Failed to deploy the application!

[Lynette García]

I was trying to reinstall dataverse, I reinstaled payara, but I got this error when I tried to deploy the application:

Deploying the application (dataverse.war)
remote failure: Error occurred during deployment: Exception while loading the app : EJB Container initialization error. Please see server.log for more details.
Command deploy failed.
Failed to deploy the application!

This is the error on server.log:

[2022-10-04T00:14:52.217+0000] [] [INFO] [NCLS-GFLAUNCHER-00005] [javax.enterprise.launcher] [tid: _ThreadID=1 _ThreadName=main] [timeMillis: 1664842492217] [levelValue: 800] [[
  JVM invocation command line:
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-cp
/usr/local/payara5/glassfish/modules/glassfish.jar
-XX:+UnlockDiagnosticVMOptions
--add-opens=java.base/java.net=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.jrt=ALL-UNNAMED
--add-opens=java.management/sun.management=ALL-UNNAMED
--add-exports=java.base/jdk.internal.ref=ALL-UNNAMED
--add-opens=java.naming/javax.naming.spi=ALL-UNNAMED
--add-opens=jdk.management/com.sun.management.internal=ALL-UNNAMED
--add-opens=java.base/java.nio=ALL-UNNAMED
--add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
--add-opens=java.base/java.lang=ALL-UNNAMED
--add-opens=java.logging/java.util.logging=ALL-UNNAMED
--add-opens=java.base/sun.net.www.protocol.jar=ALL-UNNAMED
--add-opens=java.base/jdk.internal.loader=ALL-UNNAMED
--add-opens=java.base/java.util=ALL-UNNAMED
--add-opens=java.base/sun.nio.ch=ALL-UNNAMED
-XX:MetaspaceSize=256m
-XX:NewRatio=2
-XX:+DisableExplicitGC
-XX:MaxMetaspaceSize=512m
-XX:+UseStringDeduplication
-XX:+UseG1GC
-Xbootclasspath/a:/usr/local/payara5/glassfish/lib/grizzly-npn-api.jar
-Xmx3978m
-server
-javaagent:/usr/local/payara5/glassfish/lib/monitor/flashlight-agent.jar
-Djavax.xml.accessExternalSchema=all
-Ddataverse.siteUrl=http://ceia1.uvg.edu.gt:8080
-Djdk.tls.rejectClientInitiatedRenegotiation=true
-Ddataverse.files.file.directory=/usr/local/payara5/glassfish/domains/domain1/files
-Djdk.corba.allowOutputStreamSubclass=true
-Dfelix.fileinstall.dir=/usr/local/payara5/glassfish/modules/autostart/
-Dcom.sun.aas.installRoot=/usr/local/payara5/glassfish
-Ddataverse.auth.password-reset-timeout-in-minutes=60
-Ddataverse.lang.directory=/usr/local/dataverse/langBundles
-Ddataverse.rserve.password=${ALIAS=rserve_password_alias}
-Dorg.glassfish.grizzly.DEFAULT_MEMORY_MANAGER=org.glassfish.grizzly.memory.HeapMemoryManager
-Ddoi.username=UPTY
-Dfelix.fileinstall.bundles.new.start=true
-Dgosh.args=--nointeractive
-Dcom.sun.enterprise.security.httpsOutboundKeyAlias=s1as
