proper support for retroactive entity linking

cli.py

@@ -321,12 +321,14 @@ def find_entities(tsv_file, tsv_out_file, ner_rest_endpoint, ned_rest_endpoint,
 
     out_columns = ['No.', 'TOKEN', 'NE-TAG', 'NE-EMB', 'ID', 'url_id', 'left', 'right', 'top', 'bottom']
 
+    supported_ent = {'PER', 'LOC', 'ORG'}
+
     if noproxy:
         os.environ['no_proxy'] = '*'
 
     tsv = pd.read_csv(tsv_file, sep='\t', comment='#', quoting=3)
 
-    parts = extract_doc_links(tsv_out_file)
+    parts = extract_doc_links(tsv_file)
 
     urls = [part['url'] for part in parts]
 
@@ -342,7 +344,7 @@ def find_entities(tsv_file, tsv_out_file, ner_rest_endpoint, ned_rest_endpoint,
             tmp = tsv.copy()
             tmp['sen'] = (tmp['No.'] == 0).cumsum()
 
-            ner_result = [[{'word': row.TOKEN, 'prediction': row['NE-TAG']} for _, row in sen.iterrows()]
+            ner_result = [[{'word': str(row.TOKEN), 'prediction': row['NE-TAG'] if len(row['NE-TAG']) == 1 or row['NE-TAG'][-3:] in supported_ent else 'O' } for _, row in sen.iterrows()]
                           for _, sen in tmp.groupby('sen')]
         else:
             raise RuntimeError("Either NER rest endpoint or NER-TAG information within tsv_file required.")
@@ -364,7 +366,6 @@ def find_entities(tsv_file, tsv_out_file, ner_rest_endpoint, ned_rest_endpoint,
             pd.DataFrame([], columns=out_columns). to_csv(tsv_out_file, sep="\t", quoting=3, index=False)
 
             for url_id, part in tsv.groupby('url_id'):
-
                 with open(tsv_out_file, 'a') as f:
                     f.write('# ' + urls[url_id] + '\n')