Installing Dataverse on Redhat 6.6

[TJ Bryant]

I have ran the install script and restarted the glassfish server.  When it was trying to start back up it failed with the following error.  Can anyone point me in a direction of how to resolve this?

Waiting for domain1 to start ....Error starting domain domain1.

The server exited prematurely with exit code 0.

Before it died, it produced the following output:

Listening for transport dt_socket at address: 9009

Launching GlassFish on Felix platform

Registered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishRuntime@190c05e2 in service registry.

Found populator: com.sun.enterprise.v3.server.GFDomainXml

#!## LogManagerService.postConstruct : rootFolder=/usr/local/glassfish4/glassfish

#!## LogManagerService.postConstruct : templateDir=/usr/local/glassfish4/glassfish/lib/templates

#!## LogManagerService.postConstruct : src=/usr/local/glassfish4/glassfish/lib/templates/logging.properties

#!## LogManagerService.postConstruct : dest=/usr/local/glassfish4/glassfish/domains/domain1/config/logging.properties

Completed shutdown of Log manager service

Completed shutdown of GlassFish runtime

ERROR: Bundle org.glassfish.fighterfish.osgi-web-container [291] Error starting file:/usr/local/glassfish4/glassfish/modules/autostart/osgi-web-container.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.glassfish.fighterfish.osgi-web-container [291]: Unable to resolve 291.0: missing requirement [291.0] osgi.wiring.package; (&(osgi.wiring.package=com.sun.enterprise.web)(version>=4.0.0)))

ERROR: Bundle org.glassfish.fighterfish.osgi-http [297] Error starting file:/usr/local/glassfish4/glassfish/modules/autostart/osgi-http.jar (org.osgi.framework.BundleException: Unresolved constraint in bundle org.glassfish.fighterfish.osgi-http [297]: Unable to resolve 297.0: missing requirement [297.0] osgi.wiring.package; (&(osgi.wiring.package=com.sun.enterprise.web)(version>=3.1.1)))

Apr 20, 2015 7:39:14 AM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner createBundleProvisioner

INFO: Create bundle provisioner class = class com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner.

Apr 20, 2015 7:39:14 AM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner$DefaultCustomizer getLocations

WARNING: Skipping entry  because it is not an absolute URI.

Apr 20, 2015 7:39:14 AM com.sun.enterprise.glassfish.bootstrap.osgi.BundleProvisioner$DefaultCustomizer getLocations

WARNING: Skipping entry  because it is not an absolute URI.

Apr 20, 2015 7:39:15 AM org.jvnet.hk2.config.ConfigParser handleElement

SEVERE: Ignoring unrecognized element management-rules at Line number = 475

Column number = 25

System Id = null

Public Id = null

Location Uri= null

CharacterOffset = 33193

Can't load log handler "com.sun.enterprise.server.logging.GFFileHandler"

java.lang.ClassNotFoundException: com.sun.enterprise.server.logging.GFFileHandler

java.lang.ClassNotFoundException: com.sun.enterprise.server.logging.GFFileHandler

at java.net.URLClassLoader$1.run(URLClassLoader.java:366)

at java.net.URLClassLoader$1.run(URLClassLoader.java:355)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:354)

at java.lang.ClassLoader.loadClass(ClassLoader.java:425)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)

at java.lang.ClassLoader.loadClass(ClassLoader.java:358)

at java.util.logging.LogManager$4.run(LogManager.java:808)

at java.security.AccessController.doPrivileged(Native Method)

at java.util.logging.LogManager.loadLoggerHandlers(LogManager.java:802)

at java.util.logging.LogManager.initializeGlobalHandlers(LogManager.java:1406)

at java.util.logging.LogManager.access$1500(LogManager.java:148)

at java.util.logging.LogManager$RootLogger.accessCheckedHandlers(LogManager.java:1493)

at java.util.logging.Logger.getHandlers(Logger.java:1350)

at com.sun.enterprise.server.logging.LogManagerService.postConstruct(LogManagerService.java:355)

at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:329)

at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:377)

at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:461)

at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:227)

at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:84)

at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2258)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:105)

at org.jvnet.hk2.internal.ServiceLocatorImpl.getService(ServiceLocatorImpl.java:647)

at org.jvnet.hk2.internal.ThreeThirtyResolver.resolve(ThreeThirtyResolver.java:77)

at org.jvnet.hk2.internal.ClazzCreator.resolve(ClazzCreator.java:214)

at org.jvnet.hk2.internal.ClazzCreator.resolveAllDependencies(ClazzCreator.java:237)

at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:360)

at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:461)

at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:227)

at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:84)

at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2258)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:105)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:87)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1162)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1147)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$UpOneLevel.run(CurrentTaskFuture.java:753)

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:745)

[#|2015-04-20T07:39:15.345-0700|INFO|glassfish 4.1|javax.enterprise.logging|_ThreadID=16;_ThreadName=RunLevelControllerThread-1429540755254;_TimeMillis=1429540755345;_LevelValue=800;_MessageID=NCLS-LOGGING-00009;|Running GlassFish Version: GlassFish Server Open Source Edition  4.1  (build 13)|#]

