Yet another Python3 bug

[olgabot]

Upon embarking on an existing datapackage, we run into a string/bytes error:

import flotilla

study = flotilla.embark('REDACTED', flotilla_dir=flotilla_dir)

2016-08-08 11:13:09 Reading datapackage from /projects/ps-yeolab/obotvinnik/flotilla_projects/REDACTED/datapackage.json
2016-08-08 11:13:09 Parsing datapackage to create a Study object
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-42-33d8552efa65> in <module>()
      1 import flotilla
      2 
----> 3 study = flotilla.embark('REDACTED', flotilla_dir=flotilla_dir)

/home/obotvinnik/anaconda/envs/py3k/lib/python3.5/site-packages/flotilla/__init__.py in embark(study_name, load_species_data, flotilla_dir)
     63                                             study_name)))
     64         return Study.from_datapackage_file(filename,
---> 65                                            load_species_data=load_species_data)
     66     except IOError:
     67         return Study.from_datapackage_url(study_name,

/home/obotvinnik/anaconda/envs/py3k/lib/python3.5/site-packages/flotilla/study.py in from_datapackage_file(cls, datapackage_filename, load_species_data, species_datapackage_base_url)
    484             datapackage, datapackage_dir=datapackage_dir,
    485             load_species_data=load_species_data,
--> 486             species_datapackage_base_url=species_datapackage_base_url)
    487 
    488     @staticmethod

/home/obotvinnik/anaconda/envs/py3k/lib/python3.5/site-packages/flotilla/study.py in from_datapackage(cls, datapackage, datapackage_dir, load_species_data, species_datapackage_base_url)
    587         if load_species_data and species is not None:
    588             species_kws = cls.load_species_data(species, cls.readers,
--> 589                                                 species_datapackage_base_url)
    590 
    591         try:

/home/obotvinnik/anaconda/envs/py3k/lib/python3.5/site-packages/flotilla/study.py in load_species_data(species, readers, species_datapackage_base_url)
    631                 species_datapackage_base_url, species)
    632             species_datapackage = datapackage_url_to_dict(
--> 633                 species_data_url)
    634 
    635             for resource in species_datapackage['resources']:

/home/obotvinnik/anaconda/envs/py3k/lib/python3.5/site-packages/flotilla/datapackage.py in datapackage_url_to_dict(datapackage_url)
     25 
     26 def datapackage_url_to_dict(datapackage_url):
---> 27     filename = check_if_already_downloaded(datapackage_url)
     28 
     29     with open(filename) as f:

/home/obotvinnik/anaconda/envs/py3k/lib/python3.5/site-packages/flotilla/datapackage.py in check_if_already_downloaded(url, datapackage_name, download_dir)
     60         opener = build_opener()
     61         opened_url = opener.open(req)
---> 62         datapackage = json.loads(opened_url.read())
     63         datapackage_name = datapackage['name']
     64 

/home/obotvinnik/anaconda/envs/py3k/lib/python3.5/json/__init__.py in loads(s, encoding, cls, object_hook, parse_float, parse_int, parse_constant, object_pairs_hook, **kw)
    310     if not isinstance(s, str):
    311         raise TypeError('the JSON object must be str, not {!r}'.format(
--> 312                             s.__class__.__name__))
    313     if s.startswith(u'\ufeff'):
    314         raise JSONDecodeError("Unexpected UTF-8 BOM (decode using utf-8-sig)",

TypeError: the JSON object must be str, not 'bytes'

Is the solution here to force opened_url.read() to a string type? This is using the urllib2 package within the standard libarary.

[souravsingh]

@olgabot The error could be fixed by using a decode() method.
So the line would be:
datapackage = json.loads(opened_url.read().decode('utf-8'))