def test_load_multiple_root_dirs(self):
fp = os.path.join(self.temp_dir.name, 'multiple-root-dirs.zip')
self.archiver.save(fp)
# Add another semi-valid root dir.
second_root_dir = str(uuid.uuid4())
with zipfile.ZipFile(fp, mode='a') as zf:
zf.writestr('%s/VERSION' % second_root_dir, "foo")
with zipfile.ZipFile(fp, mode='r') as zf:
root_dir = str(self.archiver.uuid)
expected = {
'%s/VERSION' % root_dir,
'%s/metadata.yaml' % root_dir,
'%s/data/ints.txt' % root_dir,
'%s/provenance/metadata.yaml' % root_dir,
'%s/provenance/VERSION' % root_dir,
'%s/provenance/action/action.yaml' % root_dir,
'%s/VERSION' % second_root_dir
}
observed = set(zf.namelist())
self.assertEqual(observed, expected)
with self.assertRaisesRegex(ValueError, 'multiple root directories'):
Archiver.load(fp)
def test_load_empty_archive(self):
fp = os.path.join(self.temp_dir.name, 'empty.zip')
with zipfile.ZipFile(fp, mode='w') as zf:
pass
with zipfile.ZipFile(fp, mode='r') as zf:
expected = set()
observed = set(zf.namelist())
self.assertEqual(observed, expected)
with self.assertRaisesRegex(ValueError, 'visible root directory'):
Archiver.load(fp)
def test_save_excludes_dotfiles_in_data_dir(self):
def data_initializer(data_dir):
data_dir = str(data_dir)
fp = os.path.join(data_dir, 'ints.txt')
with open(fp, 'w') as fh:
fh.write('1\n')
fh.write('2\n')
fh.write('3\n')
hidden_fp = os.path.join(data_dir, '.hidden-file')
with open(hidden_fp, 'w') as fh:
fh.write("You can't see me if I can't see you\n")
hidden_dir = os.path.join(data_dir, '.hidden-dir')
os.mkdir(hidden_dir)
with open(os.path.join(hidden_dir, 'ignored-file'), 'w') as fh:
fh.write("I'm ignored because I live in a hidden dir :(\n")
archiver = Archiver.from_data(
IntSequence1, IntSequenceDirectoryFormat,
data_initializer=data_initializer)
fp = os.path.join(self.temp_dir.name, 'archive.zip')
archiver.save(fp)
root_dir = str(archiver.uuid)
expected = {
'VERSION',
'metadata.yaml',
'data/ints.txt'
}
self.assertArchiveMembers(fp, root_dir, expected)
def test_load_ignores_directory_members(self):
# Directory members aren't created by Python's zipfile module but can
# be present if the archive is unzipped and then rezipped, for example,
# using a command-line zip program.
fp = os.path.join(self.temp_dir.name, 'archive.zip')
self.archiver.save(fp)
# Add directory entries to the archive.
root_dir = str(self.archiver.uuid)
with zipfile.ZipFile(fp, mode='a') as zf:
zf.writestr('%s/' % root_dir, "")
zf.writestr('%s/data/' % root_dir, "")
zf.writestr('%s/data/nested/' % root_dir, "")
zf.writestr('%s/data/nested/foo.txt' % root_dir, "bar")
# Assert the expected files exist in the archive to verify this test
# case is testing what we want it to.
expected = {
'', # Expected path: `root_dir`/
'data/',
'data/nested/',
'VERSION',
'metadata.yaml',
'data/ints.txt',
'data/nested/foo.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp, root_dir, expected)
archiver = Archiver.load(fp)
self.assertEqual(archiver.uuid, self.archiver.uuid)
self.assertEqual(archiver.type, IntSequence1)
self.assertEqual(archiver.format, IntSequenceDirectoryFormat)
archiver.save(fp)
root_dir = str(archiver.uuid)
