MEDfl 0.1.19__tar.gz → 0.1.21__tar.gz

{Medfl-0.1.19 → Medfl-0.1.21}/MEDfl.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: Medfl
-Version: 0.1.19
+Version: 0.1.21
 Summary: Python Open-source package for simulating federated learning and differential privacy
 Home-page: https://github.com/HaithemLamri/MEDfl
 Author: MEDomics consortium

{Medfl-0.1.19 → Medfl-0.1.21}/Medfl/NetManager/network.py

@@ -35,7 +35,7 @@ class Network:
 
         db_manager = DatabaseManager() ; 
         db_manager.connect() ; 
-        self.eng = db_manager.get_connection() ;
+        self.eng = db_manager.get_connection()
 
     def validate(self):
         """Validate name"""

{Medfl-0.1.19 → Medfl-0.1.21}/Medfl/NetManager/node.py

@@ -1,10 +1,9 @@
 import pandas as pd
 
-from scripts.base import *
 from .net_helper import *
 from .net_manager_queries import *
 from Medfl.LearningManager.utils import params
-
+from Medfl.NetManager.database_connector import DatabaseManager
 
 class Node:
     """
@@ -17,7 +16,7 @@ class Node:
     """
 
     def __init__(
-        self, name: str, train: int, test_fraction: float = 0.2, engine=my_eng
+        self, name: str, train: int, test_fraction: float = 0.2, engine=None
     ):
         """
         Initialize a Node instance.
@@ -30,7 +29,11 @@ class Node:
         self.name = name
         self.train = train
         self.test_fraction = 1.0 if self.train == 0 else test_fraction
-        self.engine = engine
+       
+
+        db_manager = DatabaseManager() ; 
+        db_manager.connect() ; 
+        self.engine = db_manager.get_connection()
 
     def validate(self):
         """Validate name, train, test_fraction"""

{Medfl-0.1.19 → Medfl-0.1.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: Medfl
-Version: 0.1.19
+Version: 0.1.21
 Summary: Python Open-source package for simulating federated learning and differential privacy
 Home-page: https://github.com/HaithemLamri/MEDfl
 Author: MEDomics consortium

