MEDfl 0.1.26__py3-none-any.whl → 0.1.28__py3-none-any.whl

MEDfl/NetManager/net_manager_queries.py

@@ -0,0 +1,137 @@
+from .net_helper import is_str
+
+INSERT_DATASET = """
+    INSERT INTO DataSets(DataSetName, NodeId, {columns})
+    VALUES (:name, :NodeId, {values})
+"""
+DELETE_DATASET = """
+    DELETE FROM DataSets WHERE DataSetName = :name
+"""
+
+SELECT_ALL_DATASET_NAMES = """
+    SELECT DISTINCT DataSetName,NodeId FROM DataSets
+"""
+
+SELECT_DATASET_BY_NAME = """
+    SELECT * FROM DataSets WHERE DataSetName = :name
+"""
+
+# node queries
+# sql_queries.py
+
+INSERT_NODE_QUERY = (
+    "INSERT INTO Nodes(NodeName,NetId,train) VALUES ('{}',{}, {})"
+)
+DELETE_NODE_QUERY = "DELETE FROM Nodes WHERE NodeName = '{}'"
+SELECT_MASTER_COLUMNS_QUERY = "SELECT * FROM MasterDataset LIMIT 1"
+SELECT_DATASET_BY_COLUMN_QUERY = "SELECT * FROM MasterDataset WHERE {} = '{}'"
+SELECT_DATASET_BY_NODE_ID_QUERY = "SELECT * FROM DataSets WHERE NodeId = {}"
+
+SELECT_ALL_DATASETS_QUERY = "SELECT DISTINCT DataSetName,NodeName FROM DataSets,Nodes WHERE Nodes.NodeName = '{}' and Nodes.NodeId = DataSets.NodeId"
+SELECT_ALL_NODES_QUERY = "SELECT * FROM Nodes"
+
+
+# SQL query to insert a new network
+INSERT_NETWORK_QUERY = "INSERT INTO Networks(NetName) VALUES ('{name}')"
+
+# SQL query to delete a network
+DELETE_NETWORK_QUERY = "DELETE FROM Networks WHERE NetName = '{name}'"
+
+# SQL query to delete a network
+GET_NETWORK_QUERY = "SELECT * FROM Networks WHERE NetName = '{name}'"
+
+
+# SQL query to update a network
+UPDATE_NETWORK_QUERY = (
+    "UPDATE Networks SET FLsetupId = {FLsetupId} WHERE NetId = {id}"
+)
+
+# SQL query to retrieve all nodes for a network
+LIST_ALL_NODES_QUERY = "SELECT Nodes.NodeName, Networks.NetName FROM Nodes, Networks WHERE Networks.NetName = '{name}' AND Networks.NetId = Nodes.NetId"
+
+# SQL query to create the MasterDataset table
+CREATE_MASTER_DATASET_TABLE_QUERY = """
+CREATE TABLE IF NOT EXISTS MasterDataset (
+    PatientId INT NOT NULL AUTO_INCREMENT,
+    {},
+    PRIMARY KEY (PatientId)
+);
+"""
+
+# SQL query to create the datasets table
+CREATE_DATASETS_TABLE_QUERY = """
+CREATE TABLE IF NOT EXISTS Datasets (
+                     DataSetId INT NOT NULL AUTO_INCREMENT, 
