From jrobertson3 at hmc.psu.edu  Fri Jun 12 09:26:57 2015
From: jrobertson3 at hmc.psu.edu (Robertson, Jim)
Date: Fri, 12 Jun 2015 13:26:57 +0000
Subject: [Eagle-i-admins] Request for Release Documentation
Message-ID: <6ac5de32baa544ec9d2fb11cb8a936bf@EXCHSRVR11.mshmc.local>

All,
  The central site was upgraded to 3.7.1 on 5/11 but the wiki still shows release notes only posted up to 3.4.2.  Can the documentation please be updated to help us with our institution's upgrade planning/communication?

Regards,
Jim Robertson
Systems Analyst - Research Informatics
Phone: (717) 531-0003 x289483
Email:   jrobertson3 at hmc.psu.edu

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From mail at freelock.com  Fri Jun 12 17:13:09 2015
From: mail at freelock.com (John Locke)
Date: Fri, 12 Jun 2015 14:13:09 -0700
Subject: [Eagle-i-admins] Getting Sparqler errors,
	and "LocalNode" exceptions in API
Message-ID: <557B4B65.60009@freelock.com>

Hi,

I've been assisting FredHutch with some updates to their eagle-i node, 
and am hitting two issues:

1. Sparqler. As best I can tell, we did not have Sparqler 
configured/working previously. We updated the eagle-i node to 3.0.4 last 
fall, and now going from there to 3.5.0, and I read all the notes about 
needing to configure Sparqler. I followed all the steps here: 
https://open.med.harvard.edu/wiki/display/eaglei/Public+SPARQL+Endpoint 
... all succeeded except for the final step, #11, which failed with this 
error, followed by the same HTML error page visible at 
https://eagle-i.fhcrc.org/sparqler/query/ .

 > FAILED to create metadata for user, HTTP status=500


2. We're trying to use the API to post content into eagle-i from Drupal, 
but we're getting a similar HTTP 500 error:

> Jun 01, 2015 4:24:56 PM com.sun.jersey.spi.container.ContainerResponse 
> mapMappableContainerException
> SEVERE: The RuntimeException could not be mapped to a response, 
> re-throwing to the HTTP container
> org.springframework.beans.factory.NoSuchBeanDefinitionException: No 
> bean named 'localNode' is defined
> at 
> org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeanDefinition(DefaultListableBeanFactory.java:509)
> at 
> org.springframework.beans.factory.support.AbstractBeanFactory.getMergedLocalBeanDefinition(AbstractBeanFactory.java:1041)
> at 
> org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:273)
> at 
> org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
> at 
> org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1048)
> at 
> org.eaglei.datatools.services.EIExternalResourceService.(EIExternalResourceService.java:90)
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at 
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
> at 
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
<snip> (can provide full stack trace if useful).

We were getting this in 3.0.4 too...

I've also attached the body of a sample HTTP POST we're sending, that's 
generating this error.


What is the 'localNode' in this error? I'm wondering if I overlooked 
some critical configuration step somewhere along the upgrade?

