def __init__(self):
'''Constructor.'''
self.__nodes = {}
self.__reac_ids = {}
self.__reac_enz_rels = []
self.__org_enz_rels = []
self.__enz_man = EnzymeManager()
class TestEnzymeManager(unittest.TestCase):
'''Test class for EnzymeManager.'''
def setUp(self):
unittest.TestCase.setUp(self)
self.__manager = EnzymeManager()
def test_add_uniprot_data(self):
'''Tests add_uniprot_data method.'''
enzyme_ids = ['P19367', 'Q2KNB7']
# Test unthreaded:
self.__manager.add_uniprot_data(enzyme_ids, source='test')
self.assertEqual(len(enzyme_ids), len(self.__manager.get_nodes()))
# Test threaded:
self.__manager.add_uniprot_data(enzyme_ids,
source='test',
num_threads=24)
self.assertEqual(len(enzyme_ids), len(self.__manager.get_nodes()))
def setUp(self):
unittest.TestCase.setUp(self)
self.__manager = EnzymeManager()
class ReactionManager(object):
'''Class to implement a manager of Reaction data.'''
def __init__(self):
'''Constructor.'''
self.__nodes = {}
self.__reac_ids = {}
self.__reac_enz_rels = []
self.__org_enz_rels = []
self.__enz_man = EnzymeManager()
def get_files(self):
'''Gets neo4j import files.'''
return ([utils.write_nodes(self.__nodes.values(), 'Reaction'),
utils.write_nodes(self.__enz_man.get_nodes(), 'Enzyme')],
[utils.write_rels(self.__reac_enz_rels, 'Reaction', 'Enzyme'),
utils.write_rels(self.__enz_man.get_org_enz_rels(),
'Organism', 'Enzyme')])
def add_reaction(self, source, reac_id, properties):
'''Adds a reaction to the collection of nodes, ensuring uniqueness.'''
reac_id = self.__reac_ids[source + reac_id] \
if source + reac_id in self.__reac_ids else reac_id
if reac_id not in self.__nodes:
properties[':LABEL'] = 'Reaction'
properties['id:ID(Reaction)'] = reac_id
properties['source'] = source
properties[source] = reac_id
self.__nodes[reac_id] = properties
if 'mnx' in properties:
self.__reac_ids['mnx' + properties['mnx']] = reac_id
if 'kegg.reaction' in properties:
self.__reac_ids[
'kegg.reaction' + properties['kegg.reaction']] = reac_id
if 'rhea' in properties:
self.__reac_ids['rhea' + properties['rhea']] = reac_id
else:
self.__nodes[reac_id].update(properties)
return reac_id
def add_react_to_enz(self, data, source):
'''Submit data to the graph.'''
# Create Reaction and Enzyme nodes:
enzyme_ids = self.__create_react_enz(data, source)
# Create Enzyme nodes:
self.__enz_man.add_uniprot_data(enzyme_ids, source)
def __create_react_enz(self, data, source):
'''Creates Reaction and Enzyme nodes and their Relationships.'''
enzyme_ids = []
for reac_id, uniprot_ids in data.iteritems():
reac_id = self.add_reaction(source, reac_id, {})
for uniprot_id in uniprot_ids:
enzyme_ids.append(uniprot_id)
self.__reac_enz_rels.append([reac_id, 'catalysed_by',
uniprot_id,
{'source': source}])
return list(set(enzyme_ids))