Externalize ROBOT (#474)

Author: cthoyt

pyproject.toml

@@ -71,7 +71,6 @@ dependencies = [
     "pystow>=0.7.5",
     "bioversions>=0.8.243",
     "bioregistry>=0.12.30",
-    "bioontologies>=0.7.2",
     "ssslm>=0.0.13",
     "zenodo-client>=0.4.1",
     "class_resolver>=0.6.0",
@@ -92,6 +91,7 @@ dependencies = [
     "obographs>=0.0.8",
     "sssom_pydantic>=0.2.0",
     "pytz",
+    "robot-obo-tool",
 ]
 
 # see https://peps.python.org/pep-0735/ and https://docs.astral.sh/uv/concepts/dependencies/#dependency-groups

src/pyobo/getters.py

@@ -17,7 +17,6 @@
 from textwrap import indent
 from typing import Any, TypeVar
 
-import bioontologies.robot
 import bioregistry
 import click
 import pystow.utils
@@ -80,10 +79,10 @@ class UnhandledFormatError(NoBuildError):
 
 
 def _convert_to_obo(path: Path) -> Path:
-    import bioontologies.robot
+    import robot_obo_tool
 
     _converted_obo_path = path.with_suffix(".obo")
-    bioontologies.robot.convert(path, _converted_obo_path, check=False)
+    robot_obo_tool.convert(path, _converted_obo_path, check=False)
     return _converted_obo_path
 
 
@@ -338,6 +337,8 @@ def iter_helper_helper(
 
     :yields: A prefix and the result of the callable ``f``
     """
+    from robot_obo_tool import ROBOTError
+
     strict = kwargs.get("strict", True)
     prefixes = list(
         _prefixes(
@@ -382,7 +383,7 @@ def iter_helper_helper(
             if "DrugBank" not in str(e):
                 raise
             logger.warning("[drugbank] invalid credentials")
-        except (subprocess.CalledProcessError, bioontologies.robot.ROBOTError):
+        except (subprocess.CalledProcessError, ROBOTError):
             logger.warning("[%s] ROBOT was unable to convert OWL to OBO", prefix)
         except ValueError as e:
             if _is_xml(e):

src/pyobo/struct/functional/ontology.py

@@ -250,7 +250,7 @@ def to_funowl_args(self) -> str:
 
 def get_rdf_graph_oracle(boxes: list[Box], *, prefix_map: dict[str, str]) -> Graph:
     """Serialize to turtle via OFN and conversion with ROBOT."""
-    import bioontologies.robot
+    import robot_obo_tool
 
     ontology = Ontology(
         iri=EXAMPLE_ONTOLOGY_IRI,
@@ -265,7 +265,7 @@ def get_rdf_graph_oracle(boxes: list[Box], *, prefix_map: dict[str, str]) -> Gra
         ofn_path.write_text(text)
         ttl_path = stub.with_suffix(".ttl")
         try:
-            bioontologies.robot.convert(ofn_path, ttl_path)
+            robot_obo_tool.convert(ofn_path, ttl_path)
         except subprocess.CalledProcessError:
             raise RuntimeError(f"failed to convert axioms from:\n\n{text}") from None
         graph.parse(ttl_path)

src/pyobo/struct/obograph/export.py

@@ -33,7 +33,7 @@ def to_parsed_obograph_oracle(
     obo: Obo, *, converter: Converter | None = None
 ) -> og.StandardizedGraphDocument:
     """Serialize to OBO, convert to OBO Graph JSON with ROBOT, load, then parse."""
-    import bioontologies.robot
+    import robot_obo_tool
 
     if converter is None:
         converter = get_converter()
@@ -43,7 +43,7 @@ def to_parsed_obograph_oracle(
         obo_path = stub.with_suffix(".obo")
         obograph_path = stub.with_suffix(".json")
         obo.write_obo(obo_path)
-        bioontologies.robot.convert(input_path=obo_path, output_path=obograph_path)
+        robot_obo_tool.convert(input_path=obo_path, output_path=obograph_path)
         raw = og.read(obograph_path, squeeze=False)
     rv = raw.standardize(converter)
     for graph in rv.graphs:

src/pyobo/struct/struct.py

@@ -1067,12 +1067,12 @@ def write_ofn(self, path: str | Path) -> None:
 
     def write_owl(self, path: str | Path) -> None:
         """Write OWL, by first outputting OFN then converting with ROBOT."""
-        from bioontologies import robot
+        import robot_obo_tool
 
         with tempfile.TemporaryDirectory() as directory:
             ofn_path = Path(directory).joinpath("tmp.ofn")
             self.write_ofn(ofn_path)
-            robot.convert(ofn_path, path)
+            robot_obo_tool.convert(ofn_path, path)
 
     def write_rdf(self, path: str | Path) -> None:
         """Write as Turtle RDF."""
@@ -1312,19 +1312,19 @@ def write_default(
                 tqdm.write(f"[{self._prefix_version}] writing OBO Graph to {self._obograph_path}")
                 self.write_obograph(self._obograph_path)
             else:
-                import bioontologies.robot
+                import robot_obo_tool
 
                 tqdm.write(
                     f"[{self.ontology}] converting OFN to OBO Graph at {self._obograph_path}"
                 )
-                bioontologies.robot.convert(
+                robot_obo_tool.convert(
                     self._ofn_path, self._obograph_path, debug=True, merge=False, reason=False
                 )
         if write_owl and (not self._owl_path.is_file() or force):
             tqdm.write(f"[{self._prefix_version}] writing OWL to {self._owl_path}")
-            import bioontologies.robot
+            import robot_obo_tool
 
-            bioontologies.robot.convert(
+            robot_obo_tool.convert(
                 self._ofn_path, self._owl_path, debug=True, merge=False, reason=False
             )
         if write_ttl and (not self._ttl_path.is_file() or force):

tests/test_struct/test_obo/test_struct_obo.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 from textwrap import dedent
 
-import bioontologies.robot
+import robot_obo_tool
 
 from pyobo import default_reference
 from pyobo.struct.reference import OBOLiteral
@@ -33,7 +33,7 @@ def assert_ofn_lines(self, text: str, ontology: Obo, oracle: bool = False) -> No
             if oracle:
                 tmp_path = Path(directory).joinpath("tmp.obo")
                 ontology.write_obo(tmp_path)
-                bioontologies.robot.convert(tmp_path, in_path, check=True, debug=True)
+                robot_obo_tool.convert(tmp_path, in_path, check=True, debug=True)
             else:
                 ontology.write_ofn(in_path)
             self.assert_lines(text, in_path.read_text().splitlines())
@@ -50,7 +50,7 @@ def assert_owl_lines(self, text: str, ontology: Obo, method: str = "ofn") -> Non
             else:
                 raise ValueError
             out_path = Path(directory).joinpath("tmp.owl")
-            bioontologies.robot.convert(in_path, out_path, check=True, debug=True)
+            robot_obo_tool.convert(in_path, out_path, check=True, debug=True)
             lines = out_path.read_text().splitlines()
             lines = [
                 "" if not line.strip() else line.rstrip()