Dataverse Network Application First Impressions, Post Installation Beta mode^ Update #2

This is my second post after a long time and covers a lot of updates. After completing scoping and setting goals for the project before the break, i started the installation and configuration of Dataverse Network after the break starting from 7th January. As usual, before actually installing any software for real, you have to go via the testing phase and so did i ! Being in constant touch with the software developers of DVN at Harvard University helps a lot and they recomended me to test the DVN application using Vagrant which is a tool for building development evnironments as it lowers development envonronment setup time and increases development/production parity.

Purpose of the script- To create a VMware on centos and the necessary dependencies required to run DVN on it i.e. glassfish, java, postgre sq etc. and then install DVN, all done by the script with the help of the vagrant environment.

As i tried running the Test DVN network using vagrant following the guide dvn-vagrant i faced some issues like unable to install glassfish server on the VM - 

 After this error, i tried to run the glassfish installer manually via - "/bin/bash /root/glassfish-install.sh" which solved the installation issue but returned me another error -

and after that, when i ran the script again, it just didn't work due to some incompatibility with windows 7 OS and gave me back the iptables error.

Anyway, after one of the developers tried it on there own workstation then it worked, strangely enough (probably due to some incompatibility issue between OS'es). -

 

I went ahead with the full installation with the help of the Official DVN installation guide of the DVN application which includes installing and configuring these dependencies:

1) Oracle VMware 4.2 +

2) Glassfish 3.1.2

3) Postgresql 8.3+

4) R and Rserve

5) Some other scripts and software.

The bugs which i found during the installation and how i tackled them:

  1. Glassfish was not able to install at first. It was giving some incompatibility with java error. Able to solve by uninstalling the incorrect version and installing the correct version.
  2. Installation of postgresql was simple and easy.  Just followed the steps given in the installer’s guide. However changing the “var/lib/pgsql/data/pg_hba.conf” file was a little tricky. There were some errors in the installer’s guide as well. Had to use and learn “VIM editor” to make changes to the configuration file. Details of the change can be seen from - postgresql guide”.
  3. Installation of R and Rserve was straighforwad. Followed the installation guide.
  4. System configuration was plain and easy. opened the ports neccessary.

Now, the main part is running the installer. For the first time, the installer script asks for the confirmation of these settings in yes or no fashion-

"" Internet Address of your host: localhost.localdomain

Glassfish Directory: /usr/local/glassfish3

SMTP (mail) server to relay notification messages: localhost

Postgres Server: localhost

Postgres Server Port: 5432

Name of the Postgres Database: dvnDb

Name of the Postgres User: dvnApp

Postgres user password: secret

Rserve Server: localhost

Rserve Server Port: 6311

Rserve User Name: rserve

Rserve User Password: rserve ""

After entering the details, i recieved this error-

“””””ejbtimer.sql: No such file or directory

Could not create EJB timer entry in the database!

(command: /usr/bin/psql -d dvnDb -f ejbtimer.sql)

(psql exit code: 256)

Please consult the installation manual and/or

seek support from the DVN team.”””””””””

I think it "couldn't change directory" because I unpacked the files as a  normal user in my homedir, and then it tried to setuid to postgres to read the files, which it didn't have permission to. Possible fix might be to read in the files as the running user, and feed them to the privilege-separated command via STDIN. I fixed by changing the directory where I unzipped dvn-install from/desktop to /tmp directory.

Now, After this when I tried to run the script, it gave me the error that the script has already made a DB, so I have to delete the previous DB first or change the DB name in the script to get rid of the error.

I deleted the DB by these lines-

“Su – postgres

dropdb dvnDb“

Finally after some troubleshooting some other bugs (List is endless) I managed to install the application on the local host-

 

Here are some snapshots of the Dataverse network application while running for the first and making some tweaks in the GUI and adding dummy dataverse and files in it -

 


 

 

Immidiate goals for this week is to install and comnfigure the DVN application on the VMware which will be provided by NeSI and link it to the main NZSSDS website and start uploading the data and metadata in the newly created DVN.

I will follow up with my third update in next two weeks. Thanks. :)

Submitted by Shubham Sharma on

Comments

Why R integration?

Hey, looks like a lot of manual discovery :-) 

I wonder what is the R integration for?

Cheers, Alex

Hi Alex, Thanks for the feedback

Hi Alex, Thanks for the feedback. :) Well, R is a system for statistical computation and graphics. It consists of a language plus a run-time environment with graphics, a debugger, access to certain system functions, and the ability to run programs stored in script files and NZSSDS is a social science data service which has a lot of social science related raw data like surveys and collections which can be graphically represented and analysed by R and RServe for statistical analysis.

As they say, you can have the data but it's of no use if you can't analyse it. R serves that purpose for analysing data for the researcher's here at COMPASS research center and the students who wants to access it. Hope it helps. :)

Cheers, 

Shubham