Question: HTML display problem on Galaxy v17.09 with Bismark Pretty Report
0
gravatar for david.roquis
13 days ago by
david.roquis10
david.roquis10 wrote:

Dear Galaxy Community

Since my recent upgrade to Galaxy v17.09 (from version 17.05), I am having some issues with the tool "Bismark Pretty Report", from the package Bismark v7 2017-05-06, on the toolshed.

This tool generates an HTML report which can normally be viewed in the browser. Clicking on the eye icon on the dataset (in history) will open a page with a link to the report, and clicking on the link opens a new tab with the report ( see attached screenshot here)

Until the Galaxy update, this was working flawlessly. Since the update, clicking on the link generate a page with a lot of gibberish (see the display problem here ). However, downloading the html page locally (from the download button in history), and opening it in the browser, works perfectly (as displayed here ). I have compared the code of the HTML file generated through galaxy, and the one downloaded, and it's quite different but I have no clue why (screenshot of the code differences). This problem occurs with newly generated reports, or reports which were created way before the update to v17.09.

This problem is relatively minor, but because I use Galaxy and Bismark Pretty Report to teach to my bachelor students, it would save me some troubles if anyone has an idea on how to fix this issue.

Sincerely

David

edit: for some reasons, my screenshots are not visible in the post, you can see them here

access to the link: https://ibb.co/nDV5oR

bad report: https://ibb.co/mbNJ8R

good report: https://ibb.co/jL388R

code differences: https://ibb.co/f2Dphm

bismark html galaxy • 52 views
ADD COMMENTlink modified 13 days ago by Dannon Baker3.6k • written 13 days ago by david.roquis10
0
gravatar for Dannon Baker
13 days ago by
Dannon Baker3.6k
United States
Dannon Baker3.6k wrote:

Hi David,

Are you an administrator on the Galaxy server? If so, can you check to see if Bismarck is added to the display whitelist?

Admin-> Tool Management -> Manage whitelist

This will disable Galaxy's display sanitization on outputs of the selected tools.

ADD COMMENTlink written 13 days ago by Dannon Baker3.6k

Hi Dannon,

Thanks for your very fast answer. I am the Galaxy Admin for my group, but a very basic one ;)

I have followed your suggestion, and whitelisted Bismark Pretty Report tool. However, when I now click on any link from any report datatset for visualisation, I get a 404 not found error. The display link generated for any dataset now point to the same URL: http://frumpster.wzw.tum.de/html_report.html/

Deactivating Pretty Report form the white list provides an appropriate URL to the display link again (ex: http://frumpster.wzw.tum.de/galaxy-app/datasets/8fa2351d24b57767/display/html_report.html/), but the report is still gibberish.

Cheers

David

ADD REPLYlink written 13 days ago by david.roquis10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 114 users visited in the last hour