rm import from archetypes and core and target specific files to avoid…

… cyclic dependencies

kgforge/core/archetypes/mapper.py

@@ -16,8 +16,8 @@
 from pathlib import Path
 from typing import Any, Iterable, Iterator, List, Optional, Sequence, Union
 
-from kgforge.core import Resource
-from kgforge.core.archetypes import Mapping
+from kgforge.core.resource import Resource
+from kgforge.core.archetypes.mapping import Mapping
 from kgforge.core.commons.attributes import repr_class
 
 

kgforge/core/archetypes/model.py

@@ -20,8 +20,8 @@
 import hjson
 from pandas import DataFrame
 
-from kgforge.core import Resource
-from kgforge.core.archetypes import Mapping
+from kgforge.core.resource import Resource
+from kgforge.core.archetypes.mapping import Mapping
 from kgforge.core.commons.attributes import repr_class, sort_attrs
 from kgforge.core.commons.context import Context
 from kgforge.core.commons.exceptions import ConfigurationError, ValidationError

kgforge/core/archetypes/resolver.py

@@ -16,7 +16,7 @@
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, Union, Tuple
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.attributes import repr_class
 from kgforge.core.commons.exceptions import ConfigurationError, ResolvingError
 from kgforge.core.commons.execution import not_supported

kgforge/core/archetypes/store.py

@@ -19,8 +19,10 @@
 from pathlib import Path
 from typing import Any, Dict, List, Match, Optional, Tuple, Union, Type
 
-from kgforge.core import Resource
-from kgforge.core.archetypes import Mapping, Mapper
+from kgforge.core.resource import Resource
+from kgforge.core.archetypes.mapping import Mapping
+from kgforge.core.archetypes.resolver import Resolver
+from kgforge.core.archetypes.mapper import Mapper
 from kgforge.core.commons.attributes import repr_class
 from kgforge.core.commons.context import Context
 from kgforge.core.commons.exceptions import (
@@ -35,14 +37,13 @@
 )
 from kgforge.core.commons.execution import not_supported, run
 from kgforge.core.reshaping import collect_values
-
-# NB: Do not 'from kgforge.core.archetypes import Resolver' to avoid cyclic dependency.
-
-# FIXME: need to find a comprehensive way (different than list) to get all SPARQL reserved clauses
 from kgforge.core.wrappings.dict import DictWrapper
 
 DEFAULT_LIMIT = 100
 DEFAULT_OFFSET = 0
+
+# FIXME: need to find a comprehensive way (different than list) to get all SPARQL reserved clauses
+
 SPARQL_CLAUSES = [
     "where",
     "filter",
@@ -402,7 +403,7 @@ def _deprecate_one(self, resource: Resource) -> None:
     # Querying.
 
     def search(
-            self, resolvers: Optional[List["Resolver"]], *filters, **params
+            self, resolvers: Optional[List[Resolver]], *filters, **params
     ) -> List[Resource]:
 
         # Positional arguments in 'filters' are instances of type Filter from wrappings/paths.py

kgforge/core/commons/actions.py

@@ -15,7 +15,7 @@
 from collections import Counter
 from typing import Any, Callable, Iterable, Iterator, List, Optional, Union
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.attributes import eq_class, repr_class
 
 

kgforge/core/commons/execution.py

@@ -17,7 +17,7 @@
 from functools import wraps
 from typing import Any, Callable, List, Optional, Tuple, Union
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.actions import (Action, Actions, collect_lazy_actions,
                                           execute_lazy_actions)
 from kgforge.core.commons.exceptions import NotSupportedError

kgforge/core/conversions/dataframe.py

@@ -17,7 +17,7 @@
 import numpy as np
 from pandas import DataFrame, Series
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.context import Context
 from kgforge.core.conversions.json import as_json, from_json
 

kgforge/core/conversions/json.py

@@ -17,7 +17,7 @@
 
 import hjson
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.attributes import sort_attrs
 from kgforge.core.commons.context import Context
 from kgforge.core.conversions.rdf import as_jsonld