+                     DataSetName VARCHAR(255), 
+                     NodeId INT,
+                     {},
+                     PRIMARY KEY (DataSetId)
+                     
+);
+"""
+
+# SQL query to insert dataset values
+INSERT_DATASET_VALUES_QUERY = "INSERT INTO MasterDataset({columns}, NodeId) VALUES ('{name}', {nodeId}, {values})"
+
+
+# FL setup_queries
+# sql_queries.py
+
+CREATE_FLSETUP_QUERY = """
+    INSERT INTO FLsetup (name, description, creation_date, NetId, column_name)
+    VALUES (:name, :description, :creation_date, :net_id, :column_name)
+"""
+
+DELETE_FLSETUP_QUERY = """
+    DELETE FROM FLsetup
+    WHERE name = :name
+"""
+
+UPDATE_FLSETUP_QUERY = UPDATE_NETWORK_QUERY = (
+    "UPDATE FLsetup SET column_name ='{column_name}' WHERE name ='{FLsetupName}'"
+)
+
+
+READ_SETUP_QUERY = """
+    SELECT * FROM FLsetup
+    WHERE FLsetupId = :flsetup_id
+"""
+
+READ_ALL_SETUPS_QUERY = """
+    SELECT * FROM FLsetup
+"""
+
+READ_NETWORK_BY_ID_QUERY = """
+    SELECT * FROM Networks
+    WHERE NetId = :net_id
+"""
+
+READ_DISTINCT_NODES_QUERY = """
+SELECT DISTINCT {} FROM MasterDataset 
+"""
+
+
+# FederatedDataset Queries
+INSERT_FLDATASET_QUERY = (
+    "INSERT INTO FedDatasets(name, FLsetupId) VALUES (:name, :FLsetupId)"
+)
+DELETE_FLDATASET_BY_SETUP_AND_PIPELINE_QUERY = "DELETE FROM FedDatasets WHERE FLsetupId = :FLsetupId AND FLpipeId = :FLpipeId"
+
+
+UPDATE_FLDATASET_QUERY = (
+    "UPDATE FedDatasets SET FLpipeId = :FLpipeId WHERE FedId = :FedId"
+)
+SELECT_FLDATASET_BY_NAME_QUERY = "SELECT * FROM FedDatasets WHERE name = :name"
+
+CREATE_FLPIPELINE_QUERY = """
+INSERT INTO FLpipeline (name, description, creation_date, results)
+VALUES ('{name}', '{description}', '{creation_date}', '{result}')
+"""
+DELETE_FLPIPELINE_QUERY = "DELETE FROM FLpipeline WHERE name = '{name}'"
+
+SELECT_FLPIPELINE_QUERY = "SELECT FROM FLpipeline WHERE name = '{name}'"
+
+CREATE_TEST_RESULTS_QUERY = """
+INSERT INTO testResults (pipelineid, nodename, confusionmatrix, accuracy , sensivity, ppv , npv , f1score , fpr , tpr )
+VALUES ('{pipelineId}', '{nodeName}', '{confusion_matrix}', '{accuracy}' , '{sensivity}' , '{ppv}' , '{npv}' , '{f1score}' , '{fpr}' , '{tpr}')
+"""