expected = {
# Directory entries should not be present.
'VERSION',
'metadata.yaml',
'data/ints.txt',
'data/nested/foo.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp, root_dir, expected)
def test_load_archive(self):
fp = os.path.join(self.temp_dir.name, 'archive.zip')
self.archiver.save(fp)
archiver = Archiver.load(fp)
self.assertEqual(archiver.uuid, self.archiver.uuid)
self.assertEqual(archiver.type, IntSequence1)
self.assertEqual(archiver.format, IntSequenceDirectoryFormat)
self.assertEqual({str(p.relative_to(archiver.data_dir))
for p in archiver.data_dir.iterdir()},
{'ints.txt'})
def test_load_dotfile_only_archive(self):
fp = os.path.join(self.temp_dir.name, 'dotfiles-only.zip')
with zipfile.ZipFile(fp, mode='w') as zf:
zf.writestr('.DS_Store', "The world's most beloved file\n")
zf.writestr('.hidden-file',
"You can't see me if I can't see you\n")
zf.writestr('.hidden-dir/ignored-file',
"I'm ignored because I live in a hidden dir :(\n")
with zipfile.ZipFile(fp, mode='r') as zf:
expected = {
'.DS_Store', '.hidden-file', '.hidden-dir/ignored-file'
}
observed = set(zf.namelist())
self.assertEqual(observed, expected)
with self.assertRaisesRegex(ValueError, 'visible root directory'):
Archiver.load(fp)
def test_load_dotfile_only_archive(self):
fp = os.path.join(self.temp_dir.name, 'dotfiles-only.zip')
with zipfile.ZipFile(fp, mode='w') as zf:
zf.writestr('.DS_Store', "The world's most beloved file\n")
zf.writestr('.hidden-file',
"You can't see me if I can't see you\n")
zf.writestr('.hidden-dir/ignored-file',
"I'm ignored because I live in a hidden dir :(\n")
with zipfile.ZipFile(fp, mode='r') as zf:
expected = {
'.DS_Store',
'.hidden-file',
'.hidden-dir/ignored-file'
}
observed = set(zf.namelist())
self.assertEqual(observed, expected)
with self.assertRaisesRegex(ValueError, 'visible root directory'):
Archiver.load(fp)
def setUp(self):
prefix = "qiime2-test-temp-"
self.temp_dir = tempfile.TemporaryDirectory(prefix=prefix)
# Initialize an Archiver. The values passed to the constructor mostly
# don't matter to the Archiver, but we'll pass valid Artifact test data
# anyways in case Archiver's behavior changes in the future.
def data_initializer(data_dir):
fp = os.path.join(str(data_dir), 'ints.txt')
with open(fp, 'w') as fh:
fh.write('1\n')
fh.write('2\n')
fh.write('3\n')
self.archiver = Archiver.from_data(
IntSequence1, IntSequenceDirectoryFormat,
data_initializer=data_initializer)
def setUp(self):
prefix = "qiime2-test-temp-"
self.temp_dir = tempfile.TemporaryDirectory(prefix=prefix)
# Initialize an Archiver. The values passed to the constructor mostly
# don't matter to the Archiver, but we'll pass valid Artifact test data
# anyways in case Archiver's behavior changes in the future.
def data_initializer(data_dir):
fp = os.path.join(str(data_dir), 'ints.txt')
with open(fp, 'w') as fh:
fh.write('1\n')
fh.write('2\n')
fh.write('3\n')
self.archiver = Archiver.from_data(
IntSequence1, IntSequenceDirectoryFormat,
data_initializer=data_initializer,
provenance_capture=ImportProvenanceCapture())
def test_load_ignores_root_dotfiles(self):
fp = os.path.join(self.temp_dir.name, 'archive.zip')
self.archiver.save(fp)
# Add some dotfiles to the archive.
with zipfile.ZipFile(fp, mode='a') as zf:
zf.writestr('.DS_Store', "The world's most beloved file\n")
zf.writestr('.hidden-file',
"You can't see me if I can't see you\n")
zf.writestr('.hidden-dir/ignored-file',
"I'm ignored because I live in a hidden dir :(\n")
# Assert the expected files exist in the archive to verify this test
# case is testing what we want it to.
with zipfile.ZipFile(fp, mode='r') as zf:
root_dir = str(self.archiver.uuid)
expected = {
'.DS_Store',
'.hidden-file',
'.hidden-dir/ignored-file',
'%s/VERSION' % root_dir,
'%s/metadata.yaml' % root_dir,
'%s/data/ints.txt' % root_dir,
'%s/provenance/metadata.yaml' % root_dir,
'%s/provenance/VERSION' % root_dir,
'%s/provenance/action/action.yaml' % root_dir
}
observed = set(zf.namelist())
# Not using self.assertArchiveMembers() because it accepts paths
# relative to root_dir, and we have extra paths at the same level
# as root_dir.
self.assertEqual(observed, expected)
archiver = Archiver.load(fp)
self.assertEqual(archiver.uuid, self.archiver.uuid)
self.assertEqual(archiver.type, IntSequence1)
self.assertEqual(archiver.format, IntSequenceDirectoryFormat)
self.assertEqual({str(p.relative_to(archiver.data_dir))
for p in archiver.data_dir.iterdir()},
{'ints.txt'})
def test_save_excludes_dotfiles_in_data_dir(self):
def data_initializer(data_dir):
data_dir = str(data_dir)
fp = os.path.join(data_dir, 'ints.txt')
with open(fp, 'w') as fh:
fh.write('1\n')
fh.write('2\n')
fh.write('3\n')
hidden_fp = os.path.join(data_dir, '.hidden-file')
with open(hidden_fp, 'w') as fh:
fh.write("You can't see me if I can't see you\n")
hidden_dir = os.path.join(data_dir, '.hidden-dir')
os.mkdir(hidden_dir)
with open(os.path.join(hidden_dir, 'ignored-file'), 'w') as fh:
fh.write("I'm ignored because I live in a hidden dir :(\n")
archiver = Archiver.from_data(
IntSequence1, IntSequenceDirectoryFormat,
data_initializer=data_initializer,
provenance_capture=ImportProvenanceCapture())
fp = os.path.join(self.temp_dir.name, 'archive.zip')
archiver.save(fp)
root_dir = str(archiver.uuid)
expected = {
'VERSION',
'metadata.yaml',
'data/ints.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp, root_dir, expected)
