Description of the problem
individual member files of an archive cannot be selected if they reside within a subfolder inside the archive.
For demonstration, I'm using an archive called MNE-kiloword-data.tar.gz (URL for it is in the code below).
Inside that archive is one folder with one file in it: MNE-kiloword-data/kword_metadata-epo.fif
I want to end up with the file here: /home/username/Desktop/MNE-kiloword-data/kword_metadata-epo.fif
In other words, I want the whole archive's contents to end up on my Desktop (this is just for illustration purposes; in reality we will put it somewhere more sensible).
I have tried several combinations of fname, path, and members below, and always end up with a FileNotFound error. I've also tried explicitly passing the subdirectory inside the archive as one of the members, like this:
processor = pooch.Untar(members=['MNE-kiloword-data/', 'MNE-kiloword-data/kword_metadata-epo.fif'])
...which also didn't work.
Full code that generated the error
fname = 'kword_metadata-epo.fif'
urls = {fname: 'https://osf.io/qkvf9/download?version=1'}
registry = {fname: 'md5:3a124170795abbd2e48aae8727e719a8'}
path = '/home/username/Desktop/MNE-kiloword-data/' # <--- update with your real username
processor = pooch.Untar(members=['MNE-kiloword-data/kword_metadata-epo.fif'])
foo = pooch.retrieve(url=urls[fname], known_hash=registry[fname],
fname=fname, path=path, processor=processor)Full error message
Downloading data from 'https://osf.io/qkvf9/download?version=1' to file '/home/username/Desktop/MNE-kiloword-data/kword_metadata-epo.fif'.
Extracting 'MNE-kiloword-data/kword_metadata-epo.fif' from '/home/username/Desktop/MNE-kiloword-data/kword_metadata-epo.fif' to '/home/username/Desktop/MNE-kiloword-data/kword_metadata-epo.fif.untar'
---------------------------------------------------------------------------
FileNotFoundError Traceback (most recent call last)
<ipython-input-1-f2eb5fdc640e> in <module>
6 processor = pooch.Untar(members=['MNE-kiloword-data/kword_metadata-epo.fif'])
7
----> 8 foo = pooch.retrieve(url=urls[fname], known_hash=registry[fname],
9 fname=fname,
10 path=path, processor=processor)
/opt/miniconda3/envs/mnedev/lib/python3.8/site-packages/pooch/core.py in retrieve(url, known_hash, fname, path, processor, downloader)
237
238 if processor is not None:
--> 239 return processor(str(full_path), action, None)
240
241 return str(full_path)
/opt/miniconda3/envs/mnedev/lib/python3.8/site-packages/pooch/processors.py in __call__(self, fname, action, pooch)
78 if not os.path.exists(extract_dir):
79 os.makedirs(extract_dir)
---> 80 self._extract_file(fname, extract_dir)
81 # Get a list of all file names (including subdirectories) in our folder
82 # of unzipped files.
/opt/miniconda3/envs/mnedev/lib/python3.8/site-packages/pooch/processors.py in _extract_file(self, fname, extract_dir)
186 try:
187 # Save it to our desired file name
--> 188 with open(os.path.join(extract_dir, member), "wb") as output:
189 output.write(data_file.read())
190 finally:
FileNotFoundError: [Errno 2] No such file or directory: '/home/username/Desktop/MNE-kiloword-data/kword_metadata-epo.fif.untar/MNE-kiloword-data/kword_metadata-epo.fif'
System information
- Operating system: Linux (Xubuntu 20.04)
- Python installation (Anaconda, system, ETS): miniconda
- Version of Python: 3.8.6
- Version of this package: 1.3.0
- If using conda, paste the output of
conda list below:
output of conda list
