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 nose>=1.3.0

 httplib2>=0.8

+#for internal API-API querying (mygene-myspecies)

+requests>=2.9.1

 #Optional

 msgpack-python

View file

 import re

 import time

 import copy

+import requests

 # from pyes import ES

 # from pyes.exceptions import NotFoundException, ElasticSearchException

         kwargs['species'] = self._cleaned_species(kwargs.get('species', None))

         include_tax_tree = kwargs.pop('include_tax_tree', False)

         if include_tax_tree:

-            tq = TaxonomyQuery()

-            kwargs['species'] = tq.get_expanded_species_li(kwargs['species'])

+            headers = {'content-type': 'application/x-www-form-urlencoded',

+                      'user-agent': "Python-requests_mygene.info/%s (gzip)" % requests.__version__}

+            res = requests.post('http://s.biothings.io/v1/species?ids=' +

+                                ','.join(['{}'.format(sid) for sid in kwargs['species']]) +

+                                '&expand_species=true', headers=headers)

+            if res.status_code == requests.codes.ok:

+                kwargs['species'] = res.json()

         #this parameter is to add species filter without changing facet counts.

         kwargs['species_facet_filter'] = self._cleaned_species(kwargs.get('species_facet_filter', None),