linted

src/oaklib/__init__.py

@@ -2,6 +2,7 @@
 Oaklib
 ------
 """
+
 __version__ = "0.1.0"
 
 from oaklib.interfaces import BasicOntologyInterface  # noqa:F401

src/oaklib/cli.py

@@ -4,6 +4,7 @@
 
 Executed using "runoak" command
 """
+
 # TODO: order commands.
 # See https://stackoverflow.com/questions/47972638/how-can-i-define-the-order-of-click-sub-commands-in-help
 import itertools

src/oaklib/converters/obo_graph_to_fhir_converter.py

@@ -4,6 +4,7 @@
 - Updates issue: https://github.com/INCATools/ontology-access-kit/issues/369
 - Conversion examples: https://drive.google.com/drive/folders/1lwGQ63_fedfWlGlRemq8OeZhZsvIXN01
 """
+
 import logging
 from dataclasses import dataclass
 from typing import Any, Dict, List, Tuple, Union

src/oaklib/datamodels/association.py

@@ -98,22 +98,22 @@ class PositiveOrNegativeAssociation(YAMLRoot):
     predicate_label: Optional[str] = None
     object_label: Optional[str] = None
     negated: Optional[Union[bool, Bool]] = None
-    publications: Optional[
-        Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]
-    ] = empty_list()
+    publications: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = (
+        empty_list()
+    )
     evidence_type: Optional[Union[str, URIorCURIE]] = None
-    supporting_objects: Optional[
-        Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]
-    ] = empty_list()
+    supporting_objects: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = (
+        empty_list()
+    )
     primary_knowledge_source: Optional[Union[str, URIorCURIE]] = None
     aggregator_knowledge_source: Optional[Union[str, URIorCURIE]] = None
-    subject_closure: Optional[
-        Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]
-    ] = empty_list()
+    subject_closure: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = (
+        empty_list()
+    )
     subject_closure_label: Optional[Union[str, List[str]]] = empty_list()
-    object_closure: Optional[
-        Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]
-    ] = empty_list()
+    object_closure: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = (
+        empty_list()
+    )
     object_closure_label: Optional[Union[str, List[str]]] = empty_list()
     comments: Optional[Union[str, List[str]]] = empty_list()
 
@@ -292,12 +292,12 @@ class RollupGroup(YAMLRoot):
     class_model_uri: ClassVar[URIRef] = ONTOASSOC.RollupGroup
 
     group_object: Optional[Union[str, URIorCURIE]] = None
-    sub_groups: Optional[
-        Union[Union[dict, "RollupGroup"], List[Union[dict, "RollupGroup"]]]
-    ] = empty_list()
-    associations: Optional[
-        Union[Union[dict, Association], List[Union[dict, Association]]]
-    ] = empty_list()
+    sub_groups: Optional[Union[Union[dict, "RollupGroup"], List[Union[dict, "RollupGroup"]]]] = (
+        empty_list()
+    )
+    associations: Optional[Union[Union[dict, Association], List[Union[dict, Association]]]] = (
+        empty_list()
+    )
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.group_object is not None and not isinstance(self.group_object, URIorCURIE):
@@ -458,9 +458,9 @@ class AssociationChange(YAMLRoot):
     new_date: Optional[str] = None
     primary_knowledge_source: Optional[Union[str, URIorCURIE]] = None
     aggregator_knowledge_source: Optional[Union[str, URIorCURIE]] = None
-    publications: Optional[
-        Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]
-    ] = empty_list()
+    publications: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = (
+        empty_list()
+    )
     publication_is_added: Optional[Union[bool, Bool]] = None
     publication_is_deleted: Optional[Union[bool, Bool]] = None
     subject: Optional[Union[str, URIorCURIE]] = None
@@ -474,9 +474,9 @@ class AssociationChange(YAMLRoot):
     is_specialization: Optional[Union[bool, Bool]] = None
     is_creation: Optional[Union[bool, Bool]] = None
     is_deletion: Optional[Union[bool, Bool]] = None
-    closure_predicates: Optional[
-        Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]
-    ] = empty_list()
+    closure_predicates: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = (
+        empty_list()
+    )
     closure_delta: Optional[int] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):

src/oaklib/datamodels/cross_ontology_diff.py

@@ -109,9 +109,9 @@ class StructureDiffResultSet(YAMLRoot):
     class_name: ClassVar[str] = "StructureDiffResultSet"
     class_model_uri: ClassVar[URIRef] = XODIFF.StructureDiffResultSet
 