packages in environment at /opt/miniconda3/envs/mnedev:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
alabaster 0.7.12 py_0 conda-forge
apipkg 1.5 py_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
apptools 4.5.0 pypi_0 pypi
argon2-cffi 20.1.0 py38h1e0a361_2 conda-forge
async_generator 1.10 py_0 conda-forge
attrs 20.2.0 pyh9f0ad1d_0 conda-forge
babel 2.8.0 py_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.1 py_0 conda-forge
beautifulsoup4 4.9.3 pyhb0f4dca_0 conda-forge
bleach 3.2.1 pyh9f0ad1d_0 conda-forge
blosc 1.20.1 he1b5a44_0 conda-forge
bokeh 2.2.3 py38h32f6830_0 conda-forge
brotli 1.0.9 he1b5a44_3 conda-forge
brotlipy 0.7.0 py38h8df0ef7_1001 conda-forge
brunsli 0.1 he1b5a44_0 conda-forge
bzip2 1.0.8 h516909a_3 conda-forge
c-ares 1.16.1 h516909a_3 conda-forge
ca-certificates 2020.12.5 ha878542_0 conda-forge
cairo 1.16.0 h9f066cc_1006 conda-forge
cairocffi 1.1.0 py_0 conda-forge
cairosvg 2.4.2 py_0 conda-forge
certifi 2020.12.5 py38h578d9bd_0 conda-forge
cffi 1.14.3 py38h1bdcb99_1 conda-forge
chardet 3.0.4 py38h924ce5b_1008 conda-forge
charls 2.1.0 he1b5a44_2 conda-forge
cloudpickle 1.6.0 py_0 conda-forge
cmarkgfm 0.4.2 py38h1e0a361_3 conda-forge
codespell 1.17.1 pypi_0 pypi
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
colorspacious 1.1.2 pyh24bf2e0_0 conda-forge
configobj 5.0.6 pypi_0 pypi
coverage 5.3 py38h1e0a361_1 conda-forge
cryptography 3.2.1 py38h7699a38_0 conda-forge
cssselect2 0.2.1 pyh9f0ad1d_1 conda-forge
cudatoolkit 10.2.89 h8f6ccaa_6 conda-forge
cudnn 7.6.5.32 h01f27c4_1 conda-forge
cupy 8.1.0 py38h0c20449_0 conda-forge
cycler 0.10.0 py_2 conda-forge
cytoolz 0.11.0 py38h1e0a361_1 conda-forge
dask-core 2.30.0 py_0 conda-forge
dbus 1.13.6 hfdff14a_1 conda-forge
decopatch 1.4.8 pypi_0 pypi
decorator 4.4.2 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
dipy 1.2.0 pypi_0 pypi
docutils 0.16 py38h924ce5b_2 conda-forge
entrypoints 0.3 py38h32f6830_1002 conda-forge
envisage 4.9.2 pypi_0 pypi
execnet 1.7.1 py_0 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
fastrlock 0.5 py38h950e882_1 conda-forge
filprofiler 0.8.0 pypi_0 pypi
flake8 3.8.4 py_0 conda-forge
fontconfig 2.13.1 h7e3eb15_1002 conda-forge
freetype 2.10.4 h7ca028e_0 conda-forge
fuzzywuzzy 0.18.0 pypi_0 pypi
gettext 0.19.8.1 hf34092f_1004 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
glib 2.66.2 h58526e2_0 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
h5py 2.10.0 nompi_py38h7442b35_105 conda-forge
hdf5 1.10.6 nompi_h1022a3e_1110 conda-forge
icu 67.1 he1b5a44_0 conda-forge
idna 2.10 pyh9f0ad1d_0 conda-forge
imagecodecs 2020.5.30 py38h63741c2_4 conda-forge
imageio 2.9.0 py_0 conda-forge
imageio-ffmpeg 0.4.2 pypi_0 pypi
imagesize 1.2.0 py_0 conda-forge
importlib-metadata 2.0.0 py_1 conda-forge
importlib_metadata 2.0.0 1 conda-forge
iniconfig 1.1.1 pyh9f0ad1d_0 conda-forge
ipyevents 0.8.1 py_0 conda-forge
ipykernel 5.3.4 py38h1cdfbd6_1 conda-forge
ipympl 0.5.8 pyh9f0ad1d_0 conda-forge
ipython 7.19.0 py38h81c977d_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 pyh9f0ad1d_1 conda-forge
jedi 0.17.2 py38h32f6830_1 conda-forge
jeepney 0.4.3 py_0 conda-forge
jinja2 2.11.2 pyh9f0ad1d_0 conda-forge
joblib 0.17.0 py_0 conda-forge
jpeg 9d h36c2ea0_0 conda-forge
json5 0.9.5 pyh9f0ad1d_0 conda-forge
jsonschema 3.2.0 py_2 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 6.1.7 py_0 conda-forge
jupyter_console 6.2.0 py_0 conda-forge
jupyter_core 4.6.3 py38h32f6830_2 conda-forge
jupyterlab 2.2.9 py_0 conda-forge
