From Sukdith.Punjasthitkul at dartmouth.edu Wed Jul 8 11:16:16 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Wed, 8 Jul 2015 15:16:16 +0000 Subject: [Eagle-i-admins] Can't install Institution when updating to 3.7.2 In-Reply-To: <55919904.4010007@hms.harvard.edu> References: <55919904.4010007@hms.harvard.edu> Message-ID: eagle-i sys admins, I've updated our eagle-i node to 3.7.2. Repository and SWEET applications are working, but I'm running into issues with the Institution app: > HTTP Status 404 - > > type Status report > > message > > description The requested resource () is not available. I looked at the catalina logs and I saw this: > Jul 08, 2015 10:04:42 AM org.apache.catalina.loader.WebappClassLoader validateJarFile > INFO: validateJarFile(/data/eagle-i/apache-tomcat-6.0.33/webapps/institution/WEB-INF/lib/javax.servlet-3.0.0.v201112011016.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class > Jul 08, 2015 10:05:06 AM org.apache.catalina.core.StandardContext start > SEVERE: Error listenerStart > Jul 08, 2015 10:05:06 AM org.apache.catalina.core.StandardContext start > SEVERE: Context [/institution] startup failed due to previous errors > Jul 08, 2015 10:05:06 AM 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. > Jul 08, 2015 10:05:06 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads > SEVERE: The web application [/institution] appears to have started a thread named [Thread-10] but has failed to stop it. This is very likely to create a memory leak. > Jul 08, 2015 10:05:06 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads > SEVERE: The web application [/institution] appears to have started a thread named [Thread-11] but has failed to stop it. This is very likely to create a memory leak. > Has anyone else run into issues installing Institution app when updating to 3.7.x? I'm going to try and reinstall Institution app again. --sukie-- > On Jun 29, 2015, at 3:14 PM, Sophia K Cheng wrote: > > 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) > > 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 > 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 > > _______________________________________________ > Eagle-i-admins mailing list > Eagle-i-admins at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins From jlease at hmc.psu.edu Wed Jul 8 12:08:04 2015 From: jlease at hmc.psu.edu (Lease, Joshua) Date: Wed, 8 Jul 2015 16:08:04 +0000 Subject: [Eagle-i-admins] Eagle-i-admins Digest, Vol 22, Issue 1 In-Reply-To: References: Message-ID: <316AE04E-6A1F-4922-82DF-2C8FF5A93B46@hmc.psu.edu> I also ran into an issue during the update. However, my log includes exceptions before SEVERE: Error listenerStart. I'm not sure if the issues are related. You can see my log file in an earlier post to the admin group, but I still have not found a solution. On 7/8/15, 12:00 PM, "eagle-i-admins-bounces at open.med.harvard.edu on behalf of eagle-i-admins-request at open.med.harvard.edu" wrote: >Send Eagle-i-admins mailing list submissions to > eagle-i-admins at open.med.harvard.edu > >To subscribe or unsubscribe via the World Wide Web, visit > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins >or, via email, send a message with subject or body 'help' to > eagle-i-admins-request at open.med.harvard.edu > >You can reach the person managing the list at > eagle-i-admins-owner at open.med.harvard.edu > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Eagle-i-admins digest..." > > >Today's Topics: > > 1. Can't install Institution when updating to 3.7.2 > (Sukdith Punjasthitkul) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Wed, 8 Jul 2015 15:16:16 +0000 >From: Sukdith Punjasthitkul >To: eagle-i-admins >Subject: [Eagle-i-admins] Can't install Institution when updating to > 3.7.2 >Message-ID: >Content-Type: text/plain; charset="iso-8859-1" > >eagle-i sys admins, > >I've updated our eagle-i node to 3.7.2. Repository and SWEET applications are working, but I'm running into issues with the Institution app: > >> HTTP Status 404 - >> >> type Status report >> >> message >> >> description The requested resource () is not available. > > >I looked at the catalina logs and I saw this: > >> Jul 08, 2015 10:04:42 AM org.apache.catalina.loader.WebappClassLoader validateJarFile >> INFO: validateJarFile(/data/eagle-i/apache-tomcat-6.0.33/webapps/institution/WEB-INF/lib/javax.servlet-3.0.0.v201112011016.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class >> Jul 08, 2015 10:05:06 AM org.apache.catalina.core.StandardContext start >> SEVERE: Error listenerStart >> Jul 08, 2015 10:05:06 AM org.apache.catalina.core.StandardContext start >> SEVERE: Context [/institution] startup failed due to previous errors >> Jul 08, 2015 10:05:06 AM 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. >> Jul 08, 2015 10:05:06 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads >> SEVERE: The web application [/institution] appears to have started a thread named [Thread-10] but has failed to stop it. This is very likely to create a memory leak. >> Jul 08, 2015 10:05:06 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads >> SEVERE: The web application [/institution] appears to have started a thread named [Thread-11] but