MEDfl/NetManager/network.py

@@ -0,0 +1,174 @@
+# src/MEDfl/NetManager/network.py
+
+from MEDfl.LearningManager.utils import *
+
+from .net_helper import *
+from .net_manager_queries import (CREATE_MASTER_DATASET_TABLE_QUERY,
+                                  CREATE_DATASETS_TABLE_QUERY,
+                                  DELETE_NETWORK_QUERY,
+                                  INSERT_NETWORK_QUERY, LIST_ALL_NODES_QUERY,
+                                  UPDATE_NETWORK_QUERY, GET_NETWORK_QUERY)
+from .node import Node
+import pandas as pd
+from MEDfl.LearningManager.utils import params
+
+from sqlalchemy import text
+
+
+class Network:
+    """
+    A class representing a network.
+
+    Attributes:
+        name (str): The name of the network.
+        mtable_exists (int): An integer flag indicating whether the MasterDataset table exists (1) or not (0).
+    """
+
+    def __init__(self, name: str = ""):
+        """
+        Initialize a Network instance.
+
+        Parameters:
+            name (str): The name of the network.
+        """
+        self.name = name
+        self.mtable_exists = int(master_table_exists())
+        self.validate()
+
+        db_manager = DatabaseManager() ; 
+        db_manager.connect() ; 
+        self.eng = db_manager.get_connection()
+
+    def validate(self):
+        """Validate name"""
+
+        if not isinstance(self.name, str):
+            raise TypeError("name argument must be a string")
+
+    def create_network(self):
+        """Create a new network in the database."""
+        self.eng.execute(text(INSERT_NETWORK_QUERY.format(name=self.name)))
+        self.id = get_netid_from_name(self.name)
+
+    def use_network(self, network_name: str):
+        """Use a network in the database.
+
+        Parameters:
+            network_name (str): The name of the network to use.
+
+        Returns:
+            Network or None: An instance of the Network class if the network exists, else None.
+        
+        """
+        network = pd.read_sql(
+            text(GET_NETWORK_QUERY.format(name=network_name)),
+            self.eng,
+        )
+
+        if (network.NetId[0]):
+            self.name = network.NetName[0]
+            self.id = network.NetId[0]
+            self.mtable_exists = int(master_table_exists())
+            self.validate()
+            return self
+        else:
+            return None
+
+    def delete_network(self):
+        """Delete the network from the database."""
+        self.eng.execute(text(DELETE_NETWORK_QUERY.format(name=self.name)))
+
+    def update_network(self, FLsetupId: int):
+        """Update the network's FLsetupId in the database.
+        
+        Parameters:
+            FLsetupId (int): The FLsetupId to update.
+        """
+        self.eng.execute(
+            text(UPDATE_NETWORK_QUERY.format(FLsetupId=FLsetupId, id=self.id))
+        )
+
+    def add_node(self, node: Node):
+        """Add a node to the network.
+
+        Parameters:
+            node (Node): The node to add.
+        """
+        node.create_node(self.id)
+
+    def list_allnodes(self):
+        """List all nodes in the network.
+
+        Parameters:
+            None
+
+        Returns:
+            DataFrame: A DataFrame containing information about all nodes in the network.
+        
+        """
+        query = text(LIST_ALL_NODES_QUERY.format(name=self.name))
+        result_proxy = self.eng.execute(query)
+        result_df = pd.DataFrame(result_proxy.fetchall(), columns=result_proxy.keys())
+        return result_df
+
+    def create_master_dataset(self, path_to_csv: str = params['path_to_master_csv']):
+        """
+        Create the MasterDataset table and insert dataset values.
+
+        :param path_to_csv: Path to the CSV file containing the dataset.
+        """
+        print(path_to_csv)
+        # Read the CSV file into a Pandas DataFrame
+        data_df = pd.read_csv(path_to_csv)
+
+        # Process the data if needed (e.g., handle missing values, encode categorical variables)
+        # ...
+
+        # Check if the MasterDataset table exists
+
+        if self.mtable_exists != 1:
+            columns = data_df.columns.tolist()
+            columns_str = ",\n".join(
+                [
+                    f"{col} {column_map[str(data_df[col].dtype)]}"
+                    for col in columns
+                ]
+            )
+            self.eng.execute(
+                text(CREATE_MASTER_DATASET_TABLE_QUERY.format(columns_str))
+            )
+            self.eng.execute(text(CREATE_DATASETS_TABLE_QUERY.format(columns_str)))
+
+            # Get the list of columns in the DataFrame
+
+            data_df = process_eicu(data_df)
+            # Insert the dataset values into the MasterDataset table
+
+            for index, row in data_df.iterrows():
+                query_1 = "INSERT INTO MasterDataset(" + "".join(
+                    f"{x}," for x in columns
+                )
+                query_2 = f"VALUES (" + "".join(
+                    f"{is_str(data_df, row, x)}," for x in columns
+                )
+                query = query_1[:-1] + ")" + query_2[:-1] + ")"
+                self.eng.execute(text(query))
+
+        # Set mtable_exists flag to True
+        self.mtable_exists = 1
+
+    @staticmethod
+    def list_allnetworks():
+        """List all networks in the database.
+        Returns:
+            DataFrame: A DataFrame containing information about all networks in the database.
+        
+        """
+        db_manager = DatabaseManager() ; 
+        db_manager.connect() ; 
+        my_eng = db_manager.get_connection() ;
+
+        result_proxy = my_eng.execute("SELECT * FROM Networks")
+        result = result_proxy.fetchall()
+        return result
+

