def test_load_with_archive_filepath_modified(self):
# Save an artifact for use in the following test case.
fp = os.path.join(self.test_dir.name, 'artifact.qza')
Artifact.import_data(FourInts, [-1, 42, 0, 43]).save(fp)
# Load the artifact from a filepath then save a different artifact to
# the same filepath. Assert that both artifacts produce the correct
# views of their data.
#
# `load` used to be lazy, only extracting data when it needed to (e.g.
# when `save` or `view` was called). This was buggy as the filepath
# could have been deleted, or worse, modified to contain a different
# .qza file. Thus, the wrong archive could be extracted on demand, or
# the archive could be missing altogether. There isn't an easy
# cross-platform compatible way to solve this problem, so Artifact.load
# is no longer lazy and always extracts its data immediately. The real
# motivation for lazy loading was for quick inspection of archives
# without extracting/copying data, so that API is now provided through
# Artifact.peek.
artifact1 = Artifact.load(fp)
Artifact.import_data(FourInts, [10, 11, 12, 13]).save(fp)
artifact2 = Artifact.load(fp)
self.assertEqual(artifact1.view(list), [-1, 42, 0, 43])
self.assertEqual(artifact2.view(list), [10, 11, 12, 13])
def test_call_with_no_parameters(self):
merge_mappings = self.plugin.methods['merge_mappings']
artifact1 = Artifact.import_data(Mapping, {'foo': 'abc', 'bar': 'def'})
artifact2 = Artifact.import_data(Mapping, {'bazz': 'abc'})
result = merge_mappings(artifact1, artifact2)
# Test properties of the `Results` object.
self.assertIsInstance(result, tuple)
self.assertIsInstance(result, Results)
self.assertEqual(len(result), 1)
self.assertEqual(result.merged_mapping.view(dict), {
'foo': 'abc',
'bar': 'def',
'bazz': 'abc'
})
result = result[0]
self.assertIsInstance(result, Artifact)
self.assertEqual(result.type, Mapping)
self.assertIsInstance(result.uuid, uuid.UUID)
self.assertEqual(result.view(dict), {
'foo': 'abc',
'bar': 'def',
'bazz': 'abc'
})
def test_load_with_archive_filepath_modified(self):
# Save an artifact for use in the following test case.
fp = os.path.join(self.test_dir.name, 'artifact.qza')
Artifact.import_data(FourInts, [-1, 42, 0, 43]).save(fp)
# Load the artifact from a filepath then save a different artifact to
# the same filepath. Assert that both artifacts produce the correct
# views of their data.
#
# `load` used to be lazy, only extracting data when it needed to (e.g.
# when `save` or `view` was called). This was buggy as the filepath
# could have been deleted, or worse, modified to contain a different
# .qza file. Thus, the wrong archive could be extracted on demand, or
# the archive could be missing altogether. There isn't an easy
# cross-platform compatible way to solve this problem, so Artifact.load
# is no longer lazy and always extracts its data immediately. The real
# motivation for lazy loading was for quick inspection of archives
# without extracting/copying data, so that API is now provided through
# Artifact.peek.
artifact1 = Artifact.load(fp)
Artifact.import_data(FourInts, [10, 11, 12, 13]).save(fp)
artifact2 = Artifact.load(fp)
self.assertEqual(artifact1.view(list), [-1, 42, 0, 43])
self.assertEqual(artifact2.view(list), [10, 11, 12, 13])
def test_import_data_with_filepath_multi_file_data_layout(self):
fp = os.path.join(self.test_dir.name, 'test.txt')
with open(fp, 'w') as fh:
fh.write('42\n')
with self.assertRaisesRegex(ValueError,
"FourIntsDirectoryFormat.*directory"):
Artifact.import_data(FourInts, fp)
def test_import_data_invalid_type(self):
with self.assertRaisesRegex(TypeError,
'concrete semantic type.*Visualization'):
Artifact.import_data(qiime.core.type.Visualization, self.test_dir)
with self.assertRaisesRegex(TypeError,
'concrete semantic type.*Visualization'):
Artifact.import_data('Visualization', self.test_dir)
def test_import_data_with_unreachable_path(self):
with self.assertRaisesRegex(ValueError, "does not exist"):
Artifact.import_data(IntSequence1,
os.path.join(self.test_dir.name, 'foo.txt'))
with self.assertRaisesRegex(ValueError, "does not exist"):
Artifact.import_data(FourInts,
os.path.join(self.test_dir.name, 'bar'))
def test_import_data_with_filepath_multi_file_data_layout(self):
fp = os.path.join(self.test_dir.name, 'test.txt')
with open(fp, 'w') as fh:
fh.write('42\n')
with self.assertRaisesRegex(ValueError,
"FourIntsDirectoryFormat.*directory"):
Artifact.import_data(FourInts, fp)
def test_import_data_invalid_type(self):
with self.assertRaisesRegex(TypeError,
'concrete semantic type.*Visualization'):
Artifact.import_data(qiime.core.type.Visualization, self.test_dir)
with self.assertRaisesRegex(TypeError,
'concrete semantic type.*Visualization'):
Artifact.import_data('Visualization', self.test_dir)
def test_import_data_with_unreachable_path(self):
with self.assertRaisesRegex(ValueError, "does not exist"):
Artifact.import_data(IntSequence1,
os.path.join(self.test_dir.name, 'foo.txt'))
with self.assertRaisesRegex(ValueError, "does not exist"):
Artifact.import_data(FourInts,
os.path.join(self.test_dir.name, 'bar', ''))
def test_async(self):
concatenate_ints = self.plugin.methods['concatenate_ints']
concatenate_ints_markdown = \
self.plugin.methods['concatenate_ints_markdown']
artifact1 = Artifact.import_data(IntSequence1, [0, 42, 43])
artifact2 = Artifact.import_data(IntSequence2, [99, -22])
for method in concatenate_ints, concatenate_ints_markdown:
future = method. async (artifact1, artifact1, artifact2, 55, 1)
self.assertIsInstance(future, concurrent.futures.Future)
result = future.result()
