September 9, 2010 4:20:30 PM US/Eastern
Sep 9, 2010 4:20:33 PM org.apache.catalina.core.AprLifecycleListener  
lifecycleEvent
INFO: The Apache Tomcat Native library which allows optimal  
performance in production environments was not found on the  
java.library.path: .:/Library/Java/Extensions:/System/Library/Java/ 
Extensions:/usr/lib/java
Sep 9, 2010 4:20:33 PM org.apache.coyote.http11.Http11BaseProtocol init
INFO: Initializing Coyote HTTP/1.1 on http-8080
Sep 9, 2010 4:20:33 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 479 ms
Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardService start
INFO: Starting service Catalina
Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardEngine start
INFO: Starting Servlet Engine: Apache Tomcat/5.5.28
Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardHost start
INFO: XML validation disabled
Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader  
validateJarFile
INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache- 
tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/geronimo- 
servlet_2.5_spec-1.2.jar) - jar not loaded. See Servlet Spec 2.3,  
section 9.7.2. Offending class: javax/servlet/Servlet.class
Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader  
validateJarFile
INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache- 
tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/servlet-api-2.4.jar) -  
jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class:  
javax/servlet/Servlet.class
[main] DEBUG org.cipres.treebase.web.listeners.StartupListener -  
contextInitialized(ServletContextEvent) - 
FORMAT_DELIMITER_MSG= :FORMAT_RETURN_VALUE_NAME=return valuestart
[main] WARN org.hibernate.cache.CacheFactory - read-only cache  
configured for mutable class: staticCache
[main] WARN org.hibernate.cache.EhCacheProvider - Could not find  
configuration [org.hibernate.cache.UpdateTimestampsCache]; using  
defaults.
[main] WARN org.hibernate.cache.EhCacheProvider - Could not find  
configuration [org.hibernate.cache.StandardQueryCache]; using defaults.
[main] INFO org.cipres.treebase.service.nexus.NexusServiceMesquite -  
Setting mesquite folder location from JNDI: /Users/vgapeyev/Work/ 
TreeBase/mytomcat/mesquite-2.01.tb
Sep 9, 2010 4:20:40 PM  
org.apache.cxf.service.factory.ReflectionServiceFactoryBean  
buildServiceFromClass
INFO: Creating Service {http:// 
webservices.web.treebase.cipres.org/}StudiesContainingKeyword from  
class org.cipres.treebase.web.webservices.StudyServiceByKeyword
[main] ERROR org.springframework.web.context.ContextLoader - Context  
initialization failed
org.springframework.beans.factory.BeanCreationException: Error  
creating bean with name 'searchStudiesByKeyword': Invocation of init  
method failed; nested exception is java.lang.AbstractMethodError:  
org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
Caused by:
java.lang.AbstractMethodError:  
org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at  
org 
.apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java: 
602)
	at  
org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java:84)
	at  
org 
.apache 
.ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: 
424)
	at  
org 
.apache 
.ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: 
418)
	at  
org 
.apache 
.cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
	at  
org 
.apache 
.cxf 
.databinding 
.AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
	at  
org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java:345)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean 
.buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
	at  
org 
.apache 
.cxf 
.jaxws 
.support 
.JaxWsServiceFactoryBean 
.buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean 
.initializeServiceModel(ReflectionServiceFactoryBean.java:396)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean.create(ReflectionServiceFactoryBean.java: 
181)
	at  
org 
.apache 
.cxf 
.jaxws 
.support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java: 
163)
	at  
org 
.apache 
.cxf 
.frontend 
.AbstractWSDLBasedEndpointFactory 
.createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
	at  
org 
.apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java: 
114)
	at  
org 
.apache 
.cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java: 
164)
	at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
	at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.createBean(AbstractAutowireCapableBeanFactory.java:427)
	at org.springframework.beans.factory.support.AbstractBeanFactory 
$1.getObject(AbstractBeanFactory.java:249)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.DefaultSingletonBeanRegistry 
.getSingleton(DefaultSingletonBeanRegistry.java:155)
	at  
org 
.springframework 
.beans 
.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 
246)
	at  
org 
.springframework 
.beans 
.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 
160)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.DefaultListableBeanFactory 
.preInstantiateSingletons(DefaultListableBeanFactory.java:291)
	at  
org 
.springframework 
.context 
.support 
.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
	at org.springframework.web.context.ContextLoader.createWebApplicationContext 
(ContextLoader.java:245)
	at org.springframework.web.context.ContextLoader.initWebApplicationContext 
(ContextLoader.java:188)
	at org.springframework.web.context.ContextLoaderListener.contextInitialized 
(ContextLoaderListener.java:49)
	at  
org 
.cipres 
.treebase 
.web.listeners.StartupListener.contextInitialized(StartupListener.java: 
45)
	at  
org 
.apache 
.catalina.core.StandardContext.listenerStart(StandardContext.java:3795)
	at  
org.apache.catalina.core.StandardContext.start(StandardContext.java: 
4252)
	at  
org 
.apache 
.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: 
740)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java: 
544)
	at  
org 
.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java: 
626)
	at  
org 
.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java: 
553)
	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java: 
488)
	at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
	at  
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: 
