Upgrade to Tripal 4 + Drupal 9

[laceysanderson]

Work on this has been begun by @reynoldtan on branch 9.x-2.x. We have a PR open #81 for testing of the current upgrade and would appreciate feedback on this issue or the PR if you are interested in using this module for Tripal 4.

THIS ISSUE SHOULD NOT BE CLOSED UNTIL

• Tripal 4 stable is released
• 9.x-2.x branch is made the default branch
• all documentation has been upgraded to the Drupal 9 / Tripal 4 / Tripal BLAST 2.x

[chunhuaicheng]

Hi, is there any progress on upgrading this module to Drupal9/10? If there is a new branch available, we can help test it.

[laceysanderson]

Hi! Thanks for touching base :-) All the current work is in the 9.x-4.x branch.

My colleague @reynoldtan worked on it and I haven't gotten the chance to try it out yet myself :-) I think this was all done before Tripal Jobs were ready so it may not yet work fully but we would welcome you to try it and report back through issues and what not.

This module will definitely be upgraded for Tripal 4 well before the Drupal end of life but we are currently not planning to work on it for a couple of months... but if we see enough interest I may be able to bump it up sooner. So if you need this make sure you try it out and make issues for anything not working or complete.

[chunhuaicheng]

That is great! We'll give it a try once our new dev site is ready and report any problem we find. Thank you!

[chunhuaicheng]

Just tried and the 9.x-2.x branch could not be installed on either Drupal 9 or Drupal 10. We'll wait till it is ready for testing. Thanks!

[smriti-135]

I am in dire need of this!

As part of college course work, I am required to make a genomic database for a local website with basic features (like gene search, sequence alignment). I have installed Drupal 10.2.3 with PostgreSQL 14.11, PHP 8.3.4 and Tripal 4.0.0-alpha2.

My main doubt is, considering the time frame I have to finish this course (1 month), can I afford to wait for module upgradation to support Drupal 10/Tripal 4 or should I redo the whole project with Drupal 7? Or is there anything else I am missing? I am looking to create this as part of my course project that can be converted to a full-fledged website beyond that (so cannot redo the whole thing after Drupal 7 end-of-support in just a few months).

Note: I am new to Drupal and website development in general. Would appreciate clear instructions or redirection if I am in the wrong forum.

[laceysanderson]

Hi @smriti-135, yes you are in the right place -Welcome!
Going with Tripal 4/Drupal 10 is definitely the right plan right now 👍
I'm one of the Tripal core developers and also the main developer of this module so things have been a bit hectic lately 🤪 That said, I will test install this today and see where we are at so I can advise you better :-) Even with a month turn-around I think you continue on as you are going.

Quick question: in addition to setting up a site in Tripal, are you perhaps interested in contributing code-wise to our projects? This would look really good on your CV so may be something you want to think about depending on your background. If so, I'd be happy to guide you to make any small changes needed to get this fully upgraded with detailed instructions and links to resources :-)

[smriti-135]

Hello!
Great to hear that the module is on its way to being ready. But I wonder if the same can be said for other modules such as JBrowse... After looking around, I am thinking of sticking to Drupal 7 till the modules I require are ready for Drupal 10.

As for you question about contributing to the project, I am interested but not sure if I will fit the requirements. I am actually not from a CS background and am only now learning computer-related stuff as part of my Bioinformatics course. Considering that I am still in the learning process, I wonder if I will have the skills and time to contribute good code. If you think that would be feasible for both you and me, let's discuss things!

[laceysanderson]

Great to hear that the module is on its way to being ready. But I wonder if the same can be said for other modules such as JBrowse... After looking around, I am thinking of sticking to Drupal 7 till the modules I require are ready for Drupal 10.

I'm still not sure that is what I would recommend as the upgrade from Drupal 7 to Drupal 10 may not be very straight forward 😬 Are you part of our Tripal Community slack? I would suggest you go on there and let us know the exact modules you feel you need and we could suggest alternatives or work arounds while they are prepared. For example, with JBrowse I would suggest developing it stand-alone on the same server, maybe themeing it to look like your site and then linking to it in your menu's.

Considering that I am still in the learning process, I wonder if I will have the skills and time to contribute good code. If you think that would be feasible for both you and me, let's discuss things!

I think the time is likely your limiting factor even given that you are a beginner :-) Again, I'd love to chat more in the slack channel or in the community codefests that we hold weekly.

One example so something I think you could do with your current level of knowledge and some general guidance is to help move the specialized blast options from the old version into the new services. The form arrays did not really change between D7 and D10 so this would almost be a straight copy/paste from one version to the correct place in the new version :-)

[smriti-135]

I'm not yet a part of the Tripal Community slack so I'll probably get onboard that first. Would definitely appreciate some alternatives and workarounds. And can take forward our discussion there.
See you! :)

Edit 1: @laceysanderson I have no idea how to join the Slack community. I have joined the mailing list, but what next? How else do I contact you? From what I understand, this is more of a bug/issue forum than general queries forum.

Edit 2:

For example, with JBrowse I would suggest developing it stand-alone on the same server, maybe themeing it to look like your site and then linking to it in your menu's.

I just got my deadline bumped forward because I need to work on and submit a report in the last week. So I effectively have only 2 weeks to set things up and make it work. Is your suggestion possible in this case? Putting it here since I'm still figuring out how to join Slack.

[laceysanderson]

Darn! In that case you may need to stick with Drupal 7 / Tripal 3 🙈

Regarding the slack, apparently the page providing the invite link is broken on our site so it's no wonder you're struggling to join. We will get that fixed but in the meantime here is the invite link.