Merge branch 'main' into getter-versions

Author: cthoyt

src/pyobo/cli/cli.py

@@ -90,12 +90,7 @@ def _has_no_download(prefix: str) -> bool:
 @lru_cache(maxsize=1)
 def _no_download() -> set[str]:
     """Get the list of prefixes not available as OBO."""
-    return {
-        prefix
-        for prefix in bioregistry.read_registry()
-        if bioregistry.get_obo_download(prefix) is None
-        and bioregistry.get_owl_download(prefix) is None
-    }
+    return {resource.prefix for resource in bioregistry.resources() if not resource.has_download()}
 
 
 main.add_command(lookup)

src/pyobo/getters.py

@@ -17,6 +17,7 @@
 from textwrap import indent
 from typing import Any, TypeVar
 
+import bioontologies.robot
 import bioregistry
 import click
 import pystow.utils
@@ -252,6 +253,7 @@ def _ensure_ontology_path(
     "gwascentral.phenotype": "website is down? or API changed?",  # FIXME
     "gwascentral.study": "website is down? or API changed?",  # FIXME
     "snomedct": "dead source",
+    "ero": "dead",
 }
 
 X = TypeVar("X")
@@ -378,7 +380,7 @@ def iter_helper_helper(
             if "DrugBank" not in str(e):
                 raise
             logger.warning("[drugbank] invalid credentials")
-        except subprocess.CalledProcessError:
+        except (subprocess.CalledProcessError, bioontologies.robot.ROBOTError):
             logger.warning("[%s] ROBOT was unable to convert OWL to OBO", prefix)
         except ValueError as e:
             if _is_xml(e):

src/pyobo/struct/struct.py

@@ -940,7 +940,6 @@ def _iterate_property_pairs(self) -> Iterable[Annotation]:
             yield Annotation(v.has_license, license_literal)
 
         if description := bioregistry.get_description(self.ontology):
-            description = obo_escape_slim(description.strip())
             yield Annotation(v.has_description, OBOLiteral.string(description.strip()))
         if homepage := bioregistry.get_homepage(self.ontology):
             yield Annotation(v.has_homepage, OBOLiteral.uri(homepage))
@@ -2307,12 +2306,11 @@ def build_ontology(
     homepage: str | None = None,
     mailing_list: str | None = None,
     logo: str | None = None,
-    repository: str | None,
+    repository: str | None = None,
 ) -> Obo:
     """Build an ontology from parts."""
-    resource = bioregistry.get_resource(prefix, strict=True)
     if name is None:
-        name = resource.get_name()
+        name = bioregistry.get_name(prefix)
     # TODO auto-populate license and other properties
 
     if properties is None:

src/pyobo/utils/misc.py

@@ -39,6 +39,7 @@
     "http://purl.dataone.org/odo/SENSO/",  # like in http://purl.dataone.org/odo/SENSO/0.1.0
     "https://purl.dataone.org/odo/ADCAD/",
     "http://identifiers.org/combine.specifications/teddy.rel-",
+    "https://nfdi.fiz-karlsruhe.de/ontology/",
 ]
 VERSION_PREFIX_SPLITS = [
     "http://www.ebi.ac.uk/efo/releases/v",

tests/test_struct/test_obo/test_struct_obo.py

@@ -1,12 +1,16 @@
 """Test for OBO header."""
 
+import tempfile
 import unittest
 from collections.abc import Iterable
+from pathlib import Path
 from textwrap import dedent
 
+import bioontologies.robot
+
 from pyobo import default_reference
 from pyobo.struct.reference import OBOLiteral
-from pyobo.struct.struct import Obo, make_ad_hoc_ontology
+from pyobo.struct.struct import Obo, build_ontology, make_ad_hoc_ontology
 from pyobo.struct.struct_utils import Annotation
 from pyobo.struct.typedef import has_license
 
@@ -22,11 +26,33 @@ def assert_obo_lines(self, text, ontology: Obo) -> None:
         """Assert OBO header has the right lines."""
         self.assert_lines(text, ontology.iterate_obo_lines())
 