has failed to stop it. This is very likely to create a memory leak. >> > > >Has anyone else run into issues installing Institution app when updating to 3.7.x? I'm going to try and reinstall Institution app again. > >--sukie-- > > > > > > > >> On Jun 29, 2015, at 3:14 PM, Sophia K Cheng wrote: >> >> 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) >> >> 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 >> 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 >> >> _______________________________________________ >> Eagle-i-admins mailing list >> Eagle-i-admins at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins > > > >------------------------------ > >_______________________________________________ >Eagle-i-admins mailing list >Eagle-i-admins at open.med.harvard.edu >https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins > > >End of Eagle-i-admins Digest, Vol 22, Issue 1 >********************************************* From Sukdith.Punjasthitkul at dartmouth.edu Wed Jul 8 13:54:08 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Wed, 8 Jul 2015 17:54:08 +0000 Subject: [Eagle-i-admins] Eagle-i-admins Digest, Vol 22, Issue 1 In-Reply-To: <316AE04E-6A1F-4922-82DF-2C8FF5A93B46@hmc.psu.edu> References: <316AE04E-6A1F-4922-82DF-2C8FF5A93B46@hmc.psu.edu> Message-ID: Reinstalling Institution application did not fix the issue; I'm getting the same error messages, which seems like a memory leak issue. We use the Institution application, so unless I can figure out a solution within the next day or so, we're going to rollback our server to 3.4.2. --sukie-- > On Jul 8, 2015, at 12:08 PM, Lease, Joshua wrote: > > I also ran into an issue during the update. However, my log includes exceptions before SEVERE: Error listenerStart. I'm not sure if the issues are related. You can see my log file in an earlier post to the admin group, but I still have not found a solution. > > > On 7/8/15, 12:00 PM, "eagle-i-admins-bounces at open.med.harvard.edu on behalf of eagle-i-admins-request at open.med.harvard.edu" wrote: > >> Send Eagle-i-admins mailing list submissions to >> eagle-i-admins at open.med.harvard.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins >> or, via email, send a message with subject or body 'help' to >> eagle-i-admins-request at open.med.harvard.edu >> >> You can reach the person managing the list at >> eagle-i-admins-owner at open.med.harvard.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Eagle-i-admins digest..." >> >> >> Today's Topics: >> >> 1. Can't install Institution when updating to 3.7.2 >> (Sukdith Punjasthitkul) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Wed, 8 Jul 2015 15:16:16 +0000 >> From: Sukdith Punjasthitkul >> To: eagle-i-admins >> Subject: [Eagle-i-admins] Can't install Institution when updating to >> 3.7.2 >> Message-ID: >> Content-Type: text/plain; charset="iso-8859-1" >> >> eagle-i sys admins, >> >> I've updated our eagle-i node to 3.7.2. Repository and SWEET applications are working, but I'm running into issues with the Institution app: >> >>> HTTP Status 404 - >>> >>> type Status report >>> >>> message >>> >>> description The requested resource () is not available. >> >> >> I looked at the catalina logs and I saw this: >> >>> Jul 08, 2015 10:04:42 AM org.apache.catalina.loader.WebappClassLoader validateJarFile >>> INFO: validateJarFile(/data/eagle-i/apache-tomcat-6.0.33/webapps/institution/WEB-INF/lib/javax.servlet-3.0.0.v201112011016.jar) - jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class: javax/servlet/Servlet.class >>> Jul 08, 2015 10:05:06 AM org.apache.catalina.core.StandardContext start >>> SEVERE: Error listenerStart >>> Jul 08, 2015 10:05:06 AM org.apache.catalina.core.StandardContext start >>> SEVERE: Context [/institution] startup failed due to previous errors >>> Jul 08, 2015 10:05:06 AM 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. >>> Jul 08, 2015 10:05:06 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads >>> SEVERE: The web application [/institution] appears to have started a thread named [Thread-10] but has failed to stop it. This is very likely to create a memory leak. >>> Jul 08, 2015 10:05:06 AM org.apache.catalina.loader.WebappClassLoader clearReferencesThreads >>> SEVERE: The web application [/institution] appears to have started a thread named [Thread-11] but has failed to stop it. This is very likely to create a memory leak. >>> >> >> >> Has anyone else run into issues installing Institution app when updating to 3.7.x? I'm going to try and reinstall Institution app again. >> >> --sukie-- >> >> >> >> >> >> >> >>> On Jun 29, 2015, at 3:14 PM, Sophia K Cheng wrote: >>> >>> 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) >>> >>> 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 >>> 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 >>> >>> _______________________________________________ >>> Eagle-i-admins mailing list >>> Eagle-i-admins at open.med.harvard.edu >>> https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins >> >> >> >> ------------------------------ >> >> _______________________________________________ >> Eagle-i-admins mailing list >> Eagle-i-admins