def test_artifact_validate_min(self):
A = Artifact.import_data('IntSequence1', [1, 2, 3, 4])
A.validate(level='min')
self.assertTrue(True) # Checkpoint assertion
A = Artifact.import_data('Mapping', {'a': '1', 'b': '2'})
A.validate(level='min')
self.assertTrue(True) # Checkpoint assertion
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)
# pathlib normalizes away the `.`, it doesn't matter, but this is the
# implementation we're using, so let's test against that assumption.
output_dir = pathlib.Path(self.test_dir.name) / 'artifact-extract-test'
result_dir = Artifact.extract(fp, output_dir=output_dir)
self.assertEqual(result_dir, str(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/citations.bib',
'provenance/action/action.yaml'
}
self.assertExtractedArchiveMembers(output_dir, root_dir, expected)
def test_call_with_optional_artifacts(self):
method = self.plugin.methods['optional_artifacts_method']
ints1 = Artifact.import_data(IntSequence1, [0, 42, 43])
ints2 = Artifact.import_data(IntSequence1, [99, -22])
ints3 = Artifact.import_data(IntSequence2, [43, 43])
# No optional artifacts provided.
obs = method(ints1, 42).output
self.assertEqual(obs.view(list), [0, 42, 43, 42])
# One optional artifact provided.
obs = method(ints1, 42, optional1=ints2).output
self.assertEqual(obs.view(list), [0, 42, 43, 42, 99, -22])
# All optional artifacts provided.
obs = method(
ints1, 42, optional1=ints2, optional2=ints3, num2=111).output
self.assertEqual(obs.view(list), [0, 42, 43, 42, 99, -22, 43, 43, 111])
# Invalid type provided as optional artifact.
with self.assertRaisesRegex(TypeError,
'type IntSequence2.*subtype IntSequence1'):
method(ints1, 42, optional1=ints3)
def test_classify(self):
# test read direction detection and parallel classification
classify = feature_classifier.methods.classify_sklearn
seq_path = self.get_data_path('se-dna-sequences.fasta')
reads = Artifact.import_data('FeatureData[Sequence]', seq_path)
raw_reads = skbio.io.read(
seq_path, format='fasta', constructor=skbio.DNA)
rev_path = os.path.join(self.temp_dir.name, 'rev-dna-sequences.fasta')
skbio.io.write((s.reverse_complement() for s in raw_reads),
'fasta', rev_path)
rev_reads = Artifact.import_data('FeatureData[Sequence]', rev_path)
result = classify(reads, self.classifier)
fc = result.classification.view(pd.Series).to_dict()
result = classify(rev_reads, self.classifier)
rc = result.classification.view(pd.Series).to_dict()
for taxon in fc:
self.assertEqual(fc[taxon], rc[taxon])
result = classify(reads, self.classifier, read_orientation='same')
fc = result.classification.view(pd.Series).to_dict()
result = classify(rev_reads, self.classifier,
read_orientation='reverse-complement')
rc = result.classification.view(pd.Series).to_dict()
for taxon in fc:
self.assertEqual(fc[taxon], rc[taxon])
result = classify(reads, self.classifier, reads_per_batch=100,
n_jobs=2)
cc = result.classification.view(pd.Series).to_dict()
for taxon in fc:
self.assertEqual(fc[taxon], cc[taxon])
def test_import_data_invalid_type(self):
with self.assertRaisesRegex(TypeError,
'concrete semantic type.*Visualization'):
Artifact.import_data(qiime2.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_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(qiime2.plugin.ValidationError,
"FourIntsDirectoryFormat.*directory"):
Artifact.import_data(FourInts, fp)
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_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_artifact_validate_max(self):
A = Artifact.import_data('Mapping', {'a': '1', 'b': '2'})
A.validate()
self.assertTrue(True) # Checkpoint assertion
A.validate(level='max')
self.assertTrue(True) # Checkpoint assertion
A = Artifact.import_data('IntSequence1', [1, 2, 3, 4, 5, 6, 7, 10])
