def test_ne_same_data_different_uuid(self):
visualization1 = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
visualization2 = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
self.assertNotEqual(visualization1, visualization2)
def test_load_and_save(self):
fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv')
fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv')
visualization = Visualization._from_data_dir(self.data_dir)
visualization.save(fp1)
visualization = Visualization.load(fp1)
# Overwriting its source file works.
visualization.save(fp1)
# Saving to a new file works.
visualization.save(fp2)
root_dir = str(visualization.uuid)
expected = {
'VERSION', 'metadata.yaml', 'data/index.html', 'data/css/style.css'
}
self.assertArchiveMembers(fp1, root_dir, expected)
root_dir = str(visualization.uuid)
expected = {
'VERSION', 'metadata.yaml', 'data/index.html', 'data/css/style.css'
}
self.assertArchiveMembers(fp2, root_dir, expected)
def test_load_and_save(self):
fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv')
fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv')
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
visualization.save(fp1)
visualization = Visualization.load(fp1)
# Overwriting its source file works.
visualization.save(fp1)
# Saving to a new file works.
visualization.save(fp2)
with zipfile.ZipFile(fp1, mode='r') as zf:
fps = set(zf.namelist())
expected = {
'visualization1/VERSION',
'visualization1/metadata.yaml',
'visualization1/README.md',
'visualization1/data/index.html',
'visualization1/data/css/style.css'
}
self.assertEqual(fps, expected)
with zipfile.ZipFile(fp2, mode='r') as zf:
fps = set(zf.namelist())
expected = {
'visualization2/VERSION',
'visualization2/metadata.yaml',
'visualization2/README.md',
'visualization2/data/index.html',
'visualization2/data/css/style.css'
}
self.assertEqual(fps, expected)
def test_eq_same_uuid(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization1 = Visualization._from_data_dir(self.data_dir)
visualization1.save(fp)
visualization2 = Visualization.load(fp)
self.assertEqual(visualization1, visualization2)
def test_load(self):
saved_visualization = Visualization._from_data_dir(self.data_dir)
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
saved_visualization.save(fp)
visualization = Visualization.load(fp)
self.assertEqual(visualization.type, qiime.core.type.Visualization)
self.assertEqual(visualization.uuid, saved_visualization.uuid)
def test_extract_artifact_as_visualization(self):
artifact = Artifact._from_view(FourInts, [0, 0, 42, 1000], list,
self.provenance)
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact.save(fp)
with self.assertRaisesRegex(
TypeError, 'Visualization does not support.*FourInts'):
Visualization.extract(fp, self.test_dir)
def test_get_index_paths_single_load(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir)
visualization.save(fp)
visualization = Visualization.load(fp)
actual = visualization.get_index_paths()
expected = {'html': 'data/index.html'}
self.assertEqual(actual, expected)
def test_eq_same_uuid(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization1 = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
visualization1.save(fp)
visualization2 = Visualization.load(fp)
self.assertEqual(visualization1, visualization2)
def test_load_artifact_as_visualization(self):
artifact = Artifact._from_view(FourInts, [0, 0, 42, 1000], list,
self.provenance)
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact.save(fp)
with self.assertRaisesRegex(
TypeError, 'Artifact.*Visualization.load.*Artifact.load'):
Visualization.load(fp)
def test_ne_different_data_different_uuid(self):
visualization1 = Visualization._from_data_dir(self.data_dir)
data_dir = os.path.join(self.test_dir.name, 'mc-viz-output1')
os.mkdir(data_dir)
most_common_viz(data_dir, collections.Counter(range(42)))
visualization2 = Visualization._from_data_dir(data_dir)
self.assertNotEqual(visualization1, visualization2)
def test_load(self):
saved_visualization = Visualization._from_data_dir(self.data_dir, None)