Cheers,
John Locke
http://www.freelock.com

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{
  "instanceEntity": {
    "uri": {
      "value": ""
    },
    "label": "Pilot and Feasibility Program Grants"
  },
  "specificTypeUri": {
    "value": "http://purl.obolibrary.org/obo/ERO_0000005"
  },
  "rootType": {
    "value": "http://purl.obolibrary.org/obo/ERO_0000005"
  },
  "foreignKey": "8734",
  "source": "Fred Hutchinson Cancer Research Center",
  "linkedResources": {
    "http://purl.obolibrary.org/obo/ERO_0000021": [
      {
        "instanceEntity": {
          "uri": {
            "value": "http://eagle-i.fhcrc.org/i/00000140-0735-dc32-7ab9-126580000000"
          },
          "label": "Beverly Torok-Storb"
        },
        "specificTypeUri": {
          "value": "http://xmlns.com/foaf/0.1/Person"
        },
        "rootType": {
          "value": "http://xmlns.com/foaf/0.1/Person"
        },
        "foreignKey": "8733",
        "source": "Fred Hutchinson Cancer Research Center",
        "linkedResources": {},
        "textProperties": {
          "http://purl.obolibrary.org/obo/ERO_0000042": [
            "Beverly"
          ],
          "http://purl.obolibrary.org/obo/ERO_0000049": [
            "Torok-Storb"
          ],
          "http://purl.obolibrary.org/obo/ERO_0000041": [
            "btorokst at fredhutch.org"
          ]
        }
      }
    ],
    "http://purl.obolibrary.org/obo/ERO_0000390": [
      {
        "instanceEntity": {
          "uri": {
            "value": "http://eagle-i.fhcrc.org/i/00000140-6469-8788-7845-9b5680000000"
          },
          "label": "CCEH - Administration"
        },
        "specificTypeUri": {
          "value": "http://vivoweb.org/ontology/core#CoreLaboratory"
        },
        "rootType": {
          "value": "http://xmlns.com/foaf/0.1/Organization"
        },
        "foreignKey": "8732",
        "source": "Fred Hutchinson Cancer Research Center",
        "linkedResources": {},
        "textProperties": {
          "http://purl.obolibrary.org/obo/ERO_0000041": [
            "btorokst at fredhutch.org"
          ],
          "http://eagle-i.org/ont/app/1.0/resource_description": [
            "The CCEH Administrative Core provides scientific and budgetary oversight for all CCEH activities. This includes, in addition to the Pilot and Feasibility Program, an Enrichment Program that supports outside speakers, high school summer internships, and short-term on-sight training opportunities for NIDDK-funded trainees from anywhere in the US."
          ],
          "http://purl.obolibrary.org/obo/ERO_0000480": [
            "http://sharedresources.fhcrc.org/core-facilities/cceh-administration"
          ]
        }
      }
    ]
  },
  "textProperties": {
    "http://eagle-i.org/ont/app/1.0/resource_description": [
      "The Pilot and Feasibility Studies Program, funded by the CCEH grant, supports 5-7 one-year grants of $20,000 each. The focus of the grants is generally, but not exclusively hematology-related research. Applications that propose to use one or more of the CCEH cores are especially welcomed."
    ],
    "http://purl.obolibrary.org/obo/ERO_0000480": [
      "http://sharedresources.fhcrc.org/services/pilot-and-feasibility-program-grants"
    ]
  }
}

From sophia_cheng at hms.harvard.edu  Mon Jun 29 15:14:12 2015
From: sophia_cheng at hms.harvard.edu (Sophia K Cheng)
Date: Mon, 29 Jun 2015 15:14:12 -0400
Subject: [Eagle-i-admins] Documentation for versions 3.5.0 & 3.7.2 now
	available
Message-ID: <55919904.4010007@hms.harvard.edu>

Dear eagle-i sys admins,

The long awaited for documentation for the recent releases is now 
available.  Please note that there is no version 3.6.  There were severe 
performance issues in 3.6. Instead of stretching our release schedule, 
we decided to call 3.6 done and not releasable and move onto 3.7.x.

https://open.med.harvard.edu/wiki/display/eaglei/3.5.0+Release+Notes
https://open.med.harvard.edu/wiki/display/eaglei/3.7.2+Release+Notes+(Current+Release) 
<https://open.med.harvard.edu/wiki/display/eaglei/3.7.2+Release+Notes+%28Current+Release%29>

Notable changes in these versions are:
* solr library upgraded to 4.10.2
* functional fixes for Catalyst & Experimental API
* the url for navigation has changed

Please let us know if you have any questions or problems.  Thank you for 
your patience.

Cheerios,
Sophia
-- 

*Sophia K. Cheng*/
Technical Lead/
Harvard Catalyst | eagle-i
email:  sophia?_cheng at hms.harvard.edu <mailto:_cheng at hms.harvard.edu>
skype: sophia.k.cheng

Harvard Medical School
Harvard Catalyst | The Harvard Clinical and Translational Science Center
Landmark Center, Suite 504 West
401 Park Drive
Boston, MA 02215

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From Michael_Cherry at hms.harvard.edu  Tue Jun 30 12:07:13 2015
From: Michael_Cherry at hms.harvard.edu (Cherry, Michael)
Date: Tue, 30 Jun 2015 12:07:13 -0400
Subject: [Eagle-i-admins] June 30, 2015 leap second adjustment
Message-ID: <2D9A56628D03E943A293017B10EFD25C012EAB36D6F4@ITCCRMAIL01.MED.HARVARD.EDU>

Hi all,

Anyone responsible for an eagle-i installation should be aware that there will be a leap second added to the calendar at midnight tonight.  This can potentially cause issues with both the OS and also with Java.

