pandas.errors.EmptyDataError: No columns to parse from file
fishfree opened this issue · comments
The console log is as below:
(knowledge-graph) mememe@ubuntugpu:~/knowledge_graph$ python extract_graph.py
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:05<00:00, 5.83s/it]
Number of chunks = 23
An extensive literature search was performed, and 56 articles published in peer-reviewed journals between 2005 and 2021 were selected and analyzed. The corresponding authors' experiential knowledge served as the foundation for the analysis.
(23, 3)
Traceback (most recent call last):
File "/home/mememe/knowledge_graph/extract_graph.py", line 83, in <module>
dfg1 = pd.read_csv(outputdirectory/"graph.csv", sep="|")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mememe/.conda/envs/knowledge-graph/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv
return _read(filepath_or_buffer, kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mememe/.conda/envs/knowledge-graph/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 611, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mememe/.conda/envs/knowledge-graph/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1448, in __init__
self._engine = self._make_engine(f, self.engine)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mememe/.conda/envs/knowledge-graph/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1723, in _make_engine
return mapping[engine](f, **self.options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mememe/.conda/envs/knowledge-graph/lib/python3.11/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in __init__
self._reader = parsers.TextReader(src, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "parsers.pyx", line 586, in pandas._libs.parsers.TextReader.__cinit__
pandas.errors.EmptyDataError: No columns to parse from file
I also checked the data_output/cureus/graph.csv
, the file is empty. But the indexing process is 100% completed. Cumbersome.