Merge branch 'main' into cordis

Author: cthoyt

src/pyobo/struct/reference.py

@@ -363,8 +363,8 @@ def datetime(cls, dt: datetime_cls | str) -> OBOLiteral:
     def date(cls, dt: datetime_cls | date_cls | str) -> OBOLiteral:
         """Get a datetime literal."""
         if isinstance(dt, str):
-            dt = _parse_datetime(dt)
-        if isinstance(dt, datetime.datetime):
+            dt = datetime.date.fromisoformat(dt)
+        elif isinstance(dt, datetime.datetime):
             dt = dt.date()
         return cls(dt.isoformat(), v.xsd_date, None)
 

src/pyobo/struct/struct_utils.py

@@ -975,8 +975,7 @@ def _iterate_obo_relations(
                 case OBOLiteral(dd, datatype, _language):
                     if predicate in skip_predicate_literals:
                         continue
-                    # TODO how to clean/escape value?
-                    end = f'"{dd}" {get_preferred_curie(datatype)}'
+                    end = f'"{_escape_literal(dd)}" {get_preferred_curie(datatype)}'
                     name = None
                 case curies.Reference():  # it's a reference
                     if predicate in skip_predicate_objects:
@@ -995,6 +994,10 @@ def _iterate_obo_relations(
             yield start + end
 
 
+def _escape_literal(s: str) -> str:
+    return s.replace('"', '\\"')
+
+
 def _reference_or_literal_key(x: Reference | OBOLiteral) -> tuple[int, Reference | OBOLiteral]:
     if isinstance(x, Reference):
         return 0, x

tests/test_struct/test_obo/test_struct_term.py

@@ -713,6 +713,8 @@ def test_12_property_string_with_language(self) -> None:
 
     def test_12_property_string_with_quote(self) -> None:
         """Test emitting a string property literal with a quote in it."""
+        # see pyobo.struct.struct_utils._escape_literal for
+        # implementation of escaping for these literals
         term = Term(reference=LYSINE_DEHYDROGENASE_ACT)
         term.annotate_string(RO_DUMMY, '"value" added')
         self.assert_obo_stanza(
@@ -727,7 +729,7 @@ def test_12_property_string_with_quote(self) -> None:
             ofn="""\
                 Declaration(Class(GO:0050069))
                 AnnotationAssertion(rdfs:label GO:0050069 "lysine dehydrogenase activity")
-                AnnotationAssertion(RO:1234567 GO:0050069 "\\"value\\" added"@en)
+                AnnotationAssertion(RO:1234567 GO:0050069 "\\"value\\" added"^^xsd:string)
             """,
         )
 
@@ -791,6 +793,26 @@ def test_12_property_year(self) -> None:
             typedefs={RO_DUMMY.pair: RO_DUMMY},
         )
 
+    def test_12_property_date(self) -> None:
+        """Test emitting property literals that were annotated as a date."""
+        term = Term(reference=LYSINE_DEHYDROGENASE_ACT)
+        term.annotate_date(RO_DUMMY, "1993-01-01")
+        self.assert_obo_stanza(
+            term,
+            obo="""\
+                [Term]
+                id: GO:0050069
+                name: lysine dehydrogenase activity
+                property_value: RO:1234567 "1993-01-01" xsd:date
+            """,
+            ofn="""\
+                Declaration(Class(GO:0050069))
+                AnnotationAssertion(rdfs:label GO:0050069 "lysine dehydrogenase activity")
+                AnnotationAssertion(RO:1234567 GO:0050069 "1993-01-01"^^xsd:date)
+            """,
+            typedefs={RO_DUMMY.pair: RO_DUMMY},
+        )
+
     def test_12_property_object(self) -> None:
         """Test emitting property literals."""
         term = Term(reference=LYSINE_DEHYDROGENASE_ACT)