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You can check the documentation of the GraphRelationshipsLoader class here.

GraphRelationshipsLoader class for loading graph relationships into a Neo4j database.

GraphRelationshipsLoader

Class for loading graph relationships into a Neo4j database using the AddGraphRelationships class.

Attributes:

Name Type Description
uri str

The URI for the Neo4j database.
username str

The username for the Neo4j database.
password str

The password for the Neo4j database.
relationship_settings dict

Predefined settings for different relationship types.
Source code in chemgraphbuilder/graph_relationships_loader.py 
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class GraphRelationshipsLoader:
    """
    Class for loading graph relationships into a Neo4j database using the AddGraphRelationships class.

    Attributes:
        uri (str): The URI for the Neo4j database.
        username (str): The username for the Neo4j database.
        password (str): The password for the Neo4j database.
        relationship_settings (dict): Predefined settings for different relationship types.
    """

    def __init__(self, uri, username, password):
        """
        Initializes the GraphRelationshipsLoader with Neo4j connection details.

        Args:
            uri (str): The URI for the Neo4j database.
            username (str): The username for the Neo4j database.
            password (str): The password for the Neo4j database.
        """
        self.driver = GraphDatabase.driver(uri, auth=(username, password))
        self.logger = logging.getLogger(__name__)
        self.logger.setLevel(logging.INFO)
        handler = logging.StreamHandler()
        handler.setLevel(logging.INFO)
        formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')
        handler.setFormatter(formatter)
        self.logger.addHandler(handler)
        self.add_graph_relationships = AddGraphRelationships(self.driver)
        self.logger.info("GraphRelationshipsLoader class initialized.")

        # Predefined settings for different relationship types
        self.relationship_settings = {
            "Compound_Gene": {
                "file_path": "Data/Relationships/Compound_Gene_Relationship/Compound_Gene_Relationship*.csv",
                "source_label": "Compound",
                "destination_label": "Gene",
                "rel_type_column": "activity",
                "relationship_type": None,
                "is_directory": True
            },
            "Compound_Gene_Interaction": {
                "file_path": "Data/Relationships/Compound_Gene_Relationship/Compound_Gene_Interaction*.csv",
                "source_label": "Compound",
                "destination_label": "Gene",
                "relationship_type": "INTERACTS_WITH",
                "is_directory": True
            },
            "Assay_Compound": {
                "file_path": "Data/Relationships/Assay_Compound_Relationship_Processed/Assay_Compound_Relationship*.csv",
                "source_label": "BioAssay",
                "destination_label": "Compound",
                "rel_type_column": None,
                "relationship_type": "EVALUATES",
                "is_directory": True
            },
            "Assay_Gene": {
                "file_path": "Data/Relationships/Assay_Gene_Relationship.csv",
                "source_label": "BioAssay",
                "destination_label": "Gene",
                "rel_type_column": None,
                "relationship_type": "STUDIES"
            },
            "Compound_Transformation": {
                "file_path": "Data/Relationships/Compound_Transformation.csv",
                "source_label": "Compound",
                "destination_label": "Compound",
                "rel_type_column": None,
                "relationship_type": "IS_METABOLIZED_TO"
            },
            "Gene_Protein": {
                "file_path": "Data/Relationships/Gene_Protein_Relationship.csv",
                "source_label": "Gene",
                "destination_label": "Protein",
                "rel_type_column": None,
                "relationship_type": "ENCODES"
            },
            "Compound_Similarity": {
                "file_path": "Data/Relationships/Compound_Similarities/*.csv",
                "source_label": "Compound",
                "destination_label": "Compound",
                "rel_type_column": None,
                "relationship_type": "IS_SIMILAR_TO",
                "is_directory": True,
                "is_bidirectional": True
            },
            "Compound_Compound_CoOccurrence": {
                "file_path": "Data/Relationships/Cpd_Cpd_CoOccurrence/*.csv",
                "source_label": "Compound",
                "destination_label": "Compound",
                "rel_type_column": None,
                "relationship_type": "CO_OCCURS_IN_LITERATURE",
                "is_directory": True,
                "is_bidirectional": True
            },
            "Compound_Gene_CoOccurrence": {
                "file_path": "Data/Relationships/Cpd_Gene_CoOccurrence/*.csv",
                "source_label": "Gene",
                "destination_label": "Compound",
                "rel_type_column": None,
                "relationship_type": "CO_OCCURS_IN_LITERATURE",
                "is_directory": True,
                "is_bidirectional": True
            }
        }

    def close(self):
        """Closes the Neo4j database driver connection."""
        self.driver.close()

    def add_relationships(self, relationship_type):
        """
        Adds relationships to the Neo4j database based on the specified relationship type.

