using Bioblend with external authentication

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using Bioblend with external authentication

Hans-Rudolf Hotz
Hi

We would like to start using BioBlend on our production servers (which
use external authentication) as well.

We have changed the apache conf file by adding

      <Location "/galaxy/api">
          Satisfy Any
          Allow from all
      </Location>



Nevertheless, we still get the following error, when using one of the
example scripts:


$ python list_data_libraries.py galaxy-dev.fmi.ch ***************
Initiating Galaxy connection
Retrieving Data Library list
Traceback (most recent call last):
   File "list_data_libraries.py", line 23, in <module>
     libraries = gi.libraries.get_libraries()
   File
"/****/lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/libraries/__init__.py",
line 216, in get_libraries
     libraries = Client._get(self, deleted=deleted)
   File
"/****/lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/client.py",
line 147, in _get
     raise ConnectionError(msg)
bioblend.galaxy.client.ConnectionError: GET: error 401: '<!DOCTYPE HTML
PUBLIC "-//IETF//DTD HTML 2.0//EN">\n<html><head>\n<title>401
Authorization Required</title>\n</head><body>\n<h1>Authorization
Required</h1>\n<p>This server could not verify that you\nare authorized
to access the document\nrequested.  Either you supplied the
wrong\ncredentials (e.g., bad password), or your\nbrowser doesn\'t
understand how to supply\nthe credentials
required.</p>....</body></html>\n', 0 attempts left: None
$


Is there anything else we need to change in the conf file, or do we have
to do something different?



Thank you very much for any help with this
Hans-Rudolf



--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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Re: using Bioblend with external authentication

Dannon Baker-2
My guess is that it has to do with the prefix there.  Is the Galaxy API at galaxy-dev.fmi.ch/galaxy/api or galaxy-dev.fmi.ch/api?

On Thu, Oct 22, 2015 at 6:41 AM Hans-Rudolf Hotz <[hidden email]> wrote:
Hi

We would like to start using BioBlend on our production servers (which
use external authentication) as well.

We have changed the apache conf file by adding

      <Location "/galaxy/api">
          Satisfy Any
          Allow from all
      </Location>



Nevertheless, we still get the following error, when using one of the
example scripts:


$ python list_data_libraries.py galaxy-dev.fmi.ch ***************
Initiating Galaxy connection
Retrieving Data Library list
Traceback (most recent call last):
   File "list_data_libraries.py", line 23, in <module>
     libraries = gi.libraries.get_libraries()
   File
"/****/lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/libraries/__init__.py",
line 216, in get_libraries
     libraries = Client._get(self, deleted=deleted)
   File
"/****/lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/client.py",
line 147, in _get
     raise ConnectionError(msg)
bioblend.galaxy.client.ConnectionError: GET: error 401: '<!DOCTYPE HTML
PUBLIC "-//IETF//DTD HTML 2.0//EN">\n<html><head>\n<title>401
Authorization Required</title>\n</head><body>\n<h1>Authorization
Required</h1>\n<p>This server could not verify that you\nare authorized
to access the document\nrequested.  Either you supplied the
wrong\ncredentials (e.g., bad password), or your\nbrowser doesn\'t
understand how to supply\nthe credentials
required.</p>....</body></html>\n', 0 attempts left: None
$


Is there anything else we need to change in the conf file, or do we have
to do something different?



Thank you very much for any help with this
Hans-Rudolf



--



Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
___________________________________________________________
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:
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Re: using Bioblend with external authentication

Hans-Rudolf Hotz
Hi all

Thanks to a great effort by Dannon, we have solved the problem. Since I
took the discussion off-list after his initial reply, I now owe you the
solution:

My initial mistake was the change in the apache config file. I should
have added:

             <Location "/api">
                 Satisfy Any
                 Allow from all
             </Location>

Since our Galaxy is not served from a sub directory (such as /galaxy) -
D'OH !!


In the whole process, we identified a problem in the Galaxy code, which
is now nicely patched:

https://github.com/galaxyproject/galaxy/pull/1003

Regards, Hans-Rudolf


On 10/22/2015 04:09 PM, Dannon Baker wrote:

> My guess is that it has to do with the prefix there.  Is the Galaxy API
> at galaxy-dev.fmi.ch/galaxy/api <http://galaxy-dev.fmi.ch/galaxy/api> or
> galaxy-dev.fmi.ch/api <http://galaxy-dev.fmi.ch/api>?
>
> On Thu, Oct 22, 2015 at 6:41 AM Hans-Rudolf Hotz <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi
>
>     We would like to start using BioBlend on our production servers (which
>     use external authentication) as well.
>
>     We have changed the apache conf file by adding
>
>            <Location "/galaxy/api">
>                Satisfy Any
>                Allow from all
>            </Location>
>
>
>
>     Nevertheless, we still get the following error, when using one of the
>     example scripts:
>
>
>     $ python list_data_libraries.py galaxy-dev.fmi.ch
>     <http://galaxy-dev.fmi.ch> ***************
>     Initiating Galaxy connection
>     Retrieving Data Library list
>     Traceback (most recent call last):
>         File "list_data_libraries.py", line 23, in <module>
>           libraries = gi.libraries.get_libraries()
>         File
>     "/****/lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/libraries/__init__.py",
>     line 216, in get_libraries
>           libraries = Client._get(self, deleted=deleted)
>         File
>     "/****/lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/client.py",
>     line 147, in _get
>           raise ConnectionError(msg)
>     bioblend.galaxy.client.ConnectionError: GET: error 401: '<!DOCTYPE HTML
>     PUBLIC "-//IETF//DTD HTML 2.0//EN">\n<html><head>\n<title>401
>     Authorization Required</title>\n</head><body>\n<h1>Authorization
>     Required</h1>\n<p>This server could not verify that you\nare authorized
>     to access the document\nrequested.  Either you supplied the
>     wrong\ncredentials (e.g., bad password), or your\nbrowser doesn\'t
>     understand how to supply\nthe credentials
>     required.</p>....</body></html>\n', 0 attempts left: None
>     $
>
>
>     Is there anything else we need to change in the conf file, or do we have
>     to do something different?
>
>
>
>     Thank you very much for any help with this
>     Hans-Rudolf
>
>
>
>     --
>
>
>
>     Hans-Rudolf Hotz, PhD
>     Bioinformatics Support
>
>     Friedrich Miescher Institute for Biomedical Research
>     Maulbeerstrasse 66
>     4058 Basel/Switzerland
>     ___________________________________________________________
>     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/mailinglists/
>
___________________________________________________________
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/mailinglists/