Fix and regression test for #84

Author: apdavison

pipeline/src/base.py

@@ -77,7 +77,7 @@ def to_jsonld(self, include_empty_properties=True, embed_linked_nodes=True, with
             data["@id"] = self.id
         for property in self.__class__.properties:
             value = getattr(self, property.name)
-            if value or include_empty_properties:
+            if (value is not None) or include_empty_properties:
                 if property.multiple:
                     if value is None:
                         data[property.path] = value

pipeline/tests/test_regressions.py

@@ -61,7 +61,9 @@ def test_issue_0003(om):
     }
 
     assert (
-        node1.to_jsonld(include_empty_properties=False) == node2.to_jsonld(include_empty_properties=False) == expected
+        node1.to_jsonld(include_empty_properties=False)
+        == node2.to_jsonld(include_empty_properties=False)
+        == expected
     )
 
 
@@ -96,7 +98,9 @@ def test_issue0007(om):
         om.core.Affiliation(member_of=uni2),
     ]
 
-    actual = person.to_jsonld(include_empty_properties=False, embed_linked_nodes=False, with_context=True)
+    actual = person.to_jsonld(
+        include_empty_properties=False, embed_linked_nodes=False, with_context=True
+    )
     expected = {
         "@context": {"@vocab": "https://openminds.om-i.org/props/"},
         "@id": "_:001",
@@ -117,7 +121,9 @@ def test_issue0007(om):
     assert actual == expected
 
     c = Collection(person, uni1, uni2)
-    output_paths = c.save("issue0007.jsonld", individual_files=False, include_empty_properties=False)
+    output_paths = c.save(
+        "issue0007.jsonld", individual_files=False, include_empty_properties=False
+    )
     assert output_paths == ["issue0007.jsonld"]
 
     with open(output_paths[0]) as fp:
@@ -170,7 +176,9 @@ def test_issue0008(om):
         family_name="Professor",
         affiliations=[om.core.Affiliation(member_of=uni1, end_date=date(2023, 9, 30))],
     )
-    actual = person.to_jsonld(include_empty_properties=False, embed_linked_nodes=False, with_context=True)
+    actual = person.to_jsonld(
+        include_empty_properties=False, embed_linked_nodes=False, with_context=True
+    )
     expected = {
         "@context": {"@vocab": "https://openminds.om-i.org/props/"},
         "@id": "_:002",
@@ -196,22 +204,31 @@ def test_issue0026(om):
 
     uni1 = om.core.Organization(full_name="University of This Place", id="_:uthisp")
     person = om.core.Person(
-        given_name="A", family_name="Professor", affiliations=[om.core.Affiliation(member_of=uni1)], id="_:ap"
+        given_name="A",
+        family_name="Professor",
+        affiliations=[om.core.Affiliation(member_of=uni1)],
+        id="_:ap",
     )
 
     c = Collection(person)
 
     # uni1 was not added explicitly, but should nevertheless be included in the JSON-LD export
 
-    output_paths = c.save("issue0026.jsonld", individual_files=False, include_empty_properties=False)
+    output_paths = c.save(
+        "issue0026.jsonld", individual_files=False, include_empty_properties=False
+    )
 
     new_collection = Collection()
     new_collection.load(*output_paths, version=om.__name__.split(".")[1])
     os.remove("issue0026.jsonld")
 
-    person_again = [item for item in new_collection if isinstance(item, om.core.Person)][0]
+    person_again = [
+        item for item in new_collection if isinstance(item, om.core.Person)
+    ][0]
     assert len(person_again.affiliations) == 1
-    assert person_again.affiliations[0].member_of.full_name == "University of This Place"
+    assert (
+        person_again.affiliations[0].member_of.full_name == "University of This Place"
+    )
 
 
 @pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
@@ -222,9 +239,14 @@ def test_issue0023(om):
 
     uni1 = om.core.Organization(full_name="University of This Place", id="_:uthisp")
     person = om.core.Person(
-        given_name="A", family_name="Professor", affiliations=[om.core.Affiliation(member_of=uni1)], id="_:ap"
+        given_name="A",
+        family_name="Professor",
+        affiliations=[om.core.Affiliation(member_of=uni1)],
+        id="_:ap",
+    )
+    dv = om.core.DatasetVersion(
+        full_name="The name of the dataset version", custodians=[person], id="_:dv"
     )
-    dv = om.core.DatasetVersion(full_name="The name of the dataset version", custodians=[person], id="_:dv")
 
     c = Collection(dv)
 
@@ -234,18 +256,28 @@ def test_issue0023(om):
     person.affiliations.append(om.core.Affiliation(member_of=uni2))
     dv.repository = om.core.FileRepository(iri="http://example.com", id="_:fr")
 
-    output_paths = c.save("issue0023.jsonld", individual_files=False, include_empty_properties=False)
+    output_paths = c.save(
+        "issue0023.jsonld", individual_files=False, include_empty_properties=False
+    )
 
     new_collection = Collection()
     new_collection.load(*output_paths, version=om.__name__.split(".")[1])
     os.remove("issue0023.jsonld")
 