        Args:
            relationship_type (str): The type of the relationship.
        """
        settings = self.relationship_settings.get(relationship_type)
        if not settings:
            self.logger.error(f"Invalid relationship type: {relationship_type}")
            return

        file_path = settings["file_path"]
        source_label = settings["source_label"]
        destination_label = settings["destination_label"]
        rel_type_column = settings.get("rel_type_column")
        is_directory = settings.get("is_directory", False)
        is_bidirectional = settings.get("is_bidirectional", False)

        if is_directory:
            self.add_graph_relationships.process_and_add_relationships_from_directory(file_path,
                                                                                      settings["relationship_type"],
                                                                                      source_label,
                                                                                      destination_label,
                                                                                      rel_type_column)
        else:
            self.add_graph_relationships.process_and_add_relationships(file_path,
                                                                       settings.get("relationship_type"),
                                                                       source_label,
                                                                       destination_label,
                                                                       rel_type_column)
        if is_bidirectional:
            self.add_graph_relationships.remove_self_relationships()
            self.add_graph_relationships.make_relationships_bidirectional(settings["relationship_type"])
        else:
            self.add_graph_relationships.remove_self_relationships()

__init__(uri, username, password)

Initializes the GraphRelationshipsLoader with Neo4j connection details.

Parameters:

Name Type Description Default
uri str

The URI for the Neo4j database.

 required
username str

The username for the Neo4j database.

 required
password str

The password for the Neo4j database.

 required
Source code in chemgraphbuilder/graph_relationships_loader.py 
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def __init__(self, uri, username, password):
    """
    Initializes the GraphRelationshipsLoader with Neo4j connection details.

    Args:
        uri (str): The URI for the Neo4j database.
        username (str): The username for the Neo4j database.
        password (str): The password for the Neo4j database.
    """
    self.driver = GraphDatabase.driver(uri, auth=(username, password))
    self.logger = logging.getLogger(__name__)
    self.logger.setLevel(logging.INFO)
    handler = logging.StreamHandler()
    handler.setLevel(logging.INFO)
    formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')
    handler.setFormatter(formatter)
    self.logger.addHandler(handler)
    self.add_graph_relationships = AddGraphRelationships(self.driver)
    self.logger.info("GraphRelationshipsLoader class initialized.")

    # Predefined settings for different relationship types
    self.relationship_settings = {
        "Compound_Gene": {
            "file_path": "Data/Relationships/Compound_Gene_Relationship/Compound_Gene_Relationship*.csv",
            "source_label": "Compound",
            "destination_label": "Gene",
            "rel_type_column": "activity",
            "relationship_type": None,
            "is_directory": True
        },
        "Compound_Gene_Interaction": {
            "file_path": "Data/Relationships/Compound_Gene_Relationship/Compound_Gene_Interaction*.csv",
            "source_label": "Compound",
            "destination_label": "Gene",
            "relationship_type": "INTERACTS_WITH",
            "is_directory": True
        },
        "Assay_Compound": {
            "file_path": "Data/Relationships/Assay_Compound_Relationship_Processed/Assay_Compound_Relationship*.csv",
            "source_label": "BioAssay",
            "destination_label": "Compound",
            "rel_type_column": None,
            "relationship_type": "EVALUATES",
            "is_directory": True
        },
        "Assay_Gene": {
            "file_path": "Data/Relationships/Assay_Gene_Relationship.csv",
            "source_label": "BioAssay",
            "destination_label": "Gene",
            "rel_type_column": None,
            "relationship_type": "STUDIES"
        },
        "Compound_Transformation": {
            "file_path": "Data/Relationships/Compound_Transformation.csv",
            "source_label": "Compound",
            "destination_label": "Compound",
            "rel_type_column": None,
            "relationship_type": "IS_METABOLIZED_TO"
        },
        "Gene_Protein": {
            "file_path": "Data/Relationships/Gene_Protein_Relationship.csv",
            "source_label": "Gene",
            "destination_label": "Protein",
            "rel_type_column": None,
            "relationship_type": "ENCODES"
        },
        "Compound_Similarity": {
            "file_path": "Data/Relationships/Compound_Similarities/*.csv",
            "source_label": "Compound",
            "destination_label": "Compound",
            "rel_type_column": None,
            "relationship_type": "IS_SIMILAR_TO",
            "is_directory": True,
            "is_bidirectional": True
        },
        "Compound_Compound_CoOccurrence": {
            "file_path": "Data/Relationships/Cpd_Cpd_CoOccurrence/*.csv",
            "source_label": "Compound",
            "destination_label": "Compound",
            "rel_type_column": None,
            "relationship_type": "CO_OCCURS_IN_LITERATURE",
            "is_directory": True,
            "is_bidirectional": True
        },
        "Compound_Gene_CoOccurrence": {
            "file_path": "Data/Relationships/Cpd_Gene_CoOccurrence/*.csv",
            "source_label": "Gene",
            "destination_label": "Compound",
            "rel_type_column": None,
            "relationship_type": "CO_OCCURS_IN_LITERATURE",
            "is_directory": True,
            "is_bidirectional": True
        }
    }

