def process_text(text, save_xml_name='trips_output.xml', save_xml_pretty=True):
"""Return a TripsProcessor by processing text.
Parameters
----------
text : str
The text to be processed.
save_xml_name : Optional[str]
The name of the file to save the returned TRIPS extraction knowledge
base XML. Default: trips_output.xml
save_xml_pretty : Optional[bool]
If True, the saved XML is pretty-printed. Some third-party tools
require non-pretty-printed XMLs which can be obtained by setting this
to False. Default: True
Returns
-------
tp : TripsProcessor
A TripsProcessor containing the extracted INDRA Statements
in tp.statements.
"""
html = trips_client.send_query(text)
xml = trips_client.get_xml(html)
if save_xml_name:
trips_client.save_xml(xml, save_xml_name, save_xml_pretty)
return process_xml(xml)
def process_text(text, save_xml_name='trips_output.xml', save_xml_pretty=True):
"""Return a TripsProcessor by processing text.
Parameters
----------
text : str
The text to be processed.
save_xml_name : Optional[str]
The name of the file to save the returned TRIPS extraction knowledge
base XML. Default: trips_output.xml
save_xml_pretty : Optional[bool]
If True, the saved XML is pretty-printed. Some third-party tools
require non-pretty-printed XMLs which can be obtained by setting this
to False. Default: True
Returns
-------
tp : TripsProcessor
A TripsProcessor containing the extracted INDRA Statements
in tp.statements.
"""
html = trips_client.send_query(text)
xml = trips_client.get_xml(html)
if save_xml_name:
trips_client.save_xml(xml, save_xml_name, save_xml_pretty)
return process_xml(xml)
def test_build_model_from_ekb():
m = MRA()
html = trips_client.send_query('MEK1 phosphorylates ERK2.')
ekb_xml = trips_client.get_xml(html)
model = m.build_model_from_ekb(ekb_xml)
assert (model is not None)
assert (len(m.statements[0]) == 1)
assert (isinstance(m.statements[0][0], indra.statements.Phosphorylation))
assert (m.statements[0][0].enz.name == 'MAP2K1')
assert (m.statements[0][0].sub.name == 'MAPK1')
def test_build_model_from_ekb():
m = MRA()
html = trips_client.send_query('MEK1 phosphorylates ERK2.')
ekb_xml = trips_client.get_xml(html)
model = m.build_model_from_ekb(ekb_xml)
assert(model is not None)
assert(len(m.statements[0]) == 1)
assert(isinstance(m.statements[0][0], indra.statements.Phosphorylation))
assert(m.statements[0][0].enz.name == 'MAP2K1')
assert(m.statements[0][0].sub.name == 'MAPK1')