# Test properties of the `Results` object.
self.assertIsInstance(result, tuple)
self.assertIsInstance(result, Results)
self.assertEqual(len(result), 1)
self.assertEqual(result.concatenated_ints.view(list),
[0, 42, 43, 0, 42, 43, 99, -22, 55, 1])
result = result[0]
self.assertIsInstance(result, Artifact)
self.assertEqual(result.type, IntSequence1)
self.assertIsInstance(result.uuid, uuid.UUID)
# Can retrieve multiple views of different type.
exp_list_view = [0, 42, 43, 0, 42, 43, 99, -22, 55, 1]
self.assertEqual(result.view(list), exp_list_view)
self.assertEqual(result.view(list), exp_list_view)
exp_counter_view = collections.Counter({
0: 2,
42: 2,
43: 2,
99: 1,
-22: 1,
55: 1,
1: 1
})
self.assertEqual(result.view(collections.Counter),
exp_counter_view)
self.assertEqual(result.view(collections.Counter),
exp_counter_view)
# Accepts IntSequence1 | IntSequence2
artifact3 = Artifact.import_data(IntSequence2, [10, 20])
future = method. async (artifact3, artifact1, artifact2, 55, 1)
result, = future.result()
self.assertEqual(result.type, IntSequence1)
self.assertEqual(result.view(list),
[10, 20, 0, 42, 43, 99, -22, 55, 1])
def test_import_data_with_invalid_format_single_file(self):
fp = os.path.join(self.test_dir.name, 'foo.txt')
with open(fp, 'w') as fh:
fh.write('42\n')
fh.write('43\n')
fh.write('abc\n')
fh.write('123\n')
error_regex = "foo.txt.*IntSequenceFormat"
with self.assertRaisesRegex(ValueError, error_regex):
Artifact.import_data(IntSequence1, fp)
def test_import_data_with_invalid_format_single_file(self):
fp = os.path.join(self.test_dir.name, 'foo.txt')
with open(fp, 'w') as fh:
fh.write('42\n')
fh.write('43\n')
fh.write('abc\n')
fh.write('123\n')
error_regex = "foo.txt.*IntSequenceFormat"
with self.assertRaisesRegex(ValueError, error_regex):
Artifact.import_data(IntSequence1, fp)
def test_async(self):
mapping_viz = self.plugin.visualizers['mapping_viz']
artifact1 = Artifact.import_data(Mapping, {'foo': 'abc', 'bar': 'def'})
artifact2 = Artifact.import_data(
Mapping, {'baz': 'abc', 'bazz': 'ghi'})
future = mapping_viz.async(artifact1, artifact2, 'Key', 'Value')
self.assertIsInstance(future, concurrent.futures.Future)
result = future.result()
# Test properties of the `Results` object.
self.assertIsInstance(result, tuple)
self.assertIsInstance(result, Results)
self.assertEqual(len(result), 1)
self.assertEqual(result.visualization, result[0])
result = result[0]
self.assertIsInstance(result, Visualization)
self.assertEqual(result.type, qiime.core.type.Visualization)
self.assertIsInstance(result.uuid, uuid.UUID)
