Implementing NodeDeletion which was earlier a comment. (#791)

* Implementing NodeDeletion which was earlier a comment.

* formmatted

* tox -e format

* updated version of kgcl-schema

pyproject.toml

@@ -19,7 +19,7 @@ sssom = "^0.4.4"
 ratelimit = ">=2.2.1"
 appdirs = ">=1.4.4"
 semsql = ">=0.3.1"
-kgcl-schema = "^0.6.8"
+kgcl-schema = "^0.6.9"
 
 funowl = ">=0.2.0"
 gilda = {version = ">=1.0.0", optional = true}

src/oaklib/implementations/simpleobo/simple_obo_implementation.py

@@ -912,9 +912,8 @@ def _tv_dict(stanza: Stanza) -> Dict[str, List[str]]:
                         id=_id(), about_node=t1id, new_value=vals2list[0], old_value=None
                     )
                 else:
-                    #! KGCL may have NameDeletion in the future.
-                    yield kgcl.NodeRename(
-                        id=_id(), about_node=t2id, old_value=vals2list[0], new_value=None
+                    yield kgcl.NodeDeletion(
+                        id=_id(), about_node=t1id, old_value=vals1list[0], new_value=None
                     )
             elif tag == TAG_DEFINITION:
                 if node_is_deleted:

src/oaklib/implementations/sqldb/sql_implementation.py

@@ -365,10 +365,10 @@ def __post_init__(self):
             logging.info(f"Locator, post-processed: {locator}")
             self.engine = create_engine(locator)
 
-            if(logging.root.level <= logging.DEBUG):
-                #If oaklib is running at DEBUG level logging; record all queries from sqlachemy on execution.
-                #This line is equivalent to create_engine(locator,echo=True)
-                logging.getLogger('sqlalchemy.engine.Engine').setLevel(logging.INFO)
+            if logging.root.level <= logging.DEBUG:
+                # If oaklib is running at DEBUG level logging; record all queries from sqlachemy on execution.
+                # This line is equivalent to create_engine(locator,echo=True)
+                logging.getLogger("sqlalchemy.engine.Engine").setLevel(logging.INFO)
 
     @property
     def session(self):

src/oaklib/utilities/lexical/lexical_indexer.py

@@ -82,7 +82,6 @@ def add_labels_from_uris(oi: BasicOntologyInterface):
             oi.set_label(curie, label)
 
 
-
 def create_lexical_index(
     oi: BasicOntologyInterface,
     pipelines: Optional[List[LexicalTransformationPipeline]] = None,

tests/integration_tests/test_sqlite_full.py

@@ -6,7 +6,6 @@
 from oaklib.utilities.mapping.cross_ontology_diffs import (
     calculate_pairwise_relational_diff,
 )
-
 from tests import EXTERNAL_DB_DIR
 
 DB_FOLDER = EXTERNAL_DB_DIR / "unreciprocated-mapping-test.obo"

tests/test_cli.py

@@ -12,6 +12,8 @@
 from click.testing import CliRunner
 from kgcl_schema.datamodel.kgcl import MappingCreation, NodeChange, RemoveMapping
 from linkml_runtime.loaders import json_loader, yaml_loader
+from sssom.parsers import parse_sssom_table, to_mapping_set_document
+
 from oaklib import get_adapter
 from oaklib.cli import clear_cli_settings, main
 from oaklib.datamodels import fhir, obograph, taxon_constraints
@@ -22,8 +24,6 @@
     SKOS_EXACT_MATCH,
 )
 from oaklib.utilities.kgcl_utilities import parse_kgcl_files
-from sssom.parsers import parse_sssom_table, to_mapping_set_document
-
 from tests import (
     ATOM,
     CATALYTIC_ACTIVITY,

