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:80808c25bc83f6f9e4001dd21eb7b64f063f *

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 <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-5469 Personal Email: rob.leclerc@aya.yale.edu

Dannon, *Thank you* you're absolutely right! ...Now I just have to deal with the permission denied errors. (The I set the galaxy admin to my userID/email). Cheers! Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-5469 Personal Email: rob.leclerc@aya.yale.edu On Fri, Mar 8, 2013 at 3:46 PM, Dannon Baker <dannon.baker@gmail.com> wrote:

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:80808c25bc83f6f9e4001dd21eb7b64f063f *

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 <http://www.linkedin.com/in/robleclerc><https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-5469 Personal Email: rob.leclerc@aya.yale.edu

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