# TODO qiime.sdk.Visualization doesn't have an API to access its
# contents yet. For now, save and assert the correct files are present.
filepath = os.path.join(self.test_dir.name, 'visualization.qzv')
result.save(filepath)
root_dir = str(result.uuid)
expected = {
'VERSION',
'metadata.yaml',
'data/index.html',
'data/css/style.css',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml',
'provenance/artifacts/%s/metadata.yaml' % artifact1.uuid,
'provenance/artifacts/%s/VERSION' % artifact1.uuid,
'provenance/artifacts/%s/action/action.yaml' % artifact1.uuid,
'provenance/artifacts/%s/metadata.yaml' % artifact2.uuid,
'provenance/artifacts/%s/VERSION' % artifact2.uuid,
'provenance/artifacts/%s/action/action.yaml' % artifact2.uuid
}
self.assertArchiveMembers(filepath, root_dir, expected)
def test_async(self):
concatenate_ints = self.plugin.methods['concatenate_ints']
concatenate_ints_markdown = \
self.plugin.methods['concatenate_ints_markdown']
artifact1 = Artifact.import_data(IntSequence1, [0, 42, 43])
artifact2 = Artifact.import_data(IntSequence2, [99, -22])
for method in concatenate_ints, concatenate_ints_markdown:
future = method.async(artifact1, artifact1, artifact2, 55, 1)
self.assertIsInstance(future, concurrent.futures.Future)
result = future.result()
# Test properties of the `Results` object.
self.assertIsInstance(result, tuple)
self.assertIsInstance(result, Results)
self.assertEqual(len(result), 1)
self.assertEqual(result.concatenated_ints.view(list),
[0, 42, 43, 0, 42, 43, 99, -22, 55, 1])
result = result[0]
self.assertIsInstance(result, Artifact)
self.assertEqual(result.type, IntSequence1)
self.assertIsInstance(result.uuid, uuid.UUID)
# Can retrieve multiple views of different type.
exp_list_view = [0, 42, 43, 0, 42, 43, 99, -22, 55, 1]
self.assertEqual(result.view(list), exp_list_view)
self.assertEqual(result.view(list), exp_list_view)
exp_counter_view = collections.Counter(
{0: 2, 42: 2, 43: 2, 99: 1, -22: 1, 55: 1, 1: 1})
self.assertEqual(result.view(collections.Counter),
exp_counter_view)
self.assertEqual(result.view(collections.Counter),
exp_counter_view)
# Accepts IntSequence1 | IntSequence2
artifact3 = Artifact.import_data(IntSequence2, [10, 20])
future = method.async(artifact3, artifact1, artifact2, 55, 1)
result, = future.result()
self.assertEqual(result.type, IntSequence1)
self.assertEqual(result.view(list),
[10, 20, 0, 42, 43, 99, -22, 55, 1])
def test_visualizer_callable_output(self):
artifact = Artifact.import_data(Mapping, {'foo': 'abc', 'bar': 'def'})
# Callable returns a value from `return_vals`
return_vals = (True, False, [], {}, '', 0, 0.0)
for return_val in return_vals:
def func(output_dir: str, foo: dict) -> None:
return return_val
self.plugin.visualizers.register_function(
func, {'foo': Mapping}, {}, '', ''
)
visualizer = self.plugin.visualizers['func']
with self.assertRaisesRegex(TypeError, "should not return"):
visualizer(foo=artifact)
# Callable returns None (default function return)
def func(output_dir: str, foo: dict) -> None:
return None
self.plugin.visualizers.register_function(
func, {'foo': Mapping}, {}, '', ''
)
visualizer = self.plugin.visualizers['func']
# Should not raise an exception
output = visualizer(foo=artifact)
self.assertIsInstance(output, Results)
self.assertIsInstance(output.visualization, Visualization)
def test_async_with_multiple_outputs(self):
split_ints = self.plugin.methods['split_ints']
split_ints_markdown = self.plugin.methods['split_ints_markdown']
artifact = Artifact.import_data(IntSequence1, [0, 42, -2, 43, 6])
for method in split_ints, split_ints_markdown:
future = method.async(artifact)
self.assertIsInstance(future, concurrent.futures.Future)
result = future.result()
self.assertIsInstance(result, tuple)
self.assertEqual(len(result), 2)
for output_artifact in result:
self.assertIsInstance(output_artifact, Artifact)
self.assertEqual(output_artifact.type, IntSequence1)
self.assertIsInstance(output_artifact.uuid, uuid.UUID)
# Output artifacts have different UUIDs.
self.assertNotEqual(result[0].uuid, result[1].uuid)
# Index lookup.
self.assertEqual(result[0].view(list), [0, 42])
self.assertEqual(result[1].view(list), [-2, 43, 6])