at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins >> >> >> End of Eagle-i-admins Digest, Vol 22, Issue 1 >> ********************************************* > _______________________________________________ > Eagle-i-admins mailing list > Eagle-i-admins at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins From sophia_cheng at hms.harvard.edu Thu Jul 9 12:56:47 2015 From: sophia_cheng at hms.harvard.edu (Sophia K Cheng) Date: Thu, 9 Jul 2015 12:56:47 -0400 Subject: [Eagle-i-admins] Eagle-i-admins Digest, Vol 22, Issue 1 In-Reply-To: References: <316AE04E-6A1F-4922-82DF-2C8FF5A93B46@hmc.psu.edu> Message-ID: <559EA7CF.70608@hms.harvard.edu> Hi Sukie, What does it say in your institution.log? What kind of issues are you running into specifically? If there is nothing informative in your institution.log, could you turn the log settings to debug? You can do this in the institution.log4j.properties file: log4j.logger.org.eaglei=DEBUG, CA, R Thanks, Sophia > Sukdith Punjasthitkul > July 8, 2015 at 1:54 PM > Reinstalling Institution application did not fix the issue; I'm > getting the same error messages, which seems like a memory leak issue. > We use the Institution application, so unless I can figure out a > solution within the next day or so, we're going to rollback our server > to 3.4.2. > > --sukie-- > > > > > > > _______________________________________________ > Eagle-i-admins mailing list > Eagle-i-admins at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins > Lease, Joshua > July 8, 2015 at 12:08 PM > I also ran into an issue during the update. However, my log includes > exceptions before SEVERE: Error listenerStart. I'm not sure if the > issues are related. You can see my log file in an earlier post to the > admin group, but I still have not found a solution. > > > _______________________________________________ > Eagle-i-admins mailing list > Eagle-i-admins at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From sophia_cheng at hms.harvard.edu Thu Jul 9 13:04:28 2015 From: sophia_cheng at hms.harvard.edu (Sophia K Cheng) Date: Thu, 9 Jul 2015 13:04:28 -0400 Subject: [Eagle-i-admins] Exception when Upgrading to 3.7.2 In-Reply-To: <0E580A54-59E3-4F6A-AC1D-2826F581D8BD@hmc.psu.edu> References: <0E580A54-59E3-4F6A-AC1D-2826F581D8BD@hmc.psu.edu> Message-ID: <559EA99C.2010809@hms.harvard.edu> Hi Joshua, Could you try the following: - stop tomcat & verify that it really has stopped +==> I've encountered similar errors because tomcat failed to shut down cleanly and I actually had two instances of tomcat running - drop the exploded institution war +==> I've also encountered different issues with my tomcat not updating the exploded war properly when changing war versions - drop the search folder again (per Dave's email) - check your eagle-i-apps.properties file and make sure there are no properties with that are named solr - start tomcat - cross fingers Thanks, Sophia > Lease, Joshua > June 30, 2015 at 2:57 PM > 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.(SolrCore.java:881) > at org.apache.solr.core.SolrCore.(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.(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.(IndexWriter.java:753) > at org.apache.solr.update.SolrIndexWriter.(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.(EagleISolrConfig.java:155) > at > org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) > at > org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) > at > org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() > 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.(EagleISolrConfig.java:155) > at > org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) > at > org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) > at > org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() > 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.(EagleISolrConfig.java:155) > at > org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) > at > org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) > at > org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() > 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.(EagleISolrConfig.java:155) > at > org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) > at > org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) > at > org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() > 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 > -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From sophia_cheng at hms.harvard.edu Thu Jul 9 13:56:27 2015 From: sophia_cheng at hms.harvard.edu (Sophia K Cheng) Date: Thu, 9 Jul 2015 13:56:27 -0400 Subject: [Eagle-i-admins] Exception when Upgrading to 3.7.2 In-Reply-To: References: <0E580A54-59E3-4F6A-AC1D-2826F581D8BD@hmc.psu.edu> <559EA99C.2010809@hms.harvard.edu> Message-ID: <559EB5CB.5010802@hms.harvard.edu> Hi Joshua, It seems like your application is unable to read the schema.xml file that is located ~tomcat/eaglei/solrhome/search/Search-core/conf/ One thing that might be happening is permissions. If the user you are running tomcat as doesn't have permission to read/write to solrhome, this might happen. Can you check your folder & user permissions? In my set up, I have solrhome & all