-Dorg.jboss.weld.serialization.beanIdentifierIndexOptimization=false
-Ddataverse.files.file.type=file
-Dosgi.shell.telnet.ip=127.0.0.1
-Djdk.attach.allowAttachSelf=true
-Ddataverse.rserve.user=rserve
-Djava.awt.headless=true
-Dcom.ctc.wstx.returnNullForDefaultNamespace=true
-Djdbc.drivers=org.h2.Driver
-Djavax.net.ssl.trustStore=/usr/local/payara5/glassfish/domains/domain1/config/cacerts.jks
-Ddataverse.timerServer=true
-Ddoi.password=${ALIAS=doi_password_alias}
-Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl
-Dorg.glassfish.additionalOSGiBundlesToStart=org.apache.felix.shell,org.apache.felix.gogo.runtime,org.apache.felix.gogo.shell,org.apache.felix.gogo.command,org.apache.felix.shell.remote,org.apache.felix.fileinstall
-Dfelix.fileinstall.poll=5000
-Djava.security.policy=/usr/local/payara5/glassfish/domains/domain1/config/server.policy
-Ddataverse.rserve.host=localhost
-Dosgi.shell.telnet.maxconn=1
-Dfelix.fileinstall.bundles.startTransient=true
-Dcom.sun.enterprise.config.config_environment_factory_class=com.sun.enterprise.config.serverbeans.AppserverConfigEnvironmentFactory
-Dfelix.fileinstall.log.level=2
-Ddataverse.fqdn=ceia1.uvg.edu.gt
-Ddoi.dataciterestapiurlstring=https://api.test.datacite.org
-Djavax.net.ssl.keyStore=/usr/local/payara5/glassfish/domains/domain1/config/keystore.jks
-Djava.security.auth.login.config=/usr/local/payara5/glassfish/domains/domain1/config/login.conf
-Dfelix.fileinstall.disableConfigSave=false
-Ddataverse.rserve.port=6311
-Dcom.sun.aas.instanceRoot=/usr/local/payara5/glassfish/domains/domain1
-Dosgi.shell.telnet.port=6666
-Dfish.payara.classloading.delegate=false
-Ddataverse.files.directory=/usr/local/payara5/glassfish/domains/domain1/files
-DANTLR_USE_DIRECT_CLASS_LOADING=true
-Ddataverse.files.file.label=file
-Ddoi.baseurlstring=https://mds.test.datacite.org
-Dorg.glassfish.grizzly.nio.DefaultSelectorHandler.force-selector-spin-detection=true
-Djava.library.path=/usr/local/payara5/glassfish/lib:/usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
com.sun.enterprise.glassfish.bootstrap.ASMain
-upgrade
false
-domaindir
/usr/local/payara5/glassfish/domains/domain1
-read-stdin
true
-asadmin-args
--host,,,localhost,,,--port,,,4848,,,--secure=false,,,--terse=false,,,--extraterse=false,,,--echo=false,,,--interactive=true,,,--autoname=false,,,start-domain,,,--verbose=false,,,--watchdog=false,,,--debug=false,,,--domaindir,,,/usr/local/payara5/glassfish/domains,,,domain1
-domainname
domain1
-instancename
server
-type
DAS
-verbose
false
-asadmin-classpath
/usr/local/payara5/glassfish/lib/client/appserver-cli.jar
-debug
false
-asadmin-classname
com.sun.enterprise.admin.cli.AdminMain
-watchdog
false]]

