cognite-neat 0.87.6__py3-none-any.whl → 0.88.0__py3-none-any.whl

cognite/neat/legacy/graph/transformations/transformer.py

@@ -1,322 +0,0 @@
-"""Methods to transform Domain Knowledge Graph to App Knowledge Graph"""
-
-import logging
-import time
-import traceback
-from typing import Any
-
-import pandas as pd
-from cognite.client import CogniteClient
-from prometheus_client import Gauge
-from pydantic import BaseModel
-from rdflib import RDF, Graph
-from rdflib.term import Literal, Node
-
-from cognite.neat.legacy.graph.exceptions import NamespaceRequired
-from cognite.neat.legacy.graph.transformations.query_generator.sparql import build_sparql_query
-from cognite.neat.legacy.rules.models._base import EntityTypes
-from cognite.neat.legacy.rules.models.rdfpath import (
-    AllProperties,
-    AllReferences,
-    Query,
-    RawLookup,
-    Traversal,
-    parse_rule,
-)
-from cognite.neat.legacy.rules.models.rules import Rules
-from cognite.neat.utils.rdf_ import remove_namespace_from_uri
-
-prom_total_proc_rules_g = Gauge("neat_total_processed_rules", "Number of processed rules", ["state"])
-rules_processing_timing_metric = Gauge(
-    "neat_rules_processing_timing", "Transformation rules processing timing metrics", ["aggregation"]
-)
-
-
-COMMIT_BATCH_SIZE = 10000
-
-
-class RuleProcessingReportRec(BaseModel):
-    """Report record for rule processing"""
-
-    row_id: str | None = None
-    rule_name: str | None = None
-    rule_type: str | None = None
-    rule_expression: Any | None = None
-    status: str | None = None
-    error_message: str | None = None
-    elapsed_time: float = 0
-    rows_in_response: int = 0
-
-
-class RuleProcessingReport(BaseModel):
-    """Report for rule processing"""
-
-    total_rules: int = 0
-    total_success: int = 0
-    total_success_no_results: int = 0
-    total_failed: int = 0
-    records: list[RuleProcessingReportRec] = []
-    elapsed_time: float = 0
-
-
-def source2solution_graph(
-    source_knowledge_graph: Graph,
-    transformation_rules: Rules,
-    solution_knowledge_graph: Graph | None = None,
-    client: CogniteClient | None = None,
-    cdf_lookup_database: str | None = None,
-    extra_triples: list[tuple[Node, Node, Node]] | None = None,
-    stop_on_exception: bool = False,
-    missing_raw_lookup_value: str = "NaN",
-    processing_report: RuleProcessingReport | None = None,
-) -> Graph:
-    """Transforms solution knowledge graph based on Domain Knowledge Graph
-
-    Args:
-        source_knowledge_graph: Domain Knowledge Graph which represents the source graph being
-                                transformed to app/solution specific graph
-        transformation_rules: Transformation rules holding data model definition and rules to
-                              transform source/domain graph to app/solution specific graph
-        solution_knowledge_graph: Graph to store app/solution specific graph.
-                            Defaults to None (i.e., empty graph).
-        client: CogniteClient. Defaults to None.
-        cdf_lookup_database: CDF RAW database name to use for `rawlookup` rules. Defaults to None.
-        extra_triples: Additional triples to add to app/solution knowledge graph. Defaults to None.
-        stop_on_exception: To stop on exception. Defaults to False.
-        missing_raw_lookup_value: If no value is find for `rawlookup` default value to use. Defaults to "NaN".
-        processing_report: Processing report to store results to. Defaults to None.
