As to how to figure out the id for copying, there isn't an exposed method for
doing this. If you're willing to do a little work to decode it, you can do the
following in python.
For the encoded id (the "b701da857886499b" portion that you see in a dataset
url "/galaxy/datasets/b701da857886499b/display"), we use the blowfish
implementation in pycrypto, with the 'id_secret' in your universe_wsgi.ini as
the key. Given an object_id and the id_secret from Galaxy, you should be able
to do something like (code from lib/galaxy/web/security/__init__.py):
If you haven't changed it, the id_secret is literally what is used below,
"USING THE DEFAULT IS NOT SECURE!", exactly.
>>> id_secret_from_galaxy = "USING THE DEFAULT IS NOT SECURE!"
>>> obj_id = "b701da857886499b"
>>> from Crypto.Cipher import Blowfish
>>> cipher = Blowfish.new(id_secret_from_galaxy)
>>> cipher.decrypt( obj_id.decode('hex')).lstrip("!")
'70'
And from this ID, we know to grab dataset_70.dat from the
galaxy_root/database/files/000/ folder (assuming the default file storage path).
Let me know if this isn't clear and I'll try and help out.
-Dannon
On Jul 3, 2011, at 3:28 PM, colin molter wrote:
> Hi,
> thx for the reply. I will try to make a proper install of galaxy as soon as i
> have some time.
> But as for now, more importantly, i just need to make a unix copy of the
> files that interest me.
>
> so yes, having something from within galaxy could be cool. But a unix copy
> could make the trick for my first tests. Still I have a problem. I noticed
> that all my history is located in database/files/
> However, how can i know which file corresponds to a given file in my history?
> Of course, i could work with the file size and the date of creation, but a
> more reliable and intuitive link would be nice.
> Could I find it somewhere?
>
> thx
> colin
>
>
> 2011/7/1 Jennifer Jackson <j...@bx.psu.edu>
> Hello Colin,
>
> For #1, we have some wiki help pages that go through the set-up steps for
> this type of proxy configuration. Please see:
>
> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
> -- scroll to "Make the proxy handle uploads and downloads" which links to
> these two docs:
>
> Apache:
> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
> -- the section "Sending files using Apache" specifically addresses downloads.
>
> nginx:
> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy
> -- also has a section for this function, titled "Sending files using nginx"
>
> For #2, a unix copy of the files could be done directly or by an external
> script, but it sounds as if you want to do this configured from within Galaxy
> itself. This could likely be done by setting the download destination for the
> UI "save" function to be a static location in the configuration. Let's see if
> any of our dev team community has done this already and would like to share
> the method.
>
> Hopefully this helps,
>
> Best,
>
> Jen
> Galaxy team
>
>
>
> On 6/30/11 7:48 AM, colin molter wrote:
> Hello all,
> I have two related questions about getting data from the Galaxy History.
> I installed `galaxy in my server, I did some data analyses and now i
> want the resulting data back.
>
> But I am facing two problems:
>
> 1/ I just try to use the download button. If i do it with the button (or
> with curl or wget), i get the following error:
> <h1>Proxy Error</h1>
> <p>The proxy server received an invalid
> response from an upstream server.<br />
> The proxy server could not handle the request <em><a
> href="/galaxy/datasets/b701da857886499b/display">GET /galaxy/datasets/b701da857886499b/display</a></em>.<p>
> Reason: <strong>Error reading from remote server</strong></p></p>
> </body></html>
>
> any ideas? Does I am suppose to modify the universe_wsgi.ini?
>
> 2/ In fact, i would prefer to just copy the result on the same server
> (no need to use the network). Something similar that what is used to add
> data to the datalibrary. Is it a way to just copy data from within
> galaxy to some given place in the same server?
>
> thank you
> colin
> --
> Colin Molter
> University of Brussels - InSilico Team - http://insilico.ulb.ac.be/
>
>
>
> ___________________________________________________________
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>
> --
> Jennifer Jackson
> http://usegalaxy.org/
> http://galaxyproject.org/
>
>
>
> --
> Colin Molter
> University of Brussels - InSilico Team - http://insilico.ulb.ac.be/
>
> ___________________________________________________________
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