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
saved_visualization.save(fp)
visualization = Visualization.load(fp)
self.assertEqual(visualization.type, qiime.core.type.Visualization)
self.assertIsNone(visualization.provenance)
self.assertEqual(visualization.uuid, saved_visualization.uuid)
def test_get_index_paths_single_load(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
visualization.save(fp)
visualization = Visualization.load(fp)
actual = visualization.get_index_paths()
expected = {'html': 'data/index.html'}
self.assertEqual(actual, expected)
def test_peek(self):
visualization = Visualization._from_data_dir(self.data_dir)
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization.save(fp)
metadata = Visualization.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, 'Visualization')
self.assertEqual(metadata.uuid, str(visualization.uuid))
self.assertIsNone(metadata.format)
def test_peek(self):
visualization = Visualization._from_data_dir(self.data_dir, None)
fp = os.path.join(self.test_dir.name, 'visualization.qza')
visualization.save(fp)
metadata = Visualization.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, qiime.core.type.Visualization)
self.assertIsNone(metadata.provenance)
self.assertEqual(metadata.uuid, visualization.uuid)
def test_roundtrip(self):
fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv')
fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv')
visualization = Visualization._from_data_dir(self.data_dir)
visualization.save(fp1)
visualization1 = Visualization.load(fp1)
visualization1.save(fp2)
visualization2 = Visualization.load(fp2)
self.assertEqual(visualization1.type, visualization2.type)
self.assertEqual(visualization1.uuid, visualization2.uuid)
def test_ne_different_data_different_uuid(self):
visualization1 = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
data_dir = os.path.join(self.test_dir.name, 'mc-viz-output1')
os.mkdir(data_dir)
most_common_viz(data_dir,
collections.Counter(range(42)))
visualization2 = Visualization._from_data_dir(
data_dir, self.make_provenance_capture())
self.assertNotEqual(visualization1, visualization2)
def test_peek(self):
visualization = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization.save(fp)
metadata = Visualization.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, 'Visualization')
self.assertEqual(metadata.uuid, str(visualization.uuid))
self.assertIsNone(metadata.format)
def test_get_index_paths_multiple_load(self):
data_dir = os.path.join(self.test_dir.name, 'mc-viz-output1')
os.mkdir(data_dir)
most_common_viz(data_dir, collections.Counter(range(42)))
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(data_dir)
visualization.save(fp)
visualization = Visualization.load(fp)
actual = visualization.get_index_paths()
expected = {'html': 'data/index.html', 'tsv': 'data/index.tsv'}
self.assertEqual(actual, expected)
def test_get_index_paths_multiple_html_load(self):
data_dir = os.path.join(self.test_dir.name, 'multi-html-viz1')
os.mkdir(data_dir)
multi_html_viz(data_dir, [1, 42])
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(data_dir)
visualization.save(fp)
visualization = Visualization.load(fp)
with self.assertRaises(ValueError):
visualization.get_index_paths()
def test_roundtrip(self):
fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv')
fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv')
visualization = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
visualization.save(fp1)
visualization1 = Visualization.load(fp1)
visualization1.save(fp2)
visualization2 = Visualization.load(fp2)
self.assertEqual(visualization1.type, visualization2.type)
self.assertEqual(visualization1.uuid, visualization2.uuid)
def test_get_index_paths_multiple_html_load(self):
data_dir = os.path.join(self.test_dir.name, 'multi-html-viz1')
os.mkdir(data_dir)
multi_html_viz(data_dir, [1, 42])
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(data_dir,
self.provenance)
visualization.save(fp)
visualization = Visualization.load(fp)
