Fresh installation of Dataverse 4.4 on Centos6.8 - deployed successfully can't access from URL.
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susan borda
Jul 25, 2016, 12:52:57 PM7/25/16
to Dataverse Users Community
Hi All-
I'm doing a fresh install of DVN 4.4 on a Centos 6.8 VM, install completes successfully (?) but I can't access the instance via the URL. I have attached the Glassfish server.log. Here is the info from the deployment. Any advice would be great.
Thanks,
susan
**** Passwords have been removed ****
Fully Qualified Domain Name of your host: dv-pilot.rci.montana.edu
Glassfish Directory: /usr/local/glassfish4
Administrator email address for this Dataverse: susan...@montana.edu
SMTP (mail) server to relay notification messages: smtp.office365.com
Postgres Server Address: 127.0.0.1
Postgres Server Port: 5432
Postgres ADMIN password:
Name of the Postgres Database: dvndb
Name of the Postgres User: dvnapp
Postgres user password:
Remote SOLR indexing service: LOCAL
Will this Dataverse be using TwoRavens application: NOT INSTALLED
Rserve Server: localhost
Rserve Server Port: 6311
Rserve User Name: rserve
Rserve User Password: rserve
Checking if the application .war file is available... Yes, it is!
Found Postgres psql command, version 9.4.8.
(We'll be Using psql version 9.4)
Checking if we can talk to Postgres as the admin user...
Yes, we can!
Configuring Postgres Database:
User (role) dvnapp already exists;
Proceeding.
Creating Postgres database:
Proceeding with the Glassfish setup.
Setting the heap limit for Glassfish to 703MB.
You may need to adjust this setting to better suit
your system.
Installing the Glassfish PostgresQL driver... done!
*********************
PLEASE NOTE, SOME OF THE ASADMIN COMMANDS ARE GOING TO FAIL,
FOR EXAMPLE, IF A CONFIGURATION SETTING THAT WE ARE TRYING
TO CREATE ALREADY EXISTS; OR IF A JVM OPTION THAT WE ARE
DELETING DOESN'T. THESE "FAILURES" ARE NORMAL!
*********************
When/if asadmin asks you to "Enter admin user name",
it should be safe to hit return and accept the default
(which is "admin").
Press any key to continue...
openjdk version "1.8.0_101"
OpenJDK Runtime Environment (build 1.8.0_101-b13)
OpenJDK 64-Bit Server VM (build 25.101-b13, mixed mode)
domain1 not running
Trying to start domain up...
Waiting for domain1 to start ...................
Successfully started the domain : domain1
domain Location: /usr/local/glassfish4/
glassfish/domains/domain1
Log File: /usr/local/glassfish4/glassfish/domains/domain1/logs/server.log
Admin Port: 4848
Command start-domain executed successfully.
Enter admin user name [Enter to accept default]>
Admin login information for host [localhost] and port [4848] is being overwritten with credentials provided. This is because the --savelogin option was used during create-domain command.
Login information relevant to admin user name [admin] for host [localhost] and admin port [4848] stored at [/root/.gfclient/pass] successfully.
Make sure that this file remains protected. Information stored in this file will be used by administration commands to manage associated domain.
Command login executed successfully.
checking glassfish root:/usr/local/glassfish4
checking glassfish domain:/usr/local/glassfish4/glassfish/domains/domain1
Setting up your glassfish4 to support Dataverse
Glassfish directory: /usr/local/glassfish4
Domain directory: /usr/local/glassfish4/glassfish/domains/domain1
/usr/local/glassfish4/bin /var/tmp/dvinstall
domain running
remote failure: Application dataverse-4.0 is not deployed on this target [server]
Command undeploy failed.
No jvm-options were deleted (perhaps they never existed in the configuration)
Command delete-jvm-options executed successfully.
remote failure: JVM option -XX:MaxPermSize=512m already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -XX:PermSize=256m already exists in the configuration.
Command create-jvm-options failed.
No jvm-options were deleted (perhaps they never existed in the configuration)
Command delete-jvm-options executed successfully.
remote failure: JVM option -Xmx703m already exists in the configuration.
Command create-jvm-options failed.
No jvm-options were deleted (perhaps they never existed in the configuration)
Command delete-jvm-options executed successfully.