# Test properties of the `Results` object.
self.assertIsInstance(result, Results)
self.assertEqual(result.left.view(list), [0, 42])
self.assertEqual(result.right.view(list), [-2, 43, 6])
def test_visualizer_callable_output(self):
artifact = Artifact.import_data(Mapping, {'foo': 'abc', 'bar': 'def'})
# Callable returns a value from `return_vals`
return_vals = (True, False, [], {}, '', 0, 0.0)
for return_val in return_vals:
def func(output_dir: str, foo: dict) -> None:
return return_val
self.plugin.visualizers.register_function(func, {'foo': Mapping},
{}, '', '')
visualizer = self.plugin.visualizers['func']
with self.assertRaisesRegex(TypeError, "should not return"):
visualizer(foo=artifact)
# Callable returns None (default function return)
def func(output_dir: str, foo: dict) -> None:
return None
self.plugin.visualizers.register_function(func, {'foo': Mapping}, {},
'', '')
visualizer = self.plugin.visualizers['func']
# Should not raise an exception
output = visualizer(foo=artifact)
self.assertIsInstance(output, Results)
self.assertIsInstance(output.visualization, Visualization)
def test_load_different_type_with_multiple_view_types(self):
saved_artifact = Artifact.import_data(IntSequence1,
[42, 42, 43, -999, 42])
fp = os.path.join(self.test_dir.name, 'artifact.qza')
saved_artifact.save(fp)
artifact = Artifact.load(fp)
self.assertEqual(artifact.type, IntSequence1)
self.assertEqual(artifact.uuid, saved_artifact.uuid)
self.assertEqual(artifact.view(list), [42, 42, 43, -999, 42])
self.assertEqual(artifact.view(list), [42, 42, 43, -999, 42])
self.assertEqual(artifact.view(collections.Counter),
collections.Counter({
42: 3,
43: 1,
-999: 1
}))
self.assertEqual(artifact.view(collections.Counter),
collections.Counter({
42: 3,
43: 1,
-999: 1
}))
def test_async_with_multiple_outputs(self):
split_ints = self.plugin.methods['split_ints']
split_ints_markdown = self.plugin.methods['split_ints_markdown']
artifact = Artifact.import_data(IntSequence1, [0, 42, -2, 43, 6])
for method in split_ints, split_ints_markdown:
future = method. async (artifact)
self.assertIsInstance(future, concurrent.futures.Future)
result = future.result()
self.assertIsInstance(result, tuple)
self.assertEqual(len(result), 2)
for output_artifact in result:
self.assertIsInstance(output_artifact, Artifact)
self.assertEqual(output_artifact.type, IntSequence1)
self.assertIsInstance(output_artifact.uuid, uuid.UUID)
# Output artifacts have different UUIDs.
self.assertNotEqual(result[0].uuid, result[1].uuid)
# Index lookup.
self.assertEqual(result[0].view(list), [0, 42])
self.assertEqual(result[1].view(list), [-2, 43, 6])
# Test properties of the `Results` object.
self.assertIsInstance(result, Results)
self.assertEqual(result.left.view(list), [0, 42])
self.assertEqual(result.right.view(list), [-2, 43, 6])
def test_load_and_save(self):
fp1 = os.path.join(self.test_dir.name, 'artifact1.qza')
fp2 = os.path.join(self.test_dir.name, 'artifact2.qza')
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact.save(fp1)
artifact = Artifact.load(fp1)
# Overwriting its source file works.
artifact.save(fp1)
# Saving to a new file works.
artifact.save(fp2)
root_dir = str(artifact.uuid)
expected = {
'VERSION', 'metadata.yaml', 'data/file1.txt', 'data/file2.txt',
'data/nested/file3.txt', 'data/nested/file4.txt',
'provenance/metadata.yaml', 'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp1, root_dir, expected)
root_dir = str(artifact.uuid)
expected = {
'VERSION', 'metadata.yaml', 'data/file1.txt', 'data/file2.txt',
'data/nested/file3.txt', 'data/nested/file4.txt',
'provenance/metadata.yaml', 'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp2, root_dir, expected)
def test_import_data_with_unrecognized_files(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(data_dir)
with open(os.path.join(data_dir, 'file1.txt'), 'w') as fh:
fh.write('42\n')
with open(os.path.join(data_dir, 'file2.txt'), 'w') as fh:
fh.write('43\n')
nested = os.path.join(data_dir, 'nested')
os.mkdir(nested)
with open(os.path.join(nested, 'file3.txt'), 'w') as fh:
fh.write('44\n')
with open(os.path.join(nested, 'foo.txt'), 'w') as fh:
fh.write('45\n')
error_regex = ("Unrecognized.*foo.txt.*FourIntsDirectoryFormat")
with self.assertRaisesRegex(ValueError, error_regex):
Artifact.import_data(FourInts, data_dir)
def create_artifact():
request_body = request.get_json()
artifact = Artifact.import_data(request_body['type'], request_body['path'])
path = os.path.join(os.getcwd(), request_body['name'])
if not path.endswith('.qza'):
path += '.qza'
artifact.save(path)
return ''
def test_eq_same_uuid(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact1 = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact1.save(fp)
artifact2 = Artifact.load(fp)
self.assertEqual(artifact1, artifact2)
def test_async(self):
mapping_viz = self.plugin.visualizers['mapping_viz']
artifact1 = Artifact.import_data(Mapping, {'foo': 'abc', 'bar': 'def'})
artifact2 = Artifact.import_data(Mapping, {
'baz': 'abc',
'bazz': 'ghi'
})
future = mapping_viz. async (artifact1, artifact2, 'Key', 'Value')
self.assertIsInstance(future, concurrent.futures.Future)
result = future.result()