tests/test_converters/test_logical_definition_flattener_converter.py

@@ -1,12 +1,12 @@
 import unittest
 
 from linkml_runtime.loaders import json_loader
+
 from oaklib import get_adapter
 from oaklib.converters.logical_definition_flattener import LogicalDefinitionFlattener
 from oaklib.datamodels import obograph
 from oaklib.datamodels.obograph import GraphDocument
 from oaklib.datamodels.vocabulary import HAS_PART, PART_OF
-
 from tests import INPUT_DIR, OUTPUT_DIR
 from tests.test_implementations import ComplianceTester
 

tests/test_converters/test_obo_format.py

@@ -92,9 +92,9 @@
 
 import pytest
 import rdflib
-from oaklib import get_adapter
 from rdflib.compare import isomorphic
 
+from oaklib import get_adapter
 from tests import INPUT_DIR, OUTPUT_DIR
 
 logger = logging.getLogger(__name__)

tests/test_converters/test_obo_graph_to_cx.py

@@ -4,10 +4,10 @@
 import curies
 from linkml_runtime.loaders import json_loader
 from ndex2 import create_nice_cx_from_file
+
 from oaklib.converters.obo_graph_to_cx_converter import OboGraphToCXConverter
 from oaklib.datamodels.obograph import GraphDocument
 from oaklib.interfaces.basic_ontology_interface import get_default_prefix_map
-
 from tests import INPUT_DIR, OUTPUT_DIR
 from tests.test_implementations import ComplianceTester
 

tests/test_converters/test_obo_graph_to_fhir.py

@@ -7,12 +7,12 @@
 import curies
 import requests
 from linkml_runtime.loaders import json_loader
+
 from oaklib.constants import TIMEOUT_SECONDS
 from oaklib.converters.obo_graph_to_fhir_converter import OboGraphToFHIRConverter
 from oaklib.datamodels.fhir import CodeSystem
 from oaklib.datamodels.obograph import GraphDocument
 from oaklib.interfaces.basic_ontology_interface import get_default_prefix_map
-
 from tests import IMBO, INPUT_DIR, NUCLEUS, OUTPUT_DIR
 from tests.test_implementations import ComplianceTester
 

tests/test_converters/test_obo_graph_to_obo_format.py

@@ -2,14 +2,14 @@
 
 import curies
 from linkml_runtime.loaders import json_loader
+
 from oaklib import OntologyResource
 from oaklib.converters.obo_graph_to_obo_format_converter import (
     OboGraphToOboFormatConverter,
 )
 from oaklib.datamodels.obograph import GraphDocument
 from oaklib.implementations import SimpleOboImplementation
 from oaklib.interfaces.basic_ontology_interface import get_default_prefix_map
-
 from tests import INPUT_DIR, OUTPUT_DIR
 from tests.test_implementations import ComplianceTester
 

tests/test_converters/test_obo_graph_to_rdf_owl_converter.py

@@ -2,12 +2,12 @@
 
 import curies
 from linkml_runtime.loaders import json_loader
+
 from oaklib import OntologyResource
 from oaklib.converters.obo_graph_to_rdf_owl_converter import OboGraphToRdfOwlConverter
 from oaklib.datamodels.obograph import GraphDocument
 from oaklib.implementations import SparqlImplementation
 from oaklib.interfaces.basic_ontology_interface import get_default_prefix_map
-
 from tests import INPUT_DIR, OUTPUT_DIR
 from tests.test_implementations import ComplianceTester
 

tests/test_datamodels/test_obograph_datamodel.py

@@ -1,8 +1,8 @@
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.utils.introspection import package_schemaview
+
 from oaklib.datamodels import obograph
 from oaklib.datamodels.vocabulary import IS_A
-
 from tests import output_path
 from tests.test_datamodels import AbstractDatamodelTestCase
 

tests/test_datamodels/test_ontology_metadata_datamodel.py

@@ -4,8 +4,8 @@
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.loaders import yaml_loader
 from linkml_runtime.utils.introspection import package_schemaview
-from oaklib.datamodels import ontology_metadata
 