311)
	at  
org 
.apache 
.catalina 
.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 
1022)
	at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 
1014)
	at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 
443)
	at  
org.apache.catalina.core.StandardService.start(StandardService.java:448)
	at org.apache.catalina.core.StandardServer.start(StandardServer.java: 
700)
	at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
[main] ERROR org.apache.catalina.core.ContainerBase.[Catalina]. 
[localhost].[/treebase-web] - Exception sending context initialized  
event to listener instance of class org.cipres.treebase.web.listeners.StartupListener
org.springframework.beans.factory.BeanCreationException: Error  
creating bean with name 'searchStudiesByKeyword': Invocation of init  
method failed; nested exception is java.lang.AbstractMethodError:  
org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
Caused by:
java.lang.AbstractMethodError:  
org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at  
org 
.apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java: 
602)
	at  
org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java:84)
	at  
org 
.apache 
.ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: 
424)
	at  
org 
.apache 
.ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java: 
418)
	at  
org 
.apache 
.cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
	at  
org 
.apache 
.cxf 
.databinding 
.AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
	at  
org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java:345)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean 
.buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
	at  
org 
.apache 
.cxf 
.jaxws 
.support 
.JaxWsServiceFactoryBean 
.buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean 
.initializeServiceModel(ReflectionServiceFactoryBean.java:396)
	at  
org 
.apache 
.cxf 
.service 
.factory 
.ReflectionServiceFactoryBean.create(ReflectionServiceFactoryBean.java: 
181)
	at  
org 
.apache 
.cxf 
.jaxws 
.support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java: 
163)
	at  
org 
.apache 
.cxf 
.frontend 
.AbstractWSDLBasedEndpointFactory 
.createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
	at  
org 
.apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java: 
114)
	at  
org 
.apache 
.cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java: 
164)
	at org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
	at org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
	at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.AbstractAutowireCapableBeanFactory 
.createBean(AbstractAutowireCapableBeanFactory.java:427)
	at org.springframework.beans.factory.support.AbstractBeanFactory 
$1.getObject(AbstractBeanFactory.java:249)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.DefaultSingletonBeanRegistry 
.getSingleton(DefaultSingletonBeanRegistry.java:155)
	at  
org 
.springframework 
.beans 
.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 
246)
	at  
org 
.springframework 
.beans 
.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 
160)
	at  
org 
.springframework 
.beans 
.factory 
.support 
.DefaultListableBeanFactory 
.preInstantiateSingletons(DefaultListableBeanFactory.java:291)
	at  
org 
.springframework 
.context 
.support 
.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
	at org.springframework.web.context.ContextLoader.createWebApplicationContext 
(ContextLoader.java:245)
	at org.springframework.web.context.ContextLoader.initWebApplicationContext 
(ContextLoader.java:188)
	at org.springframework.web.context.ContextLoaderListener.contextInitialized 
(ContextLoaderListener.java:49)
	at  
org 
.cipres 
.treebase 
.web.listeners.StartupListener.contextInitialized(StartupListener.java: 
45)
	at  
org 
.apache 
.catalina.core.StandardContext.listenerStart(StandardContext.java:3795)
	at  
org.apache.catalina.core.StandardContext.start(StandardContext.java: 
4252)
	at  
org 
.apache 
.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: 
740)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java: 
544)
	at  
org 
.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java: 
626)
	at  
org 
.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java: 
553)
	at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java: 
488)
	at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
	at  
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: 
311)
	at  
org 
.apache 
.catalina 
.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 
1022)
	at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
	at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 
1014)
	at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 
443)
	at  
org.apache.catalina.core.StandardService.start(StandardService.java:448)
	at org.apache.catalina.core.StandardServer.start(StandardServer.java: 
700)
	at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at  
sun 
.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 
39)
	at  
sun 
.reflect 
.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 
25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
	at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Error listenerStart
Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Context [/treebase-web] startup failed due to previous errors
WARN: The method class  
org.apache.commons.logging.impl.SLF4JLogFactory#release() was invoked.
WARN: Please see http://www.slf4j.org/codes.html for an explanation.
Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Error filterStart
Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
SEVERE: Context [/balancer] startup failed due to previous errors
Sep 9, 2010 4:20:41 PM org.apache.coyote.http11.Http11BaseProtocol start
INFO: Starting Coyote HTTP/1.1 on http-8080
Sep 9, 2010 4:20:41 PM org.apache.jk.common.ChannelSocket init
INFO: JK: ajp13 listening on /0.0.0.0:8009
Sep 9, 2010 4:20:41 PM org.apache.jk.server.JkMain start
INFO: Jk running ID=0 time=0/16  config=null
Sep 9, 2010 4:20:41 PM org.apache.catalina.storeconfig.StoreLoader load
INFO: Find registry server-registry.xml at classpath resource
Sep 9, 2010 4:20:42 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 8433 ms

