def main():
my_format_string='%(asctime)s %(levelname)s %(module)s.' \
'%(funcName)s: %(message)s'
logging.basicConfig(level=logging.INFO, format=my_format_string)
chunkmap = chunkmap_factory(
pickle.load(bz2.BZ2File('test_data/5th.chunkmap.bz2')))
semrep_reader = SemrepOutput(bz2.BZ2File('test_data/5th.semrep.out.bz2'),
DEFAULT_LINES_TO_IGNORE, chunkmap)
tfidf = TF_IDF(file_mode="c")
tfidf.build_tf_from_file(semrep_reader)
semrep_reader.rewind()
semrep_grapher = SemrepCooccurrenceGraphBuilder(
node_weight_threshold=0.001,
link_weight_threshold=0.003,
tf_idf_provider=tfidf)
eval_params = EvaluationParameters()
eval_params.alpha = 0.65
work = myWorkflow(semrep_reader, semrep_grapher, TextRanker(), eval_params,
PAGERANK_CUTOFF, MESH_TREE_FILE, SAVCC_MATRIX_FILE,
lambda x: 1.0 / math.exp(x) if x >= 0 and x < 5 else 0.0,
UMLS_CONVERTER_DATA, UMLS_CONCEPT_DATA,
open(OUTPUT_FILE, 'w'))
work.run()
def main():
my_format_string='%(asctime)s %(levelname)s %(module)s.' \
'%(funcName)s: %(message)s'
logging.basicConfig(level=logging.INFO,
format=my_format_string)
chunkmap=chunkmap_factory(pickle.load(
bz2.BZ2File('test_data/5th.chunkmap.bz2')))
semrep_reader=SemrepOutput(bz2.BZ2File('test_data/5th.semrep.out.bz2'),
DEFAULT_LINES_TO_IGNORE,
chunkmap)
tfidf=TF_IDF(file_mode="c")
tfidf.build_tf_from_file(semrep_reader)
semrep_reader.rewind()
semrep_grapher=SemrepCooccurrenceGraphBuilder(node_weight_threshold=0.001,
link_weight_threshold=0.003,
tf_idf_provider=tfidf
)
eval_params=EvaluationParameters()
eval_params.alpha=0.65
work=myWorkflow(semrep_reader, semrep_grapher, TextRanker(), eval_params,
PAGERANK_CUTOFF, MESH_TREE_FILE, SAVCC_MATRIX_FILE,
lambda x: 1.0/math.exp(x) if x>=0 and x<5 else 0.0,
UMLS_CONVERTER_DATA, UMLS_CONCEPT_DATA,
open(OUTPUT_FILE, 'w'))
work.run()
def main():
my_format_string='%(asctime)s %(levelname)s %(module)s.' \
'%(funcName)s: %(message)s'
logging.basicConfig(level=logging.DEBUG, format=my_format_string)
chunkmap = chunkmap_factory(
pickle.load(bz2.BZ2File('test_data/all_abstracts.mti_chunkmap.bz2')))
reader = MtiOutput(
bz2.BZ2File('test_data/all_abstracts.mti.just_metamap.out.bz2'),
DEFAULT_LINES_TO_IGNORE, chunkmap)
eval_params = EvaluationParameters()
eval_params.alpha = 0.65
work = MtiWorkflow(
reader, None, None, eval_params, PAGERANK_CUTOFF, MESH_TREE_FILE,
SAVCC_MATRIX_FILE, lambda x: 1.0 / math.exp(x)
if x >= 0 and x < 5 else 0.0, UMLS_CONVERTER_DATA, UMLS_CONCEPT_DATA,
open(OUTPUT_FILE, 'w'))
work.run()
def main():
my_format_string='%(asctime)s %(levelname)s %(module)s.' \
'%(funcName)s: %(message)s'
logging.basicConfig(level=logging.DEBUG,
format=my_format_string)
chunkmap=chunkmap_factory(pickle.load(
bz2.BZ2File('test_data/all_abstracts.mti_chunkmap.bz2')))
reader=MtiOutput(bz2.BZ2File('test_data/all_abstracts.mti.just_metamap.out.bz2'),
DEFAULT_LINES_TO_IGNORE,
chunkmap)
eval_params=EvaluationParameters()
eval_params.alpha=0.65
work=MtiWorkflow(reader, None, None, eval_params,
PAGERANK_CUTOFF, MESH_TREE_FILE, SAVCC_MATRIX_FILE,
lambda x: 1.0/math.exp(x) if x>=0 and x<5 else 0.0,
UMLS_CONVERTER_DATA, UMLS_CONCEPT_DATA,
open(OUTPUT_FILE, 'w'))
work.run()
def setUp(self):
from MEDRank.evaluation.evaluation import EvaluationParameters
self.params=EvaluationParameters()