jupyterlab_pygments 0.1.2 pyh9f0ad1d_0 conda-forge
jupyterlab_server 1.2.0 py_0 conda-forge
jxrlib 1.1 h516909a_2 conda-forge
keyring 21.4.0 py38h32f6830_2 conda-forge
kiwisolver 1.3.1 py38h82cb98a_0 conda-forge
krb5 1.17.1 hfafb76e_3 conda-forge
latexcodec 2.0.0 pypi_0 pypi
lcms2 2.11 hcbb858e_1 conda-forge
ld_impl_linux-64 2.35 h769bd43_9 conda-forge
lerc 2.2 he1b5a44_0 conda-forge
libaec 1.0.4 he1b5a44_1 conda-forge
libblas 3.9.0 2_openblas conda-forge
libcblas 3.9.0 2_openblas conda-forge
libclang 10.0.1 default_hde54327_1 conda-forge
libcurl 7.71.1 hcdd3856_8 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libevent 2.1.10 hcdb4288_3 conda-forge
libffi 3.2.1 he1b5a44_1007 conda-forge
libgcc-ng 9.3.0 h5dbcf3e_17 conda-forge
libgfortran-ng 9.3.0 he4bcb1c_17 conda-forge
libgfortran5 9.3.0 he4bcb1c_17 conda-forge
libglib 2.66.2 hbe7bbb4_0 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 2_openblas conda-forge
libllvm10 10.0.1 he513fc3_3 conda-forge
libnghttp2 1.41.0 h8cfc5f6_2 conda-forge
libopenblas 0.3.12 pthreads_h4812303_1 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libpq 12.3 h5513abc_2 conda-forge
libsodium 1.0.18 h516909a_1 conda-forge
libssh2 1.9.0 hab1572f_5 conda-forge
libstdcxx-ng 9.3.0 h2ae2ef3_17 conda-forge
libtiff 4.1.0 h4f3a223_6 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp-base 1.1.0 h36c2ea0_3 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxkbcommon 0.10.0 he1b5a44_0 conda-forge
libxml2 2.9.10 h68273f3_2 conda-forge
libxslt 1.1.33 h572872d_1 conda-forge
libzopfli 1.0.3 he1b5a44_0 conda-forge
lineedit 0.1.5 pypi_0 pypi
llvm-openmp 11.0.0 hfc4b9b4_1 conda-forge
llvmlite 0.34.0 py38h4f45e52_2 conda-forge
lz4-c 1.9.2 he1b5a44_3 conda-forge
makefun 1.9.4 pypi_0 pypi
markupsafe 1.1.1 py38h8df0ef7_2 conda-forge
matplotlib 3.3.2 py38h32f6830_1 conda-forge
matplotlib-base 3.3.2 py38h4d1ce4f_1 conda-forge
mayavi 4.7.2 pypi_0 pypi
mccabe 0.6.1 py_1 conda-forge
memory_profiler 0.58.0 py_0 conda-forge
meshio 4.3.3 pypi_0 pypi
mistune 0.8.4 py38h1e0a361_1002 conda-forge
mkl 2020.2 256 conda-forge
mne 0.22.dev0 dev_0
mne-bids 0.6.dev0 dev_0
mnefun 0.1 dev_0
more-itertools 8.6.0 pyhd8ed1ab_0 conda-forge
mysql-common 8.0.21 2 conda-forge
mysql-libs 8.0.21 hf3661c5_2 conda-forge
nb_conda_kernels 2.3.0 py38h32f6830_3 conda-forge
nbclient 0.5.1 py_0 conda-forge
nbconvert 6.0.7 py38h32f6830_2 conda-forge
nbformat 5.0.8 py_0 conda-forge
nccl 2.7.8.1 hc6a2c23_1 conda-forge
ncurses 6.2 he1b5a44_2 conda-forge
neo 0.9.0 pypi_0 pypi
nest-asyncio 1.4.2 pyhd8ed1ab_0 conda-forge
networkx 2.5 py_0 conda-forge
nibabel 3.2.0 pypi_0 pypi
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nss 3.58 h27285de_1 conda-forge
numba 0.51.2 py38hc5bc63f_0 conda-forge
numexpr 2.7.1 py38hc5bc63f_3 conda-forge
numpy 1.19.2 py38hf89b668_1 conda-forge
numpydoc 1.0.0.dev0 pypi_0 pypi
olefile 0.46 pyh9f0ad1d_1 conda-forge
openjpeg 2.3.1 h981e76c_3 conda-forge
openssl 1.1.1i h7f98852_0 conda-forge
oset 0.1.3 pypi_0 pypi
packaging 20.4 pyh9f0ad1d_0 conda-forge
pandas 1.1.4 py38h0ef3d22_0 conda-forge
pandoc 2.11.0.4 hd18ef5c_0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parso 0.7.0 pyh9f0ad1d_0 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 8.0.1 py38h9776b28_0 conda-forge
pip 20.2.4 py_0 conda-forge
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pkginfo 1.6.1 pyh9f0ad1d_0 conda-forge
pluggy 0.13.1 py38h924ce5b_3 conda-forge
pooch 1.3.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.8.0 pyh9f0ad1d_0 conda-forge