{Medfl-0.1.19 → Medfl-0.1.21}/notebooks/banchmarking/MEDfl_benchmarks.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -19,21 +19,48 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
-     "ename": "KeyError",
-     "evalue": "'mysql'",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[1;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
-      "Cell \u001b[1;32mIn[5], line 16\u001b[0m\n\u001b[0;32m     11\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mtorch\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mnn\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mfunctional\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mF\u001b[39;00m\n\u001b[0;32m     14\u001b[0m \u001b[39m## MedFL Imports \u001b[39;00m\n\u001b[0;32m     15\u001b[0m \u001b[39m## Network Manager Imports \u001b[39;00m\n\u001b[1;32m---> 16\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mMedfl\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mNetManager\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mnode\u001b[39;00m \u001b[39mimport\u001b[39;00m Node\n\u001b[0;32m     17\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mMedfl\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mNetManager\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mnetwork\u001b[39;00m \u001b[39mimport\u001b[39;00m Network\n\u001b[0;32m     18\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mMedfl\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mNetManager\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mdataset\u001b[39;00m \u001b[39mimport\u001b[39;00m DataSet\n",
-      "File \u001b[1;32m~\\AppData\\Roaming\\Python\\Python39\\site-packages\\Medfl\\NetManager\\node.py:3\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[39mimport\u001b[39;00m \u001b[39mpandas\u001b[39;00m \u001b[39mas\u001b[39;00m \u001b[39mpd\u001b[39;00m\n\u001b[1;32m----> 3\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mscripts\u001b[39;00m\u001b[39m.\u001b[39;00m\u001b[39mbase\u001b[39;00m \u001b[39mimport\u001b[39;00m \u001b[39m*\u001b[39m\n\u001b[0;32m      4\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39m.\u001b[39;00m\u001b[39mnet_helper\u001b[39;00m \u001b[39mimport\u001b[39;00m \u001b[39m*\u001b[39m\n\u001b[0;32m      5\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39m.\u001b[39;00m\u001b[39mnet_manager_queries\u001b[39;00m \u001b[39mimport\u001b[39;00m \u001b[39m*\u001b[39m\n",
-      "File \u001b[1;32m~\\AppData\\Roaming\\Python\\Python39\\site-packages\\scripts\\base.py:16\u001b[0m\n\u001b[0;32m     14\u001b[0m config \u001b[39m=\u001b[39m ConfigParser()\n\u001b[0;32m     15\u001b[0m config\u001b[39m.\u001b[39mread(config_file_path)\n\u001b[1;32m---> 16\u001b[0m mysql_config \u001b[39m=\u001b[39m config[\u001b[39m'\u001b[39;49m\u001b[39mmysql\u001b[39;49m\u001b[39m'\u001b[39;49m]\n\u001b[0;32m     20\u001b[0m connection_string \u001b[39m=\u001b[39m (\n\u001b[0;32m     21\u001b[0m     \u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mmysql+mysqlconnector://\u001b[39m\u001b[39m{\u001b[39;00mmysql_config[\u001b[39m'\u001b[39m\u001b[39muser\u001b[39m\u001b[39m'\u001b[39m]\u001b[39m}\u001b[39;00m\u001b[39m:\u001b[39m\u001b[39m{\u001b[39;00mmysql_config[\u001b[39m'\u001b[39m\u001b[39mpassword\u001b[39m\u001b[39m'\u001b[39m]\u001b[39m}\u001b[39;00m\u001b[39m@\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[0;32m     22\u001b[0m     \u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m{\u001b[39;00mmysql_config[\u001b[39m'\u001b[39m\u001b[39mhost\u001b[39m\u001b[39m'\u001b[39m]\u001b[39m}\u001b[39;00m\u001b[39m:\u001b[39m\u001b[39m{\u001b[39;00mmysql_config[\u001b[39m'\u001b[39m\u001b[39mport\u001b[39m\u001b[39m'\u001b[39m]\u001b[39m}\u001b[39;00m\u001b[39m/\u001b[39m\u001b[39m{\u001b[39;00mmysql_config[\u001b[39m'\u001b[39m\u001b[39mdatabase\u001b[39m\u001b[39m'\u001b[39m]\u001b[39m}\u001b[39;00m\u001b[39m\"\u001b[39m\n\u001b[0;32m     23\u001b[0m )\n\u001b[0;32m     25\u001b[0m eng \u001b[39m=\u001b[39m create_engine(\n\u001b[0;32m     26\u001b[0m     connection_string,\n\u001b[0;32m     27\u001b[0m     execution_options\u001b[39m=\u001b[39m{\u001b[39m\"\u001b[39m\u001b[39mautocommit\u001b[39m\u001b[39m\"\u001b[39m: \u001b[39mTrue\u001b[39;00m},\n\u001b[0;32m     28\u001b[0m )\n",
-      "File \u001b[1;32mc:\\Python39\\lib\\configparser.py:960\u001b[0m, in \u001b[0;36mRawConfigParser.__getitem__\u001b[1;34m(self, key)\u001b[0m\n\u001b[0;32m    958\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39m__getitem__\u001b[39m(\u001b[39mself\u001b[39m, key):\n\u001b[0;32m    959\u001b[0m     \u001b[39mif\u001b[39;00m key \u001b[39m!=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mdefault_section \u001b[39mand\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mhas_section(key):\n\u001b[1;32m--> 960\u001b[0m         \u001b[39mraise\u001b[39;00m \u001b[39mKeyError\u001b[39;00m(key)\n\u001b[0;32m    961\u001b[0m     \u001b[39mreturn\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39m_proxies[key]\n",
-      "\u001b[1;31mKeyError\u001b[0m: 'mysql'"
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "C:\\Users\\HP User\\AppData\\Roaming\\Python\\Python39\\site-packages\\tqdm\\auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
+      "  from .autonotebook import tqdm as notebook_tqdm\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "getting connection\n"
+     ]
+    }
+   ],
+   "source": [
+    "from Medfl.LearningManager.utils import *\n",
+    "from Medfl.NetManager.database_connector import DatabaseManager\n",
+    "\n",
+    "set_db_config('../../scripts/config.ini')\n",
+    "\n",
+    "db_manager = DatabaseManager()\n",
+    "db_manager.connect()\n",
+    "db_manager.get_connection()\n",
+    "\n",
+    "print('getting connection')\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "2024-04-23 20:40:29,282\tINFO util.py:159 -- Missing packages: ['ipywidgets']. Run `pip install -U ipywidgets`, then restart the notebook server for rich notebook output.\n"
      ]
     }
    ],
@@ -57,7 +84,7 @@
     "from Medfl.NetManager.network import Network\n",
     "from Medfl.NetManager.dataset import DataSet\n",