[Treebase-devel] Fwd: [Treebase-guts] SF.net SVN: treebase:[731] trunk/treebase-web

From: Vladimir G. <vla...@du...> - 2010-09-09 20:26:58


Begin forwarded message:

> From: yo...@us...
> Date: July 13, 2010 12:38:00 PM EDT
> To: tre...@li...
> Subject: [Treebase-guts] SF.net SVN: treebase:[731] trunk/treebase-web
>
> Revision: 731
>          http://treebase.svn.sourceforge.net/treebase/? 
> rev=731&view=rev
> Author:   youjun
> Date:     2010-07-13 16:38:00 +0000 (Tue, 13 Jul 2010)
>
> Log Message:
> -----------
>
>
> Modified Paths:
> --------------
>    trunk/treebase-web/pom.xml
>    trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
>
> Added Paths:
> -----------
>    trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/ 
> UnTarTool.java
>    trunk/treebase-web/src/main/java/org/cipres/treebase/web/ 
> webservices/DryadImportor.java
>
> Modified: trunk/treebase-web/pom.xml
> ===================================================================
> --- trunk/treebase-web/pom.xml	2010-07-07 19:32:38 UTC (rev 730)
> +++ trunk/treebase-web/pom.xml	2010-07-13 16:38:00 UTC (rev 731)
> @@ -21,6 +21,9 @@
> 			</resource>
> 		</resources>
> 		<finalName>treebase-web</finalName>
> +		
> +		
> +		
> 		<plugins>
>
> 			<!-- Ant Task plugin-->
> @@ -80,26 +83,20 @@
> 		<repository>
> 			<id>org.tuckey.urlrewritefilter</id>
> 			<url>http://repository.jboss.org/maven2/org/tuckey/urlrewritefilter/ 
> </url>
> -		</repository>
> -
> +		</repository>
> +    	<repository>
> +      		<id>java.net</id>
> +      		<url>http://download.java.net/maven/2</url>
> +    	</repository>
> +
> +
> 	</repositories>
> +	
>
> -	<pluginRepositories>
> -		<pluginRepository>
> -			<id>Maven Snapshots</id>
> -			<url>http://snapshots.maven.codehaus.org/maven2</url>
> -			<snapshots>
> -				<enabled>true</enabled>
> -			</snapshots>
> -			<releases>
> -				<enabled>false</enabled>
> -			</releases>
> -		</pluginRepository>
> -	</pluginRepositories>
>
> -	<dependencies>
> -
> -		
> +
> +	
> +	<dependencies>		
> 		<dependency>
> 			
> 			<groupId>org.nexml.model</groupId>
> @@ -341,5 +338,36 @@
>      	<artifactId>velocity-tools-view</artifactId>
>      	<version>1.1</version>
>      </dependency>
> -	</dependencies>
> +
> +<dependency>
> +<groupId>com.sun.jersey</groupId>
> +<artifactId>jersey-client</artifactId>
> +<version>1.1.5</version>
> +</dependency>
> +
> +<dependency>
> +<groupId>com.sun.jersey</groupId>
> +<artifactId>jersey-server</artifactId>
> +<version>1.1.5</version>
> +</dependency>
> +
> +<dependency>
> +<groupId>com.sun.jersey.contribs</groupId>
> +<artifactId>jersey-multipart</artifactId>
> +<version>1.1.5</version>
> +</dependency>
> +
> +<dependency>
> +<groupId>com.sun.jersey</groupId>
> +<artifactId>jersey-bundle</artifactId>
> +<version>1.1.5</version>
> +</dependency>
> +
> +<dependency>
> +<groupId>javax.ws.rs</groupId>
> +<artifactId>jsr311-api</artifactId>
> +<version>1.0</version>
> +</dependency>
> +</dependencies>
> +		
> </project>
>
> Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/ 
> UnTarTool.java
> ===================================================================
> --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/ 
> UnTarTool.java	                        (rev 0)
> +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/util/ 
> UnTarTool.java	2010-07-13 16:38:00 UTC (rev 731)
> @@ -0,0 +1,69 @@
> +package org.cipres.treebase.web.util;
> +
> +import java.io.BufferedInputStream;
> +import java.io.File;
> +import java.io.FileInputStream;
> +import java.io.FileOutputStream;
> +import java.io.IOException;
> +import java.io.OutputStream;
> +import java.util.zip.GZIPInputStream;
> +
> +import org.apache.tools.tar.TarEntry;
> +import org.apache.tools.tar.TarInputStream;
> +
> +public class UnTarTool
> +{
> +
> +	public static void unTarGz(File file,File outDir) throws  
> IOException{
> +
> +		TarInputStream tarIn = null;
> +
> +		try{
> +
> +			tarIn = new TarInputStream(new GZIPInputStream(
> +					new BufferedInputStream(new FileInputStream(file))),
> +					1024);  		
> +			
> +			TarEntry entry = null;
> +            //tarIn.getNextEntry();
> +			//File outputDir = new File(outDir, "myBag");
> +			//outputDir.mkdirs();
> +			while( (entry = tarIn.getNextEntry()) != null ){
> +				File f = new File(outDir,entry.getName());
> +				if(entry.isDirectory()){
> +					f.mkdirs();
> +				}else{
> +					f.getParentFile().mkdirs();
> +					f.createNewFile();
> +					OutputStream out = null;
> +					try{
> +						out = new FileOutputStream(f);
> +						int length = 0;
> +						byte[] b = new byte[1024];
> +						while((length = tarIn.read(b)) != -1){
> +							out.write(b, 0, length);
> +						}
> +
> +					}catch(IOException ex){
> +						throw ex;
> +					}finally{
> +						if(out!=null)
> +						out.close();
> +					}
> +				}
> +			}
> +		}catch(IOException ex){
> +			throw ex;
> +		} finally{
> +			try{
> +				if(tarIn != null){
> +					tarIn.close();
> +				}
> +			}catch(IOException ex){
> +				throw ex;
> +			}
> +		}
> +
> +	}
> +
> +}
>
> Added: trunk/treebase-web/src/main/java/org/cipres/treebase/web/ 
> webservices/DryadImportor.java
> ===================================================================
> --- trunk/treebase-web/src/main/java/org/cipres/treebase/web/ 
> webservices/DryadImportor.java	                        (rev 0)
> +++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/ 
> webservices/DryadImportor.java	2010-07-13 16:38:00 UTC (rev 731)
> @@ -0,0 +1,104 @@
> +package org.cipres.treebase.web.webservices;
> +
> +
> +import java.io.File;
> +import java.io.FileOutputStream;
> +import java.io.IOException;
> +import java.io.InputStream;
> +import java.io.OutputStream;
> +import java.io.PrintWriter;
> +import java.io.StringWriter;
> +
> +import com.sun.jersey.multipart.*;
> +import javax.servlet.http.HttpServletRequest;
> +import javax.ws.rs.Consumes;
> +//import javax.ws.rs.POST;
> +import javax.ws.rs.PUT;
> +import javax.ws.rs.Path;
> +import javax.ws.rs.core.Context;
> +
> +import org.cipres.treebase.TreebaseUtil;
> +import org.cipres.treebase.web.util.UnTarTool;
> +
> +
> +
> +@Path("/dryadImport")
> +
> +public class DryadImportor {
> +
> +	@Context
> +	HttpServletRequest httpRequest;
> +
> +	@PUT
> +    //@POST
> +    //@GET
> +
> +    @Consumes("multipart/mixed")
> +
> +public String processMultiparts(MultiPart multiPart) {
> +
> +        String ip = httpRequest.getRemoteAddr();
> +    	if(!AllowIP.isAllowIP(ip))return "not authorized";
