Hello John,
If it is at all possible to send the data to the web service instead ... Unfortunately, I cannot push the data to the web service, because this is the BES one and the interface is defined in the spec.
As far as I understand reading the mailing list there is no way to pull data through FTP (only upload). The API key looks interesting even I do not completely understand it. Is it possible to manipulate the key(s) programmatically? It would be great to generate a temporal key, execute the service and remove the key after that.
In general I would discourage this because it is difficult to do in a generic way ... I understand that the problem is when Galaxy is behind a proxy. In my case I control the URL for the galaxy.
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
I absolutely lost here... should I know $__user_id__ or this is a variable already known to the tool? Thank you very much for the help, Dmitry On 5/6/2014 4:39 AM, John Chilton wrote:
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/74b6e23ed7882f3c091d2b66ce85...) 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 <redmitry@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:password@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 ___________________________________________________________ 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: http://lists.bx.psu.edu/
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