with self.assertRaisesRegex(ValidationError, '3 more'):
A.validate('max')
def test_class_weight(self):
# we should be able to input class_weight to fit_classifier
weights = Artifact.import_data(
'FeatureTable[RelativeFrequency]',
self.get_data_path('class_weight.biom'),
view_type='BIOMV100Format')
reads = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('se-dna-sequences.fasta'))
fitter = feature_classifier.methods.fit_classifier_naive_bayes
classifier1 = fitter(reads, self.taxonomy, class_weight=weights)
classifier1 = classifier1.classifier
class_weight = weights.view(biom.Table)
classes = class_weight.ids('observation')
class_weights = []
for wts in class_weight.iter_data():
class_weights.append(zip(classes, wts))
priors = json.dumps(list(zip(*sorted(class_weights[0])))[1])
classifier2 = fitter(reads, self.taxonomy,
classify__class_prior=priors).classifier
classify = feature_classifier.methods.classify_sklearn
result1 = classify(reads, classifier1)
result1 = result1.classification.view(pd.Series).to_dict()
result2 = classify(reads, classifier2)
result2 = result2.classification.view(pd.Series).to_dict()
self.assertEqual(result1, result2)
svc_spec = [['feat_ext',
{'__type__': 'feature_extraction.text.HashingVectorizer',
'analyzer': 'char_wb',
'n_features': 8192,
'ngram_range': [8, 8],
'alternate_sign': False}],
['classify',
{'__type__': 'linear_model.LogisticRegression'}]]
classifier_spec = json.dumps(svc_spec)
gen_fitter = feature_classifier.methods.fit_classifier_sklearn
classifier1 = gen_fitter(reads, self.taxonomy, classifier_spec,
class_weight=weights).classifier
svc_spec[1][1]['class_weight'] = dict(class_weights[0])
classifier_spec = json.dumps(svc_spec)
gen_fitter = feature_classifier.methods.fit_classifier_sklearn
classifier2 = gen_fitter(reads, self.taxonomy, classifier_spec
).classifier
result1 = classify(reads, classifier1)
result1 = result1.classification.view(pd.Series).to_dict()
result2 = classify(reads, classifier2)
result2 = result2.classification.view(pd.Series).to_dict()
self.assertEqual(set(result1.keys()), set(result2.keys()))
for k in result1:
self.assertEqual(result1[k], result2[k])
def test_load(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 = Artifact.load(fp)
self.assertEqual(artifact.type, FourInts)
self.assertEqual(artifact.uuid, saved_artifact.uuid)
self.assertEqual(artifact.view(list), [-1, 42, 0, 43])
self.assertEqual(artifact.view(list), [-1, 42, 0, 43])
def test_peek(self):
artifact = Artifact.import_data(FourInts, [0, 0, 42, 1000])
fp = os.path.join(self.test_dir.name, 'artifact.qza')
artifact.save(fp)
metadata = Artifact.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_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.*\n\n.*Line 3"
with self.assertRaisesRegex(ValidationError, error_regex):
Artifact.import_data(IntSequence1, fp)
def setUp(self):
super().setUp()
self.taxonomy = Artifact.import_data(
'FeatureData[Taxonomy]', self.get_data_path('taxonomy.tsv'))
self.seq_path = self.get_data_path('se-dna-sequences.fasta')
reads = Artifact.import_data('FeatureData[Sequence]', self.seq_path)
fitter_name = _specific_fitters[0][0]
fitter = getattr(feature_classifier.methods,
'fit_classifier_' + fitter_name)
self.classifier = fitter(reads, self.taxonomy).classifier
def test_import_data_with_bad_validation_multi_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('1\n')
with open(os.path.join(data_dir, 'file2.txt'), 'w') as fh:
fh.write('2\n')
error_regex = ("test.*RedundantSingleIntDirectoryFormat.*\n\n"
".*does not match")
with self.assertRaisesRegex(ValidationError, error_regex):
Artifact.import_data(SingleInt, data_dir)
