failed to upload file using "Open track file or URL" feature (Jbrowse)

9 views
Skip to first unread message

Michael Thang

unread,
Oct 14, 2021, 12:50:17 AM10/14/21
to apollo
Hi Apollo,
I am using the "Open track file or URL" to upload gff3 to my Jbrowse. The upload can work with the normal URL (i.e.  https://zenodo.org/api/files/6080d6d6-68ec-4ade-afef-bbd83f9b5e2b/augustus.gff3) . However, it will fail with the url containing tokens (see the links below and the attached screenshot). I wonder if there is any setting in the Apollo to resolve this issue? or it is something to do with codebase.


Many thanks,
Mike
Apollo_URL.PNG

Garrett Stevens

unread,
Oct 15, 2021, 2:29:33 PM10/15/21
to Michael Thang, apollo
Hi Mike,

What error are you seeing? I'm guessing it's a CORS error (if you open up the developer tools console you'll probably see some errors that contain "has been blocked by CORS policy"). That's something that would have to be addressed on the server those files reside on, it's not something JBrowse can fix (see here). The format of those URLs shouldn't be a problem, though.

Best,
Garrett

--
To unsubscribe from this group and stop receiving emails from it, send an email to apollo+un...@lbl.gov.

Michael Thang

unread,
Oct 17, 2021, 11:11:32 PM10/17/21
to apollo, stevens....@gmail.com, apollo, Michael Thang
Hi Stevens,
That's what I found after I posted this issue here. I am confused about where to configure the CORS ( nginx server or the apollo-config.groovy) . This apollo documentation suggests that the following lines are part of the grails-cors plugin. Then, I added these lines in apollo-config.groovy file. is it correct ? or It should be configured in the nginx server conf file ? 

cors.url.pattern = '*'
cors.enable.logging = true
cors.enabled = true
cors.headers = ['Access-Control-Allow-Origin': '*']

Many thanks,
Mike



Garrett Stevens

unread,
Oct 18, 2021, 1:57:26 PM10/18/21
to Michael Thang, apollo
Hi Mike,

This is not something that can be fixed in JBrowe or Apollo, it's a property of the places hosting those URLs. You would need to contact usegalaxy.org.au and cloudstor.aarnet.edu.au and have them update their servers.

Best,
Garrett

On Wed, Oct 13, 2021 at 10:50 PM Michael Thang <m.t...@qfab.org> wrote:
--
Reply all
Reply to author
Forward
0 new messages