with self.assertRaises(ValueError):
visualization.get_index_paths()
def test_get_index_paths_multiple_load(self):
data_dir = os.path.join(self.test_dir.name, 'mc-viz-output1')
os.mkdir(data_dir)
most_common_viz(data_dir,
collections.Counter(range(42)))
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(data_dir,
self.provenance)
visualization.save(fp)
visualization = Visualization.load(fp)
actual = visualization.get_index_paths()
expected = {'html': 'data/index.html',
'tsv': 'data/index.tsv'}
self.assertEqual(actual, expected)
def test_extract(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir)
visualization.save(fp)
root_dir = str(visualization.uuid)
output_dir = os.path.join(self.test_dir.name, 'viz-extract-test')
result_dir = Visualization.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, os.path.join(output_dir, root_dir))
expected = {
'VERSION', 'metadata.yaml', 'data/index.html', 'data/css/style.css'
}
self.assertExtractedArchiveMembers(output_dir, root_dir, expected)
def inspect_visualization(uuid):
try:
metadata = Visualization.peek(VISUALIZATIONS[uuid])
except Exception:
abort(404)
return jsonify({'uuid': metadata.uuid, 'type': metadata.type})
def inspect_visualization(uuid):
try:
metadata = Visualization.peek(VISUALIZATIONS[uuid])
except Exception:
abort(404)
return jsonify({'uuid': metadata.uuid, 'type': metadata.type})
def test_from_data_dir_with_provenance(self):
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
self.assertEqual(visualization.type, qiime.core.type.Visualization)
self.assertEqual(visualization.provenance, self.provenance)
self.assertIsInstance(visualization.uuid, uuid.UUID)
def test_get_index_paths_single_from_data_dir(self):
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
actual = visualization.get_index_paths()
expected = {'html': 'data/index.html'}
self.assertEqual(actual, expected)
def test_get_index_paths_single_from_data_dir(self):
visualization = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
actual = visualization.get_index_paths()
expected = {'html': 'data/index.html'}
self.assertEqual(actual, expected)
def test_from_data_dir(self):
visualization = Visualization._from_data_dir(self.data_dir, None)
self.assertEqual(visualization.type, qiime.core.type.Visualization)
self.assertIsNone(visualization.provenance)
# We don't know what the UUID is because it's generated within
# Visualization._from_data_dir.
self.assertIsInstance(visualization.uuid, uuid.UUID)
def view_visualization(uuid):
try:
vis = Visualization.load(VISUALIZATIONS[uuid])
filePath = vis.get_index_paths(relative=False)['html']
ACTIVE_VIS[uuid] = vis
except Exception:
abort(404)
return jsonify({'filePath': filePath})
def test_load_visualization_as_artifact(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
visualization.save(fp)
with self.assertRaisesRegex(
TypeError, 'Visualization.*Artifact.load.*Visualization.load'):
Artifact.load(fp)
def test_extract_visualization_as_artifact(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
visualization.save(fp)
with self.assertRaisesRegex(
TypeError, 'Artifact does not support.*Visualization'):
Artifact.extract(fp, self.test_dir)
def test_get_index_paths_multiple_html_from_data_dir(self):
data_dir = os.path.join(self.test_dir.name, 'multi-html-viz2')
os.mkdir(data_dir)
multi_html_viz(data_dir, [1, 42])
visualization = Visualization._from_data_dir(
data_dir, self.make_provenance_capture())
with self.assertRaises(ValueError):
visualization.get_index_paths()
def test_ne_different_type_same_uuid(self):
visualization = Visualization._from_data_dir(self.data_dir)
class Faker:
@property
def uuid(self):
return visualization.uuid
faker = Faker()
self.assertNotEqual(visualization, faker)
def test_save_visualization_warning(self):
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
fp = os.path.join(self.test_dir.name, 'visualization.zip')
with warnings.catch_warnings(record=True) as w:
visualization.save(fp)
self.assertEqual(len(w), 1)
self.assertIsInstance(w[0].message, UserWarning)
self.assertIn(Visualization.extension, str(w[0].message))