Information about checking and patching the OS:
  http://www.datastax.com/dev/blog/preparing-for-the-leap-second
  https://access.redhat.com/articles/15145
  (RedHat's testing utility also works on CentOS)

Time-zone updater tool for Java installations:
  http://www.oracle.com/technetwork/java/javase/tzupdater-readme-136440.html
  (look for "Java Time Zone Updater Tool" near the bottom of the page)

Background information about timezone data in Java:
  http://www.oracle.com/technetwork/java/javase/timezones-137583.html

Note that to be completely safe, both the OS and Java need to be able to handle the leap second.  The consequences of not patching can apparently include (but are not limited to) high CPU loads for no apparent reason, and potentially other aberrant behavior.  If your installation is not patched and experiences any odd symptoms after midnight tonight, your best/only recourse may be to stop the application server (Tomcat) and reboot the underlying operating system.

regards,
- Michael Cherry
Sr. Release Operations Engineer
Harrvard Catalyst | Center for Biomedical Informatics
Harvard Medical School





From jlease at hmc.psu.edu  Tue Jun 30 14:57:14 2015
From: jlease at hmc.psu.edu (Lease, Joshua)
Date: Tue, 30 Jun 2015 18:57:14 +0000
Subject: [Eagle-i-admins] Exception when Upgrading to 3.7.2
Message-ID: <0E580A54-59E3-4F6A-AC1D-2826F581D8BD@hmc.psu.edu>

Admins,

I'm attempting to upgrade from 3.4.2 to 3.7.2 and have an issue when starting the web server. The logs are below and you can see the exception. When attempting to access /institution, I get HTTP 404. Is there a step unique to this upgrade that I am missing? Any ideas?

