Installing Dataverse for first time on development

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Lewatle Johannes Phaladi

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Aug 22, 2018, 3:45:13 AM8/22/18
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Hi,

I am installing Dataverse for first time, and managed to install all the pre-requisites following this link : http://guides.dataverse.org/en/latest/installation/prerequisites.html 

I then run installation script as follows http://guides.dataverse.org/en/latest/installation/installation-main.html  and I receive message on CentOS terminal saying dataverse is installed successfully and i should be able to connect to it using http://ipaddress:8080 but it is not opening, please help.

Regards,
Lewatle 

Lewatle Johannes Phaladi

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Aug 22, 2018, 7:43:38 AM8/22/18
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When i open localhost:8080, i get to glassfish page not dataverse and after few minutes i get error 500
when i open http://localhost:4848 from terminal using cmd $http://localhost:4848 i get to the page but on web browser running on separate computer using IP as follows http://23.25.4.9.0:4848 i get no page to be displayed, any suggestion 

Philip Durbin

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Aug 22, 2018, 8:21:42 AM8/22/18
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It sounds like Glassfish is running but the Dataverse war file was not successfully deployed to it.

Some of the error checking may have been lost in 4.9.2 (especially on Mac, I thought CentOS was unaffected) and we plan to take another look at the installer in https://github.com/IQSS/dataverse/issues/4966

A few places to start troubleshooting:

- The complete output of the "install" script.
- The that's created that has a name like scripts/api/setup-all.sh1234
- /usr/local/glassfish4/glassfish/domains/domain1/logs/server.log

If you don't have any secrets or passwords in these files, please feel free to attach them. Or you can email them to sup...@dataverse.org to create a support ticket.

Thanks!

Phil

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Lewatle Johannes Phaladi

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Aug 22, 2018, 9:34:26 AM8/22/18
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All the following libraries failed to install, anyone with suggestion 


Installing the required R libraries

The following R packages (libraries) are required:

R2HTML
rjson
DescTools
Rserve
haven

Install them following the normal R package installation procedures. For example, with the following R commands:

install.packages("R2HTML", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )
install.packages("rjson", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )
install.packages("DescTools", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )
install.packages("Rserve", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )
install.packages("haven", repos="https://cloud.r-project.org/", lib="/usr/lib64/R/library" )

On Wednesday, 22 August 2018 09:45:13 UTC+2, Lewatle Johannes Phaladi wrote:

Philip Durbin

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Aug 22, 2018, 10:44:35 AM8/22/18
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What are the errors?

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Lewatle Johannes Phaladi

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Aug 23, 2018, 8:07:50 AM8/23/18
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Dear Philip,

Thanks a million times for help, I have attached server.log and setup-all.sh.2974.log files. please advice if I should run install script again to obtain the output or with this 2 files you may be able to locate the error.

Regards,
Lewatle 



On Wednesday, 22 August 2018 14:21:42 UTC+2, Philip Durbin wrote:
It sounds like Glassfish is running but the Dataverse war file was not successfully deployed to it.

Some of the error checking may have been lost in 4.9.2 (especially on Mac, I thought CentOS was unaffected) and we plan to take another look at the installer in https://github.com/IQSS/dataverse/issues/4966

A few places to start troubleshooting:

- The complete output of the "install" script.
- The that's created that has a name like scripts/api/setup-all.sh1234
- /usr/local/glassfish4/glassfish/domains/domain1/logs/server.log

If you don't have any secrets or passwords in these files, please feel free to attach them. Or you can email them to sup...@dataverse.org to create a support ticket.

Thanks!