[#|2015-04-20T07:39:15.346-0700|INFO|glassfish 4.1|javax.enterprise.logging|_ThreadID=16;_ThreadName=RunLevelControllerThread-1429540755254;_TimeMillis=1429540755346;_LevelValue=800;_MessageID=NCLS-LOGGING-00010;|Server log file is using Formatter class: com.sun.enterprise.server.logging.UniformLogFormatter|#]

[#|2015-04-20T07:39:15.528-0700|INFO|glassfish 4.1|org.hibernate.validator.internal.util.Version|_ThreadID=18;_ThreadName=RunLevelControllerThread-1429540755260;_TimeMillis=1429540755528;_LevelValue=800;|HV000001: Hibernate Validator 5.0.0.Final|#]

[#|2015-04-20T07:39:15.646-0700|INFO|glassfish 4.1|javax.enterprise.system.core.security|_ThreadID=17;_ThreadName=RunLevelControllerThread-1429540755255;_TimeMillis=1429540755646;_LevelValue=800;_MessageID=NCLS-SECURITY-01115;|Realm [admin-realm] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.|#]

[#|2015-04-20T07:39:15.648-0700|INFO|glassfish 4.1|javax.enterprise.system.core.security|_ThreadID=17;_ThreadName=RunLevelControllerThread-1429540755255;_TimeMillis=1429540755648;_LevelValue=800;_MessageID=NCLS-SECURITY-01115;|Realm [file] of classtype [com.sun.enterprise.security.auth.realm.file.FileRealm] successfully created.|#]

[#|2015-04-20T07:39:15.672-0700|INFO|glassfish 4.1|javax.enterprise.system.core.security|_ThreadID=17;_ThreadName=RunLevelControllerThread-1429540755255;_TimeMillis=1429540755672;_LevelValue=800;_MessageID=NCLS-SECURITY-01115;|Realm [certificate] of classtype [com.sun.enterprise.security.auth.realm.certificate.CertificateRealm] successfully created.|#]

[#|2015-04-20T07:39:15.738-0700|INFO|glassfish 4.1|org.glassfish.ha.store.spi.BackingStoreFactoryRegistry|_ThreadID=16;_ThreadName=RunLevelControllerThread-1429540755254;_TimeMillis=1429540755738;_LevelValue=800;|Registered org.glassfish.ha.store.adapter.cache.ShoalBackingStoreProxy for persistence-type = replicated in BackingStoreFactoryRegistry|#]

[#|2015-04-20T07:39:15.768-0700|INFO|glassfish 4.1|javax.enterprise.security.services|_ThreadID=17;_ThreadName=RunLevelControllerThread-1429540755255;_TimeMillis=1429540755768;_LevelValue=800;_MessageID=SEC-SVCS-00100;|Authorization Service has successfully initialized.|#]

[#|2015-04-20T07:39:15.835-0700|INFO|glassfish 4.1|javax.enterprise.system.core|_ThreadID=19;_ThreadName=RunLevelControllerThread-1429540755260;_TimeMillis=1429540755835;_LevelValue=800;_MessageID=NCLS-CORE-00087;|Grizzly Framework 2.3.15 started in: 47ms - bound to [/0.0.0.0:80]|#]

[#|2015-04-20T07:39:15.843-0700|INFO|glassfish 4.1|javax.enterprise.system.core|_ThreadID=16;_ThreadName=RunLevelControllerThread-1429540755254;_TimeMillis=1429540755843;_LevelValue=800;_MessageID=NCLS-CORE-00015;|Shutdown requested

MultiException stack 1 of 2

com.sun.enterprise.module.ResolveError: Failed to start OSGiModuleImpl:: Bundle = [org.glassfish.main.web.glue [75]], State = [NEW]

at com.sun.enterprise.module.common_impl.AbstractModulesRegistryImpl.makeModuleFor(AbstractModulesRegistryImpl.java:340)

at com.sun.enterprise.module.common_impl.AbstractModulesRegistryImpl.makeModuleFor(AbstractModulesRegistryImpl.java:311)

at org.glassfish.internal.deployment.GenericSniffer.setup(GenericSniffer.java:194)

at com.sun.enterprise.v3.server.ContainerStarter.startContainer(ContainerStarter.java:97)

at org.glassfish.kernel.javaee.WebContainerStarter.startWebContainer(WebContainerStarter.java:236)

at org.glassfish.kernel.javaee.WebContainerStarter.postConstruct(WebContainerStarter.java:180)

at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:329)

at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:377)

at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:461)

at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:227)

at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:84)

at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2258)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:105)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:87)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1162)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1147)

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:745)

Caused by: com.sun.enterprise.module.ResolveError: Failed to start OSGiModuleImpl:: Bundle = [org.glassfish.main.web.glue [75]], State = [NEW]

at org.jvnet.hk2.osgiadapter.OSGiModuleImpl.start(OSGiModuleImpl.java:218)

at org.jvnet.hk2.osgiadapter.OSGiModuleImpl.resolve(OSGiModuleImpl.java:174)

at com.sun.enterprise.module.common_impl.AbstractModulesRegistryImpl.makeModuleFor(AbstractModulesRegistryImpl.java:337)

... 18 more

Caused by: org.osgi.framework.BundleException: Unresolved constraint in bundle org.glassfish.main.web.glue [75]: Unable to resolve 75.0: missing requirement [75.0] osgi.wiring.package; (&(osgi.wiring.package=com.sun.enterprise.web.connector.grizzly)(version>=4.1.0)(!(version>=5.0.0)))

at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:955)

at org.jvnet.hk2.osgiadapter.OSGiModuleImpl.start(OSGiModuleImpl.java:210)

