HTML display problem on Galaxy v17.09 with Bismark Pretty Report

Question: HTML display problem on Galaxy v17.09 with Bismark Pretty Report

12 months ago by

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 • 420 views

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modified 12 months ago by Dannon Baker ♦ 3.7k • written 12 months ago by david.roquis • 30

12 months ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k 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 COMMENT • link written 12 months ago by Dannon Baker ♦ 3.7k

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 REPLY • link written 12 months ago by david.roquis • 30

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