Deprecated syntax, instead use:
asadmin --secure --echo create-jvm-options [options] ...
asadmin --host localhost --port 4848 --user admin --secure --interactive=true --echo=true --terse=false create-jvm-options --target server -server
NCLS-ADMIN-00010
javax.net.ssl.SSLHandshakeException: Remote host closed connection during handshake
Command create-jvm-options failed.
JDBC Connection pool dvnDbPool deleted successfully
Command delete-jdbc-connection-pool executed successfully.
JDBC connection pool dvnDbPool created successfully.
Command create-jdbc-connection-pool executed successfully.
JDBC resource jdbc/VDCNetDS created successfully.
Command create-jdbc-resource executed successfully.
configs.config.server-config.ejb-container.ejb-timer-service.timer-datasource=jdbc/VDCNetDS
Command set executed successfully.
remote failure: JVM option -Ddataverse.files.directory=/usr/local/glassfish4/glassfish/domains/domain1/files already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.rserve.host=localhost already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.rserve.port=6311 already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.rserve.user=rserve already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.rserve.password=rserve already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.fqdn=dv-pilot.rci.montana.edu already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.auth.password-reset-timeout-in-minutes=60 already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.password=apitest already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.username=apitest already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.baseurlstring=https://ezid.cdlib.org already exists in the configuration.
Command create-jvm-options failed.
server-config.network-config.protocols.protocol.http-listener-1.http.comet-support-enabled=true
Command set executed successfully.
remote failure: A connector connection pool named jms/__defaultConnectionFactory-Connection-Pool does not exist.
Command delete-connector-connection-pool failed.
remote failure: A resource named jms/IngestQueueConnectionFactoryPool already exists.
Command create-connector-connection-pool failed.
remote failure: A ConnectorResource by name jms/IngestQueueConnectionFactory already exists with resource-ref in target server.
Command create-connector-resource failed.
remote failure: A AdminObjectResource by name jms/DataverseIngest already exists with resource-ref in target server.
Command create-admin-object failed.
remote failure: A MailResource by name mail/notifyMailSession already exists with resource-ref in target server.
Command create-javamail-resource failed.
remote failure: Network Listener named jk-connector already exists.
Command create-network-listener failed.
Updates done. Restarting...
Successfully restarted the domain
Command restart-domain executed successfully.
/var/tmp/dvinstall
Glassfish setup complete
Fri Jul 22 15:24:41 MDT 2016
Copying additional configuration files... done!
Attempting to deploy the application.
Command line: /usr/local/glassfish4/bin/asadmin deploy dataverse.war
PER01003: Deployment encountered SQL Exceptions:
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAVERSE_fk_dataverse_id ON DATAVERSE (fk_dataverse_id)": org.postgresql.util.PSQLException: ERROR: column "fk_dataverse_id" does not exist
Command deploy completed with warnings.
Pre-populating the database:
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
CREATE INDEX
CREATE INDEX
CREATE INDEX
CREATE INDEX
INSERT 0 1
OK, done!
OK, the Dataverse application appears to be running...
Executing post-deployment setup script setup-all.sh... done!
Making additional configuration changes...
Executing curl -X PUT -d susan...@montana.edu http://localhost:8080/api/admin/settings/:SystemEmail
{"status":"OK","data":{":SystemEmail":"susan.borda@montana.edu"}}OK.
Executing curl -X PUT -d false http://localhost:8080/api/admin/settings/:TwoRavensTabularView
{"status":"OK","data":{":TwoRavensTabularView":"false"}}OK.
You should now have a running DVN instance at
http://dv-pilot.rci.montana.edu:8080
Log File: /usr/local/glassfish4/glassfish/domains/domain1/logs/server.log
Admin Port: 4848
Command start-domain executed successfully.
Enter admin user name [Enter to accept default]>
Admin login information for host [localhost] and port [4848] is being overwritten with credentials provided. This is because the --savelogin option was used during create-domain command.
Login information relevant to admin user name [admin] for host [localhost] and admin port [4848] stored at [/root/.gfclient/pass] successfully.
Make sure that this file remains protected. Information stored in this file will be used by administration commands to manage associated domain.
Command login executed successfully.
checking glassfish root:/usr/local/glassfish4
checking glassfish domain:/usr/local/glassfish4/glassfish/domains/domain1
Setting up your glassfish4 to support Dataverse
Glassfish directory: /usr/local/glassfish4
Domain directory: /usr/local/glassfish4/glassfish/domains/domain1
/usr/local/glassfish4/bin /var/tmp/dvinstall
domain running
remote failure: Application dataverse-4.0 is not deployed on this target [server]
Command undeploy failed.
