def test_build_model_from_ekb():
m = MRA()
html = trips_client.send_query('MAP2K1 phosphorylates ERK2.')
ekb_xml = trips_client.get_xml(html)
res = m.build_model_from_ekb(ekb_xml)
assert (res.get('model'))
assert (res.get('model_id') == 1)
assert (res.get('model_exec'))
assert (len(m.models[1]) == 1)
assert (isinstance(m.models[1][0], Phosphorylation))
assert (m.models[1][0].enz.name == 'MAP2K1')
assert (m.models[1][0].sub.name == 'MAPK1')
def get_example_extractions(fname):
"Get extractions from one of the examples in `cag_examples`."
with open(fname, 'r') as f:
sentences = f.read().splitlines()
rdf_xml_dict = {}
for sentence in sentences:
logger.info("Reading \"%s\"..." % sentence)
html = tc.send_query(sentence, 'cwms')
try:
rdf_xml_dict[sentence] = tc.get_xml(html,
'rdf:RDF',
fail_if_empty=True)
except AssertionError as e:
logger.error("Got error for %s." % sentence)
logger.exception(e)
return rdf_xml_dict
def process_text(text,
save_xml_name='trips_output.xml',
save_xml_pretty=True,
offline=False,
service_endpoint='drum'):
"""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
oflline : Optional[bool]
If True, offline reading is used with a local instance of DRUM, if
availble. Default: False
service_endpoint : Optional[str]
Selects the TRIPS/DRUM web service endpoint to use. Is a choice between
"drum" (default) and "drum-dev", a nightly build.
Returns
-------
tp : TripsProcessor
A TripsProcessor containing the extracted INDRA Statements
in tp.statements.
"""
if not offline:
html = trips_client.send_query(text, service_endpoint)
xml = trips_client.get_xml(html)
else:
if offline_reading:
try:
dr = DrumReader()
if dr is None:
raise Exception('DrumReader could not be instantiated.')
except BaseException as e:
logger.error(e)
logger.error('Make sure drum/bin/trips-drum is running in'
' a separate process')
return None
try:
dr.read_text(text)
dr.start()
except SystemExit:
pass
xml = dr.extractions[0]
else:
logger.error('Offline reading with TRIPS/DRUM not available.')
logger.error('Error message was: %s' % offline_err)
msg = """
To install DRUM locally, follow instructions at
https://github.com/wdebeaum/drum.
Next, install the pykqml package either from pip or from
https://github.com/bgyori/pykqml.
Once installed, run drum/bin/trips-drum in a separate process.
"""
logger.error(msg)
return None
if save_xml_name:
trips_client.save_xml(xml, save_xml_name, save_xml_pretty)
return process_xml(xml)