> +    	
> +        BodyPartEntity bpe = (BodyPartEntity)  
> multiPart.getBodyParts().get(0).getEntity();
> +        File unzipFold;
> +        String systemTime;
> +
> +        do{
> +        	systemTime = "" + System.currentTimeMillis();
> +        	String uploadDir =  
> httpRequest.getSession().getServletContext()
> +        	.getRealPath(TreebaseUtil.FILESEP + "DryadFileUpload")
> +        	+ TreebaseUtil.FILESEP + systemTime;
> +        	unzipFold = new File(uploadDir);
> +        }while(unzipFold.exists());
> +
> +
> +        File zipfile = new File(unzipFold,"data.tar.gz");
> +
> +        try {
> +        	unzipFold.mkdirs();
> +        	zipfile.createNewFile();
> +        	InputStream in = bpe.getInputStream();          	
> +        	OutputStream out=new FileOutputStream(zipfile);
> +
> +            byte[] buf = new byte[1024];
> +            int len;
> +            while ((len = in.read(buf)) > 0){
> +            	out.write(buf, 0, len);
> +            }
> +            in.close();
> +            out.close();
> +            UnTarTool.unTarGz(zipfile,unzipFold);
> +
> +		} catch (IOException e) {
> +			// TODO Auto-generated catch block
> +			StringWriter sw = new StringWriter();
> +			e.printStackTrace(new PrintWriter(sw));
> +			return sw.getBuffer().toString();
> +		}
> +		String[]  
> baseURL=httpRequest.getRequestURL().toString().split("handshaking");
> +        String importURL= baseURL[0] + "login.jsp?importKey=" +  
> systemTime;
> +
> +        return importURL;
> +
> +    }
> +
> +}
> +
> +class AllowIP{
> +	private static final String dryad1 = "152.1.24.8";
> +	private static final String dryad2 = "152.3.105.16";
> +	private static final String yale1 = "130.132.27.141";
> +	private static final String yale2 = "130.132.27.212";
> +
> +	static boolean isAllowIP(String ip){
> +		
> +		if (ip.compareTo(dryad1)==0) return true;
> +		if (ip.compareTo(dryad2)==0) return true;
> +		if (ip.compareTo(yale1)==0)return true;
> +		if (ip.compareTo(yale2)==0)return true;
> +		
> +	    return false;	
> +	}
> +
> +}
>
> Modified: trunk/treebase-web/src/main/webapp/WEB-INF/web.xml
> ===================================================================
> --- trunk/treebase-web/src/main/webapp/WEB-INF/web.xml	2010-07-07  
> 19:32:38 UTC (rev 730)
> +++ trunk/treebase-web/src/main/webapp/WEB-INF/web.xml	2010-07-13  
> 16:38:00 UTC (rev 731)
> @@ -120,13 +120,67 @@
>  	<!-- ========================================================== -->
>  	 <filter-mapping>
>  		<filter-name>securityFilter</filter-name>
> - 		<url-pattern>/*</url-pattern>
> + 		<url-pattern>/*</url-pattern> 	
>  	</filter-mapping>
> - 	<filter-mapping>
> + 	
> + 	 <filter-mapping>
>  		<filter-name>sitemesh</filter-name>
> - 		<url-pattern>/*</url-pattern>
> +		<url-pattern>*.html</url-pattern>
>  		<dispatcher>REQUEST</dispatcher>
>  		<dispatcher>FORWARD</dispatcher>
> +	 </filter-mapping>
> +	
> +	 <filter-mapping>
> + 		<filter-name>sitemesh</filter-name>
> +		<url-pattern>*.jsp</url-pattern>
> + 		<dispatcher>REQUEST</dispatcher>
> + 		<dispatcher>FORWARD</dispatcher>
> +	 </filter-mapping>
> +	
> +	 <filter-mapping>
> + 		<filter-name>sitemesh</filter-name>
> +		<url-pattern>*.htm</url-pattern>
> + 		<dispatcher>REQUEST</dispatcher>
> + 		<dispatcher>FORWARD</dispatcher>
> +	 </filter-mapping>
> +	
> +	 <filter-mapping>
> + 		<filter-name>sitemesh</filter-name>
> +		<url-pattern>*.rdf</url-pattern>
> + 		<dispatcher>REQUEST</dispatcher>
> + 		<dispatcher>FORWARD</dispatcher>
> +	 </filter-mapping>
> +		
> +	 <filter-mapping>
> + 		<filter-name>sitemesh</filter-name>
> +		<url-pattern>/</url-pattern>
> + 		<dispatcher>REQUEST</dispatcher>
> + 		<dispatcher>FORWARD</dispatcher>
> +	 </filter-mapping>	
> + 	 <filter-mapping>
> + 		<filter-name>sitemesh</filter-name>
> +		<url-pattern>/phylows/*</url-pattern>
> + 		<dispatcher>REQUEST</dispatcher>
> + 		<dispatcher>FORWARD</dispatcher>
> +	 </filter-mapping>
> + 	
> + 	 <filter-mapping>
> + 		<filter-name>sitemesh</filter-name>
> +		<url-pattern>/top/*</url-pattern>
> + 		<dispatcher>REQUEST</dispatcher>
> + 		<dispatcher>FORWARD</dispatcher>
> +	</filter-mapping>
> + 	
> + 	 <filter-mapping>
> + 		<filter-name>sitemesh</filter-name>
> + 		<url-pattern>/services/*</url-pattern>
> + 		<dispatcher>REQUEST</dispatcher>
> + 		<dispatcher>FORWARD</dispatcher>
> + 	</filter-mapping>
> + 	
> + 	<filter-mapping>
> + 		<filter-name>hibernateFilter</filter-name>
> + 		<url-pattern>*.html</url-pattern>
>  	</filter-mapping>	
>  	<filter-mapping>
>  		<filter-name>hibernateFilter</filter-name>
> @@ -197,8 +251,22 @@
>     	</servlet-class>
>   	</servlet>
>   	
> -	
> +	<!-- ========================================================== -->
> +	<!-- Processed by Jersey -->
> +	<!-- ========================================================== -->
> +  	<servlet>
> +  		<servlet-name>HandshakingServlet</servlet-name>
> +		<servlet-class>
> +  			com.sun.jersey.spi.container.servlet.ServletContainer
> +		</servlet-class>
> +  		<init-param>
> +    		<param-name>com.sun.jersey.config.property.packages</param- 
> name>
> +    		<param-value>org.cipres.treebase.web.webservices</param-value>
> +  		</init-param>
> +  		<load-on-startup>1</load-on-startup>
> +	</servlet>
>
> +
> 	<!-- ========================================================== -->
> 	<!-- url pattern that will be processed by DispatcherServlet    -->
> 	<!-- ========================================================== -->
> @@ -239,6 +307,14 @@
>   	<servlet-mapping>
>     	<servlet-name>CXFServlet</servlet-name>
>     	<url-pattern>/services/*</url-pattern>
> +    </servlet-mapping>
> +
> +    <!-- ==========================================================  
> -->
> +	<!-- url pattern that will be processed by CXFServlet    -->
> +	<!-- ========================================================== -- 
> > 	
> +  	<servlet-mapping>
> +    	<servlet-name>HandshakingServlet</servlet-name>
> +    	<url-pattern>/handshaking/*</url-pattern>
>     </servlet-mapping>
> 	
> 	<!-- ========================================================== -->
>
>
> This was sent by the SourceForge.net collaborative development  
> platform, the world's largest Open Source development site.
>
> ------------------------------------------------------------------------------
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Re: [Treebase-devel] [PhyloWS] interoperability of resources using CDAO -- telecon notes, FYI