No jvm-options were deleted (perhaps they never existed in the configuration)
Command delete-jvm-options executed successfully.
remote failure: JVM option -XX:MaxPermSize=512m already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -XX:PermSize=256m already exists in the configuration.
Command create-jvm-options failed.
No jvm-options were deleted (perhaps they never existed in the configuration)
Command delete-jvm-options executed successfully.
remote failure: JVM option -Xmx703m already exists in the configuration.
Command create-jvm-options failed.
No jvm-options were deleted (perhaps they never existed in the configuration)
Command delete-jvm-options executed successfully.
Deprecated syntax, instead use:
asadmin --secure --echo create-jvm-options [options] ...
asadmin --host localhost --port 4848 --user admin --secure --interactive=true --echo=true --terse=false create-jvm-options --target server -server
NCLS-ADMIN-00010
javax.net.ssl.SSLHandshakeException: Remote host closed connection during handshake
Command create-jvm-options failed.
JDBC Connection pool dvnDbPool deleted successfully
Command delete-jdbc-connection-pool executed successfully.
JDBC connection pool dvnDbPool created successfully.
Command create-jdbc-connection-pool executed successfully.
JDBC resource jdbc/VDCNetDS created successfully.
Command create-jdbc-resource executed successfully.
configs.config.server-config.ejb-container.ejb-timer-service.timer-datasource=jdbc/VDCNetDS
Command set executed successfully.
remote failure: JVM option -Ddataverse.files.directory=/usr/local/glassfish4/glassfish/domains/domain1/files already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.rserve.host=localhost already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.rserve.port=6311 already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.rserve.user=rserve already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.rserve.password=rserve already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.fqdn=dv-pilot.rci.montana.edu already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.auth.password-reset-timeout-in-minutes=60 already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.password=apitest already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.username=apitest already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.baseurlstring=https://ezid.cdlib.org already exists in the configuration.
Command create-jvm-options failed.
server-config.network-config.protocols.protocol.http-listener-1.http.comet-support-enabled=true
Command set executed successfully.
remote failure: A connector connection pool named jms/__defaultConnectionFactory-Connection-Pool does not exist.
Command delete-connector-connection-pool failed.
remote failure: A resource named jms/IngestQueueConnectionFactoryPool already exists.
Command create-connector-connection-pool failed.
remote failure: A ConnectorResource by name jms/IngestQueueConnectionFactory already exists with resource-ref in target server.
Command create-connector-resource failed.
remote failure: A AdminObjectResource by name jms/DataverseIngest already exists with resource-ref in target server.
Command create-admin-object failed.
remote failure: A MailResource by name mail/notifyMailSession already exists with resource-ref in target server.
Command create-javamail-resource failed.
remote failure: Network Listener named jk-connector already exists.
Command create-network-listener failed.
Updates done. Restarting...
Successfully restarted the domain
Command restart-domain executed successfully.
/var/tmp/dvinstall
Glassfish setup complete
Fri Jul 22 15:24:41 MDT 2016
Copying additional configuration files... done!
Attempting to deploy the application.
Command line: /usr/local/glassfish4/bin/asadmin deploy dataverse.war
PER01003: Deployment encountered SQL Exceptions:
PER01000: Got SQLException executing statement "CREATE INDEX INDEX_DATAVERSE_fk_dataverse_id ON DATAVERSE (fk_dataverse_id)": org.postgresql.util.PSQLException: ERROR: column "fk_dataverse_id" does not exist
Command deploy completed with warnings.
Pre-populating the database:
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
CREATE INDEX
CREATE INDEX
CREATE INDEX
CREATE INDEX
INSERT 0 1
OK, done!
OK, the Dataverse application appears to be running...
Executing post-deployment setup script setup-all.sh... done!
Making additional configuration changes...
Executing curl -X PUT -d susan...@montana.edu http://localhost:8080/api/admin/settings/:SystemEmail
{"status":"OK","data":{":SystemEmail":"susan.borda@montana.edu"}}OK.
Executing curl -X PUT -d false http://localhost:8080/api/admin/settings/:TwoRavensTabularView
{"status":"OK","data":{":TwoRavensTabularView":"false"}}OK.
You should now have a running DVN instance at
http://dv-pilot.rci.montana.edu:8080
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