FileNotFoundError in profiling_camelyon_pipeline.ipynb
KumoLiu opened this issue · 3 comments
KumoLiu commented
12:41:33 Running ./pathology/tumor_detection/ignite/profiling_camelyon_pipeline.ipynb
12:41:33 Checking PEP8 compliance...
12:41:34 Running notebook...
12:41:40 MONAI version: 1.3.0+51.g02973f0e
12:41:40 Numpy version: 1.22.2
12:41:40 Pytorch version: 2.1.0a0+29c30b1
12:41:40 MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
12:41:40 MONAI rev id: 02973f0e2bac4f799bb9f522de5bb7427f257ed4
12:41:40 MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py
12:41:40
12:41:40 Optional dependencies:
12:41:41 Pytorch Ignite version: 0.4.11
12:41:41 ITK version: 5.3.0
12:41:41 Nibabel version: 5.2.0
12:41:41 scikit-image version: 0.22.0
12:41:41 scipy version: 1.11.1
12:41:41 Pillow version: 9.2.0
12:41:41 Tensorboard version: 2.9.0
12:41:41 gdown version: 4.7.1
12:41:41 TorchVision version: 0.16.0a0
12:41:41 tqdm version: 4.65.0
12:41:41 lmdb version: 1.4.1
12:41:41 psutil version: 5.9.4
12:41:41 pandas version: 1.5.2
12:41:41 einops version: 0.6.1
12:41:41 transformers version: 4.36.2
12:41:41 mlflow version: 2.9.2
12:41:41 pynrrd version: 1.0.0
12:41:41 clearml version: 1.13.3rc0
12:41:41
12:41:41 For details about installing the optional dependencies, please visit:
12:41:41 https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies
12:41:41
12:41:43 papermill --progress-bar -k python3
12:41:43 /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
12:41:43 warnings.warn(
12:42:21
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12:42:21 /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:153: UserWarning: the file is not specified with any extension : -
12:42:21 warnings.warn(
12:42:21 Traceback (most recent call last):
12:42:21 File "/usr/local/bin/papermill", line 8, in <module>
12:42:21 sys.exit(papermill())
12:42:21 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
12:42:21 return self.main(*args, **kwargs)
12:42:21 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
12:42:21 rv = self.invoke(ctx)
12:42:21 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
12:42:21 return ctx.invoke(self.callback, **ctx.params)
12:42:21 File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
12:42:21 return __callback(*args, **kwargs)
12:42:21 File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
12:42:21 return f(get_current_context(), *args, **kwargs)
12:42:21 File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 254, in papermill
12:42:21 execute_notebook(
12:42:21 File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 134, in execute_notebook
12:42:21 raise_for_execution_errors(nb, output_path)
12:42:21 File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 241, in raise_for_execution_errors
12:42:21 raise error
12:42:21 papermill.exceptions.PapermillExecutionError:
12:42:21 ---------------------------------------------------------------------------
12:42:21 Exception encountered at "In [7]":
12:42:21 ---------------------------------------------------------------------------
12:42:21 FileNotFoundError Traceback (most recent call last)
12:42:21 Cell In[7], line 2
12:42:21 1 # Load NVTX Push/Pop Range Summary
12:42:21 ----> 2 summary = pd.read_csv("profile_report_nvtxppsum.csv")
12:42:21 3 # display(summary)
12:42:21 4
12:42:21 5 # Set the Range (which is the name of each range) as the index
12:42:21 6 summary.set_index("Range", inplace=True)
12:42:21
12:42:21 File /usr/local/lib/python3.10/dist-packages/pandas/util/_decorators.py:211, in deprecate_kwarg.<locals>._deprecate_kwarg.<locals>.wrapper(*args, **kwargs)
12:42:21 209 else:
12:42:21 210 kwargs[new_arg_name] = new_arg_value
12:42:21 --> 211 return func(*args, **kwargs)
12:42:21
12:42:21 File /usr/local/lib/python3.10/dist-packages/pandas/util/_decorators.py:331, in deprecate_nonkeyword_arguments.<locals>.decorate.<locals>.wrapper(*args, **kwargs)
12:42:21 325 if len(args) > num_allow_args:
12:42:21 326 warnings.warn(
12:42:21 327 msg.format(arguments=_format_argument_list(allow_args)),
12:42:21 328 FutureWarning,
12:42:21 329 stacklevel=find_stack_level(),
12:42:21 330 )
12:42:21 --> 331 return func(*args, **kwargs)
12:42:21
12:42:21 File /usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py:950, in read_csv(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, encoding_errors, dialect, error_bad_lines, warn_bad_lines, on_bad_lines, delim_whitespace, low_memory, memory_map, float_precision, storage_options)
12:42:21 935 kwds_defaults = _refine_defaults_read(
12:42:21 936 dialect,
12:42:21 937 delimiter,
12:42:21 (...)