prompt-toolkit 3.0.8 py_0 conda-forge
prompt_toolkit 3.0.8 0 conda-forge
psutil 5.7.3 py38h8df0ef7_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
py 1.9.0 pyh9f0ad1d_0 conda-forge
pybtex 0.23.0 pypi_0 pypi
pybtex-docutils 0.2.2 pypi_0 pypi
pycodestyle 2.6.0 pyh9f0ad1d_0 conda-forge
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pydocstyle 5.1.1 pypi_0 pypi
pyface 7.1.0 pyh9f0ad1d_0 conda-forge
pyflakes 2.2.0 pyh9f0ad1d_0 conda-forge
pygments 2.7.2 py_0 conda-forge
pyopenssl 19.1.0 py_1 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyqt 5.12.3 py38ha8c2ead_4 conda-forge
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtchart 5.12 pypi_0 pypi
pyqtwebengine 5.12.1 pypi_0 pypi
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pyside2 5.13.2 py38h3b90aee_3 conda-forge
pysocks 1.7.1 py38h924ce5b_2 conda-forge
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pytest 6.1.2 py38h578d9bd_0 conda-forge
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python 3.8.6 h852b56e_0_cpython conda-forge
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python_abi 3.8 1_cp38 conda-forge
pytz 2020.4 pyhd8ed1ab_0 conda-forge
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pywavelets 1.1.1 py38hab2c0dc_3 conda-forge
pyyaml 5.3.1 py38h8df0ef7_1 conda-forge
pyzmq 19.0.2 py38ha71036d_2 conda-forge
qt 5.12.9 h1f2b2cb_0 conda-forge
qtconsole 4.7.7 pyh9f0ad1d_0 conda-forge
qtpy 1.9.0 py_0 conda-forge
quantities 0.12.4 pypi_0 pypi
radian 0.5.8 pypi_0 pypi
rchitect 0.3.28 pypi_0 pypi
readline 8.0 he28a2e2_2 conda-forge
readme_renderer 27.0 pyh9f0ad1d_0 conda-forge
requests 2.24.0 pyh9f0ad1d_0 conda-forge
requests-toolbelt 0.9.1 py_0 conda-forge
rfc3986 1.4.0 pyh9f0ad1d_0 conda-forge
rstcheck 3.3.1 pypi_0 pypi
scikit-image 0.17.2 py38h0ef3d22_4 conda-forge
scikit-learn 0.23.2 py38h5d63f67_2 conda-forge
scipy 1.5.3 py38hb2138dd_0 conda-forge
scooby 0.5.6 pypi_0 pypi
seaborn 0.11.0 ha770c72_1 conda-forge
seaborn-base 0.11.0 pyhd8ed1ab_1 conda-forge
secretstorage 3.1.2 py38h32f6830_2 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 49.6.0 py38h924ce5b_2 conda-forge
six 1.15.0 pyh9f0ad1d_0 conda-forge
sklearn 0.0 pypi_0 pypi
snakeviz 2.1.0 pyh9f0ad1d_0 conda-forge
snappy 1.1.8 he1b5a44_3 conda-forge
snowballstemmer 2.0.0 py_0 conda-forge
soupsieve 2.0.1 py_1 conda-forge
sphinx 3.3.0 pyhd8ed1ab_0 conda-forge
sphinx-gallery 0.8.1 pypi_0 pypi
sphinx_bootstrap_theme 0.8.0 py_0 conda-forge
sphinx_fontawesome 0.0.6 pyh8c360ce_0 conda-forge
sphinxcontrib-applehelp 1.0.2 py_0 conda-forge
sphinxcontrib-bibtex 2.0.0 pypi_0 pypi
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 1.0.3 py_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
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spyder-kernels 1.9.4 py38h32f6830_0 conda-forge
sqlalchemy 1.3.20 py38h1e0a361_0 conda-forge
sqlite 3.33.0 h4cf870e_1 conda-forge
sswef 0.1 dev_0
statsmodels 0.12.1 py38h0b5ebd8_1 conda-forge
termcolor 1.1.0 pypi_0 pypi
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tinycss2 1.0.2 py_1 conda-forge
tk 8.6.10 hed695b0_1 conda-forge
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toolz 0.11.1 py_0 conda-forge
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tqdm 4.46.0 pypi_0 pypi
traitlets 5.0.5 py_0 conda-forge
traits 6.1.1 py38h1e0a361_0 conda-forge
traitsui 7.1.0 pyh9f0ad1d_0 conda-forge
twine 3.2.0 py38h32f6830_1 conda-forge
typing_extensions 3.7.4.3 py_0 conda-forge
urllib3 1.25.11 py_0 conda-forge