-
-    Returns:
-        Transformed knowledge graph based on transformation rules
-    """
-
-    # TODO: This is to be improved and slowly sunset domain2app_knowledge_graph
-
-    return domain2app_knowledge_graph(
-        domain_knowledge_graph=source_knowledge_graph,
-        transformation_rules=transformation_rules,
-        app_instance_graph=solution_knowledge_graph,
-        client=client,
-        cdf_lookup_database=cdf_lookup_database,
-        extra_triples=extra_triples,
-        stop_on_exception=stop_on_exception,
-        missing_raw_lookup_value=missing_raw_lookup_value,
-        processing_report=processing_report,
-    )
-
-
-def domain2app_knowledge_graph(
-    domain_knowledge_graph: Graph,
-    transformation_rules: Rules,
-    app_instance_graph: Graph | None = None,
-    client: CogniteClient | None = None,
-    cdf_lookup_database: str | None = None,
-    extra_triples: list[tuple[Node, Node, Node]] | None = None,
-    stop_on_exception: bool = False,
-    missing_raw_lookup_value: str = "NaN",
-    processing_report: RuleProcessingReport | None = None,
-) -> Graph:
-    """Generates application/solution specific knowledge graph based on Domain Knowledge Graph
-
-    Args:
-        domain_knowledge_graph: Domain Knowledge Graph which represent the source graph being
-                                transformed to app/solution specific graph
-        transformation_rules: Transformation rules holding data model definition and rules
-                              to transform source/domain graph to app/solution specific graph
-        app_instance_graph: Graph to store app/solution specific graph. Defaults to None (i.e., empty graph).
-        client: CogniteClient. Defaults to None.
-        cdf_lookup_database: CDF RAW database name to use for `rawlookup` rules. Defaults to None.
-        extra_triples: Additional triples to add to app/solution knowledge graph. Defaults to None.
-        stop_on_exception: To stop on exception. Defaults to False.
-        missing_raw_lookup_value: If no value is find for `rawlookup` default value to use. Defaults to "NaN".
-        processing_report: Processing report to store results to. Defaults to None.
-
-    Returns:
-        Transformed knowledge graph based on transformation rules
-    """
-    if transformation_rules.metadata.namespace is None:
-        raise NamespaceRequired("Transform domain to app knowledge graph")
-    rule_namespace = transformation_rules.metadata.namespace
-
-    if app_instance_graph is None:
-        app_instance_graph = Graph()
-        # Bind App namespace and prefix
-        app_instance_graph.bind(transformation_rules.metadata.prefix, rule_namespace)
-        # Bind other prefixes and namespaces
-        for prefix, namespace in transformation_rules.prefixes.items():
-            app_instance_graph.bind(prefix, namespace)
-
-    tables_by_name = {}
-    if cdf_lookup_database and client:
-        for table_name in transformation_rules.raw_tables:
-            logging.debug(f"Loading {table_name} table from database {cdf_lookup_database}")
-            table = client.raw.rows.retrieve_dataframe(cdf_lookup_database, table_name, limit=-1)
-            tables_by_name[table_name] = table
-
-    # Add references with their type first
-    types = []
-    success = 0
-    success_no_results = 0
-    failed = 0
-    commit_counter = 0
-    timing_traces = []
-    prom_total_proc_rules_g.labels(state="success_no_results").set(0)
-    prom_total_proc_rules_g.labels(state="success").set(0)
-    prom_total_proc_rules_g.labels(state="failed").set(0)
-
-    def check_commit(force_commit: bool = False):
-        """'Commit nodes to the graph if batch counter is reached or if force_commit is True"""
-
-        if force_commit:
-            logging.debug("Committing nodes")
-            app_instance_graph.commit()
-            logging.debug("Nodes committed")
-            return
-        nonlocal commit_counter
-        commit_counter += 1
-        if commit_counter >= COMMIT_BATCH_SIZE:
-            logging.info(f"Committing {COMMIT_BATCH_SIZE} nodes")
-            app_instance_graph.commit()
-            logging.info(f" {COMMIT_BATCH_SIZE} nodes committed")
-            commit_counter = 0
-
-    proc_start_time = time.perf_counter()
-    for sheet_row, rule_definition in transformation_rules.properties.items():
-        if not rule_definition.rule or rule_definition.skip_rule:
-            continue
