Implement metagraph.get_metaedge

Author: dhimmel

hetio/abbreviation.py

@@ -136,6 +136,9 @@ def metaedges_from_metapath(abbreviation, standardize_by=None):
 
 
 def metaedge_id_from_abbreviation(metagraph, abbreviation):
+    """
+    Return the metaedge_id corresponding to a metaedge abbreviation.
+    """
     source_abbrev, target_abbrev = regex.split('[a-z<>]+', abbreviation)
     edge_abbrev = regex.search('[a-z<>]+', abbreviation).group()
     abbrev_to_kind = {v: k for k, v in metagraph.kind_to_abbrev.items()}

hetio/hetnet.py

@@ -220,8 +220,19 @@ def get_metanode(self, metanode):
         # Assume metanode must be an abbreviation
         return self.get_node(self.abbrev_to_kind[metanode])
 
-    def get_metaedge(self, metanode):
-        pass
+    def get_metaedge(self, metaedge):
+        """
+        Return the metaedge specified by the input, which can be either a:
+         - MetaEdge (passthrough)
+         - metaedge_id (tuple)
+         - metaedge abbreviation
+        """
+        if isinstance(metaedge, MetaEdge):
+            return metaedge
+        if isinstance(metaedge, tuple):
+            return self.get_edge(metaedge)
+        metaedge_id = hetio.abbreviation.metaedge_id_from_abbreviation(metaedge)
+        return self.get_edge(metaedge_id)
 
     @staticmethod
     def from_edge_tuples(metaedge_tuples, kind_to_abbrev=None):

test/graph_test.py

@@ -104,8 +104,9 @@ def test_disase_gene_example():
     """
     Recreate hetnet from https://doi.org/10.1371/journal.pcbi.1004259.g002.
     """
+    metaedge_id_GaD = 'Gene', 'Disease', 'association', 'both'
     metaedge_tuples = [
-        ('Gene', 'Disease', 'association', 'both'),
+        metaedge_id_GaD,
         ('Gene', 'Tissue', 'expression', 'both'),
         ('Disease', 'Tissue', 'localization', 'both'),
         ('Gene', 'Gene', 'interaction', 'both'),
@@ -117,6 +118,11 @@ def test_disase_gene_example():
     assert metagraph.get_metanode(gene_metanode) == gene_metanode
     assert metagraph.get_metanode('Gene') == gene_metanode
     assert metagraph.get_metanode('G') == gene_metanode
+    metaedge_GaD = metagraph.get_edge(metaedge_id_GaD)
+    assert metagraph.get_metaedge(metaedge_GaD) == metaedge_GaD
+    assert metaedge_id_GaD == metaedge_GaD.get_id()
+    assert metagraph.get_metaedge(metaedge_id_GaD) == metaedge_GaD
+    assert metagraph.get_metaedge('GaD') == metaedge_GaD
 
     # Create graph
     graph = hetio.hetnet.Graph(metagraph)