Phil
On Wed, Aug 22, 2018 at 7:43 AM, Lewatle Johannes Phaladi <joem...@gmail.com> wrote:
When i open localhost:8080, i get to glassfish page not dataverse and after few minutes i get error 500
when i open http://localhost:4848 from terminal using cmd $http://localhost:4848 i get to the page but on web browser running on separate computer using IP as follows http://23.25.4.9.0:4848 i get no page to be displayed, any suggestion 

On Wednesday, 22 August 2018 09:45:13 UTC+2, Lewatle Johannes Phaladi wrote:
Hi,

I am installing Dataverse for first time, and managed to install all the pre-requisites following this link : http://guides.dataverse.org/en/latest/installation/prerequisites.html 

I then run installation script as follows http://guides.dataverse.org/en/latest/installation/installation-main.html  and I receive message on CentOS terminal saying dataverse is installed successfully and i should be able to connect to it using http://ipaddress:8080 but it is not opening, please help.

Regards,
Lewatle 

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server.log
setup-all.sh.29749.log

Lewatle Johannes Phaladi

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Aug 23, 2018, 8:27:16 AM8/23/18
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Hi, 

Now i can open glassfish successfully, after the network colleagues opened port 4848 and when i open http://ipaddress:4848 i get to glassfish, I have also created password for admin user of glassfish and now glasssfish is opening as https, the only issue i have  is that one i have reported of dataverse not opening on port 808, I am using link as http://Ipaddress:8080 and get blank page.

when i click on launch from glassfish application I get to the page displaying :


last time when i run ./install I used IP address as fully qualified domain name, previously I used  dataverse.domain.ac.za as fully qualified domain name meaning I run few installation of dataverse on same test server 

Regards,
Lewatle 


On Wednesday, 22 August 2018 09:45:13 UTC+2, Lewatle Johannes Phaladi wrote:

Philip Durbin

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Aug 23, 2018, 9:34:48 AM8/23/18
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Thanks for sending the logs. Right after "Setup the metadata blocks" we see a "404" which probably indicates that the Dataverse war file was not successfully deployed to Glassfish. Here's where that line appears: https://github.com/IQSS/dataverse/blob/v4.9.2/scripts/api/setup-all.sh#L37 . All the setup afterwards fails as well.

I would suggest following http://guides.dataverse.org/en/4.9.2/installation/installation-main.html#fresh-reinstall when ends in rerunning the installer. Next time if you can send the output of the installer it would be helpful.

Some of us are active in http://chat.dataverse.org right now if you want to ask questions there.

Thanks,

Phil

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Lewatle Johannes Phaladi

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Aug 24, 2018, 9:01:10 AM8/24/18
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Hi Phil,

I have tried the steps as you indicated and I am getting attached errors, at the moment is psql errors on postgres database, I would like to know how to resolve them, I have attached ./install output and setup-all.sh.18380.log

Regards,
Lewatle  
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screenOutPutsInstall.txt
setup-all.sh.18380.log

Philip Durbin

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Aug 24, 2018, 10:01:37 AM8/24/18
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Thanks. When you were following the "fresh reinstall" instructions, did you get any errors at the "drop database" step? I'm especially wondering about this step:

psql -U dvnapp -c 'DROP DATABASE "dvndb"' template1

This isn't mentioned in the "fresh reinstall" instructions but you could also consider moving your installation of Glassfish aside and installing a new copy.

Other thoughts are that you can practice the installation in a virtual machine on your laptop using Vagrant or you could try Ansible. The Vagrant option is described at http://guides.dataverse.org/en/4.9.2/installation/prep.html#vagrant-for-testing-only and the Ansible option is described at http://guides.dataverse.org/en/4.9.2/installation/prep.html#advanced-installation

Please do feel free to create a GitHub issue at https://github.com/IQSS/dataverse/issues because again, the installer changed in 4.9.2 and you might be encountering a bug. You could also try installing 4.9.1 instead. The instructions can be found at http://guides.dataverse.org/en/4.9.1/installation/

I hope you don't find the variety of options above overwhelming! Please keep the feedback coming and do feel free to join us in http://chat.dataverse.org if you'd like.