... 20 more

MultiException stack 2 of 2

java.lang.IllegalStateException: Unable to perform operation: post construct on org.glassfish.kernel.javaee.WebContainerStarter

at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:395)

at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:461)

at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:227)

at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:84)

at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2258)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:105)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:87)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1162)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1147)

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:745)

|#]

[#|2015-04-20T07:39:15.844-0700|SEVERE|glassfish 4.1|javax.enterprise.system.core|_ThreadID=16;_ThreadName=RunLevelControllerThread-1429540755254;_TimeMillis=1429540755844;_LevelValue=1000;_MessageID=NCLS-CORE-00016;|Startup service failed to start

MultiException stack 1 of 2

com.sun.enterprise.module.ResolveError: Failed to start OSGiModuleImpl:: Bundle = [org.glassfish.main.web.glue [75]], State = [NEW]

at com.sun.enterprise.module.common_impl.AbstractModulesRegistryImpl.makeModuleFor(AbstractModulesRegistryImpl.java:340)

at com.sun.enterprise.module.common_impl.AbstractModulesRegistryImpl.makeModuleFor(AbstractModulesRegistryImpl.java:311)

at org.glassfish.internal.deployment.GenericSniffer.setup(GenericSniffer.java:194)

at com.sun.enterprise.v3.server.ContainerStarter.startContainer(ContainerStarter.java:97)

at org.glassfish.kernel.javaee.WebContainerStarter.startWebContainer(WebContainerStarter.java:236)

at org.glassfish.kernel.javaee.WebContainerStarter.postConstruct(WebContainerStarter.java:180)

at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:329)

at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:377)

at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:461)

at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:227)

at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:84)

at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2258)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:105)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:87)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1162)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1147)

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:745)

Caused by: com.sun.enterprise.module.ResolveError: Failed to start OSGiModuleImpl:: Bundle = [org.glassfish.main.web.glue [75]], State = [NEW]

at org.jvnet.hk2.osgiadapter.OSGiModuleImpl.start(OSGiModuleImpl.java:218)

at org.jvnet.hk2.osgiadapter.OSGiModuleImpl.resolve(OSGiModuleImpl.java:174)

at com.sun.enterprise.module.common_impl.AbstractModulesRegistryImpl.makeModuleFor(AbstractModulesRegistryImpl.java:337)

... 18 more

Caused by: org.osgi.framework.BundleException: Unresolved constraint in bundle org.glassfish.main.web.glue [75]: Unable to resolve 75.0: missing requirement [75.0] osgi.wiring.package; (&(osgi.wiring.package=com.sun.enterprise.web.connector.grizzly)(version>=4.1.0)(!(version>=5.0.0)))

at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:955)

at org.jvnet.hk2.osgiadapter.OSGiModuleImpl.start(OSGiModuleImpl.java:210)

... 20 more

MultiException stack 2 of 2

java.lang.IllegalStateException: Unable to perform operation: post construct on org.glassfish.kernel.javaee.WebContainerStarter

at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:395)

at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:461)

at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:227)

at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:84)

at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2258)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:105)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:87)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1162)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1147)

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:745)

|#]

[#|2015-04-20T07:39:15.859-0700|INFO|glassfish 4.1|javax.enterprise.system.core|_ThreadID=19;_ThreadName=RunLevelControllerThread-1429540755260;_TimeMillis=1429540755859;_LevelValue=800;_MessageID=NCLS-CORE-00087;|Grizzly Framework 2.3.15 started in: 2ms - bound to [/0.0.0.0:443]|#]

[#|2015-04-20T07:39:15.867-0700|INFO|glassfish 4.1|javax.enterprise.system.core|_ThreadID=19;_ThreadName=RunLevelControllerThread-1429540755260;_TimeMillis=1429540755867;_LevelValue=800;_MessageID=NCLS-CORE-00087;|Grizzly Framework 2.3.15 started in: 2ms - bound to [/0.0.0.0:4848]|#]

[#|2015-04-20T07:39:15.882-0700|INFO|glassfish 4.1|javax.enterprise.system.core|_ThreadID=65;_ThreadName=Thread-11;_TimeMillis=1429540755882;_LevelValue=800;_MessageID=NCLS-CORE-00092;|Server shutdown initiated|#]

[#|2015-04-20T07:39:15.920-0700|INFO|glassfish 4.1|javax.enterprise.system.core|_ThreadID=17;_ThreadName=RunLevelControllerThread-1429540755255;_TimeMillis=1429540755920;_LevelValue=800;_MessageID=NCLS-CORE-00087;|Grizzly Framework 2.3.15 started in: 1ms - bound to [/0.0.0.0:3700]|#]

[#|2015-04-20T07:39:16.014-0700|SEVERE|glassfish 4.1|javax.enterprise.system.core|_ThreadID=1;_ThreadName=main;_TimeMillis=1429540756014;_LevelValue=1000;_MessageID=NCLS-CORE-00014;|Shutdown required