MEDfl/NetManager/node.py

@@ -0,0 +1,178 @@
+import pandas as pd
+
+from .net_helper import *
+from .net_manager_queries import *
+from MEDfl.LearningManager.utils import params
+from MEDfl.NetManager.database_connector import DatabaseManager
+
+class Node:
+    """
+    A class representing a node in the network.
+
+    Attributes:
+        name (str): The name of the node.
+        train (int): An integer flag representing whether the node is used for training (1) or testing (0).
+        test_fraction (float, optional): The fraction of data used for testing when train=1. Default is 0.2.
+    """
+
+    def __init__(
+        self, name: str, train: int, test_fraction: float = 0.2, engine=None
+    ):
+        """
+        Initialize a Node instance.
+
+        Parameters:
+            name (str): The name of the node.
+            train (int): An integer flag representing whether the node is used for training (1) or testing (0).
+            test_fraction (float, optional): The fraction of data used for testing when train=1. Default is 0.2.
+        """
+        self.name = name
+        self.train = train
+        self.test_fraction = 1.0 if self.train == 0 else test_fraction
+       
+
+        db_manager = DatabaseManager() ; 
+        db_manager.connect() ; 
+        self.engine = db_manager.get_connection()
+
+    def validate(self):
+        """Validate name, train, test_fraction"""
+        if not isinstance(self.name, str):
+            raise TypeError("name argument must be a string")
+
+        if not isinstance(self.train, int):
+            raise TypeError("train argument must be an int")
+
+        if not isinstance(self.test_fraction, float):
+            raise TypeError("test_fraction argument must be a float")
+
+    def create_node(self, NetId: int):
+        """Create a node in the database.
+        Parameters:
+            NetId (int): The ID of the network to which the node belongs.
+
+        Returns:
+            None
+        """
+        self.engine.execute(
+            text(INSERT_NODE_QUERY.format(self.name, NetId, self.train))
+        )
+
+    def delete_node(self):
+        """Delete the node from the database."""
+        self.engine.execute(text(DELETE_NODE_QUERY.format(self.name)))
+
+    def check_dataset_compatibility(self, data_df):
+        """Check if the dataset is compatible with the master dataset.
+        Parameters:
+            data_df (DataFrame): The dataset to check.
+
+        Returns:
+            None
+        """
+        if master_table_exists() != 1:
+            print("MasterDataset doesn't exist")
+        else:
+            columns = data_df.columns.tolist()
+            
+            # get master_dataset columns
+            result_proxy = self.engine.execute(SELECT_MASTER_COLUMNS_QUERY)
+            master_table_columns = result_proxy.keys()
+
+
+            assert [x == y for x, y in zip(master_table_columns, columns)]
+
+    def update_node(self):
+        """Update the node information (not implemented)."""
+        pass
+
+    def get_dataset(self, column_name: str = None):
+        """Get the dataset for the node based on the given column name.
+        Parameters:
+            column_name (str, optional): The column name to filter the dataset. Default is None.
+
+        Returns:
+            DataFrame: The dataset associated with the node.
+        """
+        NodeId = get_nodeid_from_name(self.name)
+        if column_name is not None:
+            query = text(SELECT_DATASET_BY_COLUMN_QUERY.format(column_name, self.name))
+        else:
+            query = text(SELECT_DATASET_BY_NODE_ID_QUERY.format(NodeId))
+
+        result_proxy = self.engine.execute(query)
+        node_dataset = pd.DataFrame(result_proxy.fetchall(), columns=result_proxy.keys())
+
+        return node_dataset
+
+    def upload_dataset(self, dataset_name: str, path_to_csv: str = params['path_to_test_csv']):
+        """Upload the dataset to the database for the node.
+        Parameters:
+            dataset_name (str): The name of the dataset.
+            path_to_csv (str, optional): Path to the CSV file containing the dataset. Default is the path in params.
+
+        Returns:
+            None
+        """
+        data_df = pd.read_csv(path_to_csv)
+
+        nodeId = get_nodeid_from_name(self.name)
+        columns = data_df.columns.tolist()
+        self.check_dataset_compatibility(data_df)
+
+        data_df = process_eicu(data_df)
+        for index, row in data_df.iterrows():
+            query_1 = "INSERT INTO DataSets(DataSetName,nodeId," + "".join(
+                f"{x}," for x in columns
+            )
+            query_2 = f" VALUES ('{dataset_name}',{nodeId}, " + "".join(
+                f"{is_str(data_df, row, x)}," for x in columns
+            )
+            query = query_1[:-1] + ")" + query_2[:-1] + ")"
+            self.engine.execute(text(query))
+
+    def assign_dataset(self, dataset_name:str):
+        """Assigning existing dataSet to node
+        Parameters:
+            dataset_name (str): The name of the dataset to assign.
+
+        Returns:
+            None
+        """
+
+        nodeId = get_nodeid_from_name(self.name)
+        query = f"UPDATE DataSets SET nodeId = {nodeId} WHERE DataSetName = '{dataset_name}'"
+        self.engine.execute(text(query))
+
+    def unassign_dataset(self, dataset_name:str):
+        """unssigning existing dataSet to node
+        Parameters:
+            dataset_name (str): The name of the dataset to assign.
+
+        Returns:
+            None
+        """
+
+        query = f"UPDATE DataSets SET nodeId = {-1} WHERE DataSetName = '{dataset_name}'"
+        self.engine.execute(text(query))
+
+    def list_alldatasets(self):
+        """List all datasets associated with the node.
+        Returns:
+            DataFrame: A DataFrame containing information about all datasets associated with the node.
+        
+        """
+        return pd.read_sql(
+            text(SELECT_ALL_DATASETS_QUERY.format(self.name)), my_eng
+        )
+
+    @staticmethod
+    def list_allnodes():
+        """List all nodes in the database.
+        Returns:
+            DataFrame: A DataFrame containing information about all nodes in the database.
+        
+        """
+        query = text(SELECT_ALL_NODES_QUERY)
+        res = pd.read_sql(query, my_eng)
+        return res