viscm 0.9 pyh5ca1d4c_0 conda-forge
vtk 9.0.1 pypi_0 pypi
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.35.1 pyh9f0ad1d_0 conda-forge
widgetsnbextension 3.5.1 py38h32f6830_4 conda-forge
wurlitzer 2.0.0 py38h32f6830_2 conda-forge
xarray 0.16.1 py_0 conda-forge
xlrd 1.2.0 pyh9f0ad1d_1 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.10 h516909a_0 conda-forge
xorg-libsm 1.2.3 h84519dc_1000 conda-forge
xorg-libx11 1.6.12 h516909a_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xorg-libxext 1.3.4 h516909a_0 conda-forge
xorg-libxrender 0.9.10 h516909a_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h516909a_0 conda-forge
zeromq 4.3.3 he1b5a44_2 conda-forge
zfp 0.5.5 he1b5a44_4 conda-forge
zipp 3.4.0 py_0 conda-forge
zlib 1.2.11 h516909a_1010 conda-forge
zstd 1.4.5 h6597ccf_2 conda-forge
Additional notes
FWIW, ultimately I will want to use the Pooch class; I had similar difficulties getting this to work with pooch.Pooch.fetch() however. My basic problem seems to be that when using a processor like Unzip() or Untar(), there is no option to put the output of the unzipping/untarring in an arbitrary location (i.e., there is only a suffix attribute). I think that if it were possible to do this:
processor = pooch.Untar(folder_to_put_untarred_content_into='/some/arbitrary/path')
...then my difficulties would go away (i.e., for my use case, if I could specify where to untar the archive, then I wouldn't need to bother with the members parameter at all, so I wouldn't hit the problem of members nested within subfolders). I suspect that implementing the target directory for Untar() is probably easier anyway, though I can imagine cases where both capabilities would be useful.
Description of the problem
individual member files of an archive cannot be selected if they reside within a subfolder inside the archive.
For demonstration, I'm using an archive called
MNE-kiloword-data.tar.gz(URL for it is in the code below).Inside that archive is one folder with one file in it:
MNE-kiloword-data/kword_metadata-epo.fifI want to end up with the file here:
/home/username/Desktop/MNE-kiloword-data/kword_metadata-epo.fifIn other words, I want the whole archive's contents to end up on my Desktop (this is just for illustration purposes; in reality we will put it somewhere more sensible).
I have tried several combinations of
fname,path, andmembersbelow, and always end up with aFileNotFounderror. I've also tried explicitly passing the subdirectory inside the archive as one of themembers, like this:...which also didn't work.
Full code that generated the error
Full error message
System information
conda listbelow:output of conda list
Additional notes
FWIW, ultimately I will want to use the Pooch class; I had similar difficulties getting this to work with
pooch.Pooch.fetch()however. My basic problem seems to be that when using a processor likeUnzip()orUntar(), there is no option to put the output of the unzipping/untarring in an arbitrary location (i.e., there is only asuffixattribute). I think that if it were possible to do this:...then my difficulties would go away (i.e., for my use case, if I could specify where to untar the archive, then I wouldn't need to bother with the
membersparameter at all, so I wouldn't hit the problem of members nested within subfolders). I suspect that implementing the target directory forUntar()is probably easier anyway, though I can imagine cases where both capabilities would be useful.