def test_get_index_paths_multiple_from_data_dir(self):
data_dir = os.path.join(self.test_dir.name, 'mc-viz-output2')
os.mkdir(data_dir)
most_common_viz(data_dir, collections.Counter(range(42)))
visualization = Visualization._from_data_dir(
data_dir, self.make_provenance_capture())
actual = visualization.get_index_paths()
expected = {'html': 'data/index.html',
'tsv': 'data/index.tsv'}
self.assertEqual(actual, expected)
def test_load_visualization(self):
saved_visualization = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
saved_visualization.save(fp)
visualization = Result.load(fp)
self.assertIsInstance(visualization, Visualization)
self.assertEqual(visualization.type, qiime.core.type.Visualization)
self.assertEqual(visualization.uuid, saved_visualization.uuid)
def test_extract(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
visualization.save(fp)
output_dir = os.path.join(self.test_dir.name, 'viz-extract-test')
result_dir = Visualization.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, output_dir)
contents = [
'visualization/VERSION',
'visualization/metadata.yaml',
'visualization/README.md',
'visualization/data/index.html',
'visualization/data/css/style.css']
for fp in contents:
expected_fp = os.path.join(output_dir, fp)
self.assertTrue(os.path.exists(expected_fp),
'File %s was not extracted.' % fp)
def test_ne_subclass_same_uuid(self):
class VisualizationSubclass(Visualization):
pass
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization1 = VisualizationSubclass._from_data_dir(self.data_dir)
visualization1.save(fp)
visualization2 = Visualization.load(fp)
self.assertNotEqual(visualization1, visualization2)
self.assertNotEqual(visualization2, visualization1)
def test_from_data_dir_and_save(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir)
visualization.save(fp)
root_dir = str(visualization.uuid)
expected = {
'VERSION', 'metadata.yaml', 'data/index.html', 'data/css/style.css'
}
self.assertArchiveMembers(fp, root_dir, expected)
def test_ne_different_type_same_uuid(self):
visualization = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
class Faker:
@property
def uuid(self):
return visualization.uuid
faker = Faker()
self.assertNotEqual(visualization, faker)
def test_peek_visualization(self):
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization.save(fp)
metadata = Result.peek(fp)
self.assertIsInstance(metadata, ResultMetadata)
self.assertEqual(metadata.type, qiime.core.type.Visualization)
self.assertEqual(metadata.provenance, self.provenance)
self.assertEqual(metadata.uuid, visualization.uuid)
def test_load_with_archive_filepath_modified(self):
# Save a visualization for use in the following test case.
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
Visualization._from_data_dir(self.data_dir).save(fp)
# Load the visualization from a filepath then save a different
# visualization to the same filepath. Assert that both visualizations
# access the correct data.
#
# `load` used to be lazy, only extracting data when it needed to (e.g.
# when `save` or `get_index_paths` was called). This was buggy as the
# filepath could have been deleted, or worse, modified to contain a
# different .qzv 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
# Visualization.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 Visualization.peek.
visualization1 = Visualization.load(fp)
new_data_dir = os.path.join(self.test_dir.name, 'viz-output2')
os.mkdir(new_data_dir)
most_common_viz(new_data_dir, collections.Counter(range(42)))
Visualization._from_data_dir(new_data_dir).save(fp)
visualization2 = Visualization.load(fp)
self.assertEqual(visualization1.get_index_paths(),
{'html': 'data/index.html'})
self.assertEqual(visualization2.get_index_paths(), {
'html': 'data/index.html',
'tsv': 'data/index.tsv'
})
def test_load_with_archive_filepath_modified(self):
# Save a visualization for use in the following test case.
fp = os.path.join(self.test_dir.name, 'visualization.qza')
Visualization._from_data_dir(self.data_dir, None).save(fp)