From: Rutger V. <rut...@gm...> - 2010-08-18 13:40:39

> We still need someone to work on the problem of reconciling different
> versions of the nexml-to-CDAO translator (XSLT).  Let me know if anyone
> wants to do that.

A functioning nexml-to-CDAO translator is vital for the TreeBASE RDF
output, so I will be involved in this, but perhaps not on my own?
Anyway, one thing that needs to happen is that the RDFa extraction
needs to be folded into the core translator so that the whole thing
becomes a one step process. On TreeBASE, for example, I now fold the
outputs of the two translations into one in java code. I'd hate to see
others having to replicate that, and it's not very performant either.

Rutger

-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

[Treebase-devel] interoperability of resources using CDAO -- telecon notes, FYI

From: Arlin S. <ar...@um...> - 2010-08-17 16:23:25

Notes from the teleconference are here (should be visible to everyone):

    http://groups.google.com/group/feas2ls/web/cdao-3-way-interop-challenge

Synopsis:
* Vivek will identify and (ideally) solve problems to view TreeBase2  
RDFs in Nexplorer3
* Arlin will start developing a set of CDAO instance test files using  
the NEXUS test files in Bio::NEXUS
* we will have another teleconference in early to mid-September

We still need someone to work on the problem of reconciling different  
versions of the nexml-to-CDAO translator (XSLT).  Let me know if  
anyone wants to do that.