Thanks,
    Joshua Lease

Jun 30, 2015 2:30:19 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent
INFO: The APR based Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Jun 30, 2015 2:30:19 PM org.apache.coyote.AbstractProtocol init
INFO: Initializing ProtocolHandler ["ajp-bio-8009"]
Jun 30, 2015 2:30:19 PM org.apache.catalina.startup.Catalina load
INFO: Initialization processed in 675 ms
Jun 30, 2015 2:30:19 PM org.apache.catalina.core.StandardService startInternal
INFO: Starting service Catalina
Jun 30, 2015 2:30:19 PM org.apache.catalina.core.StandardEngine startInternal
INFO: Starting Servlet Engine: Apache Tomcat/7.0.59
Jun 30, 2015 2:30:19 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /opt/apache-tomcat-7.0.59/webapps/sweet.war
Jun 30, 2015 2:30:20 PM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/opt/tomcat/webapps/sweet/WEB-INF/lib/javax.servlet-3.0.0.v201112011016.jar) - jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending class: javax/servlet/Servlet.class
Jun 30, 2015 2:30:25 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
log4j:WARN No appenders could be found for logger (org.eaglei.sweet.server.LoggingContextListener).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Jun 30, 2015 2:30:25 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
Jun 30, 2015 2:30:37 PM com.sun.jersey.api.core.PackagesResourceConfig init
INFO: Scanning for root resource and provider classes in the packages:
  org.eaglei.datatools.services
Jun 30, 2015 2:30:37 PM com.sun.jersey.api.core.ScanningResourceConfig logClasses
INFO: Root resource classes found:
  class org.eaglei.datatools.services.EIExternalResourceService
Jun 30, 2015 2:30:37 PM com.sun.jersey.api.core.ScanningResourceConfig init
INFO: No provider classes found.
Jun 30, 2015 2:30:37 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO: Initiating Jersey application, version 'Jersey: 1.17.1 02/28/2013 12:47 PM'
Jun 30, 2015 2:30:38 PM com.sun.jersey.api.core.PackagesResourceConfig init
INFO: Scanning for root resource and provider classes in the packages:
  org.eaglei.datatools.about
Jun 30, 2015 2:30:38 PM com.sun.jersey.api.core.ScanningResourceConfig logClasses
INFO: Root resource classes found:
  class org.eaglei.datatools.about.AboutSweetService
Jun 30, 2015 2:30:38 PM com.sun.jersey.api.core.ScanningResourceConfig init
INFO: No provider classes found.
Jun 30, 2015 2:30:38 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO: Initiating Jersey application, version 'Jersey: 1.17.1 02/28/2013 12:47 PM'
Jun 30, 2015 2:30:38 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /opt/apache-tomcat-7.0.59/webapps/sweet.war has finished in 18,502 ms
Jun 30, 2015 2:30:38 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /opt/apache-tomcat-7.0.59/webapps/institution.war
Jun 30, 2015 2:30:38 PM org.apache.catalina.loader.WebappClassLoader validateJarFile
INFO: validateJarFile(/opt/tomcat/webapps/institution/WEB-INF/lib/javax.servlet-3.0.0.v201112011016.jar) - jar not loaded. See Servlet Spec 3.0, section 10.7.2. Offending class: javax/servlet/Servlet.class
Jun 30, 2015 2:30:41 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
[06-30 14:30:42] INFO  LoggingContextListener [researchstg.hersheymed.net-startStop-1]: About to initialize logging...
[06-30 14:30:42] INFO  EILog4jConfigurationManager [researchstg.hersheymed.net-startStop-1]: ServletContext path: /institution
[06-30 14:30:42] INFO  EILog4jConfigurationManager [researchstg.hersheymed.net-startStop-1]: Looking for log4j configuration file: institution.log4j.properties
[06-30 14:30:42] INFO  EILog4jConfigurationManager [researchstg.hersheymed.net-startStop-1]: eaglei home directory = /data/java/eaglei
Jun 30, 2015 2:30:42 PM org.apache.catalina.core.ApplicationContext log
INFO: Initializing Spring root WebApplicationContext
2015-06-30 14:30:45,179 ERROR org.apache.solr.core.CoreContainer:506 - Error creating core [Search-core]: Error opening new searcher
org.apache.solr.common.SolrException: Error opening new searcher
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:881)
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:654)
at org.apache.solr.core.CoreContainer.create(CoreContainer.java:491)
at org.apache.solr.core.CoreContainer$1.call(CoreContainer.java:255)
at org.apache.solr.core.CoreContainer$1.call(CoreContainer.java:249)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724)
Caused by: org.apache.solr.common.SolrException: Error opening new searcher
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1574)
at org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:1686)
at org.apache.solr.core.SolrCore.<init>(SolrCore.java:853)
... 9 more
Caused by: org.apache.lucene.store.LockObtainFailedException: Lock obtain timed out: NativeFSLock@/data/java/eaglei/solrhome/search/Search-core/data/index/write.lock
at org.apache.lucene.store.Lock.obtain(Lock.java:89)
at org.apache.lucene.index.IndexWriter.<init>(IndexWriter.java:753)
at org.apache.solr.update.SolrIndexWriter.<init>(SolrIndexWriter.java:77)
at org.apache.solr.update.SolrIndexWriter.create(SolrIndexWriter.java:64)
at org.apache.solr.update.DefaultSolrCoreState.createMainIndexWriter(DefaultSolrCoreState.java:279)
at org.apache.solr.update.DefaultSolrCoreState.getIndexWriter(DefaultSolrCoreState.java:111)
at org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1537)
... 11 more
2015-06-30 14:30:45,184 ERROR org.springframework.web.context.ContextLoader:331 - Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'institutionSearchConfig': Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde]: Constructor threw exception; nested exception is java.lang.NullPointerException
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1093)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1038)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:762)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:757)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:480)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:403)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5524)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:649)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1081)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1877)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724)
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde]: Constructor threw exception; nested exception is java.lang.NullPointerException
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:89)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1086)
... 27 more
Caused by: java.lang.NullPointerException
at java.util.concurrent.ConcurrentHashMap.put(ConcurrentHashMap.java:1124)
at org.eaglei.solr.EagleISolrConfig.<init>(EagleISolrConfig.java:155)
at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.<init>(AbstractSearchAppConfig.java:74)
at org.eaglei.institution.server.InstitutionSearchConfig.<init>(InstitutionSearchConfig.java:46)
at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.<init>(<generated>)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
... 29 more
Jun 30, 2015 2:30:45 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.springframework.web.context.ContextLoaderListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'institutionSearchConfig': Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde]: Constructor threw exception; nested exception is java.lang.NullPointerException
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1093)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1038)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:762)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:757)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:480)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:403)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5524)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:649)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1081)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1877)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724)
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde]: Constructor threw exception; nested exception is java.lang.NullPointerException
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:89)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1086)
... 27 more
Caused by: java.lang.NullPointerException
at java.util.concurrent.ConcurrentHashMap.put(ConcurrentHashMap.java:1124)
at org.eaglei.solr.EagleISolrConfig.<init>(EagleISolrConfig.java:155)
at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.<init>(AbstractSearchAppConfig.java:74)
at org.eaglei.institution.server.InstitutionSearchConfig.<init>(InstitutionSearchConfig.java:46)
at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.<init>(<generated>)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
... 29 more