-        msg = f"Processing {sheet_row}: class <{rule_definition.class_id}> "
-        msg += f"property <{rule_definition.property_name}> rule <{rule_definition.rule}>"
-
-        processing_report_rec = RuleProcessingReportRec(
-            row_id=sheet_row,
-            rule_name=f"{rule_definition.class_id}_{rule_definition.property_name}",
-            rule_type=rule_definition.rule_type,
-            rule_expression=rule_definition.rule,
-        )
-        logging.info(msg)
-        try:
-            start_time = time.perf_counter()
-            # Parse rule:
-            rule = parse_rule(rule_definition.rule, rule_definition.rule_type)  # type: ignore[arg-type]
-
-            # Build SPARQL if needed:
-            if isinstance(rule.traversal, Query) and rule_definition.rule_type == "sparql":
-                query = rule.traversal.query
-            elif isinstance(rule.traversal, Traversal | str):
-                query = build_sparql_query(domain_knowledge_graph, rule.traversal, transformation_rules.prefixes)
-            else:
-                raise ValueError(f"Unknown traversal type {type(rule.traversal)}")
-            logging.debug(f"Query: {query}")
-
-            if query_results := list(domain_knowledge_graph.query(query)):
-                # Generate URI for class and property in target namespace
-                class_URI = rule_namespace[rule_definition.class_id]
-                property_URI = rule_namespace[rule_definition.property_name]  # type: ignore[index]
-
-                # Turn query results into dataframe
-                instance_df = pd.DataFrame(
-                    query_results, columns=[EntityTypes.subject, EntityTypes.predicate, EntityTypes.object]
-                )
-
-                # If we are not grabbing all properties for class instances
-                # then we are able to replace source property URI with target property URI
-                # otherwise we should keep source property URI
-                if not isinstance(rule.traversal, AllProperties):
-                    instance_df[EntityTypes.predicate] = property_URI
-
-                # If we are storing object from the source graph as literal value(propety type being Datatype Property)
-                # in the target graph then we should remove namespace from the object URI and store it as literal
-                if isinstance(rule.traversal, AllReferences) and rule_definition.property_type == "DatatypeProperty":
-                    instance_df[EntityTypes.object] = instance_df[EntityTypes.object].apply(
-                        lambda x: Literal(remove_namespace_from_uri(x))
-                    )
-
-                if isinstance(rule, RawLookup):
-                    lookup_map = tables_by_name[rule.table.name].set_index(rule.table.key)[rule.table.value].to_dict()
-
-                    def lookup(
-                        literal: Literal, lookup_table=lookup_map, missing_raw_lookup_value=missing_raw_lookup_value
-                    ):
-                        if new_value := lookup_table.get(literal.value):
-                            return Literal(new_value, literal.language, literal.datatype, bool(literal.normalize))
-                        elif missing_raw_lookup_value:
-                            return Literal(
-                                missing_raw_lookup_value, literal.language, literal.datatype, bool(literal.normalize)
-                            )
-                        else:
-                            return literal
-
-                    instance_df[EntityTypes.object] = instance_df[EntityTypes.object].apply(lookup)
-
-                # Add instances
-                for _, triple in instance_df.iterrows():
-                    app_instance_graph.add(triple.values)  # type: ignore[arg-type]
-                    check_commit()
-                # Setting instances type and merging them with df containing instance - type relations
-                instance_df[EntityTypes.predicate] = RDF.type
-                instance_df[EntityTypes.object] = class_URI
-                types.append(instance_df)
-                success += 1
-                prom_total_proc_rules_g.labels(state="success").inc()
-                elapsed_time = time.perf_counter() - start_time
-                timing_traces.append(elapsed_time)
-                processing_report_rec.elapsed_time = elapsed_time
-                processing_report_rec.status = "success"