Arlin

On Aug 16, 2010, at 5:56 PM, Arlin Stoltzfus wrote:

> As noted last week, a teleconference is scheduled for Tuesday at 11:00
> am EST (GMT -5).  The agenda is to discuss steps to improve
> interoperability among tools that use CDAO (see message below for
> details).
>
> To connect,
> 1. call 1-213-289-0500  (this is a long-distance call to Los Angeles),
> then
> 2. when prompted, enter 375259
>
> After the telecon is over, I will post a summary somewhere accessible.
>
> Arlin
>
> On Aug 13, 2010, at 12:35 PM, Arlin Stoltzfus wrote:
>
>> Dear CDAO developers and users--
>>
>> For the past 2 years, CDAO has been an experimental project done in
>> our spare time.  Last summer, we reached our first big milestones  
>> with
>> an initial ontology version and a publication.     This summer, we  
>> are
>> poised for another milestone where CDAO mediates interoperability
>> between real tools developed for use  by researchers.  TreeBase2
>> (phylo database used by systematists), CDAOstore (experimental
>> triplestore by CDAO developers), and Nexplorer3 (phylogenetic data
>> viewer developed and used at NIAID) are open-source projects that  
>> have
>> made recent efforts to support CDAO encodings for import or export or
>> internal representation.  They were presented at the 2010 "iEvoBio"
>> satellite meeting at Evolution 2010 in Portland this summer.
>>
>> * TreeBase2 claims to deliver CDAO instance files (RDF-XML) in
>> response to phylows URLs
>> * Both CDAOstore  and Nexplorer3 claim to be able to consume CDAO
>> instance files via a URL.
>> * CDAOstore also has a translator, so that a user can upload a NEXUS
>> or phylip file, and translate it into CDAO
>>
>> Thus, in principle, CDAOstore can be used as a query interface to a
>> TreeBase2 data entry by giving it a phyloWS URL like this:
>>
>>  http://purl.org/phylo/treebase/phylows/study/TB2:S1787?format=RDF
>>
>> and loading the result into the triplestore.  Likewise, in principle,
>> Nexplorer3 can be used as an interface to visualize a TreeBase2 data
>> entry via its phyloWS URL.  Or we could translate a NEXUS file (e.g.,
>> from TreeBase2) using CDAO-store's online translator, then view the
>> result in Nexplorer3.  To achieve this kind of interoperability would
>> fulfill the hopes of the NESCent evolutionary informatics working
>> group (2006-2009), from whose members sprang the CDAO, phyloWS and
>> nexml projects.
>>
>> But we aren't there yet.  Having tried all of the pairwise
>> interoperations listed above, I found that none of them actually
>> works.  But I'm not discouraged by that, and neither are the  
>> TreeBase,
>> CDAO-store and Nexplorer3 developers.  Now that we have actual
>> concrete targets for interoperability, we can focus on finding
>> problems and solving them.
>>
>> We have planned an initial teleconference on this issue Tuesday, the
>> 17th at 11:00 am Eastern (GMT -5).  Details will be provided later.
>>
>> Arlin
>> -------
>> Arlin Stoltzfus (ar...@um...)
>> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
>> IBBR, 9600 Gudelsky Drive, Rockville, MD
>> tel: 240 314 6208; web: www.molevol.org
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
>> Enter the BlackBerry Developer Challenge
>> http://p.sf.net/sfu/RIM-dev2dev
>> _______________________________________________
>> CDAO-discuss mailing list
>> CDA...@li...
>> https://lists.sourceforge.net/lists/listinfo/cdao-discuss
>
> -------
> Arlin Stoltzfus (ar...@um...)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
>
> -- 
> You received this message because you are subscribed to the Google  
> Groups "PhyloWS" group.
> To post to this group, send email to ph...@go....
> To unsubscribe from this group, send email to phy...@go... 
> .
> For more options, visit this group at http://groups.google.com/group/phylows?hl=en 
> .
>

-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

Re: [Treebase-devel] [PhyloWS] Re: [CDAO-discuss] interoperability of resources using CDAO -- telecon Tuesday Aug 17

From: Rutger V. <rut...@gm...> - 2010-08-17 03:06:16

I am sorry I won't be able to call in. I'm looking forward to see the
summary, though.

