def test_writer_transformer(self):
# `Artifact._from_view` invokes transformer that handles `dataframe` ->
# `WinnowedFormat` with all input, because the `WinnowedDirectoryFormat` has
# been registered as the directory format for the semantic type.
artifact = Artifact._from_view(Winnowed, [(exp_featureOrdering, exp_auc, exp_permanova)],
list, archive.ImportProvenanceCapture())
# Test that the directory and file format can be read again.
got_featureOrdering, got_auc, got_permanova = artifact.view( list )[0]
pd.testing.assert_frame_equal(
got_featureOrdering.astype(str),
exp_featureOrdering.astype(str),
check_dtype=False
) # Avoid checking values since reading df stores as objects while, hard coding in does not
# ex) bool(False) == Object(False) in pandas is False although the values function the same.
pd.testing.assert_frame_equal(
got_auc.astype(str),
exp_auc.astype(str),
check_dtype=False
)
pd.testing.assert_frame_equal(
got_permanova.astype(str),
exp_permanova.astype(str),
check_dtype=False
)
def setUp(self):
# Ignore the returned dummy plugin object, just run this to verify the
# plugin exists as the tests rely on it being loaded.
get_dummy_plugin()
# TODO standardize temporary directories created by QIIME 2
self.test_dir = tempfile.TemporaryDirectory(prefix='qiime2-test-temp-')
self.provenance_capture = archive.ImportProvenanceCapture()
def test_writer_transformer(self):
for type in IntSequence1, IntSequence2:
# `Artifact._from_view` invokes transformer that handles `list` ->
# `SingleIntFormat`, because the `SingleIntDirectoryFormat` has
# been registered as the directory format for the semantic type.
# We didn't define a `SingleIntDirectoryFormat` ->
# `SingleIntFormat` tranformer because
# `model.SingleFileDirectoryFormat` handles that transformation for
# us.
artifact = Artifact._from_view(type, [1, 2, 42, -999, 42, 0], list,
archive.ImportProvenanceCapture())
# Test that the directory and file format can be read again.
self.assertEqual(artifact.view(list), [1, 2, 42, -999, 42, 0])
def test_writer_transformer(self):
# `Artifact._from_view` invokes transformer that handles `dict` ->
# `MappingFormat`, because the `MappingDirectoryFormat` has
# been registered as the directory format for the semantic type.
# We didn't define a `MappingDirectoryFormat` ->
# `MappingFormat` tranformer because
# `model.SingleFileDirectoryFormat` handles that transformation for
# us.
artifact = Artifact._from_view(Mapping, {
'abc': 'cat',
'def': 'dog'
}, dict, archive.ImportProvenanceCapture())
# Test that the directory and file format can be read again.
self.assertEqual(artifact.view(dict), {'abc': 'cat', 'def': 'dog'})
def import_data(cls, type, view, view_type=None):
type_, type = type, __builtins__['type']
is_format = False
if isinstance(type_, str):
type_ = qiime2.sdk.parse_type(type_)
if isinstance(view_type, str):
view_type = qiime2.sdk.parse_format(view_type)
is_format = True
if view_type is None:
if type(view) is str or isinstance(view, pathlib.PurePath):
is_format = True
pm = qiime2.sdk.PluginManager()
output_dir_fmt = pm.get_directory_format(type_)
if pathlib.Path(view).is_file():
if not issubclass(output_dir_fmt,
model.SingleFileDirectoryFormatBase):
raise qiime2.plugin.ValidationError(
"Importing %r requires a directory, not %s" %
(output_dir_fmt.__name__, view))
view_type = output_dir_fmt.file.format
else:
view_type = output_dir_fmt
else:
view_type = type(view)
format_ = None
md5sums = None
if is_format:
path = pathlib.Path(view)
if path.is_file():
md5sums = {path.name: util.md5sum(path)}
elif path.is_dir():
md5sums = util.md5sum_directory(path)
else:
raise qiime2.plugin.ValidationError(
"Path '%s' does not exist." % path)
format_ = view_type
provenance_capture = archive.ImportProvenanceCapture(format_, md5sums)
return cls._from_view(type_,
view,
view_type,
provenance_capture,
validate_level='max')
def make_provenance_capture(self):
# importing visualizations is not supported, but we do that here to
# simplify testing machinery
return archive.ImportProvenanceCapture()
def make_provenance_capture(self):
# You can't actually import a visualization, but I won't tell
# visualization if you don't...
return archive.ImportProvenanceCapture()
def setUp(self):
prefix = "qiime2-test-temp-"
self.temp_dir = tempfile.TemporaryDirectory(prefix=prefix)
self.provenance_capture = archive.ImportProvenanceCapture()