MultiException stack 1 of 1

MultiException stack 1 of 2

com.sun.enterprise.module.ResolveError: Failed to start OSGiModuleImpl:: Bundle = [org.glassfish.main.web.glue [75]], State = [NEW]

at com.sun.enterprise.module.common_impl.AbstractModulesRegistryImpl.makeModuleFor(AbstractModulesRegistryImpl.java:340)

at com.sun.enterprise.module.common_impl.AbstractModulesRegistryImpl.makeModuleFor(AbstractModulesRegistryImpl.java:311)

at org.glassfish.internal.deployment.GenericSniffer.setup(GenericSniffer.java:194)

at com.sun.enterprise.v3.server.ContainerStarter.startContainer(ContainerStarter.java:97)

at org.glassfish.kernel.javaee.WebContainerStarter.startWebContainer(WebContainerStarter.java:236)

at org.glassfish.kernel.javaee.WebContainerStarter.postConstruct(WebContainerStarter.java:180)

at org.jvnet.hk2.internal.ClazzCreator.postConstructMe(ClazzCreator.java:329)

at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:377)

at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:461)

at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:227)

at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:84)

at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2258)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:105)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:87)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1162)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1147)

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:745)

Caused by: com.sun.enterprise.module.ResolveError: Failed to start OSGiModuleImpl:: Bundle = [org.glassfish.main.web.glue [75]], State = [NEW]

at org.jvnet.hk2.osgiadapter.OSGiModuleImpl.start(OSGiModuleImpl.java:218)

at org.jvnet.hk2.osgiadapter.OSGiModuleImpl.resolve(OSGiModuleImpl.java:174)

at com.sun.enterprise.module.common_impl.AbstractModulesRegistryImpl.makeModuleFor(AbstractModulesRegistryImpl.java:337)

... 18 more

Caused by: org.osgi.framework.BundleException: Unresolved constraint in bundle org.glassfish.main.web.glue [75]: Unable to resolve 75.0: missing requirement [75.0] osgi.wiring.package; (&(osgi.wiring.package=com.sun.enterprise.web.connector.grizzly)(version>=4.1.0)(!(version>=5.0.0)))

at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:955)

at org.jvnet.hk2.osgiadapter.OSGiModuleImpl.start(OSGiModuleImpl.java:210)

... 20 more

MultiException stack 2 of 2

java.lang.IllegalStateException: Unable to perform operation: post construct on org.glassfish.kernel.javaee.WebContainerStarter

at org.jvnet.hk2.internal.ClazzCreator.create(ClazzCreator.java:395)

at org.jvnet.hk2.internal.SystemDescriptor.create(SystemDescriptor.java:461)

at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.findOrCreate(AsyncRunLevelContext.java:227)

at org.glassfish.hk2.runlevel.RunLevelContext.findOrCreate(RunLevelContext.java:84)

at org.jvnet.hk2.internal.Utilities.createService(Utilities.java:2258)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:105)

at org.jvnet.hk2.internal.ServiceHandleImpl.getService(ServiceHandleImpl.java:87)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.oneJob(CurrentTaskFuture.java:1162)

at org.glassfish.hk2.runlevel.internal.CurrentTaskFuture$QueueRunner.run(CurrentTaskFuture.java:1147)

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:745)

|#]

[#|2015-04-20T07:39:16.017-0700|INFO|glassfish 4.1|javax.enterprise.system.core|_ThreadID=67;_ThreadName=Thread-12;_TimeMillis=1429540756017;_LevelValue=800;_MessageID=NCLS-CORE-00092;|Server shutdown initiated|#]

[#|2015-04-20T07:39:16.017-0700|INFO|glassfish 4.1|javax.enterprise.bootstrap|_ThreadID=1;_ThreadName=main;_TimeMillis=1429540756017;_LevelValue=800;_MessageID=NCLS-BOOTSTRAP-00027;|Registered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishImpl@fdbf8f6 as OSGi service registration: org.apache.felix.framework.ServiceRegistrationImpl@3ab167ca.|#]

[#|2015-04-20T07:39:16.024-0700|INFO|glassfish 4.1|javax.enterprise.bootstrap|_ThreadID=67;_ThreadName=Thread-12;_TimeMillis=1429540756024;_LevelValue=800;_MessageID=NCLS-BOOTSTRAP-00028;|Unregistered com.sun.enterprise.glassfish.bootstrap.osgi.EmbeddedOSGiGlassFishImpl@fdbf8f6 from service registry.|#]

[#|2015-04-20T07:39:16.029-0700|INFO|glassfish 4.1||_ThreadID=67;_ThreadName=Thread-8;_TimeMillis=1429540756029;_LevelValue=800;|FileMonitoring shutdown|#]

[#|2015-04-20T07:39:16.057-0700|INFO|glassfish 4.1|javax.enterprise.system.core|_ThreadID=67;_ThreadName=Thread-12;_TimeMillis=1429540756057;_LevelValue=800;_MessageID=NCLS-CORE-00013;|Shutdown procedure finished|#]

org.osgi.framework.BundleException: Unresolved constraint in bundle org.glassfish.fighterfish.osgi-web-container [291]: Unable to resolve 291.0: missing requirement [291.0] osgi.wiring.package; (&(osgi.wiring.package=com.sun.enterprise.web)(version>=4.0.0))

at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

at java.lang.Thread.run(Thread.java:745)

org.osgi.framework.BundleException: Unresolved constraint in bundle org.glassfish.fighterfish.osgi-http [297]: Unable to resolve 297.0: missing requirement [297.0] osgi.wiring.package; (&(osgi.wiring.package=com.sun.enterprise.web)(version>=3.1.1))

at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1291)

at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:304)

at java.lang.Thread.run(Thread.java:745)

gogo: InterruptedException: sleep interrupted

java.lang.InterruptedException: sleep interrupted

at java.lang.Thread.sleep(Native Method)

at org.apache.felix.gogo.shell.Activator.run(Activator.java:72)

at java.lang.Thread.run(Thread.java:745)

Command start-domain failed.