# Test properties of the `Results` object.
self.assertIsInstance(result, tuple)
self.assertIsInstance(result, Results)
self.assertEqual(len(result), 1)
self.assertEqual(result.visualization, result[0])
result = result[0]
self.assertIsInstance(result, Visualization)
self.assertEqual(result.type, qiime.core.type.Visualization)
self.assertIsInstance(result.uuid, uuid.UUID)
# TODO qiime.sdk.Visualization doesn't have an API to access its
# contents yet. For now, save and assert the correct files are present.
filepath = os.path.join(self.test_dir.name, 'visualization.qzv')
result.save(filepath)
root_dir = str(result.uuid)
expected = {
'VERSION', 'metadata.yaml', 'data/index.html',
'data/css/style.css', 'provenance/metadata.yaml',
'provenance/VERSION', 'provenance/action/action.yaml',
'provenance/artifacts/%s/metadata.yaml' % artifact1.uuid,
'provenance/artifacts/%s/VERSION' % artifact1.uuid,
'provenance/artifacts/%s/action/action.yaml' % artifact1.uuid,
'provenance/artifacts/%s/metadata.yaml' % artifact2.uuid,
'provenance/artifacts/%s/VERSION' % artifact2.uuid,
'provenance/artifacts/%s/action/action.yaml' % artifact2.uuid
}
self.assertArchiveMembers(filepath, root_dir, expected)
def test_eq_same_uuid(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact1 = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact1.save(fp)
artifact2 = Artifact.load(fp)
self.assertEqual(artifact1, artifact2)
def test_import_data_with_invalid_format_multi_file(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(data_dir)
with open(os.path.join(data_dir, 'file1.txt'), 'w') as fh:
fh.write('42\n')
with open(os.path.join(data_dir, 'file2.txt'), 'w') as fh:
fh.write('43\n')
nested = os.path.join(data_dir, 'nested')
os.mkdir(nested)
with open(os.path.join(nested, 'file3.txt'), 'w') as fh:
fh.write('44\n')
with open(os.path.join(nested, 'file4.txt'), 'w') as fh:
fh.write('foo\n')
error_regex = "file4.txt.*SingleIntFormat"
with self.assertRaisesRegex(ValueError, error_regex):
Artifact.import_data(FourInts, data_dir)
def test_import_data_with_invalid_format_multi_file(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(data_dir)
with open(os.path.join(data_dir, 'file1.txt'), 'w') as fh:
fh.write('42\n')
with open(os.path.join(data_dir, 'file2.txt'), 'w') as fh:
fh.write('43\n')
nested = os.path.join(data_dir, 'nested')
os.mkdir(nested)
with open(os.path.join(nested, 'file3.txt'), 'w') as fh:
fh.write('44\n')
with open(os.path.join(nested, 'file4.txt'), 'w') as fh:
fh.write('foo\n')
error_regex = "file4.txt.*SingleIntFormat"
with self.assertRaisesRegex(ValueError, error_regex):
Artifact.import_data(FourInts, data_dir)
def test_import_data_with_unrecognized_files(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(data_dir)
with open(os.path.join(data_dir, 'file1.txt'), 'w') as fh:
fh.write('42\n')
with open(os.path.join(data_dir, 'file2.txt'), 'w') as fh:
fh.write('43\n')
nested = os.path.join(data_dir, 'nested')
os.mkdir(nested)
with open(os.path.join(nested, 'file3.txt'), 'w') as fh:
fh.write('44\n')
with open(os.path.join(nested, 'foo.txt'), 'w') as fh:
fh.write('45\n')
error_regex = ("Unrecognized.*foo.txt.*FourIntsDirectoryFormat")
with self.assertRaisesRegex(ValueError, error_regex):
Artifact.import_data(FourInts, data_dir)
def test_reader_transformer(self):
fp = pkg_resources.resource_filename('q2_dummy_types.tests',
'data/int-sequence.txt')
for type in IntSequence1, IntSequence2:
artifact = Artifact.import_data(type, fp)
# `Artifact.view` invokes the transformer that handles
# the `SingleIntFormat` -> `list` transformation.
self.assertEqual(artifact.view(list), [42, -1, 9, 10, 0, 999, 0])
def test_data_import(self):
fp = pkg_resources.resource_filename('q2_dummy_types.tests',
'data/mapping.tsv')
