Fix cyclic dependency between Mapping and KnowledgeGraphForge (#362)

* attempt fix cyclic dependency

* undo

* full imports within forge

* default mapper and mapping from store

kgforge/core/archetypes/dataset_store.py

@@ -15,15 +15,13 @@
 from abc import abstractmethod, ABC
 
 from typing import Optional, Union, List, Type, Dict
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.archetypes.read_only_store import ReadOnlyStore
 from kgforge.core.archetypes.resolver import Resolver
-from kgforge.core.archetypes.model import Model
 from kgforge.core.archetypes.mapping import Mapping
 from kgforge.core.archetypes.mapper import Mapper
 from kgforge.core.commons.imports import import_class
 from kgforge.core.conversions.json import as_json, from_json
-from kgforge.core.commons.execution import not_supported
 from kgforge.core.wrappings import Filter
 
 

kgforge/core/archetypes/read_only_store.py

@@ -16,7 +16,7 @@
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.archetypes.model import Model
 from kgforge.core.archetypes.resolver import Resolver
 from kgforge.core.commons.attributes import repr_class

kgforge/core/forge.py

@@ -13,19 +13,20 @@
 # along with Blue Brain Nexus Forge. If not, see <https://choosealicense.com/licenses/lgpl-3.0/>.
 
 from copy import deepcopy
-from typing import Any, Callable, Dict, List, Optional, Tuple, Union
+from typing import Any, Callable, Dict, List, Optional, Tuple, Union, Type
 
 import numpy as np
 import yaml
 from pandas import DataFrame
 from rdflib import Graph
 
 from kgforge.core.resource import Resource
-from kgforge.core.commons.files import load_file_as_byte
 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.mapper import Mapper
 from kgforge.core.archetypes.store import Store
+from kgforge.core.commons.files import load_file_as_byte
 from kgforge.core.commons.actions import LazyAction
 from kgforge.core.commons.dictionaries import with_defaults
 from kgforge.core.commons.exceptions import ResolvingError
@@ -44,8 +45,6 @@
 )
 from kgforge.core.reshaping import Reshaper
 from kgforge.core.wrappings.paths import PathsWrapper, wrap_paths, Filter
-from kgforge.specializations.mappers import DictionaryMapper
-from kgforge.specializations.mappings import DictionaryMapping
 
 
 class KnowledgeGraphForge:
@@ -548,7 +547,7 @@ def mappings(
 
     @catch
     def mapping(
-        self, entity: str, source: str, type: Callable = DictionaryMapping
+        self, entity: str, source: str, type: Type[Mapping] = None
     ) -> Mapping:
         """
         Return a Mapping object of type 'type' for a resource type 'entity' and a source.
@@ -558,14 +557,16 @@ def mapping(
         :param type: a Mapping class
         :return: Mapping
         """
+        if type is None:
+            type = self._store.mapping
         return self._model.mapping(entity, source, type)
 
     @catch
     def map(
         self,
         data: Any,
         mapping: Union[Mapping, List[Mapping]],
-        mapper: Callable = DictionaryMapper,
+        mapper: Type[Mapper] = None,
         na: Union[Any, List[Any]] = None,
     ) -> Union[Resource, List[Resource]]:
         """
@@ -578,6 +579,8 @@ def map(
         :param na: represents missing values
         :return: Union[Resource, List[Resource]]
         """
+        if mapper is None:
+            mapper = self._store.mapper
         return mapper(self).map(data, mapping, na)
 
     # Reshaping User Interface.

kgforge/specializations/models/rdf_model.py

@@ -20,7 +20,7 @@
 from rdflib import URIRef, Literal
 from rdflib.namespace import XSD
 
-from kgforge.core.archetypes import Mapping
+from kgforge.core.archetypes.mapping import Mapping
 from kgforge.core.resource import Resource
 from kgforge.core.archetypes.store import Store
 from kgforge.core.archetypes.model import Model

kgforge/specializations/resolvers/agent_resolver.py

@@ -19,8 +19,8 @@
 from kgforge.core.commons.execution import not_supported
 from kgforge.core.commons.sparql_query_builder import SPARQLQueryBuilder
 from kgforge.core.commons.strategies import ResolvingStrategy
-from kgforge.specializations.mappers import DictionaryMapper
-from kgforge.specializations.mappings import DictionaryMapping
+from kgforge.specializations.mappers.dictionaries import DictionaryMapper
+from kgforge.specializations.mappings.dictionaries import DictionaryMapping
 from kgforge.specializations.resolvers.store_service import StoreService
 
