1st_find_bugs_and_smells.ipynb

{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"provenance":[]},"kernelspec":{"name":"python3","display_name":"Python 3"},"language_info":{"name":"python"}},"cells":[{"cell_type":"markdown","source":["# Environment"],"metadata":{"id":"sAhoqzSEVqoG"}},{"cell_type":"code","execution_count":null,"metadata":{"id":"uW_62az96Tns"},"outputs":[],"source":["import json\n","import re\n","\n","import pandas as pd\n","\n","import psycopg2\n","from psycopg2 import Error\n","\n","from tqdm.auto import tqdm"]},{"cell_type":"markdown","source":["# Load project patches Data Frame\n","### A csv example file is available on the project repository"],"metadata":{"id":"vN4nOKCQV7av"}},{"cell_type":"code","source":["# Get project patches data and check number of total cases\n","df = pd.read_csv('projects_patches.csv')\n","print('Total cases in project_patches.csv:')\n","print(len(df))"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"XGn_l5pTW85b","executionInfo":{"status":"ok","timestamp":1696098670738,"user_tz":180,"elapsed":307,"user":{"displayName":"Orestes Bastos","userId":"10763828588366877923"}},"outputId":"1b62ff8a-d78a-41c6-df1a-683c42c24837"},"execution_count":null,"outputs":[{"output_type":"stream","name":"stdout","text":["Folder csv files created!\n"]}]},{"cell_type":"markdown","source":["# Connect to database and search for bugs and smells\n","### A database example file is available on the project repository"],"metadata":{"id":"nlte2lPO23eQ"}},{"cell_type":"code","source":["# Connect to an existing local database\n","connection = psycopg2.connect(user='postgres',\n","                              password='1234',\n","                              dbname='metrics')\n","# Create a cursor to perform database operations\n","cursor = connection.cursor()\n","counter_success = 0\n","\n","try:\n","\n","    # # Manual columns creation: (Only needed if database is not created via the example file)\n","    # psql_alter_query = 'ALTER TABLE public.class ADD COLUMN smells jsonb'\n","    # cursor.execute(psql_alter_query)\n","    # connection.commit()\n","    # psql_alter_query = 'ALTER TABLE public.class ADD COLUMN bug_fix boolean'\n","    # cursor.execute(psql_alter_query)\n","    # connection.commit()\n","\n","    # Loop for all rows in the csv file\n","    for index, row in tqdm(df.iterrows()):\n","        project_csv = row['project']\n","        file_path_csv = row['file_path']\n","\n","        # Fetch classes if it's the same project name and file path as in the csv row\n","        postgreSQL_select_Query = 'SELECT * FROM public.class WHERE project = %s AND position(%s in file)>0'\n","        cursor.execute(postgreSQL_select_Query, (project_csv, file_path_csv))\n","        classes = cursor.fetchall()\n","\n","        # Loop for all classes in the database with the same project as the current csv row\n","        for case in tqdm(classes):\n","\n","            # Set or reset bug fix flag as false for each case\n","            bug_fix_flag = False\n","\n","            # Fetch methods if it's the same class id as the id of the class in case\n","            class_id = case[0]\n","            postgreSQL_select_Query = 'SELECT * FROM public.method WHERE class_id = %s'\n","            cursor.execute(postgreSQL_select_Query, (class_id,))\n","            methods = cursor.fetchall()\n","\n","            # Findall to get only the numbers from all hunks, but separates in different tuples inside the list\n","            hunks = re.findall('@@ -(.*),(.*) [+](.*),(.*) @@', row['patch'])\n","\n","            for hunk in hunks:\n","                # get line number from class and compare with hunk intervals\n","                class_line_number = case[7]\n","                hunk_start = int(hunk[0])\n","                hunk_end = int(hunk[0]) + int(hunk[1])\n","\n","                # Check if line number in class table from database is within hunk intervals\n","                if hunk_start <= class_line_number <= hunk_end:\n","\n","                    # Set bug fix flag as true if line number within intervals\n","                    bug_fix_flag = True\n","\n","                for method in methods:\n","                    method_line_number = method[7]\n","\n","                    # Check if line number in method table from database is also within hunk intervals\n","                    if hunk_start <= method_line_number <= hunk_end:\n","\n","                        # Set bug fix flag as true if line number within intervals\n","                        bug_fix_flag = True\n","\n","            # Create or reset default smells results with all false as default before testing\n","            smells_results = {\n","                'MultifacetedAbstraction': False,\n","                'UnnecessaryAbstraction': False,\n","                'InsufficientModularization': False,\n","                'WideHierarchy': False,\n","                'LongMethod': False,\n","                'ComplexMethod': False\n","            }\n","\n","            # Get metrics for code smells for each class\n","            class_metrics = case[9]\n","\n","            # TODO: Change verifying all smells to a single function if practical\n","            if 'PercentLackOfCohesion' in class_metrics:\n","                smell_LCOM = class_metrics['PercentLackOfCohesion']\n","            else:\n","                smell_LCOM = 0\n","\n","            if 'CountDeclClassVariable' in class_metrics or 'CountDeclInstanceVariable' in class_metrics:\n","                smell_NOF = class_metrics['CountDeclClassVariable'] + class_metrics['CountDeclInstanceVariable']\n","            else:\n","                smell_NOF = 0\n","\n","            if 'CountDeclMethod' in class_metrics:\n","                smell_NOM = class_metrics['CountDeclMethod']\n","            else:\n","                smell_NOM = 0\n","\n","            if 'CountDeclMethodPublic' in class_metrics:\n","                smell_NOPM = class_metrics['CountDeclMethodPublic']\n","            else:\n","                smell_NOPM = 