# `Artifact.import_data` copies `mapping.tsv` into the artifact after
# performing validation on the file.
artifact = Artifact.import_data(Mapping, fp)
self.assertEqual(artifact.type, Mapping)
self.assertIsInstance(artifact.uuid, uuid.UUID)
def test_ne_different_type_same_uuid(self):
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
class Faker:
@property
def uuid(self):
return artifact.uuid
faker = Faker()
self.assertNotEqual(artifact, faker)
def test_peek_artifact(self):
artifact = Artifact.import_data(FourInts, [0, 0, 42, 1000])
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact.save(fp)
metadata = Result.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, 'FourInts')
self.assertEqual(metadata.uuid, str(artifact.uuid))
self.assertEqual(metadata.format, 'FourIntsDirectoryFormat')
def test_ne_different_type_same_uuid(self):
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
class Faker:
@property
def uuid(self):
return artifact.uuid
faker = Faker()
self.assertNotEqual(artifact, faker)
def test_load_artifact(self):
saved_artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
fp = os.path.join(self.test_dir.name, 'artifact.qza')
saved_artifact.save(fp)
artifact = Result.load(fp)
self.assertIsInstance(artifact, Artifact)
self.assertEqual(artifact.type, FourInts)
self.assertEqual(artifact.uuid, saved_artifact.uuid)
self.assertEqual(artifact.view(list), [-1, 42, 0, 43])
def test_data_import(self):
fp = pkg_resources.resource_filename('q2_dummy_types.tests',
'data/int-sequence.txt')
for type in IntSequence1, IntSequence2:
# `Artifact.import_data` copies `int-sequence.txt` into the
# artifact after peforming validation on the file.
artifact = Artifact.import_data(type, fp)
self.assertEqual(artifact.type, type)
self.assertIsInstance(artifact.uuid, uuid.UUID)
def test_reader_transformer(self):
fp = pkg_resources.resource_filename('q2_dummy_types.tests',
'data/mapping.tsv')
artifact = Artifact.import_data(Mapping, fp)
# `Artifact.view` invokes the transformer that handles the
# `MappingFormat` -> `dict` transformation.
self.assertEqual(artifact.view(dict), {
'foo': 'abc',
'bar': 'def',
'bazz': 'ghijkl'
})
def test_call_with_no_parameters(self):
merge_mappings = self.plugin.methods['merge_mappings']
artifact1 = Artifact.import_data(Mapping, {'foo': 'abc', 'bar': 'def'})
artifact2 = Artifact.import_data(Mapping, {'bazz': 'abc'})
result = merge_mappings(artifact1, artifact2)
# Test properties of the `Results` object.
self.assertIsInstance(result, tuple)
self.assertIsInstance(result, Results)
self.assertEqual(len(result), 1)
self.assertEqual(result.merged_mapping.view(dict),
{'foo': 'abc', 'bar': 'def', 'bazz': 'abc'})
result = result[0]
self.assertIsInstance(result, Artifact)
self.assertEqual(result.type, Mapping)
self.assertIsInstance(result.uuid, uuid.UUID)
self.assertEqual(result.view(dict),
{'foo': 'abc', 'bar': 'def', 'bazz': 'abc'})
def test_import_data_with_directory_single_file(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(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('10\n')
fh.write('100\n')
artifact = Artifact.import_data(IntSequence1, data_dir)
self.assertEqual(artifact.type, IntSequence1)
self.assertIsInstance(artifact.uuid, uuid.UUID)
self.assertEqual(artifact.view(list), [-1, -2, 10, 100])
def test_import_data_with_directory_single_file(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(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('10\n')
fh.write('100\n')
artifact = Artifact.import_data(IntSequence1, data_dir)
self.assertEqual(artifact.type, IntSequence1)
self.assertIsInstance(artifact.uuid, uuid.UUID)
self.assertEqual(artifact.view(list), [-1, -2, 10, 100])
def test_import_data_with_filepath(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(data_dir)
# Filename shouldn't matter for single-file case.
fp = os.path.join(data_dir, 'foo.txt')
with open(fp, 'w') as fh:
fh.write('42\n')
fh.write('43\n')
fh.write('42\n')
fh.write('0\n')
artifact = Artifact.import_data(IntSequence1, fp)
self.assertEqual(artifact.type, IntSequence1)
self.assertIsInstance(artifact.uuid, uuid.UUID)
self.assertEqual(artifact.view(list), [42, 43, 42, 0])
def test_import_data_with_filepath(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(data_dir)
