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):
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()
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