-    results: Optional[
-        Union[Union[dict, "RelationalDiff"], List[Union[dict, "RelationalDiff"]]]
-    ] = empty_list()
+    results: Optional[Union[Union[dict, "RelationalDiff"], List[Union[dict, "RelationalDiff"]]]] = (
+        empty_list()
+    )
     left_source: Optional[Union[str, Source]] = None
     right_source: Optional[Union[str, Source]] = None
 
@@ -180,9 +180,9 @@ class RelationalDiff(YAMLRoot):
     ] = empty_list()
     right_subject_label: Optional[Union[str, Label]] = None
     right_object_label: Optional[Union[str, Label]] = None
-    right_predicate_labels: Optional[
-        Union[Union[str, Label], List[Union[str, Label]]]
-    ] = empty_list()
+    right_predicate_labels: Optional[Union[Union[str, Label], List[Union[str, Label]]]] = (
+        empty_list()
+    )
     left_subject_is_functional: Optional[str] = None
     left_object_is_functional: Optional[str] = None
     subject_mapping_predicate: Optional[Union[str, EntityReference]] = None

src/oaklib/datamodels/fhir.py

@@ -418,9 +418,9 @@ class ConceptMap(YAMLRoot):
     sourceCanonical: Optional[Union[str, URIorCURIE]] = None
     targetUri: Optional[Union[str, URIorCURIE]] = None
     targetCanonical: Optional[Union[str, URIorCURIE]] = None
-    group: Optional[
-        Union[Union[dict, "ConceptMapGroup"], List[Union[dict, "ConceptMapGroup"]]]
-    ] = empty_list()
+    group: Optional[Union[Union[dict, "ConceptMapGroup"], List[Union[dict, "ConceptMapGroup"]]]] = (
+        empty_list()
+    )
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.id is not None and not isinstance(self.id, str):

src/oaklib/datamodels/input_specification.py

@@ -195,9 +195,9 @@ class AssociationResource(Resource):
     class_model_uri: ClassVar[URIRef] = ITEMLIST.AssociationResource
 
     id: Union[str, AssociationResourceId] = None
-    normalizers: Optional[
-        Union[Union[dict, "Normalizer"], List[Union[dict, "Normalizer"]]]
-    ] = empty_list()
+    normalizers: Optional[Union[Union[dict, "Normalizer"], List[Union[dict, "Normalizer"]]]] = (
+        empty_list()
+    )
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self._is_empty(self.id):

src/oaklib/datamodels/item_list.py

@@ -84,9 +84,9 @@ class ItemListCollection(YAMLRoot):
     class_name: ClassVar[str] = "ItemListCollection"
     class_model_uri: ClassVar[URIRef] = ITEMLIST.ItemListCollection
 
-    itemLists: Optional[
-        Union[Union[dict, "ItemList"], List[Union[dict, "ItemList"]]]
-    ] = empty_list()
+    itemLists: Optional[Union[Union[dict, "ItemList"], List[Union[dict, "ItemList"]]]] = (
+        empty_list()
+    )
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if not isinstance(self.itemLists, list):
@@ -126,12 +126,12 @@ class ItemList(YAMLRoot):
     ] = empty_dict()
     categories: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = empty_list()
     keywords: Optional[Union[str, List[str]]] = empty_list()
-    additionalType: Optional[
-        Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]
-    ] = empty_list()
-    wasGeneratedBy: Optional[
-        Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]
-    ] = empty_list()
+    additionalType: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = (
+        empty_list()
+    )
+    wasGeneratedBy: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = (
+        empty_list()
+    )
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.id is not None and not isinstance(self.id, URIorCURIE):
@@ -236,9 +236,9 @@ class Thing(YAMLRoot):
     id: Union[str, ThingId] = None
     name: Optional[str] = None
     url: Optional[Union[str, URI]] = None
-    identifiers: Optional[
-        Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]
-    ] = empty_list()
+    identifiers: Optional[Union[Union[str, URIorCURIE], List[Union[str, URIorCURIE]]]] = (
+        empty_list()
+    )
     description: Optional[str] = None
     type: Optional[Union[str, URIorCURIE]] = None
 