+from oaklib.datamodels import ontology_metadata
 from tests import output_path
 
 

tests/test_datamodels/test_search_datamodel.py

@@ -1,6 +1,7 @@
 import unittest
 
 from linkml_runtime.utils.introspection import package_schemaview
+
 from oaklib.datamodels import search_datamodel
 from oaklib.datamodels.search import create_search_configuration
 from oaklib.datamodels.search_datamodel import SearchProperty, SearchTermSyntax

tests/test_datamodels/test_text_annotator_datamodel.py

@@ -2,8 +2,8 @@
 
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.utils.introspection import package_schemaview
-from oaklib.datamodels import text_annotator
 
+from oaklib.datamodels import text_annotator
 from tests import NUCLEUS, output_path
 
 

tests/test_datamodels/test_validation_datamodel.py

@@ -1,10 +1,10 @@
 import logging
 import unittest
 
-import oaklib.datamodels.validation_datamodel as vdm
 from linkml_runtime.dumpers import yaml_dumper
 from linkml_runtime.utils.introspection import package_schemaview
 
+import oaklib.datamodels.validation_datamodel as vdm
 from tests import output_path
 
 

tests/test_implementations/__init__.py

@@ -17,6 +17,7 @@
 from kgcl_schema.datamodel.kgcl import Change, NodeObsoletion
 from kgcl_schema.grammar.render_operations import render
 from linkml_runtime.dumpers import json_dumper, yaml_dumper
+
 from oaklib import BasicOntologyInterface, get_adapter
 from oaklib.datamodels import obograph
 from oaklib.datamodels.association import Association
@@ -78,7 +79,6 @@
 from oaklib.interfaces.semsim_interface import SemanticSimilarityInterface
 from oaklib.interfaces.summary_statistics_interface import SummaryStatisticsInterface
 from oaklib.utilities.kgcl_utilities import generate_change_id
-
 from tests import (
     ARCHAEA,
     BACTERIA,

tests/test_implementations/test_aggregator.py

@@ -2,14 +2,14 @@
 import unittest
 
 from linkml_runtime.dumpers import yaml_dumper
+
 from oaklib.datamodels.vocabulary import IS_A, PART_OF
 from oaklib.implementations.aggregator.aggregator_implementation import (
     AggregatorImplementation,
 )
 from oaklib.implementations.pronto.pronto_implementation import ProntoImplementation
 from oaklib.resource import OntologyResource
 from oaklib.utilities.obograph_utils import graph_as_dict
-
 from tests import (
     CELLULAR_COMPONENT,
     CYTOPLASM,

tests/test_implementations/test_bioportal.py

@@ -4,11 +4,11 @@
 from unittest import mock
 
 from linkml_runtime.dumpers import yaml_dumper
+
 from oaklib.implementations.ontoportal.bioportal_implementation import (
     BioPortalImplementation,
 )
 from oaklib.utilities.apikey_manager import get_apikey_value
-
 from tests import CELLULAR_COMPONENT, CYTOPLASM, DIGIT, HUMAN, NEURON, VACUOLE
 
 

tests/test_implementations/test_cx.py

@@ -2,7 +2,6 @@
 
 from oaklib.implementations.cx.cx_implementation import CXImplementation
 from oaklib.resource import OntologyResource
-
 from tests import INPUT_DIR
 from tests.test_implementations import ComplianceTester
 

tests/test_implementations/test_funowl.py

@@ -4,12 +4,12 @@
 from funowl import EquivalentClasses, SubClassOf
 from funowl.writers.FunctionalWriter import FunctionalWriter
 from kgcl_schema.datamodel import kgcl
+
 from oaklib.implementations.funowl.funowl_implementation import FunOwlImplementation
 from oaklib.interfaces.obograph_interface import OboGraphInterface
 from oaklib.interfaces.owl_interface import AxiomFilter
 from oaklib.resource import OntologyResource
 from oaklib.utilities.kgcl_utilities import generate_change_id
-
 from tests import CHEBI_NUCLEUS, HUMAN, INPUT_DIR, NUCLEUS, VACUOLE
 
