Rob,

The request below library_create_library looks like it has the wrong url, it should be:

./library_create_library.py 8c25bc83f6f9e4001dd21eb7b64f063f http://localhost:8080/api/libraries api_test 'API Test Library'

-Dannon

On Fri, Mar 8, 2013 at 11:40 AM, Rob Leclerc <robert.leclerc@gmail.com> wrote:

I'm have the same error when I run library_create_library.py with the documentation laid out in the galaxy-central/tip//scrips/api/README

from:

/galaxy-dist/scripts/api/

% ./library_create_library.py 8c25bc83f6f9e4001dd21eb7b64f063f http://localhost:8080/libraries api_test 'API Test Library'

Traceback (most recent call last):

  File "./library_create_library.py", line 19, in <module>

    submit( sys.argv[1], sys.argv[2], data )

  File "./common.py", line 100, in submit

    r = post( api_key, url, data )

  File "./common.py", line 42, in post

    return simplejson.loads( urllib2.urlopen( req ).read() )

  File "build/bdist.macosx-10.6-intel/egg/simplejson/__init__.py", line 384, in loads

  File "build/bdist.macosx-10.6-intel/egg/simplejson/decoder.py", line 402, in decode

  File "build/bdist.macosx-10.6-intel/egg/simplejson/decoder.py", line 420, in raw_decode

simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0)

-Rob

On Fri, Mar 8, 2013 at 11:23 AM, Sytchev, Ilya <isytchev@hsph.harvard.edu> wrote:

JSONDecodeError will be raised if the given JSON document is not valid.

http://simplejson.readthedocs.org/en/latest/

Ilya

From: Rob Leclerc <robert.leclerc@gmail.com>
Date: Friday, March 8, 2013 12:01 AM
To: "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu>
Subject: [galaxy-dev] BioBlend: Problem Running Example file

I had trouble running blend4j, so I tried to jump into python (a language I have little experience with).

I tried running the example run_import_workflow.py 

% python run_imported_workflow.py http://localhost:8080 8c25bc83f6f9e4001dd21eb7b64f063f

but I get an error:

Initiating Galaxy connection

Importing workflow

Creating data library 'Imported data for API demo'

Traceback (most recent call last):

  File "run_imported_workflow.py", line 53, in <module>

    library_dict = gi.libraries.create_library(library_name)

  File "build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/libraries/__init__.py", line 27, in create_library

  File "build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/client.py", line 53, in _post

  File "build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/__init__.py", line 132, in make_post_request

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/requests-1.1.0-py2.7.egg/requests/models.py", line 604, in json

    return json.loads(self.text or self.content)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/__init__.py", line 454, in loads

    return _default_decoder.decode(s)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py", line 374, in decode

    obj, end = self.raw_decode(s)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py", line 393, in raw_decode

    return self.scan_once(s, idx=_w(s, idx).end())

simplejson.scanner.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

Is there anything I am missing from the stock configuration which would cause this not to run out of the box?

Cheers,

Rob

--
Rob Leclerc, PhD

P: (US) +1-(917)-873-3037

P: (Shanghai) +86-1-(861)-612-5469

Personal Email: rob.leclerc@aya.yale.edu

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