subfolders set to tomcat:tomcat and I start tomcat as tomcat. Thanks, Sophia > Lease, Joshua > July 9, 2015 at 1:47 PM > Sophia, > > Tomcat does not cleanly shutdown when this issue occurs; so, I've been > stopping it manually. I deleted the exploded institution war and the > contents of the search directory, but encountered the same issue. My > eagle-i-apps.properties has all options that contain the keyword solr > commented out. Do you have any other ideas? > > I have attached my institution log at the trace level. > > Thanks, > Joshua Lease > > From: Sophia K Cheng > Date: Thursday, July 9, 2015 at 1:04 PM > To: Joshua M Lease > Cc: "eagle-i-admins at open.med.harvard.edu > " > Subject: Re: [Eagle-i-admins] Exception when Upgrading to 3.7.2 > > Hi Joshua, > > Could you try the following: > > - stop tomcat & verify that it really has stopped > +==> I've encountered similar errors because tomcat failed to shut > down cleanly and I actually had two instances of tomcat running > - drop the exploded institution war > +==> I've also encountered different issues with my tomcat not > updating the exploded war properly when changing war versions > - drop the search folder again (per Dave's email) > - check your eagle-i-apps.properties file and make sure there are no > properties with that are named solr > - start tomcat > - cross fingers > > > Thanks, > Sophia > > > > > Sophia K Cheng > July 9, 2015 at 1:04 PM > Hi Joshua, > > Could you try the following: > > - stop tomcat & verify that it really has stopped > +==> I've encountered similar errors because tomcat failed to shut > down cleanly and I actually had two instances of tomcat running > - drop the exploded institution war > +==> I've also encountered different issues with my tomcat not > updating the exploded war properly when changing war versions > - drop the search folder again (per Dave's email) > - check your eagle-i-apps.properties file and make sure there are no > properties with that are named solr > - start tomcat > - cross fingers > > > Thanks, > Sophia > > > > > Lease, Joshua > June 30, 2015 at 2:57 PM > 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.(SolrCore.java:881) > at org.apache.solr.core.SolrCore.(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.(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.(IndexWriter.java:753) > at org.apache.solr.update.SolrIndexWriter.(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.(EagleISolrConfig.java:155) > at > org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) > at > org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) > at > org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() > 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.(EagleISolrConfig.java:155) > at > org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) > at > org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) > at > org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() > 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.(EagleISolrConfig.java:155) > at > org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) > at > org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) > at > org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() > 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.(EagleISolrConfig.java:155) > at > org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) > at > org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) > at > org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() > 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 > -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From jlease at hmc.psu.edu Thu Jul 9 13:47:47 2015 From: jlease at hmc.psu.edu (Lease, Joshua) Date: Thu, 9 Jul 2015 17:47:47 +0000 Subject: [Eagle-i-admins] Exception when Upgrading to 3.7.2 In-Reply-To: <559EA99C.2010809@hms.harvard.edu> References: <0E580A54-59E3-4F6A-AC1D-2826F581D8BD@hmc.psu.edu> <559EA99C.2010809@hms.harvard.edu> Message-ID: Sophia, Tomcat does not cleanly shutdown when this issue occurs; so, I've been stopping it manually. I deleted the exploded institution war and the contents of the search directory, but encountered the same issue. My eagle-i-apps.properties has all options that contain the keyword solr commented out. Do you have any other ideas? I have attached my institution log at the trace level. Thanks, Joshua Lease From: Sophia K Cheng Date: Thursday, July 9, 2015 at 1:04 PM To: Joshua M Lease Cc: "eagle-i-admins at open.med.harvard.edu" Subject: Re: [Eagle-i-admins] Exception when Upgrading to 3.7.2 Hi Joshua, Could you try the following: - stop tomcat & verify that it really has stopped +==> I've encountered similar errors because tomcat failed to shut down cleanly and I actually had two instances of tomcat running - drop the exploded institution war +==> I've also encountered different issues with my tomcat not updating the exploded war properly when changing war versions - drop the search folder again (per Dave's email) - check your eagle-i-apps.properties file and make sure there are no properties with that are named solr - start tomcat - cross fingers Thanks, Sophia Lease, Joshua June 30, 2015 at 2:57 PM 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.