 TEST_ONT = INPUT_DIR / "go-nucleus.ofn"

tests/test_implementations/test_gilda.py

@@ -4,7 +4,6 @@
 
 from oaklib.datamodels.text_annotator import TextAnnotationConfiguration
 from oaklib.implementations import GildaImplementation
-
 from tests import CELL_CORTEX
 
 try:

tests/test_implementations/test_ncbigene.py

@@ -7,7 +7,6 @@
 from oaklib.interfaces.association_provider_interface import (
     AssociationProviderInterface,
 )
-
 from tests import CYTOPLASM, INPUT_DIR
 from tests.input.mock_ncbi_objects import NCBI_ASSOCIATIONS
 

tests/test_implementations/test_obograph.py

@@ -3,6 +3,7 @@
 from copy import deepcopy
 
 from kgcl_schema.datamodel import kgcl
+
 from oaklib.datamodels import obograph
 from oaklib.datamodels.search import SearchConfiguration
 from oaklib.datamodels.search_datamodel import SearchProperty, SearchTermSyntax
@@ -22,7 +23,6 @@
     index_graph_edges_by_subject,
     index_graph_nodes,
 )
-
 from tests import (
     CELL,
     CELLULAR_COMPONENT,

tests/test_implementations/test_ols.py

@@ -3,11 +3,11 @@
 import unittest
 
 from linkml_runtime.dumpers import yaml_dumper
+
 from oaklib.datamodels.search import SearchConfiguration, SearchProperty
 from oaklib.datamodels.vocabulary import IS_A
 from oaklib.implementations.ols.ols_implementation import OlsImplementation
 from oaklib.resource import OntologyResource
-
 from tests import CELLULAR_COMPONENT, CYTOPLASM, DIGIT, VACUOLE
 
 

tests/test_implementations/test_ontobee.py

@@ -6,7 +6,6 @@
 from oaklib.datamodels.vocabulary import IS_A, PART_OF
 from oaklib.implementations.ontobee.ontobee_implementation import OntobeeImplementation
 from oaklib.resource import OntologyResource
-
 from tests import CELLULAR_COMPONENT, DIGIT, INPUT_DIR, OUTPUT_DIR, SHAPE, VACUOLE
 
 TEST_ONT = INPUT_DIR / "go-nucleus.obo"

tests/test_implementations/test_pantherdb.py

@@ -1,6 +1,7 @@
 import unittest
 
 import pytest
+
 from oaklib import get_adapter
 from oaklib.interfaces.association_provider_interface import (
     AssociationProviderInterface,

tests/test_implementations/test_pronto.py

@@ -3,6 +3,7 @@
 
 import pronto
 from kgcl_schema.datamodel import kgcl
+
 from oaklib import get_adapter
 from oaklib.datamodels import obograph
 from oaklib.datamodels.search import SearchConfiguration
@@ -22,7 +23,6 @@
 from oaklib.utilities.validation.definition_ontology_rule import (
     DefinitionOntologyRule,
 )
-
 from tests import (
     CELL,
     CELLULAR_COMPONENT,

tests/test_implementations/test_robot_template.py

@@ -2,6 +2,7 @@
 import pytest
 from kgcl_schema.datamodel import kgcl
 from linkml_runtime.dumpers import yaml_dumper
+
 from oaklib import BasicOntologyInterface, get_adapter
 from oaklib.implementations.tabular.robot_template_implementation import (
     template_modify,
@@ -10,7 +11,6 @@
 from oaklib.interfaces.dumper_interface import DumperInterface
 from oaklib.interfaces.patcher_interface import PatcherInterface
 from oaklib.utilities.kgcl_utilities import tidy_change_object
-
 from tests import INPUT_DIR, OUTPUT_DIR
 
 TEMPLATES = INPUT_DIR / "obi-templates"