Re: [galaxy-dev] Create a new datatype svg

2017-02-08 Thread Daniel Blankenberg 
Hi Jochen,

I’m not sure I follow exactly. The SVG format is basically an XML file that can 
be visualized as a graphic. Whether it will be displayed as a graphic within 
your browser or as text generally depends upon the mime type that is set. If 
the mime type is set as text/plain, it will render as plain text, if it is set 
as image/svg+xml it will be rendered as an image; the previously mentioned flag 
will control which is used for this datatype. However, the actual file contents 
are the same.


Dan


> On Feb 8, 2017, at 2:46 AM, Jochen Bick  wrote:
> 
> Thanks Dan,
> 
> I would like to have it as plain text but no as a separate file in the
> history but more like the solution of bam and bai files. Do you know how
> to do that?
> 
> Cheers Jochen
> 
> On 07.02.2017 21:26, Daniel Blankenberg wrote:
>> Just a quick note, if you want svg to be rendered as a graphics correctly 
>> via the eye preview, you’ll need to set “serve_xss_vulnerable_mimetypes = 
>> True" in galaxy.ini. Otherwise it will appear as plaintext xml. But do be 
>> aware of the security concerns if you change this setting.  
>> Downloading/saving the svg and then manually opening will work regardless.
>> 
>> 
>> Thanks for using Galaxy,
>> 
>> Dan
>> 
> 

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Re: [galaxy-dev] Issue when using xsendfile with galaxy release_16.07

2017-02-08 Thread SAPET, Frederic 
Hi John

Thank you for this answer.
You're right, it works now. I think that my apache server was started since a 
while, without the good user (as root).
By the way I don't understand why it was ok for some type of file and not for 
others.

Thank you.

Fred

-Message d'origine-
De : John Chilton [mailto:jmchil...@gmail.com] 
Envoyé : mardi 7 février 2017 18:56
À : SAPET, Frederic 
Cc : galaxy-dev@lists.galaxyproject.org
Objet : Re: [galaxy-dev] Issue when using xsendfile with galaxy release_16.07

Sorry for the delay in responding - are you sure this is due to a change in 
Galaxy and not a configuration difference between your development and 
production server?

This line:

[Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] (13)Permission 
denied: xsendfile: cannot open file:
/softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer:
http:

Makes it seem like the problem is a Unix permission usage. What are the 
permissions for this file?

ls -lsah softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat

It is probably owned by the Galaxy user right? If the user that the apache 
server runs as does not match this could definitely explain the problem. You'll 
want to make sure that the apache user is the Galaxy user or more realistically 
that the apache user belongs to the group that "owns" those files - perhaps a 
"galaxy" group. In this second case - you'll also need to make sure Galaxy 
files are group readable.

-John



On Tue, Feb 7, 2017 at 11:43 AM, SAPET, Frederic  
wrote:
> Hello
>
>
>
> I can still reproduce this issue with release_16.10
>
>
>
> I’m unable to preview some files (txt, pasted entry) until I have 
> changed their type (ie : to tabular).
>
>
>
> I’ve switch off the feature but it seems to be better regarding 
> performances so if you could help me to find why it doesn’t work it would be 
> nice.
>
>
>
> Thank you.
>
>
>
> Fred
>
>
>
> De : galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] De 
> la part de SAPET, Frederic Envoyé : mercredi 24 août 2016 17:19 À : 
> galaxy-dev@lists.galaxyproject.org
> Objet : [galaxy-dev] Issue when using xsendfile with galaxy 
> release_16.07
>
>
>
> Hello
>
>
>
> I’m trying the latest Galaxy (git status gives me : # On branch
> release_16.07)
>
>
>
> I’ve set the xsend option in galaxy.ini (in order to run Galaxy behind 
> a web server proxy, and apply all methods described here :
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy)
>
> apache_xsendfile = True
>
>
>
> HTML, gff3,tabular files are just fine but the preview of some other 
> files (txt, csv)  is broken on the interface.
>
>
>
> When I want to preview a txt file :
>
> Not Found
>
> The requested URL /datasets/fd1df6a9052810d5/display/ was not found on 
> this server.
>
>
>
> And apache says :
>
> [Thu Aug 18 15:33:48 2016] [error] [client 192.168.29.12] 
> (13)Permission
> denied: xsendfile: cannot open file:
> /softs/bioinfo/galaxy-prod/database/files/000/dataset_19.dat, referer: http:
>
>
>
> But it looks like this is not really a problem related to access.
>
> Indeed, from the same file, I switch it from txt to tabular (edit 
> attributes), the preview works.
>
>
>
> Are you able to reproduce the behavior ?
>
> The same problem occurs on release_16.01.
>
> It’s fine with  the release v15.05 which is my production server right now.
>
>
>
> Fred
>
>
>
>
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