(SolrCore.java:881) at org.apache.solr.core.SolrCore.(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.(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.(IndexWriter.java:753) at org.apache.solr.update.SolrIndexWriter.(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.(EagleISolrConfig.java:155) at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) at org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() 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.(EagleISolrConfig.java:155) at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) at org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() 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.(EagleISolrConfig.java:155) at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) at org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() 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.(EagleISolrConfig.java:155) at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) at org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() 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 -- -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: institution.log Type: application/octet-stream Size: 209996 bytes Desc: institution.log URL: From jlease at hmc.psu.edu Thu Jul 9 15:42:33 2015 From: jlease at hmc.psu.edu (Lease, Joshua) Date: Thu, 9 Jul 2015 19:42:33 +0000 Subject: [Eagle-i-admins] Exception when Upgrading to 3.7.2 In-Reply-To: <559EB5CB.5010802@hms.harvard.edu> References: <0E580A54-59E3-4F6A-AC1D-2826F581D8BD@hmc.psu.edu> <559EA99C.2010809@hms.harvard.edu> <559EB5CB.5010802@hms.harvard.edu> Message-ID: <8345A806-5A93-4DF7-B897-EF1F77A717C3@hmc.psu.edu> Sophia, Here's the permissions on the file: -rw-r--r--. 1 tomcat tomcat 15912 Jul 9 15:19 schema.xml The entire solrhome directory tree is owned by tomcat with read and write permissions. I tried starting tomcat as root to help rule out permissions issues and got the same error. Your email suggested that the eagle-i home should be stored in ~tomcat/eaglei, but our eagle-i home is at /data/java/eaglei as evidenced in the institution.log. Is this just a difference between your eagle-i home location and ours, or is it hardcoded to the tomcat home? 2015-07-09 13:21:29,669 TRACE org.eaglei.solr.EagleISolrConfig:180 - verify setup with eagleiHome = /data/java/eaglei and solrhome = /data/java/eaglei/solrhome Thanks, Joshua Lease From: Sophia K Cheng Date: Thursday, July 9, 2015 at 1:56 PM To: Joshua M Lease Cc: "eagle-i-admins at open.med.harvard.edu" Subject: Re: [Eagle-i-admins] Exception when Upgrading to 3.7.2 Hi Joshua, It seems like your application is unable to read the schema.xml file that is located ~tomcat/eaglei/solrhome/search/Search-core/conf/ One thing that might be happening is permissions. If the user you are running tomcat as doesn't have permission to read/write to solrhome, this might happen. Can you check your folder & user permissions? In my set up, I have solrhome & all subfolders set to tomcat:tomcat and I start tomcat as tomcat. Thanks, Sophia Lease, Joshua July 9, 2015 at 1:47 PM Sophia, Tomcat does not cleanly shutdown when this issue occurs; so, I've been stopping it manually. I deleted the exploded institution war and the contents of the search directory, but encountered the same issue. My eagle-i-apps.properties has all options that contain the keyword solr commented out. Do you have any other ideas? I have attached my institution log at the trace level. Thanks, Joshua Lease From: Sophia K Cheng Date: Thursday, July 9, 2015 at 1:04 PM To: Joshua M Lease Cc: "eagle-i-admins at open.med.harvard.edu" Subject: Re: [Eagle-i-admins] Exception when Upgrading to 3.7.2 Hi Joshua, Could you try the following: - stop tomcat & verify that it really has stopped +==> I've encountered similar errors because tomcat failed to shut down cleanly and I actually had two instances of tomcat running - drop the exploded institution war +==> I've also encountered different issues with my tomcat not updating the exploded war properly when changing war versions - drop the search folder again (per Dave's email) - check your eagle-i-apps.properties file and make sure there are no properties with that are named solr - start tomcat - cross fingers Thanks, Sophia Sophia K Cheng July 9, 2015 at 1:04 PM Hi Joshua, Could you try the following: - stop tomcat & verify that it really has stopped +==> I've encountered similar errors because tomcat failed to shut down cleanly and I actually had two instances of tomcat running - drop the exploded institution war +==> I've also encountered different issues with my tomcat not updating the exploded war properly when changing war versions - drop the search folder again (per Dave's email) - check your eagle-i-apps.properties file and make sure there are no properties with that are named solr - start tomcat - cross fingers Thanks, Sophia Lease, Joshua June 30, 2015 at 2:57 PM 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.(SolrCore.java:881) at org.apache.solr.core.SolrCore.(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.(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.(IndexWriter.java:753) at org.apache.solr.update.SolrIndexWriter.