def test_asynchronous(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.asynchronous(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, qiime2.core.type.Visualization)
self.assertIsInstance(result.uuid, uuid.UUID)
# TODO qiime2.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',
'checksums.md5',
'metadata.yaml',
'data/index.html',
'data/css/style.css',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/citations.bib',
'provenance/action/action.yaml',
'provenance/artifacts/%s/metadata.yaml' % artifact1.uuid,
'provenance/artifacts/%s/VERSION' % artifact1.uuid,
'provenance/artifacts/%s/citations.bib' % 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/citations.bib' % artifact2.uuid,
'provenance/artifacts/%s/action/action.yaml' % artifact2.uuid
}
self.assertArchiveMembers(filepath, root_dir, expected)
def test_call_with_variadic_inputs(self):
method = self.plugin.methods['variadic_input_method']
ints = [Artifact.import_data(IntSequence1, [1, 2, 3]),
Artifact.import_data(IntSequence2, [4, 5, 6])]
int_set = {Artifact.import_data(SingleInt, 7),
Artifact.import_data(SingleInt, 8)}
nums = {9, 10}
opt_nums = [11, 12, 13]
result, = method(ints, int_set, nums, opt_nums)
self.assertEqual(result.view(list), list(range(1, 14)))
def setUp(self):
super().setUp()
reads = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('se-dna-sequences.fasta'))
taxonomy = Artifact.import_data(
'FeatureData[Taxonomy]', self.get_data_path('taxonomy.tsv'))
classifier = fit_classifier_naive_bayes(reads, taxonomy)
pipeline = classifier.classifier.view(Pipeline)
transformer = self.get_transformer(
Pipeline, TaxonomicClassiferTemporaryPickleDirFmt)
self._sklp = transformer(pipeline)
sklearn_pipeline = self._sklp.sklearn_pipeline.view(PickleFormat)
self.sklearn_pipeline = str(sklearn_pipeline)
def test_populate_class_weight(self):
# should populate the class weight of a pipeline
weights = Artifact.import_data(
'FeatureTable[RelativeFrequency]',
self.get_data_path('class_weight.biom'),
view_type='BIOMV100Format')
table = weights.view(biom.Table)
svc_spec = [['feat_ext',
{'__type__': 'feature_extraction.text.HashingVectorizer',
'analyzer': 'char_wb',
'n_features': 8192,
'ngram_range': [8, 8],
'alternate_sign': False}],
['classify',
{'__type__': 'naive_bayes.GaussianNB'}]]
pipeline1 = pipeline_from_spec(svc_spec)
populate_class_weight(pipeline1, table)
classes = table.ids('observation')
class_weights = []
for wts in table.iter_data():
class_weights.append(zip(classes, wts))
svc_spec[1][1]['priors'] = list(zip(*sorted(class_weights[0])))[1]
pipeline2 = pipeline_from_spec(svc_spec)
for a, b in zip(pipeline1.get_params()['classify__priors'],
pipeline2.get_params()['classify__priors']):
self.assertAlmostEqual(a, b)
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_populate_class_weight(self):
# should populate the class weight of a pipeline
weights = Artifact.import_data(
'FeatureTable[RelativeFrequency]',
self.get_data_path('class_weight.biom'),
view_type='BIOMV100Format')
table = weights.view(biom.Table)
svc_spec = [['feat_ext',
{'__type__': 'feature_extraction.text.HashingVectorizer',
'analyzer': 'char_wb',
'n_features': 8192,
'ngram_range': [8, 8],
'alternate_sign': False}],
['classify',
{'__type__': 'naive_bayes.GaussianNB'}]]
pipeline1 = pipeline_from_spec(svc_spec)
populate_class_weight(pipeline1, table)
classes = table.ids('observation')
class_weights = []
for wts in table.iter_data():
class_weights.append(zip(classes, wts))
svc_spec[1][1]['priors'] = list(zip(*sorted(class_weights[0])))[1]
pipeline2 = pipeline_from_spec(svc_spec)
for a, b in zip(pipeline1.get_params()['classify__priors'],
pipeline2.get_params()['classify__priors']):
self.assertAlmostEqual(a, b)
def test_from_view_and_save(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
