Merge pull request #325 from biocypher/duplicate_tail_ontologies

#273: add unit test for duplicated tail ontologies

biocypher/_misc.py

@@ -115,7 +115,12 @@ def _get_inheritance_tree(inheritance_graph: Union[dict, nx.Graph]) -> dict:
         )
         if multiple_parents_present:
             logger.warning(
-                "The ontology contains multiple inheritance (one child node has multiple parent nodes). This is not visualized in the following hierarchy tree (the child node is only added once). If you want to browse all relationships of the parsed ontology write a graphml file to disk and view this file."
+                "The ontology contains multiple inheritance (one child node "
+                "has multiple parent nodes). This is not visualized in the "
+                "following hierarchy tree (the child node is only added once). "
+                "If you wish to browse all relationships of the parsed "
+                "ontologies, write a graphml file to disk using "
+                "`to_disk = <directory>` and view this file."
             )
 
         # unlist values

biocypher/_ontology.py

@@ -695,8 +695,9 @@ def show_ontology_structure(self, to_disk: str = None, full: bool = False):
         Args:
 
             to_disk (str): If specified, the ontology structure will be saved
-                to disk as a GRAPHML file, to be opened in your favourite
-                graph visualisation tool.
+                to disk as a GRAPHML file at the location (directory) specified
+                by the `to_disk` string, to be opened in your favourite graph
+                visualisation tool.
 
             full (bool): If True, the full ontology structure will be shown,
                 including all nodes and edges. If False, only the nodes and

test/test_misc.py

@@ -1,7 +1,6 @@
 import logging
 
 import pytest
-import treelib
 import networkx as nx
 
 from biocypher._misc import create_tree_visualisation

test/test_ontology.py

@@ -1,4 +1,5 @@
 import os
+import logging
 
 import pytest
 import networkx as nx
@@ -217,3 +218,38 @@ def test_simple_ontology(simple_ontology):
         "entity",
         "Thing",
     ]
+
+
+def test_duplicated_tail_ontologies(caplog, extended_ontology_mapping):
+    ontology = Ontology(
+        head_ontology={
+            "url": "https://github.com/biolink/biolink-model/raw/v3.2.1/biolink-model.owl.ttl",
+            "root_node": "entity",
+        },
+        ontology_mapping=extended_ontology_mapping,
+        tail_ontologies={
+            "so": {
+                "url": "test/ontologies/so.owl",
+                "head_join_node": "sequence variant",
+                "tail_join_node": "sequence_variant",
+            },
+            "so_2": {
+                "url": "test/ontologies/so.owl",
+                "head_join_node": "device",
+                "tail_join_node": "sequence_variant",
+            },
+            "mondo": {
+                "url": "test/ontologies/mondo.owl",
+                "head_join_node": "disease",
+                "tail_join_node": "human disease",
+            },
+        },
+    )
+    assert ontology
+    with caplog.at_level(logging.INFO):
+        tree = ontology.show_ontology_structure()
+    assert tree
+    assert any(
+        "The ontology contains multiple inheritance" in record.message
+        for record in caplog.records
+    )