(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.(EagleISolrConfig.java:155) at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) at org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() 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.(EagleISolrConfig.java:155) at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) at org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() 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.(EagleISolrConfig.java:155) at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) at org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() 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.(EagleISolrConfig.java:155) at org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig.(AbstractSearchAppConfig.java:74) at org.eaglei.institution.server.InstitutionSearchConfig.(InstitutionSearchConfig.java:46) at org.eaglei.institution.server.InstitutionSearchConfig$$EnhancerBySpringCGLIB$$f7420dde.() 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 -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From fcoldren at mail.med.upenn.edu Mon Jul 13 10:07:42 2015 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Mon, 13 Jul 2015 10:07:42 -0400 Subject: [Eagle-i-admins] upgrad from 3.2.0 to 3.7.2 Message-ID: Hi, Can eagle-i be upgraded from 3.2.0 to 3.7.2 directly? Thanks, Faith -------------- next part -------------- An HTML attachment was scrubbed... URL: From sophia_cheng at hms.harvard.edu Mon Jul 13 12:07:22 2015 From: sophia_cheng at hms.harvard.edu (Sophia K Cheng) Date: Mon, 13 Jul 2015 12:07:22 -0400 Subject: [Eagle-i-admins] upgrad from 3.2.0 to 3.7.2 In-Reply-To: References: Message-ID: <55A3E23A.4020509@hms.harvard.edu> Hi Faith, Yes, that is fine. There is no data migration required between 3.2.0 and 3.7.2. FYI - we just released 4.0.0. I will be sending out release notes shortly (today). Thanks, Sophia > Faith Coldren > July 13, 2015 at 10:07 AM > Hi, > > Can eagle-i be upgraded from 3.2.0 to 3.7.2 directly? > > Thanks, > Faith -- -------------- next part -------------- An HTML attachment was scrubbed... URL: From sophia_cheng at hms.harvard.edu Mon Jul 13 16:12:29 2015 From: sophia_cheng at hms.harvard.edu (Sophia K Cheng) Date: Mon, 13 Jul 2015 16:12:29 -0400 Subject: [Eagle-i-admins] Version 4.0.0 now available Message-ID: <55A41BAD.1050803@hms.harvard.edu> Dear eagle-i sys admins, We are pleased to announce the release of version 4.0.0 of the eagle-i software. Release notes are available https://open.med.harvard.edu/wiki/display/eaglei/4.0.0+Release+Notes+(Current+Release). Notable changes in this version are: * Significant ontology update * Repository now uses encrypted passwords Please note that because of the change to use encrypted passwords, upgraded repository user databases will not be compatible with pre 4.0.0 versions. Also, there are significant ontology changes around the disease ontology. We have documented expected compatibility issues if upgrades are not done. We strongly recommend institutions to upgrade. Please let us know if you have any questions. Thanks, Sophia -- *Sophia K. Cheng*/ Technical Lead/ Harvard Catalyst | eagle-i email: sophia?_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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sukdith.Punjasthitkul at dartmouth.edu Wed Jul 15 13:28:40 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Wed, 15 Jul 2015 17:28:40 +0000 Subject: [Eagle-i-admins] Eagle-i-admins Digest, Vol 22, Issue 1 In-Reply-To: <559EA7CF.70608@hms.harvard.edu> References: <316AE04E-6A1F-4922-82DF-2C8FF5A93B46@hmc.psu.edu> <559EA7CF.70608@hms.harvard.edu> Message-ID: <72D30E0D-AB29-4BD8-9520-D402F0C96206@dartmouth.edu> Hi Sophia, I've updated our institution.log4j.properties file to run in debug mode and this is the output from institution.log: 2015-07-15 13:10:22,776 INFO org.eaglei.utilities.servlet.EILog4jConfigurationManager:123 - Found and loaded file: /data/eagle-i/eaglei/conf/institution.log4j.properties 2015-07-15 13:10:27,214 INFO org.eaglei.institution.server.InstitutionContextListener:64 - About to shutdown Solr CoreContainer for Institution if embedded Solr. 2015-07-15 13:10:27,219 INFO org.eaglei.institution.server.LoggingContextListener:56 - About to shutdown: org.eaglei.utilities.servlet.EILog4jConfigurationManager 2015-07-15 13:10:27,220 INFO org.eaglei.utilities.servlet.EILog4jConfigurationManager:138 - About to call LogManager.shutdown() --sukie-- > On Jul 9, 2015, at 12:56 PM, Sophia K Cheng wrote: > > Hi Sukie, > > What does it say in your institution.log? What kind of issues are you running into specifically? If there is nothing informative in your institution.log, could you turn the log settings to debug? > > You can do this in the institution.log4j.properties file: > > log4j.logger.org.eaglei=DEBUG, CA, R > > Thanks, > Sophia > >> Sukdith Punjasthitkul July 8, 2015 at 1:54 PM >> Reinstalling Institution application did not fix the issue; I'm getting the same error messages, which seems like a memory leak issue. We use the Institution application, so unless I can figure out a solution within the next day or so, we're going to rollback our server to 