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Missing file? #2

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etsi123 opened this issue Jul 14, 2020 · 0 comments
Open

Missing file? #2

etsi123 opened this issue Jul 14, 2020 · 0 comments

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@etsi123
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etsi123 commented Jul 14, 2020

Could be totally wrong and just missed a query file, but is this missing a file?
Running mp-benchmark-model.ipynb leads to the error

FileNotFoundError Traceback (most recent call last)
in
26 X, y, X_header = mp.load_design_matrix(co,
27 df_additional_data=df_static[vars_static],
---> 28 data_ext='_' + data_ext)
29
30 # SVM parameters tuned by cross-validation

/Volumes/drive/MIMIC_III/mp_utils.py in load_design_matrix(co, df_additional_data, data_ext, path, diedWithin)
532 print(path + 'design_matrix' + data_ext + '.csv')
533
--> 534 df_offset = pd.read_csv(path + 'icustays_offset' + data_ext + '.csv')
535 df_offset['intime'] = pd.to_datetime(df_offset['intime'])
536 df_offset['outtime'] = pd.to_datetime(df_offset['outtime'])

~/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)
683 )
684
--> 685 return _read(filepath_or_buffer, kwds)
686
687 parser_f.name = name

~/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds)
455
456 # Create the parser.
--> 457 parser = TextFileReader(fp_or_buf, **kwds)
458
459 if chunksize or iterator:

~/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py in init(self, f, engine, **kwds)
893 self.options["has_index_names"] = kwds["has_index_names"]
894
--> 895 self._make_engine(self.engine)
896
897 def close(self):

~/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py in _make_engine(self, engine)
1133 def _make_engine(self, engine="c"):
1134 if engine == "c":
-> 1135 self._engine = CParserWrapper(self.f, **self.options)
1136 else:
1137 if engine == "python":

~/opt/anaconda3/lib/python3.7/site-packages/pandas/io/parsers.py in init(self, src, **kwds)
1915 kwds["usecols"] = self.usecols
1916
-> 1917 self._reader = parsers.TextReader(src, **kwds)
1918 self.unnamed_cols = self._reader.unnamed_cols
1919

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader.cinit()

pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source()

FileNotFoundError: [Errno 2] File b'icustays_offset_base.csv' does not exist: b'icustays_offset_base.csv'

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