Jun 30, 2015 2:30:45 PM org.apache.catalina.core.StandardContext listenerStart
SEVERE: Exception sending context initialized event to listener instance of class org.eaglei.institution.server.InstitutionContextListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'institutionSearchConfig': Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde]: Constructor threw exception; nested exception is java.lang.NullPointerException
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1093)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1038)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:762)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:757)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:480)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:403)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5524)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:649)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1081)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1877)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724)
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde]: Constructor threw exception; nested exception is java.lang.NullPointerException
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:89)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1086)
... 27 more
Caused by: java.lang.NullPointerException
at java.util.concurrent.ConcurrentHashMap.put(ConcurrentHashMap.java:1124)
at org.eaglei.solr.EagleISolrConfig.<init>(EagleISolrConfig.java:155)
at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.<init>(AbstractSearchAppConfig.java:74)
at org.eaglei.institution.server.InstitutionSearchConfig.<init>(InstitutionSearchConfig.java:46)
at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.<init>(<generated>)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
... 29 more

Jun 30, 2015 2:30:45 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Error listenerStart
Jun 30, 2015 2:30:45 PM org.apache.catalina.core.StandardContext startInternal
SEVERE: Context [/institution] startup failed due to previous errors
Jun 30, 2015 2:30:45 PM org.apache.catalina.core.StandardContext listenerStop
SEVERE: Exception sending context destroyed event to listener instance of class org.eaglei.institution.server.InstitutionContextListener
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'institutionSearchConfig': Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde]: Constructor threw exception; nested exception is java.lang.NullPointerException
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1093)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1038)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:504)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:476)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:298)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:193)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:762)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:757)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:480)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:403)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:306)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:106)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5016)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5524)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:649)
at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1081)
at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1877)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724)
Caused by: org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde]: Constructor threw exception; nested exception is java.lang.NullPointerException
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:163)
at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:89)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateBean(AbstractAutowireCapableBeanFactory.java:1086)
... 27 more
Caused by: java.lang.NullPointerException
at java.util.concurrent.ConcurrentHashMap.put(ConcurrentHashMap.java:1124)
at org.eaglei.solr.EagleISolrConfig.<init>(EagleISolrConfig.java:155)
at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.<init>(AbstractSearchAppConfig.java:74)
at org.eaglei.institution.server.InstitutionSearchConfig.<init>(InstitutionSearchConfig.java:46)
at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.<init>(<generated>)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:526)
at org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:147)
... 29 more