3.4.2. >> >> --sukie-- >> >> >> >> >> >> >> _______________________________________________ >> Eagle-i-admins mailing list >> Eagle-i-admins at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins >> Lease, Joshua July 8, 2015 at 12:08 PM >> I also ran into an issue during the update. However, my log includes exceptions before SEVERE: Error listenerStart. I'm not sure if the issues are related. You can see my log file in an earlier post to the admin group, but I still have not found a solution. >> >> >> _______________________________________________ >> Eagle-i-admins mailing list >> Eagle-i-admins at open.med.harvard.edu >> https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins > > -- > > > _______________________________________________ > Eagle-i-admins mailing list > Eagle-i-admins at open.med.harvard.edu > https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins From Sukdith.Punjasthitkul at dartmouth.edu Fri Jul 17 09:38:55 2015 From: Sukdith.Punjasthitkul at dartmouth.edu (Sukdith Punjasthitkul) Date: Fri, 17 Jul 2015 13:38:55 +0000 Subject: [Eagle-i-admins] Eagle-i-admins Digest, Vol 22, Issue 1 In-Reply-To: <72D30E0D-AB29-4BD8-9520-D402F0C96206@dartmouth.edu> References: <316AE04E-6A1F-4922-82DF-2C8FF5A93B46@hmc.psu.edu> <559EA7CF.70608@hms.harvard.edu> <72D30E0D-AB29-4BD8-9520-D402F0C96206@dartmouth.edu> Message-ID: Hi Sophia, Attached is a screenshot of the error I'm seeing when trying to access the institution app. I'm getting a 404 error, "The requested resource () is not available." Joshua, were you able to get your Institution app running on 3.7.2? --sukie-- [cid:FFF154D6-867C-4360-9DEB-007258F7B13A at dartmouth.edu] On Jul 15, 2015, at 1:28 PM, sukdith punjasthitkul > wrote: Hi Sophia, I've updated our institution.log4j.properties file to run in debug mode and this is the output from institution.log: 2015-07-15 13:10:22,776 INFO org.eaglei.utilities.servlet.EILog4jConfigurationManager:123 - Found and loaded file: /data/eagle-i/eaglei/conf/institution.log4j.properties 2015-07-15 13:10:27,214 INFO org.eaglei.institution.server.InstitutionContextListener:64 - About to shutdown Solr CoreContainer for Institution if embedded Solr. 2015-07-15 13:10:27,219 INFO org.eaglei.institution.server.LoggingContextListener:56 - About to shutdown: org.eaglei.utilities.servlet.EILog4jConfigurationManager 2015-07-15 13:10:27,220 INFO org.eaglei.utilities.servlet.EILog4jConfigurationManager:138 - About to call LogManager.shutdown() --sukie-- On Jul 9, 2015, at 12:56 PM, Sophia K Cheng > wrote: Hi Sukie, What does it say in your institution.log? What kind of issues are you running into specifically? If there is nothing informative in your institution.log, could you turn the log settings to debug? You can do this in the institution.log4j.properties file: log4j.logger.org.eaglei=DEBUG, CA, R Thanks, Sophia Sukdith Punjasthitkul July 8, 2015 at 1:54 PM Reinstalling Institution application did not fix the issue; I'm getting the same error messages, which seems like a memory leak issue. We use the Institution application, so unless I can figure out a solution within the next day or so, we're going to rollback our server to 3.4.2. --sukie-- _______________________________________________ Eagle-i-admins mailing list Eagle-i-admins at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins Lease, Joshua July 8, 2015 at 12:08 PM I also ran into an issue during the update. However, my log includes exceptions before SEVERE: Error listenerStart. I'm not sure if the issues are related. You can see my log file in an earlier post to the admin group, but I still have not found a solution. _______________________________________________ Eagle-i-admins mailing list Eagle-i-admins at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins -- _______________________________________________ Eagle-i-admins mailing list Eagle-i-admins at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: eagle-i_3-7-2_institution_bug.png Type: image/png Size: 104911 bytes Desc: eagle-i_3-7-2_institution_bug.png URL: From jlease at hmc.psu.edu Fri Jul 17 09:44:25 2015 From: jlease at hmc.psu.edu (Lease, Joshua) Date: Fri, 17 Jul 2015 13:44:25 +0000 Subject: [Eagle-i-admins] Eagle-i-admins Digest, Vol 22, Issue 1 In-Reply-To: References: <316AE04E-6A1F-4922-82DF-2C8FF5A93B46@hmc.psu.edu> <559EA7CF.70608@hms.harvard.edu> <72D30E0D-AB29-4BD8-9520-D402F0C96206@dartmouth.edu> Message-ID: Not yet. We're still trying to get to the root cause of my issue. From: Sukdith Punjasthitkul Date: Friday, July 17, 2015 at 9:38 AM To: Sophia K Cheng Cc: "eagle-i-admins at open.med.harvard.edu", Joshua M Lease Subject: Re: [Eagle-i-admins] Eagle-i-admins Digest, Vol 22, Issue 1 Hi Sophia, Attached is a screenshot of the error I'm seeing when trying to access the institution app. I'm getting a 404 error, "The requested resource () is not available." Joshua, were you able to get your Institution app running on 3.7.2? --sukie-- [cid:FFF154D6-867C-4360-9DEB-007258F7B13A at dartmouth.edu] On Jul 15, 2015, at 1:28 PM, sukdith punjasthitkul > wrote: Hi Sophia, I've updated our institution.log4j.properties file to run in debug mode and this is the output from institution.log: 