def test_downloader(tmp_path, request_mocker):
# Sandboxing test
# ===============
# When nilearn downloads a file, everything is first downloaded in a
# temporary directory (sandbox) and moved to the "real" data directory if
# all files are present. In case of error, the sandbox is deleted.
# To test this feature, we do as follow:
# - create the data dir with a file that has a specific content
# - try to download the dataset but make it fail on purpose (by requesting a
# file that is not in the archive)
# - check that the previously created file is untouched :
# - if sandboxing is faulty, the file would be replaced by the file of the
# archive
# - if sandboxing works, the file must be untouched.
local_archive = Path(
__file__).parent / "data" / "craddock_2011_parcellations.tar.gz"
url = "http://example.com/craddock_atlas"
request_mocker.url_mapping["*craddock*"] = local_archive
datasetdir = tmp_path / 'craddock_2012'
datasetdir.mkdir()
# Create a dummy file. If sandboxing is successful, it won't be overwritten
dummy_file = datasetdir / "random_all.nii.gz"
with dummy_file.open("w") as f:
f.write('stuff')
opts = {'uncompress': True}
files = [
('random_all.nii.gz', url, opts),
# The following file does not exists. It will cause an abortion of
# the fetching procedure
('bald.nii.gz', url, opts)
]
pytest.raises(IOError,
utils._fetch_files,
str(tmp_path / 'craddock_2012'),
files,
verbose=0)
with dummy_file.open("r") as f:
stuff = f.read(5)
assert stuff == 'stuff'
# Downloading test
# ================
# Now, we use the regular downloading feature. This will override the dummy
# file created before.
atlas.fetch_atlas_craddock_2012(data_dir=str(tmp_path))
with dummy_file.open() as f:
stuff = f.read()
assert stuff == ''
def test_downloader(tmp_path):
# Sandboxing test
# ===============
# When nilearn downloads a file, everything is first downloaded in a
# temporary directory (sandbox) and moved to the "real" data directory if
# all files are present. In case of error, the sandbox is deleted.
# To test this feature, we do as follow:
# - create the data dir with a file that has a specific content
# - try to download the dataset but make it fail on purpose (by requesting a
# file that is not in the archive)
# - check that the previously created file is untouched :
# - if sandboxing is faulty, the file would be replaced by the file of the
# archive
# - if sandboxing works, the file must be untouched.
local_url = "file:" + _urllib.request.pathname2url(
os.path.join(tst.datadir, "craddock_2011_parcellations.tar.gz"))
datasetdir = str(tmp_path / 'craddock_2012')
os.makedirs(datasetdir)
# Create a dummy file. If sandboxing is successful, it won't be overwritten
dummy = open(os.path.join(datasetdir, 'random_all.nii.gz'), 'w')
dummy.write('stuff')
dummy.close()
opts = {'uncompress': True}
files = [
('random_all.nii.gz', local_url, opts),
# The following file does not exists. It will cause an abortion of
# the fetching procedure
('bald.nii.gz', local_url, opts)
]
pytest.raises(IOError,
utils._fetch_files,
str(tmp_path / 'craddock_2012'),
files,
verbose=0)
dummy = open(os.path.join(datasetdir, 'random_all.nii.gz'), 'r')
stuff = dummy.read(5)
dummy.close()
assert stuff == 'stuff'
# Downloading test
# ================
# Now, we use the regular downloading feature. This will override the dummy
# file created before.
atlas.fetch_atlas_craddock_2012(data_dir=str(tmp_path), url=local_url)
dummy = open(os.path.join(datasetdir, 'random_all.nii.gz'), 'r')
stuff = dummy.read()
dummy.close()
assert stuff == ''
def test_downloader():