# Load the visualization from a filepath then save a different
# visualization to the same filepath. Assert that both visualizations
# access the correct data.
#
# `load` used to be lazy, only extracting data when it needed to (e.g.
# when `save` or `get_index_paths` was called). This was buggy as the
# filepath could have been deleted, or worse, modified to contain a
# different .qzv 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
# Visualization.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 Visualization.peek.
visualization1 = Visualization.load(fp)
new_data_dir = os.path.join(self.test_dir.name, 'viz-output2')
os.mkdir(new_data_dir)
most_common_viz(new_data_dir, collections.Counter(range(42)))
Visualization._from_data_dir(new_data_dir, None).save(fp)
visualization2 = Visualization.load(fp)
self.assertEqual(visualization1.get_index_paths(),
{'html': 'data/index.html'})
self.assertEqual(visualization2.get_index_paths(),
{'html': 'data/index.html', 'tsv': 'data/index.tsv'})
def test_get_index_paths_relative_false(self):
data_dir = os.path.join(self.test_dir.name, 'mc-viz-output2')
os.mkdir(data_dir)
most_common_viz(data_dir, collections.Counter(range(42)))
visualization = Visualization._from_data_dir(data_dir,
self.provenance)
def get_abs_path(rel):
return os.path.join(visualization._archiver._temp_dir, rel)
actual = visualization.get_index_paths(relative=False)
expected = {'html': get_abs_path('data/index.html'),
'tsv': get_abs_path('data/index.tsv')}
self.assertEqual(actual, expected)
def test_ne_subclass_same_uuid(self):
class VisualizationSubclass(Visualization):
pass
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization1 = VisualizationSubclass._from_data_dir(
self.data_dir, self.make_provenance_capture())
visualization1.save(fp)
visualization2 = Visualization.load(fp)
self.assertNotEqual(visualization1, visualization2)
self.assertNotEqual(visualization2, visualization1)
def test_get_index_paths_relative_false(self):
data_dir = os.path.join(self.test_dir.name, 'mc-viz-output2')
os.mkdir(data_dir)
most_common_viz(data_dir, collections.Counter(range(42)))
visualization = Visualization._from_data_dir(
data_dir, self.make_provenance_capture())
def get_abs_path(rel):
return str(visualization._archiver.root_dir / rel)
actual = visualization.get_index_paths(relative=False)
expected = {'html': get_abs_path('data/index.html'),
'tsv': get_abs_path('data/index.tsv')}
self.assertEqual(actual, expected)
def test_extract(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
visualization.save(fp)
root_dir = str(visualization.uuid)
output_dir = os.path.join(self.test_dir.name, 'viz-extract-test')
result_dir = Visualization.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, os.path.join(output_dir, root_dir))
expected = {
'VERSION',
'metadata.yaml',
'data/index.html',
'data/css/style.css',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertExtractedArchiveMembers(output_dir, root_dir, expected)
def test_load_and_save(self):
fp1 = os.path.join(self.test_dir.name, 'visualization1.qzv')
fp2 = os.path.join(self.test_dir.name, 'visualization2.qzv')
visualization = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
visualization.save(fp1)
visualization = Visualization.load(fp1)
# Overwriting its source file works.
visualization.save(fp1)
# Saving to a new file works.
visualization.save(fp2)
root_dir = str(visualization.uuid)
expected = {
'VERSION',
'metadata.yaml',
'data/index.html',
'data/css/style.css',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp1, root_dir, expected)
root_dir = str(visualization.uuid)
expected = {
'VERSION',
'metadata.yaml',
'data/index.html',
'data/css/style.css',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp2, root_dir, expected)
def get_visualizations():
global VISUALIZATIONS
VISUALIZATIONS = {}
path = os.getcwd()
viz_paths = list(glob.glob(os.path.join(path, '*.qzv')))
visualizations = []
for viz_path in viz_paths:
try:
metadata = Visualization.peek(viz_path)
name, _ = os.path.splitext(os.path.basename(viz_path))
VISUALIZATIONS[str(metadata.uuid)] = viz_path
visualizations.append(
_result_record(metadata, name, '.inspect_visualization'))
except Exception:
pass # TODO: do better things when this happens
return jsonify({'visualizations': visualizations})
def get_visualizations():
global VISUALIZATIONS
VISUALIZATIONS = {}
path = os.getcwd()
viz_paths = list(glob.glob(os.path.join(path, '*.qzv')))
visualizations = []
for viz_path in viz_paths:
try:
metadata = Visualization.peek(viz_path)
name, _ = os.path.splitext(os.path.basename(viz_path))
VISUALIZATIONS[metadata.uuid] = viz_path
visualizations.append(
_result_record(metadata, name, '.inspect_visualization'))
except Exception:
pass # TODO: do better things when this happens
return jsonify({'visualizations': visualizations})
def test_from_data_dir_and_save(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
visualization.save(fp)
with zipfile.ZipFile(fp, mode='r') as zf:
fps = set(zf.namelist())
expected = {
'visualization/VERSION',
'visualization/metadata.yaml',
'visualization/README.md',
'visualization/data/index.html',
'visualization/data/css/style.css'
}
self.assertEqual(fps, expected)
def test_from_data_dir_and_save(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
visualization.save(fp)
root_dir = str(visualization.uuid)
expected = {
'VERSION',
'metadata.yaml',
'data/index.html',
'data/css/style.css',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp, root_dir, expected)
def test_extract_visualization(self):
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization = Visualization._from_data_dir(self.data_dir,
self.provenance)
visualization.save(fp)
output_dir = os.path.join(self.test_dir.name, 'viz-extract-test')
result_dir = Result.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, output_dir)
contents = [
'visualization/VERSION', 'visualization/metadata.yaml',
'visualization/README.md', 'visualization/data/index.html',
'visualization/data/css/style.css'
]
for fp in contents:
expected_fp = os.path.join(output_dir, fp)
self.assertTrue(os.path.exists(expected_fp),
'File %s was not extracted.' % fp)
def test_save_visualization_auto_extension(self):
visualization = Visualization._from_data_dir(
self.data_dir, self.make_provenance_capture())