2015-07-15 13:10:22,776 INFO org.eaglei.utilities.servlet.EILog4jConfigurationManager:123 - Found and loaded file: /data/eagle-i/eaglei/conf/institution.log4j.properties 2015-07-15 13:10:27,214 INFO org.eaglei.institution.server.InstitutionContextListener:64 - About to shutdown Solr CoreContainer for Institution if embedded Solr. 2015-07-15 13:10:27,219 INFO org.eaglei.institution.server.LoggingContextListener:56 - About to shutdown: org.eaglei.utilities.servlet.EILog4jConfigurationManager 2015-07-15 13:10:27,220 INFO org.eaglei.utilities.servlet.EILog4jConfigurationManager:138 - About to call LogManager.shutdown() --sukie-- On Jul 9, 2015, at 12:56 PM, Sophia K Cheng > wrote: Hi Sukie, What does it say in your institution.log? What kind of issues are you running into specifically? If there is nothing informative in your institution.log, could you turn the log settings to debug? You can do this in the institution.log4j.properties file: log4j.logger.org.eaglei=DEBUG, CA, R Thanks, Sophia Sukdith PunjasthitkulJuly 8, 2015 at 1:54 PM Reinstalling Institution application did not fix the issue; I'm getting the same error messages, which seems like a memory leak issue. We use the Institution application, so unless I can figure out a solution within the next day or so, we're going to rollback our server to 3.4.2. --sukie-- _______________________________________________ Eagle-i-admins mailing list Eagle-i-admins at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins Lease, Joshua July 8, 2015 at 12:08 PM I also ran into an issue during the update. However, my log includes exceptions before SEVERE: Error listenerStart. I'm not sure if the issues are related. You can see my log file in an earlier post to the admin group, but I still have not found a solution. _______________________________________________ Eagle-i-admins mailing list Eagle-i-admins at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins -- _______________________________________________ Eagle-i-admins mailing list Eagle-i-admins at open.med.harvard.edu https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: eagle-i_3-7-2_institution_bug.png Type: image/png Size: 104911 bytes Desc: eagle-i_3-7-2_institution_bug.png URL: From mail at freelock.com Sun Jul 19 13:02:23 2015 From: mail at freelock.com (John Locke) Date: Sun, 19 Jul 2015 10:02:23 -0700 Subject: [Eagle-i-admins] Experimental Docker image now available for eagle-i Message-ID: <55ABD81F.7000400@freelock.com> Hi, We've been working with Docker for the past few months, and find it a very useful tool for managing complex software installations. I've created a Docker container for eagle-i, and published it on the Docker registry... right now it comes in 3 versions, 3.5.0, 3.7.2, and 4.0.0. We used it specifically to help Fred Hutch upgrade to the current version. Now that the Dockerfile is built, this becomes a very fast way to deploy and upgrade eagle-i! It's also helping us create dev/test copies so we can figure out what's going on with the "Experimental API." You can check it out here: https://registry.hub.docker.com/u/freelock/eaglei/ And the source for this build is here: https://github.com/freelock/eaglei-docker Cheers, -- John Locke Freelock LLC 206-577-0540x20 john at freelock.com http://www.freelock.com From fcoldren at mail.med.upenn.edu Tue Jul 21 09:39:27 2015 From: fcoldren at mail.med.upenn.edu (Faith Coldren) Date: Tue, 21 Jul 2015 09:39:27 -0400 Subject: [Eagle-i-admins] upgrad from 3.2.0 to 3.7.2 In-Reply-To: <55A3E23A.4020509@hms.harvard.edu> References: <55A3E23A.4020509@hms.harvard.edu> Message-ID: Hi, Is it possible to go from 3.2.0 to 4.0.0? Thanks! Faith On Mon, Jul 13, 2015 at 12:07 PM, Sophia K Cheng < sophia_cheng at hms.harvard.edu> wrote: > Hi Faith, > > Yes, that is fine. There is no data migration required between 3.2.0 and > 3.7.2. > > FYI - we just released 4.0.0. I will be sending out release notes shortly > (today). > > Thanks, > Sophia > > Faith Coldren > July 13, 2015 at 10:07 AM > Hi, > > Can eagle-i be upgraded from 3.2.0 to 3.7.2 directly? > > Thanks, > Faith > > > -- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sophia_cheng at hms.harvard.edu Wed Jul 22 17:03:33 2015 From: sophia_cheng at hms.harvard.edu (Sophia K Cheng) Date: Wed, 22 Jul 2015 17:03:33 -0400 Subject: [Eagle-i-admins] upgrad from 3.2.0 to 3.7.2 In-Reply-To: References: <55A3E23A.4020509@hms.harvard.edu> Message-ID: <55B00525.4000501@hms.harvard.edu> Hi Faith, Yes, you may do this. There is no data migration between those two versions. For future reference, we've compiled a guide to help determine this. Thanks, Sophia > Faith Coldren > July 21, 2015 at 9:39 AM > Hi, > > Is it possible to go from 3.2.0 to 4.0.0? > > Thanks! > Faith > > > Sophia K Cheng > July 13, 2015 at 12:07 PM > Hi Faith, > > Yes, that is fine. There is no data migration required between 3.2.0 > and 3.7.2. > > FYI - we just released 4.0.0. I will be sending out release notes > shortly (today). > > Thanks, > Sophia > > > Faith Coldren > July 13, 2015 at 10:07 AM > Hi, > > Can eagle-i be upgraded from 3.2.0 to 3.7.2 directly? > > Thanks, > Faith -- -------------- next part -------------- An HTML attachment was scrubbed... URL: