[dvnuser@libsandbox dvinstall]$ sudo ./install using hard-coded default configuration values (default.config not found) No pre-configured user found; using root. #################################################################### It is recommended that this script not be run as root. Consider creating a glassfish service account, giving it ownership on the glassfish/domains/domain1/ and glassfish/lib/ directories, along with the JVM-specified files.dir location, and running this installer as the user who will launch Glassfish. #################################################################### uid=0(root) gid=0(root) groups=0(root) Welcome to the Dataverse installer. You will be guided through the process of setting up a NEW instance of the dataverse application This appears to be a RedHat system; good. Please enter the following configuration values: (hit [RETURN] to accept the default value) Fully Qualified Domain Name of your host: (enter numeric IP address, if FQDN is unavailable) [sandbox.domain.ac.za] 263.258.3.6 Glassfish service account username: This user will be running Glassfish service on your system. - If this is a dev. environment, this should be your own username; - In production, we suggest "glassfish" or another unprivileged user : [root] dvnuser Glassfish Directory: [/usr/local/glassfish4] Checking your Glassfish installation...OK! Administrator email address for this Dataverse: (please enter a valid email address!) [] user@domain.ac.za SMTP (mail) server to relay notification messages: [mail.hmdc.harvard.edu] mgmail.domain.ac.za Postgres Server Address: [127.0.0.1] Postgres Server Port: [5432] Postgres ADMIN password: - We will need this to create the user and database that the Dataverse application will be using. (Hit RETURN if access control is set to "trust" for this connection in pg_hba.conf) : [secret] Name of the Postgres Database: [dvndb] Name of the Postgres User: - This is the Postgres user that the Dataverse app will be using to talk to the database : [dvnapp] Postgres user password: [secret] Remote SOLR indexing service? - Leave this set to "LOCAL" if the SOLR will be running on the same (this) server. Otherwise, please enter the host AND THE PORT NUMBER of the remote SOLR service, colon-separated (for example: foo.edu:8983) : [LOCAL] Rserve Server: [localhost] Rserve Server Port: [6311] Rserve User Name: [rserve] Rserve User Password: [rserve] OK, please confirm what you've entered: Fully Qualified Domain Name of your host: 12.236.256.336 Glassfish service account username: dvnuser Glassfish Directory: /usr/local/glassfish4 Administrator email address for this Dataverse: user@domain.ac.za SMTP (mail) server to relay notification messages: mgimail.domai.ac.za Postgres Server Address: 127.0.0.1 Postgres Server Port: 5432 Postgres ADMIN password: secret Name of the Postgres Database: dvndb Name of the Postgres User: dvnapp Postgres user password: secret Remote SOLR indexing service: LOCAL Rserve Server: localhost Rserve Server Port: 6311 Rserve User Name: rserve Rserve User Password: rserve Is this correct? [y/n] y Checking if the application .war file is available... Yes, it is! /bin Found Postgres psql command, version 9.6.10. (We'll be Using psql version 9.6) 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: OK, done! Finished configuring postgres Proceeding with the Glassfish setup. We must be running in Docker! Fancy! /sys/fs/cgroup/memory/memory.limit_in_bytes: 9223372036854771712 Docker limit_in_kb = 9007199254740988 but ignoring Setting the heap limit for Glassfish to 2933MB. 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... h openjdk version "1.8.0_181" OpenJDK Runtime Environment (build 1.8.0_181-b13) OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode) domain appears to be up... Enter admin user name [Enter to accept default]> Enter admin password> Admin login information for host [localhost] and port [4848] is being overwritten with credentials pr ovided. 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] stor ed at [/root/.gfclient/pass] successfully. Make sure that this file remains protected. Information stored in this file will be used by administr ation 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 /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 -Ddataverse.files.directory=/usr/local/glassfish4/glassfish/domains/domain 1/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=146.141.12.29 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 th e 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. remote failure: JVM option -Ddataverse.timerServer=true 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: Network Listener named jk-connector already exists. Command create-network-listener failed. No jvm-options were deleted (perhaps they never existed in the configuration) Command delete-jvm-options executed successfully. remote failure: JVM option -Xmx2933m already exists in the configuration. Command create-jvm-options failed. remote failure: A resource named dvnDbPool already exists. Command create-jdbc-connection-pool failed. remote failure: A JdbcResource by name jdbc/VDCNetDS already exists with resource-ref in target server. Command create-jdbc-resource failed. configs.config.server-config.ejb-container.ejb-timer-service.timer-datasource=jdbc/VDCNetDS Command set executed successfully. 