-                processing_report_rec.rows_in_response = len(instance_df)
-            else:
-                success_no_results += 1
-                prom_total_proc_rules_g.labels(state="success_no_results").inc()
-                elapsed_time = time.perf_counter() - start_time
-                timing_traces.append(elapsed_time)
-                processing_report_rec.elapsed_time = elapsed_time
-                processing_report_rec.status = "success_no_results"
-
-        except Exception as e:
-            failed += 1
-            elapsed_time = time.perf_counter() - start_time
-            processing_report_rec.elapsed_time = elapsed_time
-            processing_report_rec.status = "failed"
-            processing_report_rec.error_message = str(e)
-            prom_total_proc_rules_g.labels(state="failed").inc()
-            logging.error(
-                f" Error while processing rule {rule_definition.rule} for class {rule_definition.class_id} \
-                and property {rule_definition.property_name}"
-            )
-            logging.error(traceback.format_exc())
-            if stop_on_exception:
-                raise e
-
-        if processing_report:
-            processing_report.records.append(processing_report_rec)
-
-    if processing_report:
-        processing_report.total_rules = len(transformation_rules.properties)
-        processing_report.total_success = success
-        processing_report.total_success_no_results = success_no_results
-        processing_report.total_failed = failed
-        processing_report.elapsed_time = time.perf_counter() - proc_start_time
-
-    if timing_traces:
-        df = pd.Series(timing_traces)
-        rules_processing_timing_metric.labels(aggregation="sum").set(df.sum())
-        rules_processing_timing_metric.labels(aggregation="std_div").set(df.std())
-        rules_processing_timing_metric.labels(aggregation="min").set(df.min())
-        rules_processing_timing_metric.labels(aggregation="max").set(df.max())
-        rules_processing_timing_metric.labels(aggregation="mean").set(df.mean())
-
-    type_df = pd.concat(types).drop_duplicates(EntityTypes.subject).reset_index(drop=True)
-
-    # Add instance - RDF Type relations
-    for _, triple in type_df.iterrows():  # type: ignore[assignment]
-        app_instance_graph.add(triple.values)  # type: ignore[arg-type]
-        check_commit()
-
-    for i, triple in enumerate(extra_triples or []):  # type: ignore[assignment]
-        try:
-            app_instance_graph.add(triple)  # type: ignore[arg-type]
-            check_commit()
-        except ValueError as e:
-            raise ValueError(f"Triple {i} in extra_triples is not correct and cannot be added!") from e
-
-    check_commit(force_commit=True)
-    return app_instance_graph

cognite/neat/legacy/rules/analysis.py

@@ -1,231 +0,0 @@
-import warnings
-from collections import defaultdict
-
-import pandas as pd
-
-from cognite.neat.legacy.rules.models.rdfpath import TransformationRuleType
-from cognite.neat.legacy.rules.models.rules import Property, Rules
-
-
-def get_defined_classes(transformation_rules: Rules) -> set[str]:
-    """Returns classes that have properties defined for them in the data model.
-
-    Args:
-        transformation_rules: Instance of TransformationRules holding the data model
-
-    Returns:
-        Set of classes that have been defined in the data model
-    """
-    return {property.class_id for property in transformation_rules.properties.values()}
-
-
-def get_classes_with_properties(transformation_rules: Rules) -> dict[str, list[Property]]:
-    """Returns classes that have been defined in the data model.
-
-    Args:
-        transformation_rules: Instance of TransformationRules holding the data model
-
-    Returns:
-        Dictionary of classes with a list of properties defined for them
-    """
-
-    class_property_pairs: dict[str, list[Property]] = {}
-
-    for property_ in transformation_rules.properties.values():
-        class_ = property_.class_id
-        if class_ in class_property_pairs:
-            class_property_pairs[class_] += [property_]
-        else:
-            class_property_pairs[class_] = [property_]
-
-    return class_property_pairs
-
-
-def to_class_property_pairs(transformation_rules: Rules, only_rdfpath: bool = False) -> dict[str, dict[str, Property]]:
-    """Returns a dictionary of classes with a dictionary of properties associated with them.