Thanks,

Phil



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Lewatle Johannes Phaladi

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Aug 27, 2018, 3:48:49 AM8/27/18
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Hi Phil, 

Yes I got error when running : psql -U dvnapp -c 'DROP DATABASE "dvndb"' template1 
I have logged on directly to postgres as postgres user not owning dvndb and run the following : 

SELECT pg_terminate_backend(pid)
FROM pg_stat_activity
WHERE datname = 'dvndb';

then i manually run DROP DATABASE dvndb;

succeeded
but template1 not done anything to it.

Regards,
Lewatle  
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Lewatle Johannes Phaladi

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Aug 27, 2018, 8:43:46 AM8/27/18
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At the moment I am getting the following error while installing version 4.9.2 :

Attempting to deploy the application.
Command line: /usr/local/glassfish4/bin/asadmin deploy dataverse.war
remote failure: Error occurred during deployment: Exception while loading the app : EJB Container initialization error. Please see s                                                                                                         erver.log for more details.
Command deploy failed.
Failed to deploy the application! WAR file: dataverse.war.
(exit code: 256)
Aborting.
Finished configuring postgres
/usr/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:

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
CREATE INDEX
INSERT 0 1

OK, done!
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  1086  100  1086    0     0   138k      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...

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www                                                                                                         .w3.org/1999/xhtml"><head><title>GlassFish Server Open Source Edition  4.1.2  - Error report</title><style type="text/css"><!--H1 {f                                                                                                         ont-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;col                                                                                                         or: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;c                                                                                                         olor:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color :                                                                                                          black;}HR {color : #525D76;}--></style> </head><body><h1>HTTP Status 403 - Forbidden</h1><hr/><p><b>type</b> Status report</p><p><b                                                                                                         >message</b>Forbidden</p><p><b>description</b>Access to the specified resource has been forbidden.</p><hr/><h3>GlassFish Server Open                                                                                                          Source Edition  4.1.2 </h3></body></html>OK.



You should now have a running DVN instance at

Pete Meyer

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Aug 27, 2018, 10:27:40 AM8/27/18
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On Monday, August 27, 2018 at 8:43:46 AM UTC-4, Lewatle Johannes Phaladi wrote:
At the moment I am getting the following error while installing version 4.9.2 :

Attempting to deploy the application.
Command line: /usr/local/glassfish4/bin/asadmin deploy dataverse.war
remote failure: Error occurred during deployment: Exception while loading the app : EJB Container initialization error. Please see s                                                                                                         erver.log for more details.
Command deploy failed.
Failed to deploy the application! WAR file: dataverse.war.
(exit code: 256)
Aborting.


Is there anything informative in server.log?
 

Lewatle Johannes Phaladi

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Aug 29, 2018, 3:13:51 AM8/29/18
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Hi Peter and Colleagues,

I have attached server log as requested.

Regards,
Lewatle 
server.log

Pete Meyer

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Aug 29, 2018, 10:58:19 AM8/29/18
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Hi Lewatle,

Thanks - that log file is consistent with an installation that deployed the application, but failed to create the root dataverse.  Two things I suspect could cause this are a problem with the glassfish/postgresql connection, or the glassfish domain that dataverse is deployed to not listening for traffic from localhost:8080 (on the system that the installer is being run from).

Possible things to check:
- `curl http://localhost:8080/api/info/version` should return something like `{"status":"OK","data":{"version":"4.9.2","build":"940-4ad7bf5"}}`.  If not, that suggests a problem with glassfish domain configuration (assuming that `asadmin list-applications` shows data verse as being deployed).
- double-check that the database does not exist prior to running the installer, and that the postgresql credentials are correct (from your earlier messages, this sounds less likely to be an issue).

Best,
Pete

Philip Durbin

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Sep 6, 2018, 2:24:13 PM9/6/18
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Hi Lewatle,

I'm catching up on email after being away and I hope you were able to get Dataverse installed. If not, please let us know here or via a support ticket at sup...@dataverse.org

Thanks!

Phil

Pete
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