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 setUp(self): from MEDRank.evaluation.evaluation import EvaluationParameters self.params=EvaluationParameters()