# Using four-ints data layout because it has multiple files, some of
# which are in a nested directory.
artifact = Artifact._from_view(FourInts, [-1, 42, 0, 43], list,
self.provenance_capture)
artifact.save(fp)
root_dir = str(artifact.uuid)
expected = {
'VERSION',
'checksums.md5',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/citations.bib',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp, root_dir, expected)
def setUp(self):
super().setUp()
seqs = skbio.io.read(self.get_data_path('dna-sequences.fasta'),
format='fasta', constructor=skbio.DNA)
tmpseqs = os.path.join(self.temp_dir.name, 'temp-seqs.fasta')
skbio.io.write((s for s in islice(seqs, 10)), 'fasta', tmpseqs)
self.sequences = Artifact.import_data('FeatureData[Sequence]', tmpseqs)
def inspect_artifact(uuid):
try:
metadata = Artifact.peek(ARTIFACTS[uuid])
except Exception:
abort(404)
return jsonify({'uuid': metadata.uuid, 'type': metadata.type})
def test_mismatched_taxonomy(self):
wrong_taxa_fp = self.get_data_path('another-ref-taxa.tsv')
wrong_taxa = Artifact.import_data('FeatureData[Taxonomy]',
wrong_taxa_fp)
with self.assertRaisesRegex(ValueError,
'Not all OTUs.*1 feature.*\n.*879972'):
self.action(self.input_sequences, self.tree, wrong_taxa)
def inspect_artifact(uuid):
try:
metadata = Artifact.peek(ARTIFACTS[uuid])
except Exception:
abort(404)
return jsonify({'uuid': metadata.uuid, 'type': metadata.type})
def setUp(self):
super().setUp()
seqs = skbio.io.read(self.get_data_path('dna-sequences.fasta'),
format='fasta', constructor=skbio.DNA)
tmpseqs = os.path.join(self.temp_dir.name, 'temp-seqs.fasta')
skbio.io.write((s for s in islice(seqs, 10)), 'fasta', tmpseqs)
self.sequences = Artifact.import_data('FeatureData[Sequence]', tmpseqs)
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']
artifact = Artifact.import_data(IntSequence1, [0, 42, -2, 43, 6])
future = split_ints.asynchronous(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_filter_features_nooverlap(self):
# Just load up the reference tree instead of creating new test data
wrong_tree_fp = self.get_data_path('ref-tree.nwk')
wrong_tree = Artifact.import_data('Phylogeny[Rooted]', wrong_tree_fp)
with self.assertRaisesRegex(ValueError,
'Not a single fragment.*empty'):
self.action(self.table, wrong_tree)
def test_from_view_and_save(self):
fp = os.path.join(self.test_dir.name, 'artifact.qza')
# Using four-ints data layout because it has multiple files, some of
# which are in a nested directory.
artifact = Artifact._from_view(FourInts, [-1, 42, 0, 43], list,
self.provenance_capture)
artifact.save(fp)
root_dir = str(artifact.uuid)
expected = {
'VERSION',
'checksums.md5',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/citations.bib',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp, root_dir, expected)
def test_write_v1_archive(self):
fp = os.path.join(self.temp_dir.name, 'artifact_v1.qza')
with artifact_version(1):
artifact = Artifact._from_view(FourInts, [-1, 42, 0, 43], list,
self.provenance_capture)
artifact.save(fp)
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(fp, root_dir, expected)
with zipfile.ZipFile(fp, mode='r') as zf:
version = zf.read(os.path.join(root_dir, 'VERSION'))
self.assertRegex(str(version), '^.*archive: 1.*$')
def test_async_with_multiple_outputs_matched_types(self):
split_ints = self.plugin.methods['split_ints']
artifact = Artifact.import_data(IntSequence2, [0, 42, -2, 43, 6])
future = split_ints.asynchronous(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, IntSequence2)
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_low_memory_multinomial_nb(self):
# results should not depend on chunk size
fitter = feature_classifier.methods.fit_classifier_sklearn
classify = feature_classifier.methods.classify_sklearn
reads = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('se-dna-sequences.fasta'))
spec = [['feat_ext',
{'__type__': 'feature_extraction.text.HashingVectorizer',
'analyzer': 'char',
'n_features': 8192,
'ngram_range': [8, 8],
'alternate_sign': False}],
['classify',
{'__type__': 'custom.LowMemoryMultinomialNB',
'alpha': 0.01,
'chunk_size': 20000}]]
classifier_spec = json.dumps(spec)
result = fitter(reads, self.taxonomy, classifier_spec)
result = classify(reads, result.classifier)
gc = result.classification.view(pd.Series).to_dict()
spec[1][1]['chunk_size'] = 20
classifier_spec = json.dumps(spec)
result = fitter(reads, self.taxonomy, classifier_spec)
result = classify(reads, result.classifier)
sc = result.classification.view(pd.Series).to_dict()
for taxon in gc:
self.assertEqual(gc[taxon], sc[taxon])
def test_call_with_multiple_outputs(self):
split_ints = self.plugin.methods['split_ints']
artifact = Artifact.import_data(IntSequence1, [0, 42, -2, 43, 6])
result = split_ints(artifact)
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_reader_transformer(self):
fp = pkg_resources.resource_filename(
'q2_winnowing.tests', 'sample_data/test_in_dir')
artifact = Artifact.import_data(Winnowed, fp)
featureOrdering_df, auc_df, permanova_df = artifact.view( list )[0]
