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.lecl...@aya.yale.edu On Fri, Mar 8, 2013 at 3:46 PM, Dannon Baker <dannon.ba...@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.lecl...@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 <isytc...@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.lecl...@gmail.com> >>> Date: Friday, March 8, 2013 12:01 AM >>> To: "galaxy-...@bx.psu.edu" <galaxy-...@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.lecl...@aya.yale.edu >> >> ___________________________________________________________ >> 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/ >> > >
___________________________________________________________ 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/