[Philip Durbin]

Hmm. I wish I knew a quick fix for you...

Do you think you could replicate this problem in Vagrant? The Vagrantfile file here uses CentOS, which is quite similar to RHEL: https://github.com/IQSS/dataverse/blob/master/Vagrantfile

See also http://guides.dataverse.org/en/latest/developers/tools.html#vagrant

Thanks for your interest in installing Dataverse 4.0! We haven't even tagged it in git yet! :)

Phil

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[TJ Bryant]

The central IT group here only supports Redhat so I have to use that OS.

This is actually the second issue I encountered.  It seems that the domain.xml file included in the distribution was missing the security configuration section.  I copied it over from the backup that was created.  Could that be related to this problem?

[Philip Durbin]

Let's back up a moment. Are you trying to install DVN 3.6.2 or Dataverse 4.0?

The former is available at http://sourceforge.net/projects/dvn/files/dvn/3.6.2/

The latter isn't available yet as a downloadable package.

Phil

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[TJ Bryant]

I am installing 3.6.2 and encountered these issues.

[Philip Durbin]

Thanks. From the logs you've posted it seems like you're trying to install DVN 3.6.2 on Glassfish 4.x. I've never tried this so I think you'd have better luck with Glassfish 3.x. We use Glassfish 3.x in the Vagrant environment for DVN 3.6 here: https://github.com/dvn/dvn-install-demo

That said, I wonder if you'd be interested in trying to install Dataverse 4.0! We haven't actually posted installers yet but we plan to soon. I'm sure we'll update https://github.com/IQSS/dataverse/blob/master/README.md once we've packaged up 4.0 to explain where to download it. You can also check out some preliminary info at http://guides.dataverse.org/en/latest/installation/ . We'd love feedback (and help perhaps) on how we can make the installation process as easy as possible!

Phil

On Tue, Apr 21, 2015 at 11:13 AM, TJ Bryant <dela...@gmail.com> wrote:

I am installing 3.6.2 and encountered these issues.

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[TJ Bryant]

Ok, I'll give DVN 4.0 a shot.  Should I still stick with Glassfish 3.x?

On Tuesday, April 21, 2015 at 12:50:15 PM UTC-4, Philip Durbin wrote:

Thanks. From the logs you've posted it seems like you're trying to install DVN 3.6.2 on Glassfish 4.x. I've never tried this so I think you'd have better luck with Glassfish 3.x. We use Glassfish 3.x in the Vagrant environment for DVN 3.6 here: https://github.com/dvn/dvn-install-demo

That said, I wonder if you'd be interested in trying to install Dataverse 4.0! We haven't actually posted installers yet but we plan to soon. I'm sure we'll update https://github.com/IQSS/dataverse/blob/master/README.md once we've packaged up 4.0 to explain where to download it. You can also check out some preliminary info at http://guides.dataverse.org/en/latest/installation/ . We'd love feedback (and help perhaps) on how we can make the installation process as easy as possible!

Phil

On Tue, Apr 21, 2015 at 11:13 AM, TJ Bryant <dela...@gmail.com> wrote:

I am installing 3.6.2 and encountered these issues.

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[Philip Durbin]

Nope! Glassfish 4.1 for Dataverse 4.0 please! (We call it "Dataverse 4.0" rather than "DVN 4.0".)

On Tue, Apr 21, 2015 at 12:56 PM, TJ Bryant <dela...@gmail.com> wrote:

Ok, I'll give DVN 4.0 a shot.  Should I still stick with Glassfish 3.x?

On Tuesday, April 21, 2015 at 12:50:15 PM UTC-4, Philip Durbin wrote:

Thanks. From the logs you've posted it seems like you're trying to install DVN 3.6.2 on Glassfish 4.x. I've never tried this so I think you'd have better luck with Glassfish 3.x. We use Glassfish 3.x in the Vagrant environment for DVN 3.6 here: https://github.com/dvn/dvn-install-demo

That said, I wonder if you'd be interested in trying to install Dataverse 4.0! We haven't actually posted installers yet but we plan to soon. I'm sure we'll update https://github.com/IQSS/dataverse/blob/master/README.md once we've packaged up 4.0 to explain where to download it. You can also check out some preliminary info at http://guides.dataverse.org/en/latest/installation/ . We'd love feedback (and help perhaps) on how we can make the installation process as easy as possible!

Phil

On Tue, Apr 21, 2015 at 11:13 AM, TJ Bryant <dela...@gmail.com> wrote:

I am installing 3.6.2 and encountered these issues.

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[Mercè Crosas]

Here is a demo instance of Dataverse 4.0, in case you'd like to test all the cool new functionality and improved user interface and experience:

https://dataverse-demo.iq.harvard.edu/

And here is our updated production instance at Harvard, with Dataverse 4.0:

https://dataverse.harvard.edu/

Very much worth installing Dataverse 4.0! Let us know how it goes.