 

kgforge/specializations/resolvers/demo_resolver.py

@@ -21,8 +21,8 @@
 from kgforge.core.commons.exceptions import ConfigurationError
 from kgforge.core.commons.execution import not_supported
 from kgforge.core.commons.strategies import ResolvingStrategy
-from kgforge.specializations.mappers import DictionaryMapper
-from kgforge.specializations.mappings import DictionaryMapping
+from kgforge.specializations.mappers.dictionaries import DictionaryMapper
+from kgforge.specializations.mappings.dictionaries import DictionaryMapping
 
 
 class DemoResolver(Resolver):

kgforge/specializations/resolvers/entity_linking/entity_linker_elastic.py

@@ -15,8 +15,9 @@
 from typing import Callable, Dict, Optional, Union, Any
 
 from kgforge.core.commons.execution import not_supported
-from kgforge.specializations.mappers import DictionaryMapper
-from kgforge.specializations.mappings import DictionaryMapping
+from kgforge.specializations.mappers.dictionaries import DictionaryMapper
+from kgforge.specializations.mappings.dictionaries import DictionaryMapping
+
 from kgforge.specializations.resolvers.entity_linking import EntityLinker
 from kgforge.specializations.resolvers.entity_linking.service.entity_linking_elastic_service import EntityLinkerElasticService
 

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

@@ -22,8 +22,8 @@
 from kgforge.core.conversions.json import as_json
 from kgforge.core.resource import encode
 from kgforge.core.wrappings import Filter, FilterOperator
-from kgforge.specializations.mappers import DictionaryMapper
-from kgforge.specializations.mappings import DictionaryMapping
+from kgforge.specializations.mappers.dictionaries import DictionaryMapper
+from kgforge.specializations.mappings.dictionaries import DictionaryMapping
 from kgforge.specializations.resolvers.entity_linking.service.entity_linking_service import (
     EntityLinkerService,
 )

kgforge/specializations/resolvers/ontology_resolver.py

@@ -19,8 +19,8 @@
 from kgforge.core.commons.execution import not_supported
 from kgforge.core.commons.sparql_query_builder import SPARQLQueryBuilder
 from kgforge.core.commons.strategies import ResolvingStrategy
-from kgforge.specializations.mappers import DictionaryMapper
-from kgforge.specializations.mappings import DictionaryMapping
+from kgforge.specializations.mappers.dictionaries import DictionaryMapper
+from kgforge.specializations.mappings.dictionaries import DictionaryMapping
 from kgforge.specializations.resolvers.store_service import StoreService
 
 

kgforge/specializations/stores/bluebrain_nexus.py

@@ -59,8 +59,8 @@
 from kgforge.core.conversions.rdf import as_jsonld
 from kgforge.core.wrappings.dict import DictWrapper
 from kgforge.core.wrappings.paths import Filter, create_filters_from_dict
-from kgforge.specializations.mappers import DictionaryMapper
-from kgforge.specializations.mappings import DictionaryMapping
+from kgforge.specializations.mappers.dictionaries import DictionaryMapper
+from kgforge.specializations.mappings.dictionaries import DictionaryMapping
 from kgforge.specializations.stores.nexus.service import BatchAction, Service, _error_message
 
 

kgforge/specializations/stores/demo_store.py

@@ -16,7 +16,7 @@
 from pathlib import Path
 from typing import Dict, List, Optional, Union, Type, Tuple, Any
 from uuid import uuid4
-from kgforge.core import Resource
+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

kgforge/specializations/stores/sparql/sparql_service.py

@@ -15,7 +15,7 @@
 import copy
 from typing import Dict, List, Optional, Union, Tuple
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.context import Context
 from kgforge.core.wrappings.dict import wrap_dict
 

kgforge/specializations/stores/sparql_store.py

@@ -15,13 +15,13 @@
 import requests
 from typing import Dict, List, Optional, Union, Any, Type, Tuple
 
-from kgforge.core import Resource
-from kgforge.core.archetypes import Mapper
+from kgforge.core.resource import Resource
+from kgforge.core.archetypes.mapper import Mapper
 from kgforge.core.archetypes.resolver import Resolver
 from kgforge.core.archetypes.model import Model
 from kgforge.core.archetypes.dataset_store import DatasetStore
 from kgforge.core.commons import Context
-from kgforge.specializations.mappers import DictionaryMapper
+from kgforge.specializations.mappers.dictionaries import DictionaryMapper
 from kgforge.specializations.stores.sparql.sparql_service import SPARQLService
 from kgforge.core.wrappings.paths import create_filters_from_dict, Filter
 from kgforge.core.wrappings.dict import DictWrapper

tests/conftest.py

@@ -18,7 +18,8 @@
 import pytest
 from pytest_bdd import given, parsers, then, when
 