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: A MailResource by name mail/notifyMailSession already exists with resource-ref in target server. Command create-javamail-resource failed. Updates done. Restarting... Server is not running, will attempt to start it... Corrupt domain. The config directory does not exist. I was looking for it here: /usr/local/glassfish4/glassfish/domains/domain1/config Command restart-domain failed. /tmp/dvinstall Glassfish setup complete Fri Aug 24 14:20:49 SAST 2018 Copying additional configuration files... done! Attempting to deploy the application. Command line: /usr/local/glassfish4/bin/asadmin deploy dataverse.war remote failure: Error occurred during deployment: Exception while deploying the app [dataverse] : Exception [EclipseLink-4019] (Eclipse Persistence Services - 2.6.1.v20150605-31e8258): org.eclipse.persistence.exceptions.DatabaseException Exception Description: Error while obtaining information about the database. Refer to the nested exception for more details.. Please see server.log for more details. Command deploy failed. Failed to deploy the application! WAR file: dataverse.war. (exit code: 256) Aborting. Finished configuring postgres /bin Found Postgres psql command, version 9.6.10. (We'll be Using psql version 9.6) Checking if we can talk to Postgres as the admin user... Pre-populating the database: psql:reference_data.sql:2: ERROR: relation "foreignmetadataformatmapping" does not exist LINE 1: INSERT INTO foreignmetadataformatmapping(id, name, startelem... ^ psql:reference_data.sql:3: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:4: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:5: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:6: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:7: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:8: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:9: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:10: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:11: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:12: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:13: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:14: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:15: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:16: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:17: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:18: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:19: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:20: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:21: ERROR: relation "foreignmetadatafieldmapping" does not exist LINE 1: INSERT INTO foreignmetadatafieldmapping (id, foreignfieldxpa... ^ psql:reference_data.sql:27: ERROR: relation "guestbook" does not exist LINE 1: INSERT INTO guestbook( ^ psql:reference_data.sql:31: ERROR: relation "dataverse" does not exist psql:reference_data.sql:32: ERROR: relation "authenticateduser" does not exist psql:reference_data.sql:33: ERROR: relation "builtinuser" does not exist psql:reference_data.sql:38: ERROR: relation "datasetversion" does not exist psql:reference_data.sql:51: ERROR: relation "worldmapauth_tokentype" does not exist LINE 1: INSERT INTO worldmapauth_tokentype ^ OK, done! % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 1086 100 1086 0 0 142k 0 --:--:-- --:--:-- --:--:-- 151k It appears that the Dataverse application is not running... Even though the "asadmin deploy" command had succeeded earlier. Aborting - sorry... OK, the Dataverse application appears to be running... using default contact email for root dataverse Executing post-deployment setup script setup-all.sh... done! Making additional configuration changes... Executing curl -X PUT -d user@domain.ac.za http://localhost:8080/api/admin/settings/:SystemEmail GlassFish Server Open Source Edition 4.1.2 - Error report

HTTP Status 403 - Forbidden

type Status report

messageForbidden

descriptionAccess to the specified resource has been forbidden.

GlassFish Server Open Source Edition 4.1.2

OK. You should now have a running DVN instance at http://148.146.13.21:8080