     "from Medfl.NetManager.flsetup import FLsetup\n",
-    "from Medfl.NetManager.database_connector import DatabaseManager\n",
+    "\n",
     "# flower imports \n",
     "import flwr as fl\n",
     "\n",
@@ -78,7 +105,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -108,7 +135,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -117,7 +144,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -128,7 +155,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -138,7 +165,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -148,7 +175,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -375,7 +402,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -413,7 +440,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -423,7 +450,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -437,7 +464,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -484,7 +511,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -520,7 +547,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -549,7 +576,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -560,18 +587,29 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 17,
    "metadata": {},
    "outputs": [
     {
-     "ename": "NameError",
-     "evalue": "name 'benchmarks_config' is not defined",
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Executing the: TL configurations\n",
+      "Executing th confuguration\n",
+      "{'Tl': True, 'train_test': True, 'train_portion': 0.5, 'aggreg_algo': 'FedAvg', 'dp_activate': False, 'n_clients': 10}\n"
+     ]
+    },
+    {
+     "ename": "CalledProcessError",
+     "evalue": "Command '['python', 'C:\\\\Users\\\\HP User\\\\AppData\\\\Roaming\\\\Python\\\\Python39\\\\site-packages\\\\Medfl\\\\NetManager\\\\..\\\\scripts\\\\create_db.py', '../data/masterDataSet/Mimic_ouael.csv']' returned non-zero exit status 2.",
      "output_type": "error",
      "traceback": [
       "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
-      "Cell \u001b[1;32mIn[3], line 2\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[39m# Loop Over the benchmark configs\u001b[39;00m\n\u001b[1;32m----> 2\u001b[0m \u001b[39mfor\u001b[39;00m key \u001b[39min\u001b[39;00m benchmarks_config\u001b[39m.\u001b[39mkeys():\n\u001b[0;32m      3\u001b[0m     \u001b[39mprint\u001b[39m(\u001b[39m\"\u001b[39m\u001b[39mExecuting the: \u001b[39m\u001b[39m\"\u001b[39m \u001b[39m+\u001b[39m key \u001b[39m+\u001b[39m \u001b[39m\"\u001b[39m\u001b[39m configurations\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[0;32m      4\u001b[0m     \u001b[39mfor\u001b[39;00m config \u001b[39min\u001b[39;00m benchmarks_config[key]:\n",
-      "\u001b[1;31mNameError\u001b[0m: name 'benchmarks_config' is not defined"
+      "\u001b[1;31mCalledProcessError\u001b[0m                        Traceback (most recent call last)",
+      "Cell \u001b[1;32mIn[17], line 14\u001b[0m\n\u001b[0;32m      9\u001b[0m     \u001b[39mbreak\u001b[39;00m\n\u001b[0;32m     10\u001b[0m \u001b[39m# Create the MEDfl pipeline for each config\u001b[39;00m\n\u001b[1;32m---> 14\u001b[0m db_manager\u001b[39m.\u001b[39;49mcreate_MEDfl_db(path_to_csv\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39m../data/masterDataSet/Mimic_ouael.csv\u001b[39;49m\u001b[39m\"\u001b[39;49m)\n\u001b[0;32m     16\u001b[0m \u001b[39m# if the differential privac is activated change the epsilon and delta on the params file \u001b[39;00m\n\u001b[0;32m     17\u001b[0m \u001b[39mif\u001b[39;00m(config[\u001b[39m\"\u001b[39m\u001b[39mdp_activate\u001b[39m\u001b[39m\"\u001b[39m]):\n",
+      "File \u001b[1;32m~\\AppData\\Roaming\\Python\\Python39\\site-packages\\Medfl\\NetManager\\database_connector.py:40\u001b[0m, in \u001b[0;36mDatabaseManager.create_MEDfl_db\u001b[1;34m(self, path_to_csv)\u001b[0m\n\u001b[0;32m     37\u001b[0m create_db_script_path \u001b[39m=\u001b[39m os\u001b[39m.\u001b[39mpath\u001b[39m.\u001b[39mjoin(current_directory, \u001b[39m'\u001b[39m\u001b[39m..\u001b[39m\u001b[39m'\u001b[39m, \u001b[39m'\u001b[39m\u001b[39mscripts\u001b[39m\u001b[39m'\u001b[39m, \u001b[39m'\u001b[39m\u001b[39mcreate_db.py\u001b[39m\u001b[39m'\u001b[39m)\n\u001b[0;32m     39\u001b[0m \u001b[39m# Execute the create_db.py script\u001b[39;00m\n\u001b[1;32m---> 40\u001b[0m subprocess\u001b[39m.\u001b[39;49mrun([\u001b[39m'\u001b[39;49m\u001b[39mpython\u001b[39;49m\u001b[39m'\u001b[39;49m, create_db_script_path, path_to_csv], check\u001b[39m=\u001b[39;49m\u001b[39mTrue\u001b[39;49;00m)\n\u001b[0;32m     42\u001b[0m \u001b[39mreturn\u001b[39;00m\n",
+      "File \u001b[1;32mc:\\Python39\\lib\\subprocess.py:528\u001b[0m, in \u001b[0;36mrun\u001b[1;34m(input, capture_output, timeout, check, *popenargs, **kwargs)\u001b[0m\n\u001b[0;32m    526\u001b[0m     retcode \u001b[39m=\u001b[39m process\u001b[39m.\u001b[39mpoll()\n\u001b[0;32m    527\u001b[0m     \u001b[39mif\u001b[39;00m check \u001b[39mand\u001b[39;00m retcode:\n\u001b[1;32m--> 528\u001b[0m         \u001b[39mraise\u001b[39;00m CalledProcessError(retcode, process\u001b[39m.\u001b[39margs,\n\u001b[0;32m    529\u001b[0m                                  output\u001b[39m=\u001b[39mstdout, stderr\u001b[39m=\u001b[39mstderr)\n\u001b[0;32m    530\u001b[0m \u001b[39mreturn\u001b[39;00m CompletedProcess(process\u001b[39m.\u001b[39margs, retcode, stdout, stderr)\n",
+      "\u001b[1;31mCalledProcessError\u001b[0m: Command '['python', 'C:\\\\Users\\\\HP User\\\\AppData\\\\Roaming\\\\Python\\\\Python39\\\\site-packages\\\\Medfl\\\\NetManager\\\\..\\\\scripts\\\\create_db.py', '../data/masterDataSet/Mimic_ouael.csv']' returned non-zero exit status 2."
      ]
     }
    ],
@@ -588,13 +626,7 @@
     "                break\n",
     "            # Create the MEDfl pipeline for each config\n",
     "\n",
-    "            set_db_config('../../scripts/config.ini')\n",
-    "\n",
-    "            db_manager = DatabaseManager()\n",
-    "            db_manager.connect()\n",
-    "            db_manager.get_connection()\n",
-    "\n",
-    "            print('getting connection')\n",
+    "            \n",
     "\n",
     "            db_manager.create_MEDfl_db(path_to_csv=\"../data/masterDataSet/Mimic_ouael.csv\")\n",
     "\n",