add_relationships(relationship_type)

Adds relationships to the Neo4j database based on the specified relationship type.

Parameters:

Name Type Description Default
relationship_type str

The type of the relationship.

 required
Source code in chemgraphbuilder/graph_relationships_loader.py 
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def add_relationships(self, relationship_type):
    """
    Adds relationships to the Neo4j database based on the specified relationship type.

    Args:
        relationship_type (str): The type of the relationship.
    """
    settings = self.relationship_settings.get(relationship_type)
    if not settings:
        self.logger.error(f"Invalid relationship type: {relationship_type}")
        return

    file_path = settings["file_path"]
    source_label = settings["source_label"]
    destination_label = settings["destination_label"]
    rel_type_column = settings.get("rel_type_column")
    is_directory = settings.get("is_directory", False)
    is_bidirectional = settings.get("is_bidirectional", False)

    if is_directory:
        self.add_graph_relationships.process_and_add_relationships_from_directory(file_path,
                                                                                  settings["relationship_type"],
                                                                                  source_label,
                                                                                  destination_label,
                                                                                  rel_type_column)
    else:
        self.add_graph_relationships.process_and_add_relationships(file_path,
                                                                   settings.get("relationship_type"),
                                                                   source_label,
                                                                   destination_label,
                                                                   rel_type_column)
    if is_bidirectional:
        self.add_graph_relationships.remove_self_relationships()
        self.add_graph_relationships.make_relationships_bidirectional(settings["relationship_type"])
    else:
        self.add_graph_relationships.remove_self_relationships()

close()

Closes the Neo4j database driver connection.

Source code in chemgraphbuilder/graph_relationships_loader.py 
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def close(self):
    """Closes the Neo4j database driver connection."""
    self.driver.close()

main()

Main function to handle command-line arguments and run the GraphRelationshipsLoader.

Source code in chemgraphbuilder/graph_relationships_loader.py 
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def main():
    """Main function to handle command-line arguments and run the GraphRelationshipsLoader."""
    parser = argparse.ArgumentParser(description="Load graph relationships into"
                                                 "a Neo4j database.")
    parser.add_argument("--uri", type=str, required=True,
                        help="URI for the Neo4j database.")
    parser.add_argument("--username", type=str, required=True,
                        help="Username for the Neo4j database.")
    parser.add_argument("--password", type=str, required=True,
                        help="Password for the Neo4j database.")
    parser.add_argument("--relationship_type", type=str, required=True,
                        choices=['Assay_Compound', 'Assay_Gene', 'Gene_Protein',
                                 'Compound_Gene', 'Compound_Similarity',
                                 'Compound_Compound_CoOccurrence',
                                 'Compound_Gene_CoOccurrence',
                                 'Compound_Gene_Interaction',
                                 'Compound_Transformation'],
                        help="Type of the relationship to add.")

    args = parser.parse_args()

    loader = GraphRelationshipsLoader(args.uri, args.username, args.password)
    loader.add_relationships(args.relationship_type)
    loader.close()