Do I have to reinstall java too?

[Don Sizemore]

Hello,

Which version of Dataverse, and which version of Payara? There may be a quick fix depending on these versions.

If Payara wasn't shut down cleanly, you may just need to clean out some entries in the DB.

Don

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[Lynette García]

I installed payara-5.2021.6. using the prerequisite page link, and dataverse version I think is 5.11. 

Thank you

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[Don Sizemore]

Hello,

You might try to stop Payara, remove /usr/local/payara5/glassfish/domains/domain1/generated and /usr/local/payara5/glassfish/domains/domain1/osgi-cache , start Payara, then try to deploy again?

Later versions of Payara require that you remove the EJB directory entirely, but I'm not aware that this is the case for payara-5.2021.6.

Don

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[Lynette García]

Thanks for the answer. I deleted   /usr/local/payara5/glassfish/domains/domain1/generated and /usr/local/payara5/glassfish/domains/domain1/osgi-cache. I tried to deploy and I got this error:

remote failure: Error occurred during deployment: Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.7.7.payara-p3): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: java.sql.SQLException: Error in allocating a connection. Cause: Connection could not be allocated because: FATAL: password authentication failed for user "dataverse"
Error Code: 0. Please see server.log for more details.
Command deploy failed.

I deleted those folders again and tried to reinstall dataverse using the install.py file, because it creates that user and password in the database, but I got the same error message.

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[Don Sizemore]

Lynette,

This is a problem between your specified database credentials within Dataverse, and the credentials allowed by your Postgres service. Can you double-check that they're correct?

Don

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[Lynette García]

Yes, I double checked, I changed that user password and I could deploy dataverse. But now it is not working. I got this message after a successful install 

"You should now have a running Dataverse instance at
  http://192.168.10.125:8080"

But this is what I see:

The server is working I can access to other pages, but not dataverse

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[Don Sizemore]

Does the server's firewall allow you to connect on port 8080 from external machines?

From on the server, can you try a "curl http://localhost:8080/api/info/version" ?

Don

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[Lynette García]

I think so, this is the output of   "curl http://localhost:8080/api/info/version"

{"status":"OK","data":{"version":"5.11.1","build":"1069-02e3e92"}}

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[Don Sizemore]

Do you have Apache or Nginx installed on the server?

What happens if you take the ":8080" off the URL in your browser?

Currently, the Apache proxy stuff is documented as part of the Shibboleth installation, even if you're not using Shibboleth: https://guides.dataverse.org/en/latest/installation/shibboleth.html

Don

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[Lynette García]

Do you have Apache or Nginx installed on the server? Yes, I installed iRedMail and it installed both, I uninstalled apache and stopped Nginx service. The browser doesn't show anything with or without 8080. Solr service is running and Payara domain1 is running too. Dataverse is deployed with status OK

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[Don Sizemore]

Okay. Payara listens on port 8080 by default, but your firewall likely doesn't allow this port.

If this is a test server, allowing port 8080 is probably fine, but if this will be a public server you'll want nginx or Apache running in front of Payara, particularly if you'd like to use https.

It sounds like your Dataverse installation itself succeeded, you'll just want to put some sort of proxy in front of Payara?

Don

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[Philip Durbin]

Hi Lynette, just checking if you're all set now. Please let us know!

Thanks,

Phil

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--

Philip Durbin
Software Developer for http://dataverse.org
http://www.iq.harvard.edu/people/philip-durbin

[Lynette García]

Nop, trying to configure smtp server, something closed my ssh access. In Rocky 9 test server If I undeploy dataverse I see payara home page but when I deploy it again I get http error 500 and this error in server.logjavax.ejb.EJBException: getSingleResult() did not retrieve any entities.
        at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTran>
        at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionMa>
        at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionMan>
        at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4592)
        at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2125)
        at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2095)
        at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler>
        at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocatio>
        at com.sun.proxy.$Proxy300.findRootDataverse(Unknown Source)
        at edu.harvard.iq.dataverse.__EJB31_Generated__DataverseServiceBean__Intf____Bean__.findRootData>
        at edu.harvard.iq.dataverse.SettingsWrapper.getRootDataverse(SettingsWrapper.java:562)
        at edu.harvard.iq.dataverse.SettingsWrapper$Proxy$_$$_WeldClientProxy.getRootDataverse(Unknown S>
        at edu.harvard.iq.dataverse.DataversePage.init(DataversePage.java:322)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:>
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorIm>
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at com.sun.el.util.ReflectionUtil.invokeMethod(ReflectionUtil.java:163)
        at com.sun.el.parser.AstValue.invoke(AstValue.java:261)
 
I already did this with no luck remove /usr/local/payara5/glassfish/domains/domain1/generated and /usr/local/payara5/glassfish/domains/domain1/osgi-cache 

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[Philip Durbin]

Sorry, I've been busy with other things. Were you able to make any progress? When Dataverse is deployed, you should see a version number when you curl http://localhost:8080/api/info/version

It might be more efficient if you can join me (and Don, if he's available) to talk through this sometime in https://chat.dataverse.org

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