kgforge/core/forge.py

@@ -20,9 +20,12 @@
 from pandas import DataFrame
 from rdflib import Graph
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.files import load_file_as_byte
-from kgforge.core.archetypes import Mapping, Model, Resolver, Store
+from kgforge.core.archetypes.mapping import Mapping
+from kgforge.core.archetypes.model import Model
+from kgforge.core.archetypes.resolver import Resolver
+from kgforge.core.archetypes.store import Store
 from kgforge.core.commons.actions import LazyAction
 from kgforge.core.commons.dictionaries import with_defaults
 from kgforge.core.commons.exceptions import ResolvingError

kgforge/core/reshaping.py

@@ -14,7 +14,7 @@
 
 from typing import Callable, Dict, Iterator, List, Union
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.attributes import repr_class
 from kgforge.core.commons.execution import dispatch
 from kgforge.core.conversions.json import as_json

kgforge/core/resource.py

@@ -85,6 +85,12 @@ def _sync_resource(item, vlist, sync_value=True):
             else:
                 vlist.append(item)
 
+    def set_validated(self, validation_status: bool):
+        self._validated = validation_status
+
+    def set_last_action(self, action: "Action"):
+        self._last_action = action
+
     def _get_synchronized(self) -> bool:
         inner = []
         for v in self.__dict__.values():
@@ -160,12 +166,12 @@ def _(d: Union[Dict, List[Dict]], nas: List[Any]) -> Resource:
         return [_(d, nas) for d in data] if isinstance(data, List) else _(data, nas)
 
 
-def encode(data: Any) -> Union[str, Dict]:
+def encode(data: Any) -> Union[str, Dict, set]:
     if isinstance(data, Resource):
         return {k: v for k, v in data.__dict__.items() if k not in data._RESERVED}
     if type(data).__name__ == "LazyAction":
         return str(data)
-    if isinstance(data, set) or isinstance(data, list):
+    if isinstance(data, (set, list)):
         return {encode(r) for r in data}
 
     return data.__dict__

kgforge/core/wrappings/paths.py

@@ -33,7 +33,7 @@ def __init__(self, path: List[str], operator: Union[str, FilterOperator], value:
         try:
             self.operator: str = operator.value if isinstance(operator, FilterOperator) \
                 else FilterOperator(operator).value
-        except Exception as e:
+        except Exception:
             raise ValueError(
                 f"Invalid operator value '{operator}'. Allowed operators are {[member.value for name, member in FilterOperator.__members__.items()]}"
             )
@@ -90,7 +90,7 @@ def __init__(self, path: List[str]) -> None:
 
 class PathsWrapper(FilterMixin):
     def __init__(self, path: List[str], paths: Dict) -> None:
-        check_collisions(self._RESERVED, paths.keys())
+        check_collisions(FilterMixin._RESERVED, paths.keys())
         super().__init__(path)
         self.__dict__ = paths
 
@@ -107,7 +107,7 @@ def _wrap(data: Any, path: List[str]) -> Union[PathsWrapper, PathWrapper]:
 
 
 def create_filters_from_dict(filter_dict: Dict, path_prefix=None) -> List[Filter]:
-    filters = list()
+    filters = []
     if path_prefix is None:
         path_prefix = []
     for k, v in filter_dict.items():

kgforge/specializations/mappers/dictionaries.py

@@ -16,8 +16,9 @@
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Union
 
-from kgforge.core import Resource
-from kgforge.core.archetypes import Mapper, Mapping
+from kgforge.core.resource import Resource
+from kgforge.core.archetypes.mapper import Mapper
+from kgforge.core.archetypes.mapping import Mapping
 from kgforge.core.conversions.json import from_json
 from kgforge.core.wrappings.dict import DictWrapper, wrap_dict
 
@@ -30,8 +31,9 @@ class DictionaryMapper(Mapper):
     def __init__(self, forge: Optional["KnowledgeGraphForge"] = None) -> None:
         super().__init__(forge)
 
