YeoLab / flotilla

Reproducible machine learning analysis of gene expression and alternative splicing data
http://yeolab.github.io/flotilla/docs
BSD 3-Clause "New" or "Revised" License
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Can't embark on study name only #307

Open olgabot opened 9 years ago

olgabot commented 9 years ago

This should work flawlessly:

import flotilla
study = flotilla.embark('singlecell_pnm_post_kmeans_outliers')
2015-05-22 13:09:30 Reading datapackage from singlecell_pnm_post_kmeans_outliers
:0: FutureWarning: IPython widgets are experimental and may change in the future.
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-1-94ff691f22ea> in <module>()
      1 import flotilla
----> 2 study = flotilla.embark('singlecell_pnm_post_kmeans_outliers')

/home/obotvinnik/workspace-git/flotilla/flotilla/__init__.pyc in embark(study_name, load_species_data, flotilla_dir)
     45         try:
     46             return Study.from_datapackage_file(
---> 47                 study_name, load_species_data=load_species_data)
     48         except IOError:
     49             pass

/home/obotvinnik/workspace-git/flotilla/flotilla/data_model/study.pyc in from_datapackage_file(cls, datapackage_filename, load_species_data, species_datapackage_base_url)
    457             sys.stdout.write('{}\tReading datapackage from {}\n'.format(
    458                 timestamp(), datapackage_filename))
--> 459             datapackage = json.load(f)
    460         datapackage_dir = os.path.dirname(datapackage_filename)
    461         return cls.from_datapackage(

/home/obotvinnik/anaconda/lib/python2.7/json/__init__.pyc in load(fp, encoding, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
    288         parse_float=parse_float, parse_int=parse_int,
    289         parse_constant=parse_constant, object_pairs_hook=object_pairs_hook,
--> 290         **kw)
    291 
    292 

/home/obotvinnik/anaconda/lib/python2.7/json/__init__.pyc in loads(s, encoding, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
    336             parse_int is None and parse_float is None and
    337             parse_constant is None and object_pairs_hook is None and not kw):
--> 338         return _default_decoder.decode(s)
    339     if cls is None:
    340         cls = JSONDecoder

/home/obotvinnik/anaconda/lib/python2.7/json/decoder.pyc in decode(self, s, _w)
    364 
    365         """
--> 366         obj, end = self.raw_decode(s, idx=_w(s, 0).end())
    367         end = _w(s, end).end()
    368         if end != len(s):

/home/obotvinnik/anaconda/lib/python2.7/json/decoder.pyc in raw_decode(self, s, idx)
    382             obj, end = self.scan_once(s, idx)
    383         except StopIteration:
--> 384             raise ValueError("No JSON object could be decoded")
    385         return obj, end

ValueError: No JSON object could be decoded

Instead only this works:

import flotilla
study = flotilla.embark('/home/obotvinnik/flotilla_projects/singlecell_pnm_post_kmeans_outliers/datapackage.json')