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')]