-    def _map_one(self, data: Union[Path, Dict], mappings: List[Mapping], nas: List[Any]
-                 ) -> List[Resource]:
+    def _map_one(
+            self, data: Union[Path, Dict], mappings: List[Mapping], nas: List[Any]
+    ) -> List[Resource]:
         variables = {
             "forge": self.forge,
             "x": self._load_one(data),

kgforge/specializations/models/demo_model.py

@@ -17,8 +17,9 @@
 from pathlib import Path
 from typing import Callable, Dict, List, Optional, Tuple, Union
 
-from kgforge.core import Resource
-from kgforge.core.archetypes import Mapping, Model
+from kgforge.core.resource import Resource
+from kgforge.core.archetypes.mapping import Mapping
+from kgforge.core.archetypes.model import Model
 from kgforge.core.commons.context import Context
 from kgforge.core.commons.exceptions import ValidationError
 

kgforge/specializations/models/rdf/service.py

@@ -19,7 +19,7 @@
 from pyshacl.shapes_graph import ShapesGraph
 from rdflib import Graph, URIRef, RDF, XSD
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.context import Context
 from kgforge.core.commons.exceptions import ConfigurationError
 from kgforge.core.conversions.rdf import as_graph

kgforge/specializations/models/rdf/store_service.py

@@ -20,7 +20,7 @@
 
 from kgforge.core.commons.exceptions import RetrievalError
 from kgforge.core.conversions.rdf import as_jsonld, as_graph
-from kgforge.core.archetypes import Store
+from kgforge.core.archetypes.store import Store
 from kgforge.specializations.models.rdf.node_properties import NodeProperties
 from kgforge.specializations.models.rdf.service import RdfService, ShapesGraphWrapper
 from kgforge.specializations.stores.nexus import Service

kgforge/specializations/models/rdf_model.py

@@ -20,8 +20,9 @@
 from rdflib import URIRef, Literal
 from rdflib.namespace import XSD
 
-from kgforge.core import Resource
-from kgforge.core.archetypes import Model, Store
+from kgforge.core.resource import Resource
+from kgforge.core.archetypes.store import Store
+from kgforge.core.archetypes.model import Model
 from kgforge.core.commons.actions import Action
 from kgforge.core.commons.context import Context
 from kgforge.core.commons.exceptions import ValidationError
@@ -115,15 +116,16 @@ def _validate_many(self, resources: List[Resource], type_: str) -> None:
         for resource in resources:
             conforms, graph, _ = self.service.validate(resource, type_=type_)
             if conforms:
-                resource._validated = True
+                resource.set_validated(True)
                 action = Action(self._validate_many.__name__, conforms, None)
             else:
-                resource._validated = False
+                resource.set_validated(False)
                 violations = set(" ".join(re.findall('[A-Z][^A-Z]*', as_term(o)))
                                  for o in graph.objects(None, SH.sourceConstraintComponent))
                 message = f"violation(s) of type(s) {', '.join(sorted(violations))}"
                 action = Action(self._validate_many.__name__, conforms, ValidationError(message))
-            resource._last_action = action
+
+            resource.set_last_action(action)
 
     def _validate_one(self, resource: Resource, type_: str) -> None:
         conforms, _, report = self.service.validate(resource, type_)

kgforge/specializations/resolvers/agent_resolver.py

@@ -14,7 +14,7 @@
 from pathlib import Path
 from typing import List, Dict, Any, Optional, Callable, Union
 
-from kgforge.core.archetypes import Resolver
+from kgforge.core.archetypes.resolver import Resolver
 from kgforge.core.archetypes.resolver import _build_resolving_query
 from kgforge.core.commons.execution import not_supported
 from kgforge.core.commons.sparql_query_builder import SPARQLQueryBuilder

kgforge/specializations/resolvers/demo_resolver.py

@@ -17,7 +17,7 @@
 from pathlib import Path
 from typing import Callable, Dict, Iterator, List, Optional, Union, Any
 
-from kgforge.core.archetypes import Resolver
+from kgforge.core.archetypes.resolver import Resolver
 from kgforge.core.commons.exceptions import ConfigurationError
 from kgforge.core.commons.execution import not_supported
 from kgforge.core.commons.strategies import ResolvingStrategy

kgforge/specializations/resolvers/entity_linking/entity_linker.py

@@ -14,7 +14,7 @@
 from abc import ABCMeta
 from typing import Dict, List, Optional, Tuple, Union, Any
 