{Medfl-0.1.19 → Medfl-0.1.21}/scripts/create_db.py

@@ -6,17 +6,14 @@ from mysql.connector import Error
 from configparser import ConfigParser
 import os
 
+from Medfl.NetManager.database_connector import DatabaseManager
+
 def main(csv_file_path):
     try:
-        # Get the directory of the current script
-        current_directory = os.path.dirname(os.path.abspath(__file__))
-
-        # Load configuration from the config file
-        config_file_path = os.path.join(current_directory, 'config.ini')
-
-        config = ConfigParser()
-        config.read(config_file_path)
-        mysql_config = config['mysql']
+        db_manager = DatabaseManager() ; 
+        db_manager.connect() ; 
+        mysql_config = db_manager.get_connection()
+        
 
         mydb = mysql.connector.connect(host=mysql_config['host'], user=mysql_config['user'], password=mysql_config['password'])
         mycursor = mydb.cursor()

{Medfl-0.1.19 → Medfl-0.1.21}/setup.py

@@ -14,7 +14,7 @@ with open('requirements.txt') as f:
 
 setup(
     name="Medfl",
-    version="0.1.19",
+    version="0.1.21",
     author="MEDomics consortium",
     author_email="medomics.info@gmail.com",
     description="Python Open-source package for simulating federated learning and differential privacy",