Fix eFP-Seq browser JS to work with Safari

The eFP-Seq browser is unable to connect with IGB while using the Safari web browser. When an eFP-Seq user clicks the Alignments in IGB hyperlink, they are directed to https://bioviz.org/bar.html. Safari does not allow https sites to communicate with http://localhost.

There are two issues that need to be addressed to allow users to use the eFP-Seq browser on the Safari web browser. For the first issue, we can use similar logic employed for galaxy.html (IGBF-2987) where the bar.js file checks if the user is using Safari and if they are on http or https. If they are on https and using safari, we will redirect the users to http://bioviz.org/bar.html.

For the second issue, we will need to make changes to the BioViz playbook to alter the Apache configuration. Currently, Apache is configured to redirect all http://bioviz.org traffic to https except if the request URI is galaxy.html (IGBF-2505). We would need to extend this logic to bar.html.

There is an issue occurring in bar.js that is causing the data to not load in IGB when on Safari on http. In the addCoordinatesForGeneId method, the xhr.status is not returning a 200 for some reason. Need to investigate further to understand why.

Update: The issue was the /cgi-bin/geneIdLookup.py was being redirected to https and this was being blocked by Safari. Updated the httpd.conf to not redirect /cgi-bin/geneIdLookup.py to https.

Commits:
BioViz: https://bitbucket.org/nfreese/bioviz/commits/11fb44a36ecfd8e0792b73bb934dc9a4d90921e1
BioViz-playbooks: https://bitbucket.org/nfreese/bioviz-playbooks/commits/9ed7f05ac0689682871c7b1b12c920b980c71b5e?at=IGBF-2999

Changes are manually implemented on bioviztest.bioviz.org.

To test:
Turn on IGB.
Open the Safari web browser.
Copy and paste this URL into Safari.
The Arabidopsis genome should load in IGB and data should appear.
Remove the data file from IGB.

Repeat the test on Chrome, Firefox, and Edge. The bar.html page should remain on https and the data should load without issue.

Changes look great. Thanks for improving the apache configuration. Please submit PR.

BioViz pull request: https://bitbucket.org/lorainelab/bioviz/pull-requests/71/igbf-2999-redirect-safari-web-browser-to
BioViz-playbooks pull request: https://bitbucket.org/lorainelab/bioviz-playbooks/pull-requests/10/igbf-2999-do-not-redirect-barhtml-and

PR's are both merged. New code is deployed to bioviz.org main site. Please test.

New link for testing: https://bioviz.org/bar.html?version=A_thaliana_Jun_2009&gene_id=AT2G24270&feature_url_0=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&genome=A_thaliana_Jun_2009&annotation_set=Araport11&query_url=https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/aerial/ERR274310/accepted_hits.bam&server_url=bar

Above link is getting error 500 from the server. Please check snapshot ' data loading'.

I have attached the error (error.txt) I am seeing in the logs (/var/log/httpd) for the BioViz EC2 when I try to hit either https or http bioviz.org/cgi-bin/geneIdLookup.py?gene_id=AT2G24270

[~aloraine] - I'm not sure what is causing this issue.

Tested the URL on edge, chrome, firefox and safari latest versions. The link is working and the data is loaded in IGB. Please check the snapshot edge, firefox, chrome and data.

Testing using this link.

Working on Safari Version 15.0 (16612.1.29.41.4, 16612)
Working on Chrome Version 94.0.4606.81 (Official Build) (x86_64)
Working on Firefox 94.0.2 (64-bit)
Working on Edge Version 95.0.1020.53 (Official build) (x86_64)

Omkar and I have both tested this issue on the various browsers and are no longer seeing the 500 error. My best guess is that redeploying bioviz.org fixed the issue.

Closing ticket.