MEDfl/__init__.py

@@ -0,0 +1,2 @@
+from .LearningManager import *
+from .NetManager import *

{MEDfl-0.1.26.data → MEDfl-0.1.28.data}/scripts/setup_mysql.sh

@@ -1,22 +1,22 @@
-echo '#!/bin/bash
-
-# Update package lists
-sudo apt update
-
-# Install MySQL
-sudo apt install mysql-server
-
-# Secure MySQL installation
-sudo mysql_secure_installation
-
-# Install phpMyAdmin
-sudo apt install phpmyadmin
-
-# Create symbolic link for Apache
-sudo ln -s /etc/phpmyadmin/apache.conf /etc/apache2/conf-available/phpmyadmin.conf
-sudo a2enconf phpmyadmin
-sudo systemctl reload apache2
-
-# Print completion message
-echo "MySQL and phpMyAdmin setup complete."
-' > setup_mysql.sh && chmod +x setup_mysql.sh && python3 scripts/create_db.py
+echo '#!/bin/bash
+
+# Update package lists
+sudo apt update
+
+# Install MySQL
+sudo apt install mysql-server
+
+# Secure MySQL installation
+sudo mysql_secure_installation
+
+# Install phpMyAdmin
+sudo apt install phpmyadmin
+
+# Create symbolic link for Apache
+sudo ln -s /etc/phpmyadmin/apache.conf /etc/apache2/conf-available/phpmyadmin.conf
+sudo a2enconf phpmyadmin
+sudo systemctl reload apache2
+
+# Print completion message
+echo "MySQL and phpMyAdmin setup complete."
+' > setup_mysql.sh && chmod +x setup_mysql.sh && python3 scripts/create_db.py