Enable https, pretty index, add README for maven.bioviz.org

Prof. [~aloraine], could you please email me the login credentials?
Thanks

Attching a file with the configuration steps which one needs to follow in order to configure https as well as for enabling the pretty indexing and creation of the README.md file.
Changes are live and can be checked using the following link http://maven.bioviz.org.

Please take a look at comments for

• https://jira.transvar.org/browse/IGBF-1931

There may be a problem with some extant pipelines and poms. Maybe due to how redirected/rewritten URLs are handled in bitbucket pipeline build environment.

Can you look into it?

Noor Zahara can show you.

The reason why mentioned exception was occurring in the bitbucket pipeline is because we've shifted the maven repository to https and when the pipeline is trying to build the project when it encounters the need to import remote dependency, it sends a request to the maven repository server. At this point of time the SSL handshake is happening and the client tries to to find public certificate file in the default java keystore which exists in the lib/security/cacerts of JRE. Since the certificate is no there it is throwing the exception. For local machine, there are some commands which we can use to transfer the valid certificate in the default folder. But, for pipeline we need to change the JRE bundles which the docker image is using so that we can transfer the public certificate in the default directory which would eventually fix the problem.
For reference:
https://confluence.atlassian.com/kb/how-to-import-a-public-ssl-certificate-into-a-jvm-867025849.html#HowtoimportapublicSSLcertificateintoaJVM-commandline

Prof. [~aloraine], please let me know if we could do that or not. If yes, then I would need docker hub credentials.
Thanks.

I have a followup question/concern:

One thing that confuses me about is that the same certificates are being used to enable SSL for https://nexus.bioviz.org. That site is using also using Apache for hosting, but is configured differently.

I'll send you a link to some documentation describing how I set up and configured that site.

Can you read it over and think about how and why that site is working but maven.bioviz.org is not?

Follow-up:

I looked at: ssl.conf
This line was commented: SSLCertificateChainFile /etc/pki/tls/certs/DigiCertCA.crt
Next, I re-ran bitbucket pipeline for https://bitbucket.org/lorainelab/protannot/src/master/
It has passed.

Prutha Kulkarni - can you check the other pipelines?

This seems like the fix we need, but it should be checked out for other repositories.

Sure. I will check it for other repositories.
Thanks.

Prof. [~aloraine], I checked it for each repository. The pipeline is building successfully.
I have uncommented the line in the document also.
Shall I go ahead and change the repository links in the pom from http to https or the rewrite rule will take care of it?
Please let me know.

Sure, yes, that would be great - we should change http to https.
There are a lot of POMs – could take a while but definitely worth the effort.

HTTPS is working fine but pretty indexing is failing.
Returning to To-Do and re-assigning to Prutha Kulkarni

Prof. [~aloraine], I have checked the config file and fixed the fancyindexing issue.
It's working fine now. I have also changed the documentation accordingly and uploaded the updated one n the same ticket.
You can check it by accessing following link:
https://maven.bioviz.org/
Thanks.

It looks very nice – many thanks!
For the next steps, I would like make some edits to the documentation (readme file).
For that, would you assign the ticket to my user and move it back to "To-Do" for me to work on next?
Prutha Kulkarni

Sure Prof. [~aloraine]

Added some new text explaining what the site is. Copied everything, including styling code, to a dropbox for backup.
Marking this as done and re-assigning to original developer.