formatted with black

Author: apdavison

build.py

@@ -16,7 +16,7 @@
 include_instances = True  # to speed up the build during development, set this to False
 
 parser = argparse.ArgumentParser(prog=sys.argv[0], description="Generate Python package for openMINDS")
-parser.add_argument('--branch', help="The branch to build from ('main' or 'development')", default="main")
+parser.add_argument("--branch", help="The branch to build from ('main' or 'development')", default="main")
 args = parser.parse_args()
 
 print("*******************************************************************************")
@@ -59,13 +59,14 @@
     class_to_module_map = {}
     for schema_file_path in schemas_file_paths:
         emb, lnk = PythonBuilder(schema_file_path, schema_loader.schemas_sources).get_edges()
-        class_to_module_map=PythonBuilder(schema_file_path, schema_loader.schemas_sources).update_class_to_module_map(class_to_module_map)
+        class_to_module_map = PythonBuilder(
+            schema_file_path, schema_loader.schemas_sources
+        ).update_class_to_module_map(class_to_module_map)
         embedded.update(emb)
         linked.update(lnk)
     conflicts = linked.intersection(embedded)
     if conflicts:
-        print(f"Found schema(s) in version {schema_version} "
-              f"that are both linked and embedded: {conflicts}")
+        print(f"Found schema(s) in version {schema_version} " f"that are both linked and embedded: {conflicts}")
         # conflicts should not happen in new versions.
         # There is one conflict in v1.0, QuantitativeValue,
         # which we treat as embedded
@@ -79,7 +80,7 @@
             schema_loader.schemas_sources,
             instances=instances.get(schema_version, None),
             additional_methods=additional_methods,
-        ).build(embedded=embedded,class_to_module_map=class_to_module_map)
+        ).build(embedded=embedded, class_to_module_map=class_to_module_map)
 
         parts = module_path.split(".")
         parent_path = ".".join(parts[:-1])
@@ -109,10 +110,7 @@
     with open(init_file_path, "w") as fp:
         fp.write(f"from . import ({', '.join(sorted(module_list))})\n")
 
-env = Environment(
-    loader=FileSystemLoader(os.path.dirname(os.path.realpath(__file__))),
-    autoescape=select_autoescape()
-)
+env = Environment(loader=FileSystemLoader(os.path.dirname(os.path.realpath(__file__))), autoescape=select_autoescape())
 context = {
     "version": "0.3.0",
 }

pipeline/src/base.py

@@ -27,9 +27,7 @@ def value_to_jsonld(value, include_empty_properties=True, embed_linked_nodes=Tru
             )
         else:
             if hasattr(value, "id") and value.id is None:
-                raise ValueError(
-                    "Exporting as a stand-alone JSON-LD document requires @id to be defined."
-                )
+                raise ValueError("Exporting as a stand-alone JSON-LD document requires @id to be defined.")
             item = {"@id": value.id}
     elif isinstance(value, EmbeddedMetadata):
         item = value.to_jsonld(
@@ -64,9 +62,7 @@ def has_property(self, name):
                 return True
         return False
 
-    def to_jsonld(
-        self, include_empty_properties=True, embed_linked_nodes=True, with_context=True
-    ):
+    def to_jsonld(self, include_empty_properties=True, embed_linked_nodes=True, with_context=True):
         """
         Return a represention of this metadata node as a dictionary that can be directly serialized to JSON-LD.
         """

pipeline/src/collection.py

@@ -85,12 +85,12 @@ def save(self, path, individual_files=False, include_empty_properties=False):
         # we first re-add all child nodes to the collection.
         # This is probably not the most elegant or fast way to do this, but it is simple and robust.
         for node in tuple(self.nodes.values()):
-            
+
             if node.type_.startswith("https://openminds.ebrains.eu/"):
                 data_context = {"@vocab": "https://openminds.ebrains.eu/vocab/"}
             else:
                 data_context = {"@vocab": "https://openminds.om-i.org/props/"}
-            
+
             for linked_node in node.links:
                 self._add_node(linked_node)
         # Now we can actually save the nodes
@@ -118,7 +118,9 @@ def save(self, path, individual_files=False, include_empty_properties=False):
             if not os.path.exists(path):
                 os.makedirs(path, exist_ok=True)
             if not os.path.isdir(path):
-                raise OSError(f"If saving to multiple files, `path` must be a directory. path={path}, pwd={os.getcwd()}")
+                raise OSError(
+                    f"If saving to multiple files, `path` must be a directory. path={path}, pwd={os.getcwd()}"
+                )
             output_paths = []
             for node in self:
                 if node.id.startswith("http"):
@@ -161,12 +163,12 @@ def load(self, *paths):
                 data = json.load(fp)
             if "@graph" in data:
                 if data["@context"]["@vocab"].startswith("https://openminds.ebrains.eu/"):
-                    version="v3"
+                    version = "v3"
                 else:
-                    version="latest"
+                    version = "latest"
                 for item in data["@graph"]:
                     if "@type" in item:
-                        cls = lookup_type(item["@type"],version=version)
+                        cls = lookup_type(item["@type"], version=version)
                         node = cls.from_jsonld(item)
                     else:
                         # allow links to metadata instances outside this collection

