Hello Dmitry,

This use case isn't really addressed by Galaxy currently.

There is not a generic way of doing grabbing the users credentials
like this or producing URLs from inside the tool. This depends on a
lot of different things - how Galaxy's proxy is configured, etc... so
in many (all?) cases Galaxy would not be able to fetch the users raw
credentials. Your best bet is going to be to use the Galaxy's API -
tools can fetch a user's API key and you can use Galaxy's API to build
a URL that includes this key.

Your users will all need API keys set to use the tool. There have been
some other galaxy-dev discussions about using the API from tools -
http://osdir.com/ml/galaxy-development-source-control/2013-12/msg00105.html.
In general I would discourage this because it is difficult to do in a
generic way - for instance there is no way for the tool to accurately
determine what the URL of Galaxy should be - but it should be possible
to tailor something to your setup if absolutely needed.

If you are really keen to use the Galaxy API to do this and you
understand the limitations - we can try to work through the exact
details.

If it is at all possible to send the data to the web service instead
of sending a reference - the genomespace exporter
(https://bitbucket.org/galaxy/galaxy-central/src/74b6e23ed7882f3c091d2b66ce85025241372017/tools/genomespace/genomespace_exporter.xml?at=default)
might be a good example of how to do this in a more generic fashion.

-John


On Tue, Apr 29, 2014 at 11:16 AM, Dmitry <redmi...@list.ru> wrote:
> Hello,
>
> Is there any way to provide a protected resource link to the external
> application?
> My tool is supposed to call a Web service via SSL which should access to the
> Galaxy resources.
> In ideal it would be something like
> ftp://user:passw...@mygalaxy.net/fasta.gz
>
> The Web service then downloads the resource and do the computation.
>
> Since user is already provided the login to galaxy, I do not want to ask the
> password again on a tool page.
>
> Sincerely,
>
> Dmitry
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