Update src/tagging_text.py

src/tagging_text.py

@@ -1,102 +1,102 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Mon Aug 24 16:21:23 2020
-
-@author: luol2
-"""
-
-import argparse
-from ssplit_tokenzier import ssplit_token_pos_lemma
-from ml_ner import ml_tagging,ml_tagging_allngram
-from combine_result import combine_ml_dict
-from restore_index import restore_index_nest_fn
-from dic_ner import dic_ont
-from post_processing import combine_overlap
-from abbre_resolution import postprocess_abbr
-import os
-import time
-import json
-
-#hybrid method
-def bioTag(session,text,biotag_dic,ml_model,onlyLongest=False, abbrRecog=False, Threshold=0.95):
-
-    # startTime=time.time()
-    ssplit_token=ssplit_token_pos_lemma(text)
-#    print(ssplit_token) 
-    # print('ssplit token:',time.time()-startTime)
-    
-    # startTime=time.time()
-    dict_tsv=biotag_dic.matching(ssplit_token)
-#    print('dict tsv:\n',dict_tsv)
-    # print('dict ner:',time.time()-startTime)
-  
-    # startTime=time.time()
-    ml_tsv=ml_tagging(session,ssplit_token,ml_model,Threshold)
-    #print('ml_tsv:\n',ml_tsv)
-    # print('ml ner:',time.time()-startTime)
-    
-    # startTime=time.time()
-    combine_tsv=combine_ml_dict(dict_tsv,ml_tsv)
-    #combine_tsv=combine_ml_dict_fn(ml_tsv,dict_tsv)
-    #print('combine:\n',combine_tsv)
-    # print('combine:',time.time()-startTime)
-    
-    # startTime=time.time()
-    final_result=  restore_index_nest_fn(text,combine_tsv)
-#    print('final ner:',time.time()-startTime)
-    if onlyLongest==True:
-        final_result=combine_overlap(final_result)
-    if abbrRecog==True:
-        final_result=postprocess_abbr(final_result,text)
-#    print('final result:') 
-#    print(final_result)
-    # print('final ner:',time.time()-startTime)
-    
-    return final_result
-
-# only machine learning-based method
-def bioTag_ml(text,ml_model,onlyLongest=False,abbrRecog=False, Threshold=0.95):
-
-#    startTime=time.time()
-    ssplit_token=ssplit_token_pos_lemma(text)
-#    print(ssplit_token) 
-#    print('ssplit token:',time.time()-startTime)
-    
-#    startTime=time.time()
-    ml_tsv=ml_tagging_allngram(ssplit_token,ml_model,Threshold)
-#    print('ml_tsv:\n',ml_tsv)
-#    print('ml ner:',time.time()-startTime)
-       
-    final_result=  restore_index_nest_fn(text,ml_tsv)
-#    print('final ner:',time.time()-startTime)
-    if onlyLongest==True:
-        final_result=combine_overlap(final_result)
-    
-    if abbrRecog==True:
-        final_result=postprocess_abbr(final_result,text)
-    
-    return final_result
-
-# only dict method
-def bioTag_dic(text,biotag_dic,onlyLongest=False, abbrRecog=False):
-
-#    startTime=time.time()
-    ssplit_token=ssplit_token_pos_lemma(text)
-#    print(ssplit_token) 
-#    print('ssplit token:',time.time()-startTime)
-    
-#    startTime=time.time()
-    dict_tsv=biotag_dic.matching(ssplit_token)
-#    print('dict tsv:\n',dict_tsv)
-#    print('dict ner:',time.time()-startTime)
-    
-    final_result=  restore_index_nest_fn(text,dict_tsv)
-#    print('final ner:',time.time()-startTime)
-    if onlyLongest==True:
-        final_result=combine_overlap(final_result)
-    
-    if abbrRecog==True:
-        final_result=postprocess_abbr(final_result,text)
-    
-    return final_result
-
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Aug 24 16:21:23 2020
+
+@author: luol2
+"""
+
+import argparse
+from src.ssplit_tokenzier import ssplit_token_pos_lemma
+from src.ml_ner import ml_tagging,ml_tagging_allngram
+from src.combine_result import combine_ml_dict
+from src.restore_index import restore_index_nest_fn
+from src.dic_ner import dic_ont
+from src.post_processing import combine_overlap
+from src.abbre_resolution import postprocess_abbr
+import os
+import time
+import json
+
+#hybrid method
+def bioTag(session,text,biotag_dic,ml_model,onlyLongest=False, abbrRecog=False, Threshold=0.95):
+
+    # startTime=time.time()
+    ssplit_token=ssplit_token_pos_lemma(text)
+#    print(ssplit_token) 
+    # print('ssplit token:',time.time()-startTime)
+    
+    # startTime=time.time()
+    dict_tsv=biotag_dic.matching(ssplit_token)
+#    print('dict tsv:\n',dict_tsv)
+    # print('dict ner:',time.time()-startTime)
+  
+    # startTime=time.time()
+    ml_tsv=ml_tagging(session,ssplit_token,ml_model,Threshold)
+    #print('ml_tsv:\n',ml_tsv)
+    # print('ml ner:',time.time()-startTime)
+    
+    # startTime=time.time()
+    combine_tsv=combine_ml_dict(dict_tsv,ml_tsv)
+    #combine_tsv=combine_ml_dict_fn(ml_tsv,dict_tsv)
+    #print('combine:\n',combine_tsv)
+    # print('combine:',time.time()-startTime)
+    
+    # startTime=time.time()
+    final_result=  restore_index_nest_fn(text,combine_tsv)
+#    print('final ner:',time.time()-startTime)
+    if onlyLongest==True:
+        final_result=combine_overlap(final_result)
+    if abbrRecog==True:
+        final_result=postprocess_abbr(final_result,text)
+#    print('final result:') 
+#    print(final_result)
+    # print('final ner:',time.time()-startTime)
+    
+    return final_result
+
+# only machine learning-based method
+def bioTag_ml(text,ml_model,onlyLongest=False,abbrRecog=False, Threshold=0.95):
+
+#    startTime=time.time()
+    ssplit_token=ssplit_token_pos_lemma(text)
+#    print(ssplit_token) 
+#    print('ssplit token:',time.time()-startTime)
+    
+#    startTime=time.time()
+    ml_tsv=ml_tagging_allngram(ssplit_token,ml_model,Threshold)
+#    print('ml_tsv:\n',ml_tsv)
+#    print('ml ner:',time.time()-startTime)
+       
+    final_result=  restore_index_nest_fn(text,ml_tsv)
+#    print('final ner:',time.time()-startTime)
+    if onlyLongest==True:
+        final_result=combine_overlap(final_result)
+    
+    if abbrRecog==True:
+        final_result=postprocess_abbr(final_result,text)
+    
+    return final_result
+
+# only dict method
+def bioTag_dic(text,biotag_dic,onlyLongest=False, abbrRecog=False):
+
+#    startTime=time.time()
+    ssplit_token=ssplit_token_pos_lemma(text)
+#    print(ssplit_token) 
+#    print('ssplit token:',time.time()-startTime)
+    
+#    startTime=time.time()
+    dict_tsv=biotag_dic.matching(ssplit_token)
+#    print('dict tsv:\n',dict_tsv)
+#    print('dict ner:',time.time()-startTime)
+    
+    final_result=  restore_index_nest_fn(text,dict_tsv)
+#    print('final ner:',time.time()-startTime)
+    if onlyLongest==True:
+        final_result=combine_overlap(final_result)
+    
+    if abbrRecog==True:
+        final_result=postprocess_abbr(final_result,text)
+    
+    return final_result
+