Best,

Merce

Mercè Crosas, Ph.D.

Director of Data Science, IQSS

Harvard University

http://scholar.harvard.edu/mercecrosas

To view this discussion on the web visit https://groups.google.com/d/msgid/dataverse-community/CABbxx8HnQa1X2ETNR48eJQAiddDb%3DURN_Dc9Lbkj2SKaqEomzA%40mail.gmail.com.

[TJ Bryant]

Thanks for the info.  As far as installing Dataverse 4.0, is it as simple as running the installation script or are there new prerequisites?  I do have a R and postgresql installed already.

On Tuesday, April 21, 2015 at 1:05:55 PM UTC-4, Merce wrote:

Here is a demo instance of Dataverse 4.0, in case you'd like to test all the cool new functionality and improved user interface and experience:

https://dataverse-demo.iq.harvard.edu/

And here is our updated production instance at Harvard, with Dataverse 4.0:

https://dataverse.harvard.edu/

Very much worth installing Dataverse 4.0! Let us know how it goes.

Best,

Merce

Mercè Crosas, Ph.D.

Director of Data Science, IQSS

Harvard University

http://scholar.harvard.edu/mercecrosas

On Tue, Apr 21, 2015 at 1:00 PM, Philip Durbin <philip...@harvard.edu> wrote:

Nope! Glassfish 4.1 for Dataverse 4.0 please! (We call it "Dataverse 4.0" rather than "DVN 4.0".)

On Tue, Apr 21, 2015 at 12:56 PM, TJ Bryant <dela...@gmail.com> wrote:

Ok, I'll give DVN 4.0 a shot.  Should I still stick with Glassfish 3.x?

On Tuesday, April 21, 2015 at 12:50:15 PM UTC-4, Philip Durbin wrote:

Thanks. From the logs you've posted it seems like you're trying to install DVN 3.6.2 on Glassfish 4.x. I've never tried this so I think you'd have better luck with Glassfish 3.x. We use Glassfish 3.x in the Vagrant environment for DVN 3.6 here: https://github.com/dvn/dvn-install-demo

That said, I wonder if you'd be interested in trying to install Dataverse 4.0! We haven't actually posted installers yet but we plan to soon. I'm sure we'll update https://github.com/IQSS/dataverse/blob/master/README.md once we've packaged up 4.0 to explain where to download it. You can also check out some preliminary info at http://guides.dataverse.org/en/latest/installation/ . We'd love feedback (and help perhaps) on how we can make the installation process as easy as possible!

Phil

On Tue, Apr 21, 2015 at 11:13 AM, TJ Bryant <dela...@gmail.com> wrote:

I am installing 3.6.2 and encountered these issues.

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[Philip Durbin]

You'll need Solr for sure. For details, please see http://guides.dataverse.org/en/latest/installation/

You *might* want to wait a little longer until we've improved those docs in https://github.com/IQSS/dataverse/issues/913

Also, there's no Dataverse 4.0 war file yet to download. :)

That said, some eager people have been able to get it running! Ben here might be building his own war file: https://github.com/IQSS/dataverse/issues/2003

We will, of course, be releasing actual war files we want people to use!

Thanks again for your interest! We'll try to get something out there soon!

Phil

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[TJ Bryant]

So far I have packaged the war and created these server resources:

Connection Pool for postgres

JDBC

VDCNetDS

VDCNetDS_nontx

VDCDNetDS_pm

JMS factories and destinations:

DSBIngest

IndexMessage

DataverseIngest

I am trying to install the war through the admin console and getting this exception.  Any ideas?