pipeline/src/properties.py

@@ -118,7 +118,7 @@ def validate(self, value, ignore=None):
                             failures["type"].append(
                                 f"{self.name}: Expected {', '.join(t.__name__ for t in self.types)}, "
                                 f"value contains {type(item)}"
-                        )
+                            )
                     elif isinstance(item, (Node, IRI)):
                         failures.update(item.validate(ignore=ignore))
                 if self.min_items:
@@ -148,7 +148,8 @@ def validate(self, value, ignore=None):
             elif not isinstance(value, self.types):
                 if "type" not in ignore:
                     failures["type"].append(
-                        f"{self.name}: Expected {', '.join(t.__name__ for t in self.types)}, " f"value is {type(value)}"
+                        f"{self.name}: Expected {', '.join(t.__name__ for t in self.types)}, "
+                        f"value is {type(value)}"
                     )
             elif isinstance(value, (Node, IRI)):
                 failures.update(value.validate(ignore=ignore))

pipeline/src/registry.py

@@ -68,6 +68,7 @@ def lookup_type(class_type: str, version: str = "latest") -> Node:
 
 class Registry(type):
     """Metaclass for registering Knowledge Graph classes."""
+
     properties: List[Property] = []
     type_: Union[str, List[str]]
     context: Dict[str, str]
@@ -107,4 +108,3 @@ def property_names(cls) -> List[str]:
     @property
     def required_property_names(cls) -> List[str]:
         return [p.name for p in cls.properties if p.required]
-

pipeline/tests/test_instantiation.py

@@ -55,10 +55,7 @@ def test_json_roundtrip():
 
 
 def test_IRI():
-    valid_iris = [
-        "https://example.com/path/to/my/file.txt",
-        "file:///path/to/my/file.txt"
-    ]
+    valid_iris = ["https://example.com/path/to/my/file.txt", "file:///path/to/my/file.txt"]
     for value in valid_iris:
         iri = IRI(value)
         assert iri.value == value
@@ -67,9 +64,7 @@ def test_IRI():
             assert not failures
         else:
             assert failures["value"][0] == "IRI points to a local file path"
-    invalid_iris = [
-        "/path/to/my/file.txt"
-    ]
+    invalid_iris = ["/path/to/my/file.txt"]
     for value in invalid_iris:
         with pytest.raises(ValueError) as exc_info:
             iri = IRI(value)

pipeline/tests/test_regressions.py

@@ -44,7 +44,7 @@ def test_issue_0003():
         "format": {
             "@type": "https://openminds.om-i.org/types/ContentType",
             "name": "application/zip",
-            },
+        },
         "sourceData": [
             {
                 "@type": "https://openminds.om-i.org/types/File",
@@ -98,15 +98,11 @@ def test_issue0007():
         "affiliation": [
             {
                 "@type": "https://openminds.om-i.org/types/Affiliation",
-                "memberOf": {
-                    "@id": "_:002"
-                },
+                "memberOf": {"@id": "_:002"},
             },
             {
                 "@type": "https://openminds.om-i.org/types/Affiliation",
-                "memberOf": {
-                    "@id": "_:003"
-                },
+                "memberOf": {"@id": "_:003"},
             },
         ],
     }
@@ -128,15 +124,11 @@ def test_issue0007():
                 "affiliation": [
                     {
                         "@type": "https://openminds.om-i.org/types/Affiliation",
-                        "memberOf": {
-                            "@id": "_:002"
-                        },
+                        "memberOf": {"@id": "_:002"},
                     },
                     {
                         "@type": "https://openminds.om-i.org/types/Affiliation",
-                        "memberOf": {
-                            "@id": "_:003"
-                        },
+                        "memberOf": {"@id": "_:003"},
                     },
                 ],
                 "familyName": "Professor",
@@ -178,9 +170,7 @@ def test_issue0008():
             {
                 "@type": "https://openminds.om-i.org/types/Affiliation",
                 "endDate": "2023-09-30",
-                "memberOf": {
-                    "@id": "_:001"
-                },
+                "memberOf": {"@id": "_:001"},
             }
         ],
         "familyName": "Professor",
@@ -196,10 +186,7 @@ def test_issue0026():
 
     uni1 = omcore.Organization(full_name="University of This Place", id="_:uthisp")
     person = omcore.Person(
-        given_name="A",
-        family_name="Professor",
-        affiliations = [omcore.Affiliation(member_of=uni1)],
-        id="_:ap"
+        given_name="A", family_name="Professor", affiliations=[omcore.Affiliation(member_of=uni1)], id="_:ap"
     )
 
     c = Collection(person)
@@ -224,16 +211,9 @@ def test_issue0023():
 
     uni1 = omcore.Organization(full_name="University of This Place", id="_:uthisp")
     person = omcore.Person(
-        given_name="A",
-        family_name="Professor",
-        affiliations = [omcore.Affiliation(member_of=uni1)],
-        id="_:ap"
-    )
-    dv = omcore.DatasetVersion(
-        full_name="The name of the dataset version",
-        custodians=[person],
-        id="_:dv"
+        given_name="A", family_name="Professor", affiliations=[omcore.Affiliation(member_of=uni1)], id="_:ap"
     )
+    dv = omcore.DatasetVersion(full_name="The name of the dataset version", custodians=[person], id="_:dv")
 
     c = Collection(dv)