Fix obonet caching (#314)

This PR makes sure that the parsed obonet file is actually cached. It
also makes sure the tests don't pollute the active cache directory

src/pyobo/getters.py

@@ -34,7 +34,7 @@
 )
 from .identifier_utils import ParseError, wrap_norm_prefix
 from .plugins import has_nomenclature_plugin, run_nomenclature_plugin
-from .reader import from_obo_path
+from .reader import from_obo_path, from_obonet
 from .struct import Obo
 from .utils.io import get_writer
 from .utils.path import ensure_path, prefix_directory_join
@@ -110,16 +110,30 @@ def get_ontology(
         logger.info("UBERON has so much garbage in it that defaulting to non-strict parsing")
         strict = False
 
-    if cache:
+    if not cache:
+        logger.debug("[%s] caching was turned off, so dont look for an obonet file", prefix)
+        obonet_json_gz_path = None
+    else:
         obonet_json_gz_path = prefix_directory_join(
             prefix, name=f"{prefix}.obonet.json.gz", ensure_exists=False, version=version
         )
+        logger.debug(
+            "[%s] caching is turned on, so look for an obonet file at %s",
+            prefix,
+            obonet_json_gz_path,
+        )
         if obonet_json_gz_path.exists() and not force:
-            from .reader import from_obonet
             from .utils.cache import get_gzipped_graph
 
             logger.debug("[%s] using obonet cache at %s", prefix, obonet_json_gz_path)
-            return from_obonet(get_gzipped_graph(obonet_json_gz_path))
+            return from_obonet(
+                get_gzipped_graph(obonet_json_gz_path),
+                strict=strict,
+                version=version,
+                upgrade=upgrade,
+            )
+        else:
+            logger.debug("[%s] no obonet cache found at %s", prefix, obonet_json_gz_path)
 
     if has_nomenclature_plugin(prefix):
         obo = run_nomenclature_plugin(prefix, version=version)
@@ -128,8 +142,6 @@ def get_ontology(
             obo.write_default(force=force_process)
         return obo
 
-    logger.debug("[%s] no obonet cache found at %s", prefix, obonet_json_gz_path)
-
     ontology_format, path = _ensure_ontology_path(prefix, force=force, version=version)
     if path is None:
         raise NoBuildError(prefix)
@@ -144,7 +156,14 @@ def get_ontology(
     else:
         raise UnhandledFormatError(f"[{prefix}] unhandled ontology file format: {path.suffix}")
 
-    obo = from_obo_path(path, prefix=prefix, strict=strict, version=version, upgrade=upgrade)
+    obo = from_obo_path(
+        path,
+        prefix=prefix,
+        strict=strict,
+        version=version,
+        upgrade=upgrade,
+        _cache_path=obonet_json_gz_path,
+    )
     if cache:
         obo.write_default(force=force_process)
     return obo

src/pyobo/reader.py

@@ -42,6 +42,7 @@
 from .struct.struct_utils import Annotation, Stanza
 from .struct.typedef import comment as has_comment
 from .struct.typedef import default_typedefs, has_ontology_root_term
+from .utils.cache import write_gzipped_graph
 from .utils.misc import STATIC_VERSION_REWRITES, cleanup_version
 
 __all__ = [
@@ -60,6 +61,7 @@ def from_obo_path(
     version: str | None,
     upgrade: bool = True,
     ignore_obsolete: bool = False,
+    _cache_path: Path | None = None,
 ) -> Obo:
     """Get the OBO graph from a path."""
     path = Path(path).expanduser().resolve()
@@ -87,6 +89,10 @@ def from_obo_path(
         # Make sure the graph is named properly
         _clean_graph_ontology(graph, prefix)
 
+    if _cache_path:
+        logger.info("[%s] writing obonet cache to %s", prefix, _cache_path)
+        write_gzipped_graph(path=_cache_path, graph=graph)
+
     # Convert to an Obo instance and return
     return from_obonet(graph, strict=strict, version=version, upgrade=upgrade)
 

tests/test_obo_reader/test_get.py

@@ -270,7 +270,7 @@ class TestGet(unittest.TestCase):
     def setUp(self) -> None:
         """Set up the test with the mock ChEBI OBO file."""
         with chebi_patch:
-            self.ontology = get_ontology("chebi")
+            self.ontology = get_ontology("chebi", cache=False)
 
     def test_get_id_alts_mapping(self):
         """Make sure the alternative ids are mapped properly.