Log Entry Detail

Timestamp

Apr 21, 2015 13:09:16.003

Log Level

SEVERE

Logger

javax.enterprise.system.core

Name-Value Pairs

{levelValue=1000, timeMillis=1429646956003}

Record Number

1425

Message ID

Complete Message

Exception while loading the app : javax.ejb.CreateException: Initialization failed for Singleton IngestServiceBean javax.ejb.CreateException: Initialization failed for Singleton IngestServiceBean at com.sun.ejb.containers.AbstractSingletonContainer.createSingletonEJB(AbstractSingletonContainer.java:476) at com.sun.ejb.containers.AbstractSingletonContainer.access$000(AbstractSingletonContainer.java:74) at com.sun.ejb.containers.AbstractSingletonContainer$SingletonContextFactory.create(AbstractSingletonContainer.java:647) at com.sun.ejb.containers.AbstractSingletonContainer.instantiateSingletonInstance(AbstractSingletonContainer.java:389) at org.glassfish.ejb.startup.SingletonLifeCycleManager.initializeSingleton(SingletonLifeCycleManager.java:219) at org.glassfish.ejb.startup.SingletonLifeCycleManager.initializeSingleton(SingletonLifeCycleManager.java:180) at org.glassfish.ejb.startup.SingletonLifeCycleManager.doStartup(SingletonLifeCycleManager.java:158) at org.glassfish.ejb.startup.EjbApplication.start(EjbApplication.java:166) at org.glassfish.internal.data.EngineRef.start(EngineRef.java:122) at org.glassfish.internal.data.ModuleInfo.start(ModuleInfo.java:291) at org.glassfish.internal.data.ApplicationInfo.start(ApplicationInfo.java:352) at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:500) at com.sun.enterprise.v3.server.ApplicationLifecycle.deploy(ApplicationLifecycle.java:219) at org.glassfish.deployment.admin.DeployCommand.execute(DeployCommand.java:491) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:539) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2$1.run(CommandRunnerImpl.java:535) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:356) at com.sun.enterprise.v3.admin.CommandRunnerImpl$2.execute(CommandRunnerImpl.java:534) at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:565) at com.sun.enterprise.v3.admin.CommandRunnerImpl$3.run(CommandRunnerImpl.java:557) at java.security.AccessController.doPrivileged(Native Method) at javax.security.auth.Subject.doAs(Subject.java:356) at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:556) at com.sun.enterprise.v3.admin.CommandRunnerImpl.doCommand(CommandRunnerImpl.java:1464) at com.sun.enterprise.v3.admin.CommandRunnerImpl.access$1300(CommandRunnerImpl.java:109) at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1846) at com.sun.enterprise.v3.admin.CommandRunnerImpl$ExecutionContext.execute(CommandRunnerImpl.java:1722) at org.glassfish.admin.rest.utils.ResourceUtil.runCommand(ResourceUtil.java:253) at org.glassfish.admin.rest.utils.ResourceUtil.runCommand(ResourceUtil.java:231) at org.glassfish.admin.rest.utils.ResourceUtil.runCommand(ResourceUtil.java:275) at org.glassfish.admin.rest.resources.TemplateListOfResource.createResource(TemplateListOfResource.java:133) at sun.reflect.GeneratedMethodAccessor594.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:151) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:171) at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:152) at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:104) at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:387) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:331) at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:103) at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:271) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271) at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267) at org.glassfish.jersey.internal.Errors.process(Errors.java:315) at org.glassfish.jersey.internal.Errors.process(Errors.java:297) at org.glassfish.jersey.internal.Errors.process(Errors.java:267) at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:297) at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:254) at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1028) at org.glassfish.jersey.grizzly2.httpserver.GrizzlyHttpContainer.service(GrizzlyHttpContainer.java:365) at org.glassfish.admin.rest.adapter.RestAdapter$2.service(RestAdapter.java:316) at org.glassfish.admin.rest.adapter.RestAdapter.service(RestAdapter.java:179) at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459) at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167) at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201) at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175) at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235) at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201) at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133) at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112) at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77) at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561) at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56) at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545) at java.lang.Thread.run(Thread.java:745) Caused by: java.lang.IllegalStateException: Exception attempting to inject Res-Ref-Env-Property: edu.harvard.iq.dataverse.ingest.IngestServiceBean/fac...@javax.jms.QueueConnectionFactory@ resolved as: jndi: jms/IngestQueueConnectionFactory@res principal: null@mail: null No Runtime properties Database Vendor : null Create Tables at Deploy : false Delete Tables at Undeploy : false into class edu.harvard.iq.dataverse.ingest.IngestServiceBean: Lookup failed for 'java:comp/env/edu.harvard.iq.dataverse.ingest.IngestServiceBean/factory' in SerialContext[myEnv={java.naming.factory.initial=com.sun.enterprise.naming.impl.SerialInitContextFactory, java.naming.factory.state=com.sun.corba.ee.impl.presentation.rmi.JNDIStateFactoryImpl, java.naming.factory.url.pkgs=com.sun.enterprise.naming} at org.glassfish.weld.services.InjectionServicesImpl.aroundInject(InjectionServicesImpl.java:175) at org.jboss.weld.injection.InjectionContextImpl.run(InjectionContextImpl.java:46) at org.jboss.weld.injection.producer.DefaultInjector.inject(DefaultInjector.java:68) at org.jboss.weld.injection.producer.ejb.SessionBeanInjectionTarget.inject(SessionBeanInjectionTarget.java:133) at org.glassfish.weld.services.JCDIServiceImpl.injectEJBInstance(JCDIServiceImpl.java:257) at com.sun.ejb.containers.BaseContainer.injectEjbInstance(BaseContainer.java:1748) at com.sun.ejb.containers.AbstractSingletonContainer.createSingletonEJB(AbstractSingletonContainer.java:436) ... 