Truely Embed JBrowse

[laceysanderson]

With JBrowse release 1.14.1, it should now be possible to embed JBrowse in a Drupal page without an iFrame! This was my original design goal back when this module was created and thanks to git, the code is still there! 36e5015

Here is the original template: 36e5015#diff-536353ccb1e44f0c85ac43303aa53fdc
and the original module file: 36e5015#diff-75d77511f4513b21d1a231432afdd006

Ideally we would use the libraries api this time around and have a single source of the jbrowse code to make updates easier.

[laceysanderson]

This is started in branch 7.x-3.x. Currently having troubles loading the "chunks" ;-)

My current approach is for JBrowse instances to be stored in sites/all/files. I need to find a way to set the base directory for the JBrowse package manager (webpack I think? ).

NOTE: I can't just change webpack.conf.js since it is only used when the chunks are first built, not when they're served to the browser. Unless I repackage JBrowse 👀

[laceysanderson]

One way to fix this is to set the publicPath to [your drupal site]/sites/default/files which would be most extensible done via an environmental variable. However, environmental variable are set when the module is packed meaning we would have to rebuild JBrowse 😞

Perhaps we need a drush script/command that downloads JBrowse in the correct spot, sets the environmental variable and rebuilds using webpack? Unfortunately this would require installing webpack...

[laceysanderson]

A quick fix is to change src=i.p+""+({}[t]||t)+".bundle.js" to src="https://my.drupalsite.com/"+i.p+""+({}[t]||t)+".bundle.js" in dist/main.bundle.js

This results in the following error: Must provide a 'baseUrl' in configuration

[laceysanderson]

Revisiting this JBrowse2 on Drupal 9 / Tripal 4

I was prompted to play with this quickly by @scottcain who got this working. He created a node and added javascript in the body field. It was a quick implementation with hard-coded location/URLs just to make sure that the JBrowse js didn't clash with Drupal and it worked! He used this tutorial: https://jbrowse.org/jb2/docs/tutorials/embed_linear_genome_view/02_simple_site/.

And his final result rendered as:

I tested this out myself and documented it in a Gist for later development into this module: https://gist.github.com/laceysanderson/c241b816cb5a254797b19e3abe7776eb