Best wishes,

Rutger

On Tue, Aug 17, 2010 at 5:56 AM, Arlin Stoltzfus <ar...@um...> wrote:
> As noted last week, a teleconference is scheduled for Tuesday at 11:00 am
> EST (GMT -5).  The agenda is to discuss steps to improve interoperability
> among tools that use CDAO (see message below for details).
>
> To connect,
> 1. call 1-213-289-0500  (this is a long-distance call to Los Angeles), then
> 2. when prompted, enter 375259
>
> After the telecon is over, I will post a summary somewhere accessible.
>
> Arlin
>
> On Aug 13, 2010, at 12:35 PM, Arlin Stoltzfus wrote:
>
>> Dear CDAO developers and users--
>>
>> For the past 2 years, CDAO has been an experimental project done in
>> our spare time.  Last summer, we reached our first big milestones with
>> an initial ontology version and a publication.     This summer, we are
>> poised for another milestone where CDAO mediates interoperability
>> between real tools developed for use  by researchers.  TreeBase2
>> (phylo database used by systematists), CDAOstore (experimental
>> triplestore by CDAO developers), and Nexplorer3 (phylogenetic data
>> viewer developed and used at NIAID) are open-source projects that have
>> made recent efforts to support CDAO encodings for import or export or
>> internal representation.  They were presented at the 2010 "iEvoBio"
>> satellite meeting at Evolution 2010 in Portland this summer.
>>
>> * TreeBase2 claims to deliver CDAO instance files (RDF-XML) in
>> response to phylows URLs
>> * Both CDAOstore  and Nexplorer3 claim to be able to consume CDAO
>> instance files via a URL.
>> * CDAOstore also has a translator, so that a user can upload a NEXUS
>> or phylip file, and translate it into CDAO
>>
>> Thus, in principle, CDAOstore can be used as a query interface to a
>> TreeBase2 data entry by giving it a phyloWS URL like this:
>>
>>  http://purl.org/phylo/treebase/phylows/study/TB2:S1787?format=RDF
>>
>> and loading the result into the triplestore.  Likewise, in principle,
>> Nexplorer3 can be used as an interface to visualize a TreeBase2 data
>> entry via its phyloWS URL.  Or we could translate a NEXUS file (e.g.,
>> from TreeBase2) using CDAO-store's online translator, then view the
>> result in Nexplorer3.  To achieve this kind of interoperability would
>> fulfill the hopes of the NESCent evolutionary informatics working
>> group (2006-2009), from whose members sprang the CDAO, phyloWS and
>> nexml projects.
>>
>> But we aren't there yet.  Having tried all of the pairwise
>> interoperations listed above, I found that none of them actually
>> works.  But I'm not discouraged by that, and neither are the TreeBase,
>> CDAO-store and Nexplorer3 developers.  Now that we have actual
>> concrete targets for interoperability, we can focus on finding
>> problems and solving them.
>>
>> We have planned an initial teleconference on this issue Tuesday, the
>> 17th at 11:00 am Eastern (GMT -5).  Details will be provided later.
>>
>> Arlin
>> -------
>> Arlin Stoltzfus (ar...@um...)
>> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
>> IBBR, 9600 Gudelsky Drive, Rockville, MD
>> tel: 240 314 6208; web: www.molevol.org
>>
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
>> Enter the BlackBerry Developer Challenge
>> http://p.sf.net/sfu/RIM-dev2dev
>> _______________________________________________
>> CDAO-discuss mailing list
>> CDA...@li...
>> https://lists.sourceforge.net/lists/listinfo/cdao-discuss
>
> -------
> Arlin Stoltzfus (ar...@um...)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
>
> --
> You received this message because you are subscribed to the Google Groups
> "PhyloWS" group.
> To post to this group, send email to ph...@go....
> To unsubscribe from this group, send email to
> phy...@go....
> For more options, visit this group at
> http://groups.google.com/group/phylows?hl=en.
>
>



-- 
Dr. Rutger A. Vos
School of Biological Sciences
Philip Lyle Building, Level 4
University of Reading
Reading
RG6 6BX
United Kingdom
Tel: +44 (0) 118 378 7535
http://www.nexml.org
http://rutgervos.blogspot.com

Re: [Treebase-devel] [CDAO-discuss] interoperability of resources using CDAO -- telecon Tuesday Aug 17

From: Arlin S. <ar...@um...> - 2010-08-16 21:57:01

As noted last week, a teleconference is scheduled for Tuesday at 11:00  
am EST (GMT -5).  The agenda is to discuss steps to improve  
interoperability among tools that use CDAO (see message below for  
details).

To connect,
1. call 1-213-289-0500  (this is a long-distance call to Los Angeles),  
then
2. when prompted, enter 375259

After the telecon is over, I will post a summary somewhere accessible.

Arlin

On Aug 13, 2010, at 12:35 PM, Arlin Stoltzfus wrote:

> Dear CDAO developers and users--
>
> For the past 2 years, CDAO has been an experimental project done in
> our spare time.  Last summer, we reached our first big milestones with
> an initial ontology version and a publication.     This summer, we are
> poised for another milestone where CDAO mediates interoperability
> between real tools developed for use  by researchers.  TreeBase2
> (phylo database used by systematists), CDAOstore (experimental
> triplestore by CDAO developers), and Nexplorer3 (phylogenetic data
> viewer developed and used at NIAID) are open-source projects that have
> made recent efforts to support CDAO encodings for import or export or
> internal representation.  They were presented at the 2010 "iEvoBio"
> satellite meeting at Evolution 2010 in Portland this summer.
>
> * TreeBase2 claims to deliver CDAO instance files (RDF-XML) in
> response to phylows URLs
> * Both CDAOstore  and Nexplorer3 claim to be able to consume CDAO
> instance files via a URL.
> * CDAOstore also has a translator, so that a user can upload a NEXUS
> or phylip file, and translate it into CDAO
>
> Thus, in principle, CDAOstore can be used as a query interface to a
> TreeBase2 data entry by giving it a phyloWS URL like this:
>
>   http://purl.org/phylo/treebase/phylows/study/TB2:S1787?format=RDF
>
> and loading the result into the triplestore.  Likewise, in principle,
> Nexplorer3 can be used as an interface to visualize a TreeBase2 data
> entry via its phyloWS URL.  Or we could translate a NEXUS file (e.g.,
> from TreeBase2) using CDAO-store's online translator, then view the
> result in Nexplorer3.  To achieve this kind of interoperability would
> fulfill the hopes of the NESCent evolutionary informatics working
> group (2006-2009), from whose members sprang the CDAO, phyloWS and
> nexml projects.
>
> But we aren't there yet.  Having tried all of the pairwise
> interoperations listed above, I found that none of them actually
> works.  But I'm not discouraged by that, and neither are the TreeBase,
> CDAO-store and Nexplorer3 developers.  Now that we have actual
> concrete targets for interoperability, we can focus on finding
> problems and solving them.
>
> We have planned an initial teleconference on this issue Tuesday, the
> 17th at 11:00 am Eastern (GMT -5).  Details will be provided later.
>
> Arlin
> -------
> Arlin Stoltzfus (ar...@um...)
> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
> IBBR, 9600 Gudelsky Drive, Rockville, MD
> tel: 240 314 6208; web: www.molevol.org
>
>
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-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