73 more Caused by: com.sun.enterprise.container.common.spi.util.InjectionException: Exception attempting to inject Res-Ref-Env-Property: edu.harvard.iq.dataverse.ingest.IngestServiceBean/fac...@javax.jms.QueueConnectionFactory@ resolved as: jndi: jms/IngestQueueConnectionFactory@res principal: null@mail: null No Runtime properties Database Vendor : null Create Tables at Deploy : false Delete Tables at Undeploy : false into class edu.harvard.iq.dataverse.ingest.IngestServiceBean: Lookup failed for 'java:comp/env/edu.harvard.iq.dataverse.ingest.IngestServiceBean/factory' in SerialContext[myEnv={java.naming.factory.initial=com.sun.enterprise.naming.impl.SerialInitContextFactory, java.naming.factory.state=com.sun.corba.ee.impl.presentation.rmi.JNDIStateFactoryImpl, java.naming.factory.url.pkgs=com.sun.enterprise.naming} at com.sun.enterprise.container.common.impl.util.InjectionManagerImpl._inject(InjectionManagerImpl.java:740) at com.sun.enterprise.container.common.impl.util.InjectionManagerImpl.inject(InjectionManagerImpl.java:507) at com.sun.enterprise.container.common.impl.util.InjectionManagerImpl.injectInstance(InjectionManagerImpl.java:170) at org.glassfish.weld.services.InjectionServicesImpl.aroundInject(InjectionServicesImpl.java:165) ... 79 more Caused by: javax.naming.NamingException: Lookup failed for 'java:comp/env/edu.harvard.iq.dataverse.ingest.IngestServiceBean/factory' in SerialContext[myEnv={java.naming.factory.initial=com.sun.enterprise.naming.impl.SerialInitContextFactory, java.naming.factory.state=com.sun.corba.ee.impl.presentation.rmi.JNDIStateFactoryImpl, java.naming.factory.url.pkgs=com.sun.enterprise.naming} [Root exception is javax.naming.NamingException: Lookup failed for 'jms/IngestQueueConnectionFactory' in SerialContext[myEnv={java.naming.factory.initial=com.sun.enterprise.naming.impl.SerialInitContextFactory, java.naming.factory.state=com.sun.corba.ee.impl.presentation.rmi.JNDIStateFactoryImpl, java.naming.factory.url.pkgs=com.sun.enterprise.naming, com.sun.enterprise.naming.logicalName=java:comp/env/edu.harvard.iq.dataverse.ingest.IngestServiceBean/factory} [Root exception is javax.naming.NameNotFoundException: IngestQueueConnectionFactory not found]] at com.sun.enterprise.naming.impl.SerialContext.lookup(SerialContext.java:491) at com.sun.enterprise.naming.impl.SerialContext.lookup(SerialContext.java:438) at javax.naming.InitialContext.lookup(InitialContext.java:411) at javax.naming.InitialContext.lookup(InitialContext.java:411) at com.sun.enterprise.container.common.impl.util.InjectionManagerImpl._inject(InjectionManagerImpl.java:636) ... 82 more Caused by: javax.naming.NamingException: Lookup failed for 'jms/IngestQueueConnectionFactory' in SerialContext[myEnv={java.naming.factory.initial=com.sun.enterprise.naming.impl.SerialInitContextFactory, java.naming.factory.state=com.sun.corba.ee.impl.presentation.rmi.JNDIStateFactoryImpl, java.naming.factory.url.pkgs=com.sun.enterprise.naming, com.sun.enterprise.naming.logicalName=java:comp/env/edu.harvard.iq.dataverse.ingest.IngestServiceBean/factory} [Root exception is javax.naming.NameNotFoundException: IngestQueueConnectionFactory not found] at com.sun.enterprise.naming.impl.SerialContext.lookup(SerialContext.java:491) at com.sun.enterprise.naming.impl.SerialContext.lookup(SerialContext.java:438) at javax.naming.InitialContext.lookup(InitialContext.java:411) at javax.naming.InitialContext.lookup(InitialContext.java:411) at com.sun.enterprise.naming.util.JndiNamingObjectFactory.create(JndiNamingObjectFactory.java:90) at com.sun.enterprise.naming.util.JndiInitializationNamingObjectFactory.create(JndiInitializationNamingObjectFactory.java:110) at com.sun.enterprise.naming.impl.GlassfishNamingManagerImpl.lookup(GlassfishNamingManagerImpl.java:745) at com.sun.enterprise.naming.impl.GlassfishNamingManagerImpl.lookup(GlassfishNamingManagerImpl.java:715) at com.sun.enterprise.naming.impl.JavaURLContext.lookup(JavaURLContext.java:159) at com.sun.enterprise.naming.impl.SerialContext.lookup(SerialContext.java:471) ... 86 more Caused by: javax.naming.NameNotFoundException: IngestQueueConnectionFactory not found at com.sun.enterprise.naming.impl.TransientContext.doLookup(TransientContext.java:237) at com.sun.enterprise.naming.impl.TransientContext.lookup(TransientContext.java:204) at com.sun.enterprise.naming.impl.TransientContext.lookup(TransientContext.java:208) at com.sun.enterprise.naming.impl.SerialContextProviderImpl.lookup(SerialContextProviderImpl.java:66) at com.sun.enterprise.naming.impl.LocalSerialContextProviderImpl.lookup(LocalSerialContextProviderImpl.java:114) at com.sun.enterprise.naming.impl.SerialContext.lookup(SerialContext.java:478) ... 95 more

[Philip Durbin]

I'm seeing "IngestQueueConnectionFactory not found" which suggests that https://github.com/IQSS/dataverse/blob/master/scripts/installer/glassfish-setup.sh was not called. That script is typically called from https://github.com/IQSS/dataverse/blob/master/scripts/installer/install

I can't recommend enough letting Vagrant run all these scripts for you just to see how the app is put together. :)

When you look at the "provision" lines in https://github.com/IQSS/dataverse/blob/master/Vagrantfile you'll see that the following scripts are called (in order):

- https://github.com/IQSS/dataverse/blob/master/scripts/vagrant/setup.sh
- https://github.com/IQSS/dataverse/blob/master/scripts/vagrant/setup-solr.sh
- https://github.com/IQSS/dataverse/blob/master/scripts/vagrant/install-dataverse.sh

If nothing else, studying these script a bit should give you a sense of how to get Dataverse 4.0 installed.

Again, we'll do a real release soon! I hope this helps!

Phil

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