def process_xml(xml_string): tp = TripsProcessor(xml_string) tp.get_complexes() tp.get_phosphorylation() tp.get_activating_mods() tp.get_activations() return tp
def process_xml(xml_string): """Return a TripsProcessor by processing a TRIPS EKB XML string. Parameters ---------- xml_string : str A TRIPS extraction knowledge base (EKB) string to be processed. http://trips.ihmc.us/parser/api.html Returns ------- tp : TripsProcessor A TripsProcessor containing the extracted INDRA Statements in tp.statements. """ tp = TripsProcessor(xml_string) if tp.tree is None: return None tp.get_complexes() tp.get_phosphorylation() tp.get_activating_mods() tp.get_activations() tp.get_activations_causal() return tp
def process_xml(xml_string): tp = TripsProcessor(xml_string) tp.get_complexes() tp.get_phosphorylation() tp.get_activating_mods() return tp
def process_text(text): html = trips_client.send_query(text) xml = trips_client.get_xml(html) with open('test.xml','w') as f: f.write(xml) return process_xml(xml) def process_xml(xml_string): tp = TripsProcessor(xml_string) tp.get_complexes() tp.get_phosphorylation() tp.get_activating_mods() return tp if __name__ == '__main__': input_fname = 'phosphorylate.xml' if len(sys.argv) > 1: input_fname = sys.argv[1] try: fh = open(input_fname, 'rt') except IOError: print 'Could not open file %s' % input_fname sys.exit() xml_string = fh.read() tp = TripsProcessor(xml_string) tp.get_complexes() tp.get_phosphorylation()
def process_text(text, save_xml_name='trips_output.xml'): html = trips_client.send_query(text) xml = trips_client.get_xml(html) if save_xml_name: trips_client.save_xml(xml, save_xml_name) return process_xml(xml) def process_xml(xml_string): tp = TripsProcessor(xml_string) tp.get_complexes() tp.get_phosphorylation() tp.get_activating_mods() tp.get_activations() return tp if __name__ == '__main__': input_fname = 'phosphorylate.xml' if len(sys.argv) > 1: input_fname = sys.argv[1] try: fh = open(input_fname, 'rt') except IOError: print 'Could not open file %s' % input_fname sys.exit() xml_string = fh.read() tp = TripsProcessor(xml_string) tp.get_complexes() tp.get_phosphorylation()