From StewartA@si.edu Wed Jul 24 11:35:11 2013
From: "Stewart, Andrew" <StewartA@si.edu>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] HTML output with external Javascript
Date: Wed, 24 Jul 2013 15:34:39 +0000
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Hi Gromobir,

The file that Gift is producing is already an html file and there's
already an html datatype in Galaxy by default.  The output file in
question just invokes remote javascript libraries inside <script> tags,
and this seems to be tripping up Galaxy's data viewer.  We've tried
turning off the the html sanitizer, as mentioned below, but this doesn't
seem to have any effect.  We've tried downloading and referencing the
javascript libraries in /static/js as well.

I know that the new visualization platform in Galaxy uses a lot of
external javascript libraries like D3Š does anyone know how that is being
handled differently?


Thanks,
Andrew


--
Andrew Stewart
Office of Research Information Services (ORIS),
Office of the Chief Information Officer (OCIO),
Smithsonian Institution
202-633-2840




On 7/23/13 12:00 PM, "galaxy-dev-request(a)lists.bx.psu.edu"
<galaxy-dev-request(a)lists.bx.psu.edu> wrote:

>On 07/23/2013 05:14 PM, Sinthong, Phanwadee wrote:
>>Hi galaxy-dev,
>>
>>I have a tool that generates a HTML output file which uses some
>>javascript library. I cannot view the output file with the eye button in
>>Galaxy, but it still works fine from the HTML file opened out of the
>>file directory.
>>I changed the sanitize_all_html = False and restarted the galaxy server
>>as some earlier post suggested but still couldn't view the output file.
>>What else can I do to execute Javascript in the Galaxy browser?
>>
>Which library are you trying to use?
>You may have to define your own datatype and add something like the
>following to the file "datatypes_conf.xml"afterwards:
>
><datatype extension="html" type="galaxay.datatypes.xml:Html"
>mimetype="application/html">



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From jeremy.goecks@emory.edu Thu Jul 25 08:36:42 2013
From: Jeremy Goecks <jeremy.goecks@emory.edu>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] HTML output with external Javascript
Date: Thu, 25 Jul 2013 08:36:31 -0400
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> The file that Gift is producing is already an html file and there's
> already an html datatype in Galaxy by default.  The output file in
> question just invokes remote javascript libraries inside <script> tags,
> and this seems to be tripping up Galaxy's data viewer. =20

Setting up relative paths to images and scripts inside your HTML output shoul=
d work; this is done in FastQC and other similar tools.

> We've tried downloading and referencing the
> javascript libraries in /static/js as well.

This should work as well and is the approach used by the rGenetics tools, but=
 the path you want is /static/scripts/ Note that Galaxy already has many jQue=
ry libraries in /static/scripts/libs/jquery, which could simplify development.

> I know that the new visualization platform in Galaxy uses a lot of
> external javascript libraries like D3=C5=A0 does anyone know how that is be=
ing
> handled differently?

For now, the viz framework is a different code base that's not relevant for d=
isplaying datasets.

Best,
J.

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