[Treebase-devel] interoperability of resources using CDAO -- planned telecon Tuesday Aug 17

From: Arlin S. <ar...@um...> - 2010-08-13 16:35:58

Dear CDAO developers and users--

For the past 2 years, CDAO has been an experimental project done in  
our spare time.  Last summer, we reached our first big milestones with  
an initial ontology version and a publication.     This summer, we are  
poised for another milestone where CDAO mediates interoperability  
between real tools developed for use  by researchers.  TreeBase2  
(phylo database used by systematists), CDAOstore (experimental  
triplestore by CDAO developers), and Nexplorer3 (phylogenetic data  
viewer developed and used at NIAID) are open-source projects that have  
made recent efforts to support CDAO encodings for import or export or  
internal representation.  They were presented at the 2010 "iEvoBio"  
satellite meeting at Evolution 2010 in Portland this summer.

* TreeBase2 claims to deliver CDAO instance files (RDF-XML) in  
response to phylows URLs
* Both CDAOstore  and Nexplorer3 claim to be able to consume CDAO  
instance files via a URL.
* CDAOstore also has a translator, so that a user can upload a NEXUS  
or phylip file, and translate it into CDAO

Thus, in principle, CDAOstore can be used as a query interface to a  
TreeBase2 data entry by giving it a phyloWS URL like this:

   http://purl.org/phylo/treebase/phylows/study/TB2:S1787?format=RDF

and loading the result into the triplestore.  Likewise, in principle,  
Nexplorer3 can be used as an interface to visualize a TreeBase2 data  
entry via its phyloWS URL.  Or we could translate a NEXUS file (e.g.,  
from TreeBase2) using CDAO-store's online translator, then view the  
result in Nexplorer3.  To achieve this kind of interoperability would  
fulfill the hopes of the NESCent evolutionary informatics working  
group (2006-2009), from whose members sprang the CDAO, phyloWS and  
nexml projects.

But we aren't there yet.  Having tried all of the pairwise  
interoperations listed above, I found that none of them actually  
works.  But I'm not discouraged by that, and neither are the TreeBase,  
CDAO-store and Nexplorer3 developers.  Now that we have actual  
concrete targets for interoperability, we can focus on finding  
problems and solving them.

We have planned an initial teleconference on this issue Tuesday, the  
17th at 11:00 am Eastern (GMT -5).  Details will be provided later.

Arlin
-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org

Re: [Treebase-devel] Disk space for treebase production database

From: William P. <wil...@ya...> - 2010-08-07 10:10:05

On Aug 6, 2010, at 3:04 PM, William Piel wrote:

> As a test file, I have a large NEXUS (attached) which I uploaded to the treebase.org site, and it took me 7 minutes 51 seconds. 

I just tested this file by uploading to http://treebase-dev.nescent.org/treebase-web/

Time taken: 9 minutes 22 seconds -- compared with 7 minutes 51 seconds. So although one took longer, they both succeeded in uploading. It's certainly possible that some larger files will run into the 15-min timeout faster with dev than normal treebase. 

In terms of searching, the performance is closer: going from an identical selection of taxa to a selection of studies took 27 seconds on treebase and 36 seconds on treebase-dev.

bp

Re: [Treebase-devel] Disk space for treebase production database

From: Jon A. <jon...@ne...> - 2010-08-06 16:27:48

I've changed treebase-dev application to connect to the 123 GB treebaseprod database, which is a restore of the production database some time back.

Please test against treebase-dev.nescent.org

Thanks,
Jon


On Aug 6, 2010, at 3:04 AM, William Piel wrote:

> 
> On Aug 6, 2010, at 8:22 AM, Hilmar Lapp wrote:
> 
>> 
>> On Aug 5, 2010, at 7:18 PM, William Piel wrote:
>> 
>>> This seems okay to me, given our constraints (Hilmar - WDYT?). 
>> 
>> 
>> Sounds OK to me too. It's hard to imagine that there'd be very little to notice at 123 GB size, but an annoying degree of slowdown at 180 GB. We just need to keep in mind that whatever slowdown we see, it's not going to be any less for the real database, but quite possibly more.
>> 
>> 	-hilmar
> 
> As a test file, I have a large NEXUS (attached) which I uploaded to the treebase.org site, and it took me 7 minutes 51 seconds. Course, I'm doing it from China (which has fairly slow internet) but I suspect that the real slowdown is with the insertions. In fact, this file is too big to delete -- once uploaded, trying to delete it causes a error trace (probably because postgres times out) -- evidently, our upload methods are more efficient than our delete methods. With 378 taxa and 15993 characters, we're looking at 6,045,354 insertions for the matrix element table alone. The submitter has uploaded a bunch of these (located in submission 10698 / study 10708), but we can't delete them.  Since we don't have "cascade delete" constraints, and with all the FKs in circular relationships, it's also not easy to issue a SQL command to delete these.  But that's beside the point. We have a benchmark file that takes a significant time to import, so we can use it for testing. 
> 
> bp
> 
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-------------------------------------------------------
Jon Auman
Systems Administrator
National Evolutionary Synthesis Center
Duke University
http:www.nescent.org
jon...@ne...
------------------------------------------------------

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