Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

new build: ConfigurationModelsSetup: Failed to create the 'displayTbox' #3911

Closed
GarrettArm opened this issue Oct 5, 2023 · 0 comments · Fixed by vivo-project/Vitro#423
Closed
Milestone

Comments

@GarrettArm
Copy link

Describe the bug
A fresh Vivo build (1.14-maint git repo) erroring at first startup.

Vivo logs pasted at bottom of message.

To Reproduce
add ENV variables:
TZ="America/New_York"
CATALINA_OPTS="-Xms512m -Xmx4g -XX:MaxPermSize=512m"

cd /usr/local
git clone https://github.com/vivo-project/Vitro.git Vitro -b rel-1.14-maint
git clone https://github.com/vivo-project/VIVO.git VIVO -b rel-1.14-maint
cd usr/local/Vitro
mvn install
cd /usr/local/VIVO
mvn clean package -s settings.xml
mvn install -s settings.xml
chmod ugo+w -R /usr/local/tomcat/temp
chmod ugo+w -R /usr/local/VIVO/home
ln -s /usr/local/tomcat/webapps/vivo/ /usr/local/tomcat/webapps/ROOT

I don't believe anything changed except the versions. Possibly I need to update some arguments or try v1.14.0. Or very possibly I'm making a user error.

Expected behavior
Build completes as it did a few months ago.

Environment (please complete the following information):
Revision info [build date: 10/5/23, 3:27 PM, level info: [[VIVO, 1.14.1-SNAPSHOT, 83ab8d0]]]
maven v3.6.3
java 11.0.16 Oracle
Debian glibc 2.31
tomcat 9.0.65
solr 8.11.2