# Filename shouldn't matter for single-file case.
fp = os.path.join(data_dir, 'foo.txt')
with open(fp, 'w') as fh:
fh.write('42\n')
fh.write('43\n')
fh.write('42\n')
fh.write('0\n')
artifact = Artifact.import_data(IntSequence1, fp)
self.assertEqual(artifact.type, IntSequence1)
self.assertIsInstance(artifact.uuid, uuid.UUID)
self.assertEqual(artifact.view(list), [42, 43, 42, 0])
def test_roundtrip(self):
fp1 = os.path.join(self.test_dir.name, 'artifact1.qza')
fp2 = os.path.join(self.test_dir.name, 'artifact2.qza')
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact.save(fp1)
artifact1 = Artifact.load(fp1)
artifact1.save(fp2)
artifact2 = Artifact.load(fp2)
self.assertEqual(artifact1.type, artifact2.type)
self.assertEqual(artifact1.format, artifact2.format)
self.assertEqual(artifact1.uuid, artifact2.uuid)
self.assertEqual(artifact1.view(list), artifact2.view(list))
# double view to make sure multiple views can be taken
self.assertEqual(artifact1.view(list), artifact2.view(list))
def test_extract(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact.save(fp)
root_dir = str(artifact.uuid)
output_dir = os.path.join(self.test_dir.name, 'artifact-extract-test')
result_dir = Artifact.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, os.path.join(output_dir, root_dir))
expected = {
'VERSION', 'metadata.yaml', 'data/file1.txt', 'data/file2.txt',
'data/nested/file3.txt', 'data/nested/file4.txt',
'provenance/metadata.yaml', 'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertExtractedArchiveMembers(output_dir, root_dir, expected)
def test_import_data_with_directory_multi_file(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(data_dir)
with open(os.path.join(data_dir, 'file1.txt'), 'w') as fh:
fh.write('42\n')
with open(os.path.join(data_dir, 'file2.txt'), 'w') as fh:
fh.write('41\n')
nested = os.path.join(data_dir, 'nested')
os.mkdir(nested)
with open(os.path.join(nested, 'file3.txt'), 'w') as fh:
fh.write('43\n')
with open(os.path.join(nested, 'file4.txt'), 'w') as fh:
fh.write('40\n')
artifact = Artifact.import_data(FourInts, data_dir)
self.assertEqual(artifact.type, FourInts)
self.assertIsInstance(artifact.uuid, uuid.UUID)
self.assertEqual(artifact.view(list), [42, 41, 43, 40])
def test_roundtrip(self):
fp1 = os.path.join(self.test_dir.name, 'artifact1.qza')
fp2 = os.path.join(self.test_dir.name, 'artifact2.qza')
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact.save(fp1)
artifact1 = Artifact.load(fp1)
artifact1.save(fp2)
artifact2 = Artifact.load(fp2)
self.assertEqual(artifact1.type, artifact2.type)
self.assertEqual(artifact1.format, artifact2.format)
self.assertEqual(artifact1.uuid, artifact2.uuid)
self.assertEqual(artifact1.view(list),
artifact2.view(list))
# double view to make sure multiple views can be taken
self.assertEqual(artifact1.view(list),
artifact2.view(list))
def test_import_data_with_directory_multi_file(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(data_dir)
with open(os.path.join(data_dir, 'file1.txt'), 'w') as fh:
fh.write('42\n')
with open(os.path.join(data_dir, 'file2.txt'), 'w') as fh:
fh.write('41\n')
nested = os.path.join(data_dir, 'nested')
os.mkdir(nested)
with open(os.path.join(nested, 'file3.txt'), 'w') as fh:
fh.write('43\n')
with open(os.path.join(nested, 'file4.txt'), 'w') as fh:
fh.write('40\n')
artifact = Artifact.import_data(FourInts, data_dir)
self.assertEqual(artifact.type, FourInts)
self.assertIsInstance(artifact.uuid, uuid.UUID)
self.assertEqual(artifact.view(list), [42, 41, 43, 40])
def test_load_different_type_with_multiple_view_types(self):
saved_artifact = Artifact.import_data(IntSequence1,
[42, 42, 43, -999, 42])
fp = os.path.join(self.test_dir.name, 'artifact.qza')
saved_artifact.save(fp)
artifact = Artifact.load(fp)
self.assertEqual(artifact.type, IntSequence1)
self.assertEqual(artifact.uuid, saved_artifact.uuid)
self.assertEqual(artifact.view(list),
[42, 42, 43, -999, 42])
self.assertEqual(artifact.view(list),
[42, 42, 43, -999, 42])
self.assertEqual(artifact.view(collections.Counter),
collections.Counter({42: 3, 43: 1, -999: 1}))
self.assertEqual(artifact.view(collections.Counter),
collections.Counter({42: 3, 43: 1, -999: 1}))
def test_load_and_save(self):
fp1 = os.path.join(self.test_dir.name, 'artifact1.qza')
fp2 = os.path.join(self.test_dir.name, 'artifact2.qza')
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact.save(fp1)
artifact = Artifact.load(fp1)
# Overwriting its source file works.
artifact.save(fp1)