Jun 30, 2015 2:30:45 PM org.apache.catalina.core.ApplicationContext log
INFO: Closing Spring root WebApplicationContext
Jun 30, 2015 2:30:45 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/institution] appears to have started a thread named [searcherExecutor-6-thread-1] but has failed to stop it. This is very likely to create a memory leak.
Jun 30, 2015 2:30:45 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/institution] appears to have started a thread named [Thread-4] but has failed to stop it. This is very likely to create a memory leak.
Jun 30, 2015 2:30:45 PM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads
SEVERE: The web application [/institution] appears to have started a thread named [Thread-5] but has failed to stop it. This is very likely to create a memory leak.
Jun 30, 2015 2:30:45 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /opt/apache-tomcat-7.0.59/webapps/institution.war has finished in 6,837 ms
Jun 30, 2015 2:30:45 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deploying web application archive /opt/apache-tomcat-7.0.59/webapps/ROOT.war
Jun 30, 2015 2:30:45 PM org.apache.catalina.startup.SetContextPropertiesRule begin
WARNING: [SetContextPropertiesRule]{Context} Setting property 'debug' to '0' did not find a matching property.
Jun 30, 2015 2:30:45 PM org.apache.tomcat.util.digester.SetPropertiesRule begin
WARNING: [SetPropertiesRule]{Context/Realm} Setting property 'debug' to '99' did not find a matching property.
log4j:WARN No appenders could be found for logger (org.apache.solr.update.SolrIndexWriter).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Jun 30, 2015 2:30:48 PM org.apache.catalina.core.ApplicationContext log
INFO: No Spring WebApplicationInitializer types detected on classpath
log4j:WARN No appenders could be found for logger (org.eaglei.repository.Lifecycle).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
***INFO*** (at Tue Jun 30 14:30:48 EDT 2015) eagle-i Configuration: /data/java/eaglei/repo, realmDatasource = jdbc/eaglei
***INFO*** (at Tue Jun 30 14:30:48 EDT 2015) eagle-i Configuration: Set up default log4j config: logfile directory: /data/java/eaglei/repo/logs
***INFO*** (at Tue Jun 30 14:30:48 EDT 2015) eagle-i Configuration: Got 0 initial log4j properties from repo configuration.
***INFO*** (at Tue Jun 30 14:30:48 EDT 2015) eagle-i Configuration: Configuring log4j with properties: {log4j.appender.repository.ImmediateFlush=false, log4j.appender.repository.BufferedIO=true, log4j.appender.repository.Append=true, log4j.appender.repository.layout=org.apache.log4j.PatternLayout, log4j.logger.org.eaglei.repository=INFO, repository, log4j.appender.repository.File=/data/java/eaglei/repo/logs/repository.log, log4j.appender.repository=org.apache.log4j.DailyRollingFileAppender, log4j.appender.repository.layout.ConversionPattern=%d{ISO8601} T=%t %p %c - %m%n, log4j.additivity.org.eaglei.repository=false, log4j.logger.org.openrdf=WARN, repository, log4j.appender.repository.Encoding=UTF-8, log4j.appender.repository.DatePattern='.'yyyy-MM-dd}
***INFO*** (at Tue Jun 30 14:30:48 EDT 2015) eagle-i Configuration: Activating log4j appender "repository" for logger org.eaglei.repository
Jun 30, 2015 2:30:48 PM com.sun.jersey.api.core.PackagesResourceConfig init
INFO: Scanning for root resource and provider classes in the packages:
  org.eaglei.repository.about
Jun 30, 2015 2:30:48 PM com.sun.jersey.api.core.ScanningResourceConfig logClasses
INFO: Root resource classes found:
  class org.eaglei.repository.about.AboutRepositoryService
Jun 30, 2015 2:30:48 PM com.sun.jersey.api.core.ScanningResourceConfig init
INFO: No provider classes found.
Jun 30, 2015 2:30:48 PM com.sun.jersey.server.impl.application.WebApplicationImpl _initiate
INFO: Initiating Jersey application, version 'Jersey: 1.17.1 02/28/2013 12:47 PM'
Jun 30, 2015 2:30:49 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /opt/apache-tomcat-7.0.59/webapps/ROOT.war has finished in 4,417 ms
Jun 30, 2015 2:30:49 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /opt/apache-tomcat-7.0.59/webapps/${catalina.base}
Jun 30, 2015 2:30:49 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /opt/apache-tomcat-7.0.59/webapps/${catalina.base} has finished in 178 ms
Jun 30, 2015 2:30:49 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /opt/apache-tomcat-7.0.59/webapps/static
Jun 30, 2015 2:30:49 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /opt/apache-tomcat-7.0.59/webapps/static has finished in 152 ms
Jun 30, 2015 2:30:49 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Jun 30, 2015 2:30:49 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 30153 ms

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