+    def assert_ofn_lines(self, text: str, ontology: Obo) -> None:
+        """Assert OFN header has the right lines."""
+        with tempfile.TemporaryDirectory() as directory:
+            in_path = Path(directory).joinpath("tmp.ofn")
+            ontology.write_ofn(in_path)
+            self.assert_lines(text, in_path.read_text().splitlines())
+
+    def assert_owl_lines(self, text: str, ontology: Obo) -> None:
+        """Assert OWL header has the right lines."""
+        with tempfile.TemporaryDirectory() as directory:
+            in_path = Path(directory).joinpath("tmp.ofn")
+            ontology.write_ofn(in_path)
+            out_path = Path(directory).joinpath("tmp.owl")
+            bioontologies.robot.convert(in_path, out_path, check=False)
+            lines = out_path.read_text().splitlines()
+            lines = [
+                "" if not line.strip() else line.rstrip()
+                for line in lines
+                if line.strip() and not line.strip().startswith("<!-- Generated by the OWL API")
+            ]
+            self.assert_lines(text, lines)
+
     def test_2_data_version(self) -> None:
         """Test ontology definition."""
-        ontology = make_ad_hoc_ontology(
-            _ontology="xxx",
-            _data_version="1.0",
+        ontology = build_ontology(
+            prefix="xxx",
+            version="1.0",
         )
         self.assert_obo_lines(
             """\
@@ -174,6 +200,73 @@ def test_18_properties_bioregistry(self) -> None:
             ontology,
         )
 
+    def test_18_properties_escapes(self) -> None:
+        """Test escapes in property values, like for parentheses."""
+        ontology = build_ontology(
+            prefix="xxx",
+            description="MeSH (Medical Subject Headings)",
+        )
+        self.assert_obo_lines(
+            r"""
+            format-version: 1.4
+            idspace: dcterms http://purl.org/dc/terms/ "Dublin Core Metadata Initiative Terms"
+            ontology: xxx
+            property_value: dcterms:description "MeSH \(Medical Subject Headings\)" xsd:string
+
+            [Typedef]
+            id: dcterms:description
+            name: description
+            is_metadata_tag: true
+            """,
+            ontology,
+        )
+        self.assert_ofn_lines(
+            """
+            Prefix(dcterms:=<http://purl.org/dc/terms/>)
+            Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+            Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+            Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+            Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+
+            Ontology(<https://w3id.org/biopragmatics/resources/xxx/xxx.ofn>
+            Annotation(dcterms:description "MeSH (Medical Subject Headings)"^^xsd:string)
+
+            Declaration(AnnotationProperty(dcterms:description))
+            AnnotationAssertion(rdfs:label dcterms:description "description")
+            )
+            """,
+            ontology,
+        )
+        self.assert_owl_lines(
+            """
+            <?xml version="1.0"?>
+            <rdf:RDF xmlns="https://w3id.org/biopragmatics/resources/xxx/xxx.ofn#"
+                 xml:base="https://w3id.org/biopragmatics/resources/xxx/xxx.ofn"
+                 xmlns:owl="http://www.w3.org/2002/07/owl#"
+                 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+                 xmlns:xml="http://www.w3.org/XML/1998/namespace"
+                 xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+                 xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+                 xmlns:dcterms="http://purl.org/dc/terms/">
+                <owl:Ontology rdf:about="https://w3id.org/biopragmatics/resources/xxx/xxx.ofn">
+                    <dcterms:description>MeSH (Medical Subject Headings)</dcterms:description>
+                </owl:Ontology>
+                <!--
+                ///////////////////////////////////////////////////////////////////////////////////////
+                //
+                // Annotation properties
+                //
+                ///////////////////////////////////////////////////////////////////////////////////////
+                 -->
+                <!-- http://purl.org/dc/terms/description -->
+                <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/description">
+                    <rdfs:label>description</rdfs:label>
+                </owl:AnnotationProperty>
+            </rdf:RDF>
+            """,
+            ontology,
+        )
+
     def test_18_properties_external(self) -> None:
         """Test properties."""
         ontology = make_ad_hoc_ontology(