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Code Issues Releases Wiki Activity

make tools more robust against glitches within the input files

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This commit is contained in:
Kai Labusch 2020-07-02 11:37:54 +02:00
parent e09f40db61
commit 2dc3857770
1 changed files with 9 additions and 6 deletions
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15
cli.py
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@ -174,6 +174,7 @@ def ned(tsv, ner_result, ned_rest_endpoint, json_file=None, threshold=None):
rids = []
entity = ""
entity_type = None
tsv['ID'] = '-'
def check_entity(tag):
nonlocal entity, entity_type, rids
@ -195,7 +196,10 @@ def ned(tsv, ner_result, ned_rest_endpoint, json_file=None, threshold=None):
entity = ""
entity_type = None
for rid, row in tsv.iterrows():
ner_tmp = tsv.copy()
ner_tmp.loc[~ner_tmp['NE-TAG'].isin(['O', 'B-PER', 'B-LOC','B-ORG', 'I-PER', 'I-LOC', 'I-ORG']), 'NE-TAG'] = 'O'
for rid, row in ner_tmp.iterrows():
check_entity(row['NE-TAG'])
@ -205,7 +209,7 @@ def ned(tsv, ner_result, ned_rest_endpoint, json_file=None, threshold=None):
entity += " " if entity != "" else ""
entity += row['TOKEN']
entity += str(row['TOKEN'])
rids.append(rid)
@ -321,12 +325,10 @@ 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)
tsv = pd.read_csv(tsv_file, sep='\t', comment='#', quoting=3).rename(columns={'GND-ID': 'ID'})
parts = extract_doc_links(tsv_file)
@ -343,8 +345,9 @@ def find_entities(tsv_file, tsv_out_file, ner_rest_endpoint, ned_rest_endpoint,
tmp = tsv.copy()
tmp['sen'] = (tmp['No.'] == 0).cumsum()
tmp.loc[~tmp['NE-TAG'].isin(['O', 'B-PER', 'B-LOC','B-ORG', 'I-PER', 'I-LOC', 'I-ORG']), 'NE-TAG'] = 'O'
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()]
ner_result = [[{'word': str(row.TOKEN), 'prediction': row['NE-TAG']} 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.")