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 load(chem_manager):
'''Loads ChEBI data from libChEBIpy.'''
chebi_ids = []
rels = []
_add_node('CHEBI:24431', chebi_ids, rels, chem_manager)
return [], [utils.write_rels(rels, 'Chemical', 'Chemical')]
def load(source=__NCBITAXONOMY_URL):
'''Loads NCBI Taxonomy data.'''
nodes_filename, names_filename = _get_ncbi_taxonomy_files(source)
nodes, rels = _parse_nodes(nodes_filename)
_parse_names(nodes, names_filename)
return [utils.write_nodes(nodes.values(), 'Organism')], \
[utils.write_rels(rels, 'Organism', 'Organism')]
def load(self):
'''Loads MnxRef data from chem_prop.tsv, chem_xref.tsv,
reac_prop.tsv and reac_xref.tsv files.'''
reader = MnxRefReader()
for properties in reader.get_chem_data().values():
properties['mnx'] = properties.pop('id')
self.__chem_man.add_chemical(properties)
rels = self.__add_reac_nodes(reader.get_reac_data())
return [], [utils.write_rels(rels, 'Reaction', 'Chemical')]
