An update: looking some more, it appears that the <img> tags produced by both 17.01
and 17.05 are the same (i.e. in both cases there is no prefix). So the "missing"
prefix is not the reason for the problem in the later release, as I'd originally
thought.
In fact with the help of git bisect, as far as I'm able to tell the problem seems to
be associated with changes in commit id 6e32b0f7c119ca6c3d54a761e64f49fe6a7f8280:
and specifically those associated with the file
'static/scripts/bundled/analysis.bundled.js'.
Unfortunately I'm not able to make much sense of the diff, or to identify which parts
might be relevant to this problem. I suppose it's possible that the problem only
manifests when these changes interact with something elsewhere in another commit.
Once again any help or suggestions would be appreciated, thanks!
Best wishes
Peter
On 21/08/17 16:36, Peter Briggs wrote:
Dear devs
The rendering of images in tool XML 'help' sections is broken for release_17.05
when serving Galaxy from a subdirectory using proxy-prefix.
The <img...> tags are rendered in the tool helps but point to relative URLs which
don't include the prefix (e.g.
"admin_toolshed/static/images/756ced91f537cdf0/norm_IGVsnapshot_indFiles.png"
rather than
"<PROXY_PREFIX>/admin_toolshed/static/images/756ced91f537cdf0/norm_IGVsnapshot_indFiles.png").
I've looked at the Galaxy code but so far I haven't been able to see where these
tags are generated (nor whether the proxy prefix is even available to the Galaxy webapp).
This problem doesn't appear to be in release_17.01 (i.e. images display regardless of
proxy-prefix), but it is still present in the 'dev' branch. I believe it's
independent of the PATH_TO_IMAGES issue raised previously.
Can anyone suggest any starting points for looking into how to fix this?
Thanks for your help - I really like to get this fixed as it's breaking the very
useful inline documentation for e.g. 'deepTools', as well for a locally developed
tool we're currently trying to roll out on our production instance.
Best wishes
Peter
On 10/08/17 16:12, John Chilton wrote:
> There is an open issue for these paths not working with vanilla Galaxy
> tools
https://github.com/galaxyproject/galaxy/issues/1676.
>
> -John
>
> On Wed, Aug 9, 2017 at 10:03 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
>> I'm puzzled now too, cross reference
>>
>>
https://github.com/galaxy-iuc/standards/pull/46
>>
>> and the original:
>>
>>
https://github.com/galaxy-iuc/standards/issues/12
>>
>> Peter
>>
>>
>> On Wed, Aug 9, 2017 at 3:01 PM, Peter Briggs
>> <peter.briggs(a)manchester.ac.uk> wrote:
>>> Hello Peter
>>>
>>> Thanks for the fast response. From reading around elsewhere I'd
understood
>>> that using $PATH_TO_IMAGES was now deprecated? I think I tried it anyway and
>>> it didn't seem to help. But I might have missed something, so I'd be
>>> interested to know if it works for you.
>>>
>>> Best wishes
>>>
>>> Peter
>>>
>>>
>>> On 09/08/17 14:57, Peter Cock wrote:
>>>>
>>>> It looks like something important is not showing in the best practise
>>>> website, special variable $PATH_TO_IMAGES as per the linked example:
>>>>
>>>> .. image:: $PATH_TO_IMAGES/slop-glyph.png
>>>>
>>>> Let me look into this,
>>>>
>>>> Peter
>>>>
>>>> On Wed, Aug 9, 2017 at 2:52 PM, Peter Briggs
>>>> <peter.briggs(a)manchester.ac.uk> wrote:
>>>>>
>>>>> Dear devs
>>>>>
>>>>> I've been updating the <help> section for a locally
developed tool and
>>>>> want
>>>>> to include some images, but I've had some issues trying to see
them when
>>>>> testing locally.
>>>>>
>>>>> I've followed the instructions outlined here:
>>>>>
>>>>>
>>>>>
https://github.com/galaxy-iuc/standards/blob/master/docs/best_practices/t...
>>>>>
>>>>> (i.e. put the images files into a 'static/images/' subdir of
the tool
>>>>> directory and reference them using ".. image::
picture.png")
>>>>>
>>>>> However when I load the tool into a Galaxy using "planemo serve
..." the
>>>>> images fail to render: I just get a line of text with the image
filename.
>>>>> The same thing happens when I add the tool manually on our local
server
>>>>> (i.e. by adding a <tool file=...> reference to the tool XML in
the
>>>>> appropriate conf.xml file).
>>>>>
>>>>> If I upload the same tool files to a toolshed and then install from
>>>>> there, I
>>>>> do see the images rendered correctly.
>>>>>
>>>>> I'm a bit baffled as to why there should be a difference. Is
there an
>>>>> option
>>>>> or setting I've missed to turn on the image rendering for
>>>>> non-shed-installed
>>>>> tools? Or have I made some other mistake?
>>>>>
>>>>> Thanks for your help,
>>>>>
>>>>> Best wishes
>>>>>
>>>>> Peter
>>>>>
>>>>> --
>>>>> Peter Briggs peter.briggs(a)manchester.ac.uk
>>>>> Bioinformatics Core Facility University of Manchester
>>>>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>>>>> ___________________________________________________________
>>>>> Please keep all replies on the list by using "reply all"
>>>>> in your mail client. To manage your subscriptions to this
>>>>> and other Galaxy lists, please use the interface at:
>>>>>
https://lists.galaxyproject.org/
>>>>>
>>>>> To search Galaxy mailing lists use the unified search at:
>>>>>
http://galaxyproject.org/search/
>>>
>>>
>>> --
>>> Peter Briggs peter.briggs(a)manchester.ac.uk
>>> Bioinformatics Core Facility University of Manchester
>>> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client. To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>
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--
Peter Briggs peter.briggs(a)manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482