-from kgforge.core import Resource, KnowledgeGraphForge
+from kgforge.core.resource import Resource
+from kgforge.core.forge import KnowledgeGraphForge
 from kgforge.core.commons.actions import Action
 from kgforge.core.commons.context import Context
 from kgforge.core.conversions.rdf import _merge_jsonld, Form

tests/core/archetypes/test_read_only_store.py

@@ -15,7 +15,8 @@
 # Placeholder for the test suite for actions.
 import pytest
 
-from kgforge.core import Resource, KnowledgeGraphForge
+from kgforge.core.resource import Resource
+from kgforge.core.forge import KnowledgeGraphForge
 from kgforge.core.commons.exceptions import DownloadingError
 
 

tests/core/archetypes/test_store.py

@@ -15,7 +15,8 @@
 # Placeholder for the test suite for actions.
 import pytest
 
-from kgforge.core import Resource, KnowledgeGraphForge
+from kgforge.core.resource import Resource
+from kgforge.core.forge import KnowledgeGraphForge
 from kgforge.specializations.resources import Dataset
 from kgforge.core.wrappings.dict import wrap_dict
 import json

tests/core/commons/test_actions.py

@@ -14,7 +14,7 @@
 
 # Placeholder for the test suite for actions.
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.actions import LazyAction, collect_lazy_actions, execute_lazy_actions
 
 

tests/core/conversions/conftest.py

@@ -18,7 +18,8 @@
 from urllib.parse import urljoin
 from urllib.request import pathname2url
 
-from kgforge.core import KnowledgeGraphForge, Resource
+from kgforge.core.resource import Resource
+from kgforge.core.forge import KnowledgeGraphForge
 from kgforge.core.commons.context import Context
 from kgforge.core.conversions.rdf import _merge_jsonld
 from kgforge.core.wrappings.dict import wrap_dict

tests/core/conversions/test_dataframe.py

@@ -19,7 +19,7 @@
 
 # Test suite for conversion of resource to / from Pandas DataFrame.
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 
 
 @pytest.fixture

tests/core/conversions/test_rdf.py

@@ -24,7 +24,7 @@
 from rdflib import Graph, BNode, term
 from rdflib.namespace import RDF, Namespace
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.exceptions import NotSupportedError
 from kgforge.core.conversions.rdf import _merge_jsonld, _resolve_iri, from_jsonld, as_jsonld, Form, as_graph, from_graph, LD_KEYS
 

tests/core/test_forge.py

@@ -16,7 +16,7 @@
 
 import pytest
 
-from kgforge.core import KnowledgeGraphForge
+from kgforge.core.forge import KnowledgeGraphForge
 
 SCOPE = "terms"
 MODEL = "DemoModel"

tests/core/test_reshaping.py

@@ -14,7 +14,8 @@
 
 # Placeholder for the test suite for reshaping.
 import pytest
-from kgforge.core import Resource, KnowledgeGraphForge
+from kgforge.core.resource import Resource
+from kgforge.core.forge import KnowledgeGraphForge
 from kgforge.core.reshaping import collect_values, Reshaper
 
 

tests/core/test_resource.py

@@ -15,7 +15,7 @@
 import pytest
 from pytest_bdd import given, scenarios, then, when
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 
 # TODO To be port to the generic parameterizable test suite for resources in test_resources.py.
 #  DKE-135.

tests/specializations/mappers/test_mappers.py

@@ -17,9 +17,10 @@
 import pytest
 from contextlib import nullcontext as does_not_raise
 
-from kgforge.core import KnowledgeGraphForge, Resource
-from kgforge.specializations.mappers import DictionaryMapper
-from kgforge.specializations.mappings import DictionaryMapping
+from kgforge.core.resource import Resource
+from kgforge.core.forge import KnowledgeGraphForge
+from kgforge.specializations.mappers.dictionaries import DictionaryMapper
+from kgforge.specializations.mappings.dictionaries import DictionaryMapping
 
 
 @pytest.fixture

tests/specializations/models/test_rdf_model.py

@@ -14,7 +14,7 @@
 import json
 import pytest
 
-from kgforge.core import Resource
+from kgforge.core.resource import Resource
 from kgforge.core.commons.exceptions import ValidationError
 from kgforge.specializations.models import RdfModel
 from tests.specializations.models.data import *

tests/specializations/resources/test_datasets.py

@@ -15,7 +15,8 @@
 # Placeholder for the generic parameterizable test suite for resources.
 from typing import List
 
-from kgforge.core import KnowledgeGraphForge, Resource
+from kgforge.core.resource import Resource
+from kgforge.core.forge import KnowledgeGraphForge
 from kgforge.specializations.resources import Dataset
 
 

tests/specializations/stores/test_bluebrain_nexus.py

@@ -22,8 +22,8 @@
 import pytest
 from typing import Callable, Union, List
 
-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.context import Context
 from kgforge.core.conversions.rdf import _merge_jsonld
 from kgforge.core.wrappings.dict import wrap_dict