-
-    Args:
-        transformation_rules : Instance of TransformationRules holding the data model
-        only_rdfpath : To consider only properties which have rule `rdfpath` set. Defaults False
-
-    Returns:
-        Dictionary of classes with a dictionary of properties associated with them.
-
-    !!! note "only_rdfpath"
-        If only_rdfpath is True, only properties with RuleType.rdfpath will be returned as
-        a part of the dictionary of properties related to a class. Otherwise, all properties
-        will be returned.
-    """
-
-    class_property_pairs = {}
-
-    for class_, properties in get_classes_with_properties(transformation_rules).items():
-        processed_properties = {}
-        for property_ in properties:
-            if property_.property_id in processed_properties:
-                # TODO: use appropriate Warning class from _exceptions.py
-                # if missing make one !
-                warnings.warn(
-                    "Property has been defined more than once! Only first definition will be considered.", stacklevel=2
-                )
-                continue
-
-            if (only_rdfpath and property_.rule_type == TransformationRuleType.rdfpath) or not only_rdfpath:
-                processed_properties[property_.property_id] = property_
-        class_property_pairs[class_] = processed_properties
-
-    return class_property_pairs
-
-
-def get_class_linkage(transformation_rules: Rules) -> pd.DataFrame:
-    """Returns a dataframe with the class linkage of the data model.
-
-    Args:
-        transformation_rules: Instance of TransformationRules holding the data model
-
-    Returns:
-        Dataframe with the class linkage of the data model
-    """
-
-    class_linkage = pd.DataFrame(columns=["source_class", "target_class", "connecting_property", "max_occurrence"])
-    for property_ in transformation_rules.properties.values():
-        if property_.property_type == "ObjectProperty":
-            new_row = pd.Series(
-                {
-                    "source_class": property_.class_id,
-                    "target_class": property_.expected_value_type.suffix,
-                    "connecting_property": property_.property_id,
-                    "max_occurrence": property_.max_count,
-                    "linking_type": "hierarchy" if property_.resource_type_property else "relationship",
-                }
-            )
-            class_linkage = pd.concat([class_linkage, new_row.to_frame().T], ignore_index=True)
-
-    class_linkage.drop_duplicates(inplace=True)
-
-    return class_linkage
-
-
-def get_class_hierarchy_linkage(rules: Rules) -> pd.DataFrame:
-    """Remove linkage which is not creating asset hierarchy."""
-    class_linkage = get_class_linkage(rules)
-    return class_linkage[class_linkage.linking_type == "hierarchy"]
-
-
-def get_connected_classes(transformation_rules: Rules) -> set[str]:
-    """Return a set of classes that are connected to other classes.
-
-    Args:
-        transformation_rules: Instance of TransformationRules holding the data model
-
-    Returns:
-        Set of classes that are connected to other classes
-    """
-    class_linkage = get_class_linkage(transformation_rules)
-    return set(class_linkage.source_class.values).union(set(class_linkage.target_class.values))
-
-
-def get_disconnected_classes(transformation_rules: Rules) -> set[str]:
-    """Return a set of classes that are disconnected (i.e. isolated) from other classes.
-
-    Args:
-        transformation_rules: Instance of TransformationRules holding the data model
-
-    Returns:
-        Set of classes that are disconnected from other classes
-    """
-    return get_defined_classes(transformation_rules) - get_connected_classes(transformation_rules)
-
-
-def get_symmetric_pairs(transformation_rules: Rules) -> set[tuple[str, str]]:
-    """Returns a set of pairs of symmetrically linked classes.