# `Artifact.view` invokes the transformer that handles the
# `WinnowedFormat` -> `dataframe` transformation.
# print( featureOrdering_df, exp_featureOrdering )
pd.testing.assert_frame_equal(
featureOrdering_df.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(
auc_df.astype(str),
exp_auc.astype(str),
check_dtype=False
)
pd.testing.assert_frame_equal(
permanova_df.astype(str),
exp_permanova.astype(str),
check_dtype=False
)
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 test_fit_classifier(self):
# fit_classifier should generate a working taxonomic_classifier
reads = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('se-dna-sequences.fasta'))
classifier_specification = \
[['feat_ext',
{'__type__': 'feature_extraction.text.HashingVectorizer',
'analyzer': 'char_wb',
'n_features': 8192,
'ngram_range': [8, 8],
'non_negative': True}],
['classify',
{'__type__': 'naive_bayes.MultinomialNB',
'alpha': 0.01}]]
classifier_specification = json.dumps(classifier_specification)
fit_classifier = feature_classifier.methods.fit_classifier
result = fit_classifier(reads, self.taxonomy, classifier_specification)
classify = feature_classifier.methods.classify
result = classify(reads, result.classifier)
ref = self.taxonomy.view(pd.Series).to_dict()
cls = result.classification.view(pd.Series).to_dict()
right = 0.
for taxon in cls:
right += ref[taxon].startswith(cls[taxon])
self.assertGreater(right/len(cls), 0.5)
def test_write_v4_archive(self):
fp = os.path.join(self.temp_dir.name, 'artifact_v1.qza')
with artifact_version(4):
artifact = Artifact._from_view(FourInts, [-1, 42, 0, 43], list,
self.provenance_capture)
artifact.save(fp)
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/citations.bib',
'provenance/action/action.yaml',
}
self.assertArchiveMembers(fp, root_dir, expected)
with zipfile.ZipFile(fp, mode='r') as zf:
version = zf.read(os.path.join(root_dir, 'VERSION'))
self.assertRegex(str(version), '^.*archive: 4.*$')
def test_asynchronous(self):
concatenate_ints = self.plugin.methods['concatenate_ints']
artifact1 = Artifact.import_data(IntSequence1, [0, 42, 43])
artifact2 = Artifact.import_data(IntSequence2, [99, -22])
future = concatenate_ints.asynchronous(
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 = concatenate_ints.asynchronous(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_classify_otus_experimental(self):
ar_tree = Artifact.load(self.get_data_path('sepp_tree_tiny.qza'))
ar_repseq = Artifact.load(self.get_data_path('real_data.qza'))
obs_classification = classify_otus_experimental(
ar_repseq.view(DNASequencesDirectoryFormat),
ar_tree.view(NewickFormat))
exp_classification = pd.read_csv(
self.get_data_path('taxonomy_real_data_tiny_otus.tsv'),
index_col=0,
sep="\t").fillna("")
assert_frame_equal(obs_classification, exp_classification)
ar_tree_small = Artifact.load(
self.get_data_path('sepp_tree_small.qza'))
obs_classification_small = classify_otus_experimental(
ar_repseq.view(DNASequencesDirectoryFormat),
ar_tree_small.view(NewickFormat))
exp_classification_small = pd.read_csv(
self.get_data_path('taxonomy_real_data_small_otus.tsv'),
index_col=0,
sep="\t").fillna("")
assert_frame_equal(obs_classification_small, exp_classification_small)
ar_refphylo_tiny = Artifact.load(
self.get_data_path('reference_phylogeny_tiny.qza'))
ref_phylo_tiny = ar_refphylo_tiny.view(NewickFormat)
with self.assertRaises(ValueError):
classify_otus_experimental(
ar_repseq.view(DNASequencesDirectoryFormat), ref_phylo_tiny)
# test that missing taxon mappings result in an error
ar_taxonomy = Artifact.load(
self.get_data_path('taxonomy_missingotus.qza'))
# capture stderr message and check if its content is as expected
captured_stderr = StringIO()
with redirect_stderr(captured_stderr):
with self.assertRaises(ValueError):
classify_otus_experimental(
ar_repseq.view(DNASequencesDirectoryFormat),
ar_tree.view(NewickFormat),
reference_taxonomy=ar_taxonomy.view(pd.DataFrame))
self.assertIn('The taxonomy artifact you provided does not cont',
captured_stderr.getvalue())
self.assertIn('539572', captured_stderr.getvalue())
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_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.*\n\n.*integer"
with self.assertRaisesRegex(ValidationError, error_regex):
Artifact.import_data(FourInts, data_dir)
def test_call_with_artifacts_and_parameters(self):
concatenate_ints = self.plugin.methods['concatenate_ints']
artifact1 = Artifact.import_data(IntSequence1, [0, 42, 43])
artifact2 = Artifact.import_data(IntSequence2, [99, -22])
result = concatenate_ints(artifact1, artifact1, artifact2, 55, 1)
