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_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_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_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)
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)