# Sandboxing test
# ===============
# When nilearn downloads a file, everything is first downloaded in a
# temporary directory (sandbox) and moved to the "real" data directory if
# all files are present. In case of error, the sandbox is deleted.
# To test this feature, we do as follow:
# - create the data dir with a file that has a specific content
# - try to download the dataset but make it fail on purpose (by requesting a
# file that is not in the archive)
# - check that the previously created file is untouched :
# - if sandboxing is faulty, the file would be replaced by the file of the
# archive
# - if sandboxing works, the file must be untouched.
local_url = "file:" + _urllib.request.pathname2url(
os.path.join(tst.datadir, "craddock_2011_parcellations.tar.gz"))
datasetdir = os.path.join(tst.tmpdir, 'craddock_2012')
os.makedirs(datasetdir)
# Create a dummy file. If sandboxing is successful, it won't be overwritten
dummy = open(os.path.join(datasetdir, 'random_all.nii.gz'), 'w')
dummy.write('stuff')
dummy.close()
opts = {'uncompress': True}
files = [
('random_all.nii.gz', local_url, opts),
# The following file does not exists. It will cause an abortion of
# the fetching procedure
('bald.nii.gz', local_url, opts)
]
assert_raises(IOError, utils._fetch_files,
os.path.join(tst.tmpdir, 'craddock_2012'), files,
verbose=0)
dummy = open(os.path.join(datasetdir, 'random_all.nii.gz'), 'r')
stuff = dummy.read(5)
dummy.close()
assert_equal(stuff, 'stuff')
# Downloading test
# ================
# Now, we use the regular downloading feature. This will override the dummy
# file created before.
atlas.fetch_atlas_craddock_2012(data_dir=tst.tmpdir, url=local_url)
dummy = open(os.path.join(datasetdir, 'random_all.nii.gz'), 'r')
stuff = dummy.read()
dummy.close()
assert_equal(stuff, '')
def test_fetch_atlas_craddock_2012():
bunch = atlas.fetch_atlas_craddock_2012(data_dir=tmpdir, verbose=0)
keys = ("scorr_mean", "tcorr_mean", "scorr_2level", "tcorr_2level", "random")
filenames = [
"scorr05_mean_all.nii.gz",
"tcorr05_mean_all.nii.gz",
"scorr05_2level_all.nii.gz",
"tcorr05_2level_all.nii.gz",
"random_all.nii.gz",
]
assert_equal(len(mock_url_request.urls), 1)
for key, fn in zip(keys, filenames):
assert_equal(bunch[key], os.path.join(tmpdir, "craddock_2012", fn))
assert_not_equal(bunch.description, "")
def test_fetch_atlas_craddock_2012():
bunch = atlas.fetch_atlas_craddock_2012(data_dir=tmpdir, verbose=0)
keys = ("scorr_mean", "tcorr_mean", "scorr_2level", "tcorr_2level",
"random")
filenames = [
"scorr05_mean_all.nii.gz",
"tcorr05_mean_all.nii.gz",
"scorr05_2level_all.nii.gz",
"tcorr05_2level_all.nii.gz",
"random_all.nii.gz",
]
assert_equal(len(mock_url_request.urls), 1)
for key, fn in zip(keys, filenames):
assert_equal(bunch[key], os.path.join(tmpdir, 'craddock_2012', fn))
def test_fetch_atlas_craddock_2012(tmp_path, request_mocker):
bunch = atlas.fetch_atlas_craddock_2012(data_dir=str(tmp_path), verbose=0)
keys = ("scorr_mean", "tcorr_mean", "scorr_2level", "tcorr_2level",
"random")
filenames = [
"scorr05_mean_all.nii.gz",
"tcorr05_mean_all.nii.gz",
"scorr05_2level_all.nii.gz",
"tcorr05_2level_all.nii.gz",
"random_all.nii.gz",
]
assert len(tst.mock_url_request.urls) == 1
for key, fn in zip(keys, filenames):
assert bunch[key] == str(tmp_path / 'craddock_2012' / fn)
assert bunch.description != ''
def test_fetch_atlas_craddock_2012(tmp_path, request_mocker):
local_archive = Path(
__file__).parent / "data" / "craddock_2011_parcellations.tar.gz"
request_mocker.url_mapping["*craddock*"] = local_archive
bunch = atlas.fetch_atlas_craddock_2012(data_dir=str(tmp_path), verbose=0)
keys = ("scorr_mean", "tcorr_mean", "scorr_2level", "tcorr_2level",
"random")
filenames = [
"scorr05_mean_all.nii.gz",
"tcorr05_mean_all.nii.gz",
"scorr05_2level_all.nii.gz",
"tcorr05_2level_all.nii.gz",
"random_all.nii.gz",
]
assert request_mocker.url_count == 1
for key, fn in zip(keys, filenames):
assert bunch[key] == str(tmp_path / 'craddock_2012' / fn)
assert bunch.description != ''