# Saving to a new file works.
artifact.save(fp2)
root_dir = str(artifact.uuid)
expected = {
'VERSION',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp1, root_dir, expected)
root_dir = str(artifact.uuid)
expected = {
'VERSION',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp2, root_dir, expected)
def test_call_with_no_parameters(self):
most_common_viz = self.plugin.visualizers['most_common_viz']
artifact = Artifact.import_data(
IntSequence1, [42, 42, 10, 0, 42, 5, 0])
result = most_common_viz(artifact)
# Test properties of the `Results` object.
self.assertIsInstance(result, tuple)
self.assertIsInstance(result, Results)
self.assertEqual(len(result), 1)
self.assertEqual(result.visualization, result[0])
result = result[0]
self.assertIsInstance(result, Visualization)
self.assertEqual(result.type, qiime.core.type.Visualization)
self.assertIsInstance(result.uuid, uuid.UUID)
# TODO qiime.sdk.Visualization doesn't have an API to access its
# contents yet. For now, save and assert the correct files are present.
filepath = os.path.join(self.test_dir.name, 'visualization.qzv')
result.save(filepath)
root_dir = str(result.uuid)
expected = {
'VERSION',
'metadata.yaml',
'data/index.html',
'data/index.tsv',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml',
'provenance/artifacts/%s/metadata.yaml' % artifact.uuid,
'provenance/artifacts/%s/VERSION' % artifact.uuid,
'provenance/artifacts/%s/action/action.yaml' % artifact.uuid
}
self.assertArchiveMembers(filepath, root_dir, expected)
def test_extract_artifact(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact.save(fp)
root_dir = str(artifact.uuid)
output_dir = os.path.join(self.test_dir.name, 'artifact-extract-test')
result_dir = Result.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, os.path.join(output_dir, root_dir))
expected = {
'VERSION',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertExtractedArchiveMembers(output_dir, root_dir, expected)
def test_save_artifact_auto_extension(self):
artifact = Artifact.import_data(FourInts, [0, 0, 42, 1000])
# No extension.
fp = os.path.join(self.test_dir.name, 'artifact')
obs_fp = artifact.save(fp)
obs_filename = os.path.basename(obs_fp)
self.assertEqual(obs_filename, 'artifact.qza')
# Wrong extension.
fp = os.path.join(self.test_dir.name, 'artifact.zip')
obs_fp = artifact.save(fp)
obs_filename = os.path.basename(obs_fp)
self.assertEqual(obs_filename, 'artifact.zip.qza')
# Correct extension.
fp = os.path.join(self.test_dir.name, 'artifact.qza')
obs_fp = artifact.save(fp)
obs_filename = os.path.basename(obs_fp)
self.assertEqual(obs_filename, 'artifact.qza')
def test_call_with_no_parameters(self):
most_common_viz = self.plugin.visualizers['most_common_viz']
artifact = Artifact.import_data(IntSequence1,
[42, 42, 10, 0, 42, 5, 0])
result = most_common_viz(artifact)
# Test properties of the `Results` object.
self.assertIsInstance(result, tuple)
self.assertIsInstance(result, Results)
self.assertEqual(len(result), 1)
self.assertEqual(result.visualization, result[0])
result = result[0]
self.assertIsInstance(result, Visualization)
self.assertEqual(result.type, qiime.core.type.Visualization)
self.assertIsInstance(result.uuid, uuid.UUID)
# TODO qiime.sdk.Visualization doesn't have an API to access its
# contents yet. For now, save and assert the correct files are present.
filepath = os.path.join(self.test_dir.name, 'visualization.qzv')
result.save(filepath)
root_dir = str(result.uuid)
expected = {
'VERSION', 'metadata.yaml', 'data/index.html', 'data/index.tsv',
'provenance/metadata.yaml', 'provenance/VERSION',
'provenance/action/action.yaml',
'provenance/artifacts/%s/metadata.yaml' % artifact.uuid,
'provenance/artifacts/%s/VERSION' % artifact.uuid,
'provenance/artifacts/%s/action/action.yaml' % artifact.uuid
}
self.assertArchiveMembers(filepath, root_dir, expected)
def test_import_data_with_wrong_number_of_files(self):
data_dir = os.path.join(self.test_dir.name, 'test')
os.mkdir(data_dir)
error_regex = ("Missing.*MappingDirectoryFormat.*mapping.tsv")
with self.assertRaisesRegex(ValueError, error_regex):
Artifact.import_data(Mapping, data_dir)
def test_ne_different_data_different_uuid(self):
artifact1 = Artifact.import_data(FourInts, [-1, 42, 0, 43])
artifact2 = Artifact.import_data(FourInts, [1, 2, 3, 4])
self.assertNotEqual(artifact1, artifact2)
def test_eq_identity(self):
artifact = Artifact.import_data(FourInts, [-1, 42, 0, 43])
self.assertEqual(artifact, artifact)
