Merge pull request #164 from biolink/handle_names_in_descendants

Handle aliases in queries for  get_descendants

.github/workflows/check-dependencies.yaml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [ "3.9", "3.10" ]
+        python: [ "3.9", "3.10", "3.11" ]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

.github/workflows/initialize-toolkit-daily.yaml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [ "3.9", "3.10" ]
+        python: [ "3.9", "3.10", "3.11" ]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

.github/workflows/run-tests.yml

@@ -22,7 +22,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [ "3.9", "3.10" ]
+        python: [ "3.9", "3.10", "3.11" ]
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

bmt/toolkit.py

@@ -21,7 +21,7 @@
 Url = str
 Path = str
 
-LATEST_BIOLINK_RELEASE = "4.1.5"
+LATEST_BIOLINK_RELEASE = "4.1.6"
 
 REMOTE_PATH = f"https://raw.githubusercontent.com/biolink/biolink-model/v{LATEST_BIOLINK_RELEASE}/biolink-model.yaml"
 PREDICATE_MAP = f"https://raw.githubusercontent.com/biolink/biolink-model/v{LATEST_BIOLINK_RELEASE}/predicate_mapping.yaml"
@@ -884,8 +884,11 @@ def get_element(self, name: str) -> Optional[Element]:
         logger.debug(parsed_name)
         element = self.view.get_element(parsed_name)
         if element is None and self.view.all_aliases() is not None:
+            if parsed_name.startswith("biolink:"):
+                parsed_name = parsed_name.replace("biolink:", "")
+                parsed_name = parsed_name.replace("_", " ")
             for e in self.view.all_aliases():
-                if name in self.view.all_aliases()[e]:
+                if name in self.view.all_aliases()[e] or parsed_name in self.view.all_aliases()[e]:
                     element = self.view.get_element(e)
         if element is None and "_" in name:
             element = self.get_element(name.replace("_", " "))

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bmt"
-version = "1.1.2.post14.dev0+08be61e"
+version = "1.2.1"
 description = "Biolink Model Toolkit: A Python API for working with the Biolink Model"
 authors = ["Sierra Taylor Moxon <[email protected]>"]
 license = "BSD"

tests/unit/test_toolkit.py

@@ -130,6 +130,11 @@ def test_not_valid_edge(toolkit):
 
 def test_get_element_via_alias(toolkit):
     el = toolkit.get_element('definition')
+    pred_alias = toolkit.get_element("biolink:realized_in_response_to")
+    print(pred_alias)
+    ameliorates_aliase = toolkit.get_element("biolink:ameliorates")
+    assert ameliorates_aliase.name == "ameliorates condition"
+    assert pred_alias.name == "caused by"
     assert el.name == 'description'
 
 
@@ -885,6 +890,9 @@ def test_descendants(toolkit):
     assert INTERACTS_WITH in toolkit.get_descendants(RELATED_TO)
     assert PHENOTYPIC_FEATURE in toolkit.get_descendants(NAMED_THING)
     assert RELATED_TO not in toolkit.get_descendants(NAMED_THING)
+    assert "ameliorates condition" in toolkit.get_descendants("biolink:ameliorates")
+    assert "biolink:ameliorates_condition" in toolkit.get_descendants("biolink:ameliorates", formatted=True)
+
     with pytest.raises(ValueError):
         toolkit.get_descendants('biolink:invalid')
     assert "biolink:PhenotypicFeature" in toolkit.get_descendants(