12:42:21 946 defaults={"delimiter": ","},
12:42:21 947 )
12:42:21 948 kwds.update(kwds_defaults)
12:42:21 --> 950 return _read(filepath_or_buffer, kwds)
12:42:21
12:42:21 File /usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py:605, in _read(filepath_or_buffer, kwds)
12:42:21 602 _validate_names(kwds.get("names", None))
12:42:21 604 # Create the parser.
12:42:21 --> 605 parser = TextFileReader(filepath_or_buffer, **kwds)
12:42:21 607 if chunksize or iterator:
12:42:21 608 return parser
12:42:21
12:42:21 File /usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py:1442, in TextFileReader.__init__(self, f, engine, **kwds)
12:42:21 1439 self.options["has_index_names"] = kwds["has_index_names"]
12:42:21 1441 self.handles: IOHandles | None = None
12:42:21 -> 1442 self._engine = self._make_engine(f, self.engine)
12:42:21
12:42:21 File /usr/local/lib/python3.10/dist-packages/pandas/io/parsers/readers.py:1735, in TextFileReader._make_engine(self, f, engine)
12:42:21 1733 if "b" not in mode:
12:42:21 1734 mode += "b"
12:42:21 -> 1735 self.handles = get_handle(
12:42:21 1736 f,
12:42:21 1737 mode,
12:42:21 1738 encoding=self.options.get("encoding", None),
12:42:21 1739 compression=self.options.get("compression", None),
12:42:21 1740 memory_map=self.options.get("memory_map", False),
12:42:21 1741 is_text=is_text,
12:42:21 1742 errors=self.options.get("encoding_errors", "strict"),
12:42:21 1743 storage_options=self.options.get("storage_options", None),
12:42:21 1744 )
12:42:21 1745 assert self.handles is not None
12:42:21 1746 f = self.handles.handle
12:42:21
12:42:21 File /usr/local/lib/python3.10/dist-packages/pandas/io/common.py:856, in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)
12:42:21 851 elif isinstance(handle, str):
12:42:21 852 # Check whether the filename is to be opened in binary mode.
12:42:21 853 # Binary mode does not support 'encoding' and 'newline'.
12:42:21 854 if ioargs.encoding and "b" not in ioargs.mode:
12:42:21 855 # Encoding
12:42:21 --> 856 handle = open(
12:42:21 857 handle,
12:42:21 858 ioargs.mode,
12:42:21 859 encoding=ioargs.encoding,
12:42:21 860 errors=errors,
12:42:21 861 newline="",
12:42:21 862 )
12:42:21 863 else:
12:42:21 864 # Binary mode
12:42:21 865 handle = open(handle, ioargs.mode)
12:42:21
12:42:21 FileNotFoundError: [Errno 2] No such file or directory: 'profile_report_nvtxppsum.csv'
KumoLiu commented
The root cause is the permissions for Google Drive used in tutorials have changed.
Access denied with the following error:
Cannot retrieve the public link of the file. You may need to change
the permission to 'Anyone with the link', or have had many accesses.
You may still be able to access the file from the browser:
https://drive.google.com/uc?id=1uWS4CXKD-NP_6-SgiQbQfhFMzbs0UJIr
Access denied with the following error:
Cannot retrieve the public link of the file. You may need to change
the permission to 'Anyone with the link', or have had many accesses.
You may still be able to access the file from the browser:
https://drive.google.com/uc?id=1OxAeCMVqH9FGpIWpAXSEJe6cLinEGQtF
@drbeh, could you please help check the permissions, thanks in advance!
drbeh commented
aylward commented
Sorry, that was an accident. I had to move our shared google drive to a new account.
It should be fixed now, and there should be no need for any future account changes. These files now have a "google-permanent" home. There may be other permission errors, but I tried to be thorough.