src/oaklib/datamodels/lexical_index.py

@@ -198,9 +198,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if not isinstance(self.pipeline, list):
             self.pipeline = [self.pipeline] if self.pipeline is not None else []
         self.pipeline = [
-            v
-            if isinstance(v, LexicalTransformationPipelineName)
-            else LexicalTransformationPipelineName(v)
+            (
+                v
+                if isinstance(v, LexicalTransformationPipelineName)
+                else LexicalTransformationPipelineName(v)
+            )
             for v in self.pipeline
         ]
 

src/oaklib/datamodels/mapping_cluster_datamodel.py

@@ -336,9 +336,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
                 [self.predicate_probabilities] if self.predicate_probabilities is not None else []
             )
         self.predicate_probabilities = [
-            v
-            if isinstance(v, PredicateProbabilityPredicateId)
-            else PredicateProbabilityPredicateId(v)
+            (
+                v
+                if isinstance(v, PredicateProbabilityPredicateId)
+                else PredicateProbabilityPredicateId(v)
+            )
             for v in self.predicate_probabilities
         ]
 

src/oaklib/datamodels/mapping_rules_datamodel.py

@@ -88,9 +88,9 @@ class MappingRuleCollection(YAMLRoot):
     class_name: ClassVar[str] = "MappingRuleCollection"
     class_model_uri: ClassVar[URIRef] = MAPPINGRULES.MappingRuleCollection
 
-    rules: Optional[
-        Union[Union[dict, "MappingRule"], List[Union[dict, "MappingRule"]]]
-    ] = empty_list()
+    rules: Optional[Union[Union[dict, "MappingRule"], List[Union[dict, "MappingRule"]]]] = (
+        empty_list()
+    )
     minimum_confidence: Optional[float] = None
 
     def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
@@ -440,9 +440,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if not isinstance(self.pipeline, list):
             self.pipeline = [self.pipeline] if self.pipeline is not None else []
         self.pipeline = [
-            v
-            if isinstance(v, LexicalTransformationPipelineName)
-            else LexicalTransformationPipelineName(v)
+            (
+                v
+                if isinstance(v, LexicalTransformationPipelineName)
+                else LexicalTransformationPipelineName(v)
+            )
             for v in self.pipeline
         ]
 

src/oaklib/datamodels/obograph.py

@@ -220,9 +220,9 @@ class Graph(YAMLRoot):
     domainRangeAxioms: Optional[
         Union[Union[dict, "DomainRangeAxiom"], List[Union[dict, "DomainRangeAxiom"]]]
     ] = empty_list()
-    allValuesFromEdges: Optional[
-        Union[Union[dict, "Edge"], List[Union[dict, "Edge"]]]
-    ] = empty_list()
+    allValuesFromEdges: Optional[Union[Union[dict, "Edge"], List[Union[dict, "Edge"]]]] = (
+        empty_list()
+    )
     propertyChainAxioms: Optional[
         Union[Union[dict, "PropertyChainAxiom"], List[Union[dict, "PropertyChainAxiom"]]]
     ] = empty_list()
@@ -805,9 +805,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if not isinstance(self.restrictions, list):
             self.restrictions = [self.restrictions] if self.restrictions is not None else []
         self.restrictions = [
-            v
-            if isinstance(v, ExistentialRestrictionExpression)
-            else ExistentialRestrictionExpression(**as_dict(v))
+            (
+                v
+                if isinstance(v, ExistentialRestrictionExpression)
+                else ExistentialRestrictionExpression(**as_dict(v))
+            )
             for v in self.restrictions
         ]
 
@@ -848,9 +850,11 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
                 [self.classExpressions] if self.classExpressions is not None else []
             )
         self.classExpressions = [
-            v
-            if isinstance(v, ExistentialRestrictionExpression)
-            else ExistentialRestrictionExpression(**as_dict(v))
+            (
+                v
+                if isinstance(v, ExistentialRestrictionExpression)
+                else ExistentialRestrictionExpression(**as_dict(v))
+            )
             for v in self.classExpressions
         ]