def test_build_meta_failure(self):
p1, p2 = Pipeline(), Pipeline()
p = Pipeline._build_meta('wrong', [p1, p2])
with self.assertRaises(MetaValueError):
p(BELGraph())
def test_serialize_file(self):
p = Pipeline.from_functions(['enrich_protein_and_rna_origins'])
sio = StringIO()
p.dump(sio)
sio.seek(0)
p_reconstituted = Pipeline.load(sio)
self.assertEqual(p.protocol, p_reconstituted.protocol)
def test_serialize_file(self):
p = Pipeline.from_functions(['infer_central_dogma'])
sio = StringIO()
p.dump(sio)
sio.seek(0)
p_reconstituted = Pipeline.load(sio)
self.assertEqual(p.protocol, p_reconstituted.protocol)
def test_extend(self):
p1 = Pipeline.from_functions(['enrich_protein_and_rna_origins'])
self.assertEqual(1, len(p1))
p2 = Pipeline.from_functions(['remove_pathologies'])
p1.extend(p2)
self.assertEqual(2, len(p1))
def test_extend(self):
p1 = Pipeline.from_functions(['infer_central_dogma'])
self.assertEqual(1, len(p1))
p2 = Pipeline.from_functions(['remove_pathologies'])
p1.extend(p2)
self.assertEqual(2, len(p1))
def test_pipeline_by_function(self):
pipeline = Pipeline.from_functions([
enrich_protein_and_rna_origins,
])
result = pipeline(self.graph)
self.assertEqual(32, result.number_of_nodes())
for node in self.graph:
self.assertIn(node, result)
self.check_original_unchanged()
def test_pipeline_by_string(self):
pipeline = Pipeline.from_functions([
'infer_central_dogma',
])
result = pipeline(self.graph)
self.assertEqual(32, result.number_of_nodes())
for node in self.graph:
self.assertIn(node, result)
self.check_original_unchanged()
def test_serialize_string(self):
p = Pipeline.from_functions(['enrich_protein_and_rna_origins'])
s = p.dumps()
p_reconstituted = Pipeline.loads(s)
self.assertEqual(p.protocol, p_reconstituted.protocol)
def test_append(self):
pipeline = Pipeline()
self.assertEqual(0, len(pipeline))
pipeline.append('enrich_protein_and_rna_origins')
self.assertEqual(1, len(pipeline))
def test_fail_add(self):
pipeline = Pipeline()
with self.assertRaises(MissingPipelineFunctionError):
pipeline.append('missing function')
def test_get_function_failure(self):
p = Pipeline()
with self.assertRaises(MissingPipelineFunctionError):
p._get_function('nonsense name')
def test_append_invalid(self):
"""Test when an invalid type is given to a :class:`pybel.struct.Pipeline`."""
p = Pipeline()
with self.assertRaises(TypeError):
p.append(4)
from .tools_compat import calculate_error_by_annotation, get_tools_version, summarize_completeness
from .utils import SecurityConfigurableBlueprint as Blueprint, calculate_overlap_info
from .version import get_version as get_bel_commons_version
__all__ = [
'ui_blueprint',
]
logger = logging.getLogger(__name__)
ui_blueprint = Blueprint('ui', __name__)
time_instantiated = str(datetime.datetime.now())
extract_useful_subgraph = Pipeline.from_functions([
remove_pathologies,
remove_associations,
collapse_to_genes,
remove_isolated_nodes,
])
def _format_big_number(n: int) -> str:
if n > 1000000:
return '{}M'.format(int(round(n / 1000000)))
elif n > 1000:
return '{}K'.format(int(round(n / 1000)))
else:
return str(n)
def redirect_to_view_explorer_query(query: Query) -> flask.Response:
"""Return the response for the biological network explorer in a given query to :func:`view_explorer_query`."""
def test_serialize_string(self):
p = Pipeline.from_functions(['infer_central_dogma'])
s = p.dumps()
p_reconstituted = Pipeline.loads(s)
self.assertEqual(p.protocol, p_reconstituted.protocol)
def test_append(self):
pipeline = Pipeline()
self.assertEqual(0, len(pipeline))
pipeline.append('infer_central_dogma')
self.assertEqual(1, len(pipeline))
