glassfish web page instead of dataverse web page
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Adilia Alves
Feb 27, 2020, 6:33:34 PM2/27/20
to Dataverse Users Community
Hello.
I deploied dataverse but I see glassfish web page instead of dataverse web page on https://localhost:80. Why is this happening?
No error was reported as you can see:
"Found Postgres psql command, version 9.6.17.
(Using psql version 9.6: /bin/psql)
Checking if we can talk to Postgres as the admin user...
Yes, we can!
Configuring Postgres Database:
User (role)***********already exists;
Proceeding.
Creating Postgres database:
OK, done.
Proceeding with the Glassfish setup.
INFO: This system has the CGROUP file /sys/fs/cgroup/memory/memory.limit_in_bytes
INFO: /sys/fs/cgroup/memory/memory.limit_in_bytes: 9223372036854771712
INFO: CGROUP limit_in_kb = 9007199254740988 [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...
openjdk version "1.8.0_232"
OpenJDK Runtime Environment (build 1.8.0_232-b09)
OpenJDK 64-Bit Server VM (build 25.232-b09, 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 ***** 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**** for host [localhost] and admin port ***** 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 /usr/local/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: Password alias with the specified name already exists. Please use the update-password-alias command to change it
Command create-password-alias failed.
remote failure: Password alias with the specified name already exists. Please use the update-password-alias command to change it
Command create-password-alias failed.
remote failure: Password alias with the specified name already exists. Please use the update-password-alias command to change it
Command create-password-alias failed.
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=${ALIAS=rserve_password_alias} already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.fqdn=dados.ipb.pt already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.auth.password-reset-timeout-in-minutes=60 already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.username=FCT.IPBRAGANCA already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.password=${ALIAS=doi_password_alias} already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.baseurlstring=https://datacite.org already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.mdcbaseurlstring=https://api.datacite.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.
resources.jdbc-connection-pool.dvnDbPool.property.password=${ALIAS=db_password_alias}
Command set executed successfully.
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.
Mail resource mail/notifyMailSession deleted.
Command delete-javamail-resource executed successfully.
Mail Resource mail/notifyMailSession created.
Command create-javamail-resource executed successfully.
Updates done. Restarting...
Waiting for the domain to stop
Command stop-domain executed successfully.
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.
/usr/local/dvinstall
Glassfish setup complete
Thu Feb 27 11:21:20 WET 2020
Copying additional configuration files... done!
Attempting to deploy the application.
Command line: /usr/local/glassfish4/bin/asadmin deploy dataverse.war
Application deployed with name dataverse.
Command deploy executed successfully.
Finished configuring Glassfish and deploying the dataverse application.
populating the database with reference data:
EXECUTING PSQL COMMAND: PGPASSWORD=secret; export PGPASSWORD; /bin/psql -h 127.0.0.1 -p 5432 -U dvnapp -d dvndb -f reference_data.sql
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
INSERT 0 1
INSERT 0 1
CREATE INDEX
CREATE INDEX
CREATE INDEX
INSERT 0 1
OK, done!
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 aia...@ipb.pt http://localhost:8080/api/admin/settings/:SystemEmail
<html><head><title>Apache Tomcat/7.0.76 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 403 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>Access to the specified resource has been forbidden.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.76</h3></body></html>OK.
You should now have a running Dataverse instance at
http://dados.ipb.pt:80
Your Dataverse has been configured to use DataCite, to register DOI global identifiers in the
test name space "10.5072" with the "shoulder" "FK2"
However, you have to contact DataCite (sup...@datacite.org) and request a test account, before you
can publish datasets. Once you receive the account name and password, add them to your domain.xml,
as the following two JVM options:
<jvm-options>-Ddoi.username=...</jvm-options>
<jvm-options>-Ddoi.password=...</jvm-options>
and restart glassfish
If this is a production Dataverse and you are planning to register datasets as
"real", non-test DOIs or Handles, consult the "Persistent Identifiers and Publishing Datasets"
section of the Installataion guide, on how to configure your Dataverse with the proper registration
credentials.
$
"
(Using psql version 9.6: /bin/psql)
Checking if we can talk to Postgres as the admin user...
Yes, we can!
Configuring Postgres Database:
User (role)***********already exists;
Proceeding.
Creating Postgres database:
OK, done.
Proceeding with the Glassfish setup.
INFO: This system has the CGROUP file /sys/fs/cgroup/memory/memory.limit_in_bytes
INFO: /sys/fs/cgroup/memory/memory.limit_in_bytes: 9223372036854771712
INFO: CGROUP limit_in_kb = 9007199254740988 [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...
openjdk version "1.8.0_232"
OpenJDK Runtime Environment (build 1.8.0_232-b09)
OpenJDK 64-Bit Server VM (build 25.232-b09, 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 ***** 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**** for host [localhost] and admin port ***** 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 /usr/local/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: Password alias with the specified name already exists. Please use the update-password-alias command to change it
Command create-password-alias failed.
remote failure: Password alias with the specified name already exists. Please use the update-password-alias command to change it
Command create-password-alias failed.
remote failure: Password alias with the specified name already exists. Please use the update-password-alias command to change it
Command create-password-alias failed.