# 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])
result, = concatenate_ints(artifact3, artifact1, artifact2, 55, 1)
self.assertEqual(result.type, IntSequence1)
self.assertEqual(result.view(list),
[10, 20, 0, 42, 43, 99, -22, 55, 1])
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(ValidationError, error_regex):
Artifact.import_data(FourInts, data_dir)
def test_call_with_variadic_inputs(self):
method = self.plugin.methods['variadic_input_method']
ints = [
Artifact.import_data(IntSequence1, [1, 2, 3]),
Artifact.import_data(IntSequence2, [4, 5, 6])
]
int_set = {
Artifact.import_data(SingleInt, 7),
Artifact.import_data(SingleInt, 8)
}
nums = {9, 10}
opt_nums = [11, 12, 13]
result, = method(ints, int_set, nums, opt_nums)
self.assertEqual(result.view(list), list(range(1, 14)))
def test_validate_artifact_bad(self):
artifact = Artifact.import_data('IntSequence1', [1, 2, 3, 4])
with (artifact._archiver.root_dir / 'extra.file').open('w') as fh:
fh.write('uh oh')
with self.assertRaisesRegex(exceptions.ValidationError,
r'extra\.file'):
artifact.validate()
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, qiime2.core.type.Visualization)
self.assertIsInstance(result.uuid, uuid.UUID)
# TODO qiime2.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_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.*\n\n.*integer"
with self.assertRaisesRegex(ValidationError, 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(ValidationError, error_regex):
Artifact.import_data(FourInts, data_dir)
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',
'checksums.md5',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/citations.bib',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp1, root_dir, expected)
root_dir = str(artifact.uuid)
expected = {
'VERSION',
'checksums.md5',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/citations.bib',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp2, root_dir, expected)
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',
'checksums.md5',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/citations.bib',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp1, root_dir, expected)
root_dir = str(artifact.uuid)
expected = {
'VERSION',
'checksums.md5',
'metadata.yaml',
'data/file1.txt',
'data/file2.txt',
'data/nested/file3.txt',
'data/nested/file4.txt',
'provenance/metadata.yaml',
'provenance/VERSION',
'provenance/citations.bib',
'provenance/action/action.yaml'
}
self.assertArchiveMembers(fp2, root_dir, expected)
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 create_artifact():
request_body = request.get_json()
artifact = Artifact.import_data(request_body['type'], request_body['path'],
request_body['source_format'])
path = os.path.join(os.getcwd(), request_body['name'])
if not path.endswith('.qza'):
path += '.qza'
artifact.save(path)
return ''
def test_primitive_param_not_valid_choice(self):
pipeline = self.plugin.pipelines['failing_pipeline']
int_sequence = Artifact.import_data(IntSequence1, [0, 42, 43])
break_from = "invalid choice"
# test String not a valid choice
with self.assertRaisesRegex(TypeError,
'break_from.*\'invalid choice\''):
pipeline(int_sequence, break_from)
def setUp(self):
super().setUp()
taxonomy = Artifact.import_data('FeatureData[Taxonomy]',
self.get_data_path('taxonomy.tsv'))
self.taxonomy = taxonomy.view(pd.Series)
# TODO: use `Artifact.import_data` here once we have a transformer
# for DNASequencesDirectoryFormat -> DNAFASTAFormat
self.reads_fp = self.get_data_path('se-dna-sequences.fasta')
self.reads = DNAFASTAFormat(self.reads_fp, mode='r')
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_exercise_classify_otus_experimental(self):
obs_artifact, = self.action(self.input_sequences, self.tree,
self.taxonomy)
obs = obs_artifact.view(pd.DataFrame)
exp_artifact = Artifact.import_data(
'FeatureData[Taxonomy]', self.get_data_path('sepp-results.tsv'))
exp = exp_artifact.view(pd.DataFrame)
assert_frame_equal(obs, exp)
def test_extract_reads_expected_reverse(self):
reverse_sequences = Artifact.import_data(
'FeatureData[Sequence]',
self.get_data_path('dna-sequences-reverse.fasta'))
results = extract_reads(
reverse_sequences, f_primer=self.f_primer, r_primer=self.r_primer,
min_length=4, read_orientation='reverse')
self._test_results(results)
def test_import_data_with_good_validation_multi_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('1\n')
with open(os.path.join(data_dir, 'file2.txt'), 'w') as fh:
fh.write('1\n')
a = Artifact.import_data(SingleInt, data_dir)
self.assertEqual(1, a.view(int))