-
-    Args:
-        transformation_rules: Instance of TransformationRules holding the data model
-
-    Returns:
-        Set of pairs of symmetrically linked classes
-    """
-
-    # TODO: Find better name for this method
-    sym_pairs: set[tuple[str, str]] = set()
-
-    class_linkage = get_class_linkage(transformation_rules)
-    if class_linkage.empty:
-        return sym_pairs
-
-    for _, row in class_linkage.iterrows():
-        source = row.source_class
-        target = row.target_class
-        target_targets = class_linkage[class_linkage.source_class == target].target_class.values
-        if source in target_targets and (source, target) not in sym_pairs:
-            sym_pairs.add((source, target))
-    return sym_pairs
-
-
-def get_entity_ids(transformation_rules: Rules) -> set[str]:
-    """Returns a set of entity ids (classes and properties) defined in the data model.
-
-    Args:
-        transformation_rules: Instance of TransformationRules holding the data model
-
-    Returns:
-        Set of entity ids (classes and properties) defined in the data model
-    """
-    return set(transformation_rules.classes.keys()).union(
-        {property_.property_id for property_ in transformation_rules.properties.values()}
-    )
-
-
-def to_property_dict(transformation_rules: Rules) -> dict[str, list[Property]]:
-    """Convert list of properties to a dictionary of lists of properties with property_id as key.
-
-    Args:
-        transformation_rules: Instance of TransformationRules holding the data model
-
-    Returns:
-        Dictionary of lists of properties with property_id as key
-    """
-    property_: dict[str, list[Property]] = defaultdict(list)
-
-    for prop in transformation_rules.properties.values():
-        if not (prop.property_id and prop.property_name == "*"):
-            property_[prop.property_id].append(prop)
-
-    return property_
-
-
-def get_asset_related_properties(properties: list[Property]) -> list[Property]:
-    """Return properties that are used to define CDF Assets
-
-    Args:
-        properties: List of properties
-
-    Returns:
-        List of properties that are used to define CDF Assets
-    """
-    return [prop for prop in properties if "Asset" in prop.cdf_resource_type]
-
-
-def define_class_asset_mapping(transformation_rules: Rules, class_: str) -> dict[str, list[str]]:
-    """Define mapping between class and asset properties
-
-    Args:
-        transformation_rules: Instance of TransformationRules holding the data model
-        class_: Class id for which mapping is to be defined
-
-    Returns:
-        Dictionary with asset properties as keys and list of class properties as values
-    """
-    mapping_dict: dict[str, list[str]] = {}
-
-    class_properties = to_class_property_pairs(transformation_rules, only_rdfpath=True)[class_]
-
-    for asset_property in get_asset_related_properties(list(class_properties.values())):
-        for resource_type_property in asset_property.resource_type_property or []:
-            if resource_type_property not in mapping_dict:
-                mapping_dict[resource_type_property] = [asset_property.property_id]
-            else:
-                mapping_dict[resource_type_property] += [asset_property.property_id]
-
-    return mapping_dict

cognite/neat/legacy/rules/examples/__init__.py

@@ -1,18 +0,0 @@
-from pathlib import Path
-
-# we should make this a proper package that loads examples
-# similar how they handle it in xarray:
-# https://github.com/pydata/xarray/blob/main/xarray/tutorial.py
-# Currently there are simple paths to the examples which are then easily loaded in the notebooks
-
-_EXAMPLES = Path(__file__).parent
-
-power_grid_model = _EXAMPLES / "power-grid-example.xlsx"
-power_grid_containers = _EXAMPLES / "power-grid-containers.yaml"
-power_grid_data_model = _EXAMPLES / "power-grid-model.yaml"
-simple_example = _EXAMPLES / "sheet2cdf-transformation-rules.xlsx"
-source_to_solution_mapping = _EXAMPLES / "source-to-solution-mapping-rules.xlsx"
-nordic44 = _EXAMPLES / "Rules-Nordic44.xlsx"
-nordic44_graphql = _EXAMPLES / "Rules-Nordic44-to-graphql.xlsx"
-skos = _EXAMPLES / "skos-rules.xlsx"
-wind_energy_ontology = _EXAMPLES / "wind-energy.owl"