# No extension.
fp = os.path.join(self.test_dir.name, 'visualization')
obs_fp = visualization.save(fp)
obs_filename = os.path.basename(obs_fp)
self.assertEqual(obs_filename, 'visualization.qzv')
# Wrong extension.
fp = os.path.join(self.test_dir.name, 'visualization.zip')
obs_fp = visualization.save(fp)
obs_filename = os.path.basename(obs_fp)
self.assertEqual(obs_filename, 'visualization.zip.qzv')
# Correct extension.
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
obs_fp = visualization.save(fp)
obs_filename = os.path.basename(obs_fp)
self.assertEqual(obs_filename, 'visualization.qzv')
def test_load_from_externally_created_zipfile(self):
# If a user unzips a .qzv to inspect contents and rezips using a
# different ZIP library/implementation than the one provided by Python,
# loading, saving, etc. should still work as expected. The Python ZIP
# implementation doesn't store directories as entries when writing, but
# the `zip` Unix and OS X command line utilities include both
# directories and filepaths as entries. When reading these files with
# Python's ZIP implementation, the directory entries are visible, so
# their presence needs to be accounted for when extracting.
#
# The following visualization was created with:
#
# visualization = Visualization._from_data_dir(self.data_dir,
# self.provenance)
# visualization.save('externally_created_zipfile.qzv')
#
# Unzip and rezip using command line utility:
#
# unzip externally_created_zipfile.qzv
# rm externally_created_zipfile.qzv
# zip -r externally_created_zipfile.qzv externally_created_zipfile
#
fp = pkg_resources.resource_filename(
'qiime.sdk.tests', 'data/externally_created_zipfile.qzv')
with zipfile.ZipFile(fp, mode='r') as zf:
fps = set(zf.namelist())
expected = {
# These are extra directory entries included by `zip` command
# line utility.
'externally_created_zipfile/',
'externally_created_zipfile/data/',
'externally_created_zipfile/data/css/',
'externally_created_zipfile/VERSION',
'externally_created_zipfile/metadata.yaml',
'externally_created_zipfile/README.md',
'externally_created_zipfile/data/index.html',
'externally_created_zipfile/data/css/style.css'
}
self.assertEqual(fps, expected)
visualization = Visualization.load(fp)
self.assertEqual(visualization.type, qiime.core.type.Visualization)
self.assertEqual(visualization.provenance, self.provenance)
self.assertIsInstance(visualization.uuid, uuid.UUID)
fp = os.path.join(self.test_dir.name, 'visualization.qzv')
visualization.save(fp)
with zipfile.ZipFile(fp, mode='r') as zf:
fps = set(zf.namelist())
expected = {
# Directory entries should not be present.
'visualization/VERSION',
'visualization/metadata.yaml',
'visualization/README.md',
'visualization/data/index.html',
'visualization/data/css/style.css'
}
self.assertEqual(fps, expected)