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=${ALIAS=rserve_password_alias} already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.fqdn=dados.ipb.pt already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddataverse.auth.password-reset-timeout-in-minutes=60 already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.username=FCT.IPBRAGANCA already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.password=${ALIAS=doi_password_alias} already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.baseurlstring=https://datacite.org already exists in the configuration.
Command create-jvm-options failed.
remote failure: JVM option -Ddoi.mdcbaseurlstring=https://api.datacite.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.
resources.jdbc-connection-pool.dvnDbPool.property.password=${ALIAS=db_password_alias}
Command set executed successfully.
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.
Mail resource mail/notifyMailSession deleted.
Command delete-javamail-resource executed successfully.
Mail Resource mail/notifyMailSession created.
Command create-javamail-resource executed successfully.
Updates done. Restarting...
Waiting for the domain to stop
Command stop-domain executed successfully.
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.
/usr/local/dvinstall
Glassfish setup complete
Thu Feb 27 11:21:20 WET 2020
Copying additional configuration files... done!
Attempting to deploy the application.
Command line: /usr/local/glassfish4/bin/asadmin deploy dataverse.war
Application deployed with name dataverse.
Command deploy executed successfully.
Finished configuring Glassfish and deploying the dataverse application.
populating the database with reference data:
EXECUTING PSQL COMMAND: PGPASSWORD=secret; export PGPASSWORD; /bin/psql -h 127.0.0.1 -p 5432 -U dvnapp -d dvndb -f reference_data.sql
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
INSERT 0 1
INSERT 0 1
CREATE INDEX
CREATE INDEX
CREATE INDEX
INSERT 0 1
OK, done!
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 aia...@ipb.pt http://localhost:8080/api/admin/settings/:SystemEmail
<html><head><title>Apache Tomcat/7.0.76 - Error report</title><style><!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}A.name {color : black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 403 - </h1><HR size="1" noshade="noshade"><p><b>type</b> Status report</p><p><b>message</b> <u></u></p><p><b>description</b> <u>Access to the specified resource has been forbidden.</u></p><HR size="1" noshade="noshade"><h3>Apache Tomcat/7.0.76</h3></body></html>OK.
You should now have a running Dataverse instance at
http://dados.ipb.pt:80
Your Dataverse has been configured to use DataCite, to register DOI global identifiers in the
test name space "10.5072" with the "shoulder" "FK2"
However, you have to contact DataCite (sup...@datacite.org) and request a test account, before you
can publish datasets. Once you receive the account name and password, add them to your domain.xml,
as the following two JVM options:
<jvm-options>-Ddoi.username=...</jvm-options>
<jvm-options>-Ddoi.password=...</jvm-options>
and restart glassfish
If this is a production Dataverse and you are planning to register datasets as
"real", non-test DOIs or Handles, consult the "Persistent Identifiers and Publishing Datasets"
section of the Installataion guide, on how to configure your Dataverse with the proper registration
credentials.
$
"
What can I do to fix this?
Philip Durbin
Feb 27, 2020, 6:49:45 PM2/27/20
to dataverse...@googlegroups.com
Hi! "Access to the specified resource has been forbidden" when setting the system email is a bad sign. :(
Have you tried dataverse-ansible? It has been described* as a work of art. The artist is Don Sizemore from UNC. My main role was to add a little quickstart to the README here: https://github.com/IQSS/dataverse-ansible#quickstart
We use dataverse-ansible in our automated testing of Dataverse and couldn't have gotten to where we are so quickly without it. THANK YOU DON SIZEMORE!
Don and I are often in https://chat.dataverse.org M-F 9-5 East Coast US time if that time is convenient for you.
In addition, there is a fancy new Python installer to try if you are feeling brave. Please see https://github.com/IQSS/dataverse/blob/v4.19/scripts/installer/README_python.txt via "NEW in v.4.19" at http://guides.dataverse.org/en/4.19/installation/installation-main.html
I hope this helps!
Phil
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--
Philip Durbin
Software Developer for http://dataverse.org
http://www.iq.harvard.edu/people/philip-durbin
Software Developer for http://dataverse.org
http://www.iq.harvard.edu/people/philip-durbin
Don Sizemore
Feb 28, 2020, 10:36:42 AM2/28/20
to dataverse...@googlegroups.com
Adilia,
IQSS recommends that the setup script be run as an unprivileged user (usually glassfish) but if you're like me and launch the installer with sudo -u glassfish, you'll need to first make sure that the unprivileged user can write to the working directory when you launch the script.
If I forget to do this on a test system, the setup-all.sh portion fails and leaves me in the state you describe.
Let me know if that doesn't do the trick?
D
On Thu, Feb 27, 2020 at 6:33 PM Adilia Alves <aidc...@gmail.com> wrote:
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