-    dv_again = [item for item in new_collection if isinstance(item, om.core.DatasetVersion)][0]
+    dv_again = [
+        item for item in new_collection if isinstance(item, om.core.DatasetVersion)
+    ][0]
     assert isinstance(dv_again.repository, om.core.FileRepository)
     assert dv_again.repository.iri.value == "http://example.com"
     assert len(dv_again.custodians[0].affiliations) == 2
-    assert dv_again.custodians[0].affiliations[0].member_of.full_name == "University of This Place"
-    assert dv_again.custodians[0].affiliations[1].member_of.full_name == "University of That Place"
+    assert (
+        dv_again.custodians[0].affiliations[0].member_of.full_name
+        == "University of This Place"
+    )
+    assert (
+        dv_again.custodians[0].affiliations[1].member_of.full_name
+        == "University of That Place"
+    )
 
 
 @pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
@@ -258,12 +290,14 @@ def test_issue0056(om):
     dataset = om.core.Dataset(
         digital_identifier=[
             om.core.DOI(identifier="abc"),
-            om.core.DOI(identifier="def")
+            om.core.DOI(identifier="def"),
         ]
     )
     failures = dataset.validate(ignore=["required"])
     assert len(failures) == 1
-    assert failures["multiplicity"] == ['digital_identifier does not accept multiple values, but contains 2']
+    assert failures["multiplicity"] == [
+        "digital_identifier does not accept multiple values, but contains 2"
+    ]
     data = dataset.to_jsonld()
     json.dumps(data)  # this should not raise an Exception
 
@@ -272,14 +306,8 @@ def test_issue0056(om):
 def test_issue0073a(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/73
     # Infinite recursion in validate()
-    ds1 = om.core.DatasetVersion(
-        short_name="ds1",
-        is_alternative_version_of=None
-    )
-    ds2 = om.core.DatasetVersion(
-        short_name="ds2",
-        is_alternative_version_of=ds1
-    )
+    ds1 = om.core.DatasetVersion(short_name="ds1", is_alternative_version_of=None)
+    ds2 = om.core.DatasetVersion(short_name="ds2", is_alternative_version_of=ds1)
     ds1.is_alternative_version_of = ds2
 
     failures = ds1.validate()
@@ -289,14 +317,8 @@ def test_issue0073a(om):
 def test_issue0073b(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/issues/73
     # Infinite recursion in validate()
-    ds1 = om.core.DatasetVersion(
-        short_name="ds1",
-        is_variant_of=None
-    )
-    ds2 = om.core.DatasetVersion(
-        short_name="ds2",
-        is_variant_of=ds1
-    )
+    ds1 = om.core.DatasetVersion(short_name="ds1", is_variant_of=None)
+    ds2 = om.core.DatasetVersion(short_name="ds2", is_variant_of=ds1)
     ds1.is_variant_of = ds2
 
     failures = ds1.validate()
@@ -316,10 +338,16 @@ def test_issue0069(om):
     result = om.sands.ParcellationEntity.by_name("NODa,b")
     assert result.abbreviation == "NODa,b"
 
-    result = om.sands.CommonCoordinateSpace.by_name("MEBRAINS population-based monkey brain template")
+    result = om.sands.CommonCoordinateSpace.by_name(
+        "MEBRAINS population-based monkey brain template"
+    )
     assert result.full_name == "MEBRAINS population-based monkey brain template"
 
-    assert om.controlled_terms.BiologicalOrder.by_name("rodents") == om.controlled_terms.BiologicalOrder.by_name("Rodentia") != None
+    assert (
+        om.controlled_terms.BiologicalOrder.by_name("rodents")
+        == om.controlled_terms.BiologicalOrder.by_name("Rodentia")
+        != None
+    )
 
     # Test with "all=True"
     results = om.sands.BrainAtlasVersion.by_name("Julich-Brain Atlas", all=True)
@@ -332,16 +360,33 @@ def test_issue0069(om):
     assert len(results) == 7
     assert all("CC" in r.short_name for r in results)
 
+
 @pytest.mark.parametrize("om", [openminds.latest])
 def test_pr0083(om):
     # https://github.com/openMetadataInitiative/openMINDS_Python/pull/83
     # by_name() should return None consistently
     # when no matches are found, regardless of the 'all' parameter
-    
+
     # all=False (default) should return None when no match is found
     result = om.controlled_terms.BiologicalOrder.by_name("nonexistent_order_xyz")
     assert result is None
-    
+
     # all=True should also return None when no match is found
-    results = om.controlled_terms.BiologicalOrder.by_name("nonexistent_order_xyz", all=True)
-    assert results is None
+    results = om.controlled_terms.BiologicalOrder.by_name(
+        "nonexistent_order_xyz", all=True
+    )
+    assert results is None
+
+
+@pytest.mark.parametrize("om", [openminds.latest, openminds.v4])
+def test_issue0084(om):
+    # Properties whose value evaluates to False (e.g., zero)
+    # are not serialized if using include_empty_properties=False
+    obj = om.publications.LivePaperSection(name="test", order=0)
+    data = obj.to_jsonld(include_empty_properties=False)
+    assert data == {
+        "@context": {"@vocab": "https://openminds.om-i.org/props/"},
+        "@type": "https://openminds.om-i.org/types/LivePaperSection",
+        "name": "test",
+        "order": 0,
+    }