Additional context

#! /usr/local/tomcat/logs/vivo.all.log

2023-10-05 13:50:51,459 INFO [RevisionInfoBean] Revision info [build date: 10/5/23, 3:27 PM, level info: [[VIVO, 1.14.1-SNAPSHOT, 83ab8d0]]]
2023-10-05 13:53:01,542 WARN [StartupStatus] From FreemarkerEmailFactory$Setup: Invalid SMTP host: 'smtp.uncw.edu': refused connection on port 25 - Email functions are disabled.
2023-10-05 13:53:01,557 INFO [RDFFilesLoader] Loading rdf/display/firsttime/PropertyConfig.n3
2023-10-05 13:53:01,674 INFO [RDFFilesLoader] Loading rdf/display/firsttime/PropertyConfigSupp.n3
2023-10-05 13:53:01,681 INFO [RDFFilesLoader] Loading rdf/display/firsttime/aboutPage.n3
2023-10-05 13:53:01,688 INFO [RDFFilesLoader] Loading rdf/display/firsttime/application.owl
2023-10-05 13:53:01,705 INFO [RDFFilesLoader] Loading rdf/display/firsttime/menu.n3
2023-10-05 13:53:01,714 INFO [RDFFilesLoader] Loading rdf/display/firsttime/pageList_editableStatements.n3
2023-10-05 13:53:01,738 INFO [RDFFilesLoader] Loading rdf/display/firsttime/profilePageType.n3
2023-10-05 13:53:01,747 INFO [RDFFilesLoader] Loading rdf/i18n/en_US/display/firsttime/PropertyConfig.nt
2023-10-05 13:53:01,761 INFO [RDFFilesLoader] Loading rdf/i18n/en_US/display/firsttime/aboutPage.n3
2023-10-05 13:53:01,767 INFO [RDFFilesLoader] Loading rdf/i18n/en_US/display/firsttime/aboutQrCodes.n3
2023-10-05 13:53:01,772 INFO [RDFFilesLoader] Loading rdf/i18n/en_US/display/firsttime/menu.nt
2023-10-05 13:53:01,789 INFO [RDFFilesLoader] Loading rdf/i18n/en_US/display/firsttime/termsOfUse.n3
2023-10-05 13:53:01,845 INFO [RDFFilesLoader] Loading rdf/display/everytime/dataGetterLabels.n3
2023-10-05 13:53:01,846 INFO [RDFFilesLoader] Loading rdf/display/everytime/displayModelListViews.rdf
2023-10-05 13:53:01,848 INFO [RDFFilesLoader] Loading rdf/display/everytime/documentModifierI18nLabel.n3
2023-10-05 13:53:01,848 INFO [RDFFilesLoader] Loading rdf/display/everytime/documentModifierI18nSort.n3
2023-10-05 13:53:01,849 INFO [RDFFilesLoader] Loading rdf/display/everytime/homePageDataGetters.n3
2023-10-05 13:53:01,849 INFO [RDFFilesLoader] Loading rdf/display/everytime/localeSelectionGUI.n3
2023-10-05 13:53:01,849 INFO [RDFFilesLoader] Loading rdf/display/everytime/n3ModelChangePreprocessors.n3
2023-10-05 13:53:01,850 INFO [RDFFilesLoader] Loading rdf/display/everytime/orcidInterfaceDataGetters.n3
2023-10-05 13:53:01,850 INFO [RDFFilesLoader] Loading rdf/display/everytime/pageList.n3
2023-10-05 13:53:01,850 INFO [RDFFilesLoader] Loading rdf/display/everytime/permissions.n3
2023-10-05 13:53:01,851 INFO [RDFFilesLoader] Loading rdf/display/everytime/searchIndexerConfigurationVitro.n3
2023-10-05 13:53:01,852 INFO [RDFFilesLoader] Loading rdf/display/everytime/searchIndexerConfigurationVivo.n3
2023-10-05 13:53:01,853 INFO [RDFFilesLoader] Loading rdf/display/everytime/storedFileListView.n3
2023-10-05 13:53:01,853 INFO [RDFFilesLoader] Loading rdf/display/everytime/vitroSearchProhibited.n3
2023-10-05 13:53:01,854 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoConceptDataGetters.n3
2023-10-05 13:53:01,854 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoListViewConfig.rdf
2023-10-05 13:53:01,858 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoOrganizationDataGetters.n3
2023-10-05 13:53:01,859 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoQrCodeDataGetter.n3
2023-10-05 13:53:01,859 INFO [RDFFilesLoader] Loading rdf/display/everytime/vivoSearchProhibited.n3
2023-10-05 13:53:01,864 ERROR [StartupStatus] From ConfigurationModelsSetup: Failed to create the 'displayTbox' model (http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadataTBOX).
java.util.ConcurrentModificationException
at java.base/java.util.ArrayList$Itr.checkForComodification(ArrayList.java:1043)
at java.base/java.util.ArrayList$Itr.next(ArrayList.java:997)
at java.base/java.util.AbstractCollection.addAll(AbstractCollection.java:351)
at java.base/java.util.TreeSet.addAll(TreeSet.java:312)
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker.getModelNames(RDFServiceModelMaker.java:72)
at edu.cornell.mannlib.vitro.webapp.dao.jena.RDFServiceModelMaker.listModels(RDFServiceModelMaker.java:86)
at edu.cornell.mannlib.vitro.webapp.modelaccess.adapters.AbstractModelMakerDecorator.listModels(AbstractModelMakerDecorator.java:98)
at edu.cornell.mannlib.vitro.webapp.modelaccess.adapters.AbstractModelMakerDecorator.listModels(AbstractModelMakerDecorator.java:98)
at edu.cornell.mannlib.vitro.webapp.modelaccess.adapters.ModelMakerWithPersistentEmptyModels.listModels(ModelMakerWithPersistentEmptyModels.java:49)
at edu.cornell.mannlib.vitro.webapp.modelaccess.ontmodels.ModelMakerOntModelCache.getModelNames(ModelMakerOntModelCache.java:48)
at edu.cornell.mannlib.vitro.webapp.modelaccess.ontmodels.JoinedOntModelCache.getOntModel(JoinedOntModelCache.java:48)
at edu.cornell.mannlib.vitro.webapp.modelaccess.impl.ContextModelAccessImpl.getOntModel(ContextModelAccessImpl.java:190)
at edu.cornell.mannlib.vitro.webapp.servlet.setup.ConfigurationModelsSetup.setupModel(ConfigurationModelsSetup.java:56)
at edu.cornell.mannlib.vitro.webapp.servlet.setup.ConfigurationModelsSetup.contextInitialized(ConfigurationModelsSetup.java:40)
at edu.cornell.mannlib.vitro.webapp.startup.StartupManager.initialize(StartupManager.java:175)
at edu.cornell.mannlib.vitro.webapp.startup.StartupManager.contextInitialized(StartupManager.java:65)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4768)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5230)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:726)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:698)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:696)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1185)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1933)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:118)
at org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:1095)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:477)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1618)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:319)
at org.apache.catalina.util.LifecycleBase.fireLifecycleEvent(LifecycleBase.java:123)
at org.apache.catalina.util.LifecycleBase.setStateInternal(LifecycleBase.java:423)
at org.apache.catalina.util.LifecycleBase.setState(LifecycleBase.java:366)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:946)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:835)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1396)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1386)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.base/java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:140)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:919)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:265)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:432)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:930)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.startup.Catalina.start(Catalina.java:772)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:345)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:476)
2023-10-05 13:53:01,866 INFO [StartupManager] Called 'contextInitialized' on all listeners.
2023-10-05 13:53:01,888 INFO [JSessionStripFilter] Filtering: no jsessionids will be generated.

http://localhost:8080 shows a 500 Server Error with parts of the above error message.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

2 participants