-from kgforge.core.archetypes import Resolver
+from kgforge.core.archetypes.resolver import Resolver
 from kgforge.core.commons.actions import LazyAction
 from kgforge.core.commons.exceptions import ResolvingError
 from kgforge.core.commons.strategies import ResolvingStrategy

kgforge/specializations/resolvers/entity_linking/service/entity_linking_elastic_service.py

@@ -18,7 +18,7 @@
 
 import requests
 
-from kgforge.core.archetypes import Store
+from kgforge.core.archetypes.store import Store
 from kgforge.core.conversions.json import as_json
 from kgforge.core.resource import encode
 from kgforge.core.wrappings import Filter, FilterOperator

kgforge/specializations/resolvers/ontology_resolver.py

@@ -14,7 +14,7 @@
 from pathlib import Path
 from typing import List, Dict, Any, Optional, Callable, Union
 
-from kgforge.core.archetypes import Resolver
+from kgforge.core.archetypes.resolver import Resolver
 from kgforge.core.archetypes.resolver import _build_resolving_query
 from kgforge.core.commons.execution import not_supported
 from kgforge.core.commons.sparql_query_builder import SPARQLQueryBuilder

kgforge/specializations/resolvers/store_service.py

@@ -13,7 +13,7 @@
 # along with Blue Brain Nexus Forge. If not, see <https://choosealicense.com/licenses/lgpl-3.0/>.
 from typing import Callable, Dict, List, Optional
 
-from kgforge.core.archetypes import Store
+from kgforge.core.archetypes.store import Store
 from kgforge.core.conversions.json import as_json
 
 

kgforge/specializations/resources/datasets.py

@@ -15,7 +15,7 @@
 from typing import List, Union
 from warnings import warn
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.actions import LazyAction
 from kgforge.core.commons.execution import catch, not_supported
 from kgforge.core.forge import KnowledgeGraphForge

kgforge/specializations/resources/entity_linking_candidate.py

@@ -13,7 +13,7 @@
 # along with Blue Brain Nexus Forge. If not, see <https://choosealicense.com/licenses/lgpl-3.0/>.
 from typing import Any
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 
 
 class EntityLinkingCandidate(Resource):

kgforge/specializations/stores/bluebrain_nexus.py

@@ -37,8 +37,8 @@
 from kgforge.core.commons.dictionaries import update_dict
 from kgforge.core.commons.es_query_builder import ESQueryBuilder
 from kgforge.core.commons.sparql_query_builder import SPARQLQueryBuilder
-from kgforge.core import Resource
-from kgforge.core.archetypes import Store
+from kgforge.core.resource import Resource
+from kgforge.core.archetypes.store import Store
 from kgforge.core.commons.actions import LazyAction
 from kgforge.core.commons.context import Context
 from kgforge.core.commons.exceptions import (

kgforge/specializations/stores/demo_store.py

@@ -16,11 +16,17 @@
 from typing import Dict, List, Optional, Union, Type
 from uuid import uuid4
 
-from kgforge.core import Resource
-from kgforge.core.archetypes import Resolver, Store, Mapper, Mapping
+from kgforge.core.resource import Resource
+from kgforge.core.archetypes.resolver import Resolver
+from kgforge.core.archetypes.store import Store
+from kgforge.core.archetypes.mapper import Mapper
+from kgforge.core.archetypes.mapping import Mapping
+
 from kgforge.core.commons.context import Context
-from kgforge.core.commons.exceptions import (DeprecationError, RegistrationError,
-                                             RetrievalError, TaggingError, UpdatingError)
+from kgforge.core.commons.exceptions import (
+    DeprecationError, RegistrationError,
+    RetrievalError, TaggingError, UpdatingError
+)
 from kgforge.core.commons.execution import not_supported
 from kgforge.core.conversions.json import as_json, from_json
 from kgforge.core.wrappings.dict import wrap_dict

kgforge/specializations/stores/nexus/service.py

@@ -30,7 +30,7 @@
 from numpy import nan
 from requests import HTTPError
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.actions import (
     Action,
     collect_lazy_actions,