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,
self.make_provenance_capture()).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,
self.make_provenance_capture()).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.qzv')
Visualization._from_data_dir(self.data_dir,
self.make_provenance_capture()).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,
self.make_provenance_capture()).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_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_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_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', 'checksums.md5', 'metadata.yaml', 'data/index.html',
'data/css/style.css', 'provenance/metadata.yaml',
'provenance/VERSION', 'provenance/citations.bib',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp1, root_dir, expected)
root_dir = str(visualization.uuid)
expected = {
'VERSION', 'checksums.md5', 'metadata.yaml', 'data/index.html',
'data/css/style.css', 'provenance/metadata.yaml',
'provenance/VERSION', 'provenance/citations.bib',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp2, root_dir, 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 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 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_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(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 = Visualization.load(fp)
self.assertEqual(visualization.type, qiime2.core.type.Visualization)
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.make_provenance_capture())
visualization.save(fp)
visualization = Visualization.load(fp)
actual = visualization.get_index_paths()
expected = {'html': 'data/index.html'}
self.assertEqual(actual, expected)
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.make_provenance_capture())
visualization.save(fp)
visualization = Visualization.load(fp)
actual = visualization.get_index_paths()
expected = {'html': 'data/index.html'}
self.assertEqual(actual, expected)
def test_load(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 = Visualization.load(fp)
self.assertEqual(visualization.type, qiime2.core.type.Visualization)
self.assertEqual(visualization.uuid, saved_visualization.uuid)
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_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.make_provenance_capture())
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.make_provenance_capture())
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, self.make_provenance_capture())
visualization.save(fp)
visualization = Visualization.load(fp)
with self.assertRaises(ValueError):
visualization.get_index_paths()
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_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.make_provenance_capture())
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_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/citations.bib',
'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/citations.bib',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp2, root_dir, expected)