0\n","\n","            if 'SumCyclomaticModified' in class_metrics:\n","                smell_WMC = class_metrics['SumCyclomaticModified']\n","            else:\n","                smell_WMC = 0\n","\n","            if 'CountClassDerived' in class_metrics:\n","                smell_NC = class_metrics['CountClassDerived']\n","            else:\n","                smell_NC = 0\n","\n","            # Appears in both class and method but granularity appoints method only\n","            # if 'CountLine' in class_metrics:\n","            #     smell_LOC = class_metrics['CountLine']\n","            # else:\n","            #     smell_LOC = 0\n","\n","            # Individual test for each smell for each class\n","            if smell_LCOM >= 80 and smell_NOF >= 7 and smell_NOM >= 7:\n","                smells_results['MultifacetedAbstraction'] = True\n","\n","            if smell_NOF >= 5 and smell_NOM == 0:\n","                smells_results['UnnecessaryAbstraction'] = True\n","\n","            if smell_NOPM >= 20 or smell_NOM >= 30 or smell_WMC >= 100:\n","                smells_results['InsufficientModularization'] = True\n","\n","            if smell_NC >= 10:\n","                smells_results['WideHierarchy'] = True\n","\n","            for method in methods:\n","                # Get metrics for code smells for each method in that class\n","                method_metrics = method[9]\n","\n","                if 'CountLine' in method_metrics:\n","                    smell_LOC = method_metrics['CountLine']\n","                else:\n","                    smell_LOC = 0\n","                if 'Cyclomatic' in method_metrics:\n","                    smell_CC = method_metrics['Cyclomatic']\n","                else:\n","                    smell_CC = 0\n","\n","                # Individual test for each smell for each method\n","                if smell_LOC >= 100:\n","                    smells_results['LongMethod'] = True\n","\n","                if smell_CC >= 8:\n","                    smells_results['ComplexMethod'] = True\n","\n","            # Update class table marking as a bug fix commit\n","            postgreSQL_alter_Query = 'UPDATE public.class SET bug_fix = %s WHERE id = %s'\n","            cursor.execute(postgreSQL_alter_Query, (bug_fix_flag, class_id))\n","            connection.commit()\n","\n","            # Update database with the test for smells results\n","            postgreSQL_alter_Query = 'UPDATE public.class SET smells = %s WHERE id = %s'\n","            cursor.execute(postgreSQL_alter_Query, (json.dumps(smells_results), class_id))\n","            connection.commit()\n","\n","            # If it is a bug fix mark as a success\n","            if bug_fix_flag:\n","                counter_success += 1\n","            # # Conditional to check time needed and test script\n","            # if counter_success >= 1000:\n","                # raise Exception('Assigned counter limit reached')\n","\n","except (Exception, Error) as error:\n","    print('Error while connecting to PostgreSQL', error)\n","\n","finally:\n","    if connection:\n","        cursor.close()\n","        connection.close()\n","        print('PostgreSQL connection is closed')\n","        print('Successful cases:')\n","        print(counter_success)\n"],"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":394},"id":"zYbC9xVVWwZL","executionInfo":{"status":"error","timestamp":1696098679950,"user_tz":180,"elapsed":372,"user":{"displayName":"Orestes Bastos","userId":"10763828588366877923"}},"outputId":"4742813e-fffd-4baa-f571-542df4f68f2c"},"execution_count":null,"outputs":[{"output_type":"error","ename":"OperationalError","evalue":"ignored","traceback":["\u001b[0;31m---------------------------------------------------------------------------\u001b[0m","\u001b[0;31mOperationalError\u001b[0m                          Traceback (most recent call last)","\u001b[0;32m<ipython-input-4-f7c62c9e6d45>\u001b[0m in \u001b[0;36m<cell line: 2>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;31m# Connect to an existing database\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m connection = psycopg2.connect(user='postgres',\n\u001b[0m\u001b[1;32m      3\u001b[0m                               \u001b[0mpassword\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'1234'\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m                               dbname='metrics')\n\u001b[1;32m      5\u001b[0m \u001b[0;31m# Create a cursor to perform database operations\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n","\u001b[0;32m/usr/local/lib/python3.10/dist-packages/psycopg2/__init__.py\u001b[0m in \u001b[0;36mconnect\u001b[0;34m(dsn, connection_factory, cursor_factory, **kwargs)\u001b[0m\n\u001b[1;32m    120\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    121\u001b[0m     \u001b[0mdsn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_ext\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmake_dsn\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdsn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 122\u001b[0;31m     \u001b[0mconn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_connect\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdsn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mconnection_factory\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mconnection_factory\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwasync\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    123\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0mcursor_factory\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    124\u001b[0m         \u001b[0mconn\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcursor_factory\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcursor_factory\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n","\u001b[0;31mOperationalError\u001b[0m: connection to server on socket \"/var/run/postgresql/.s.PGSQL.5432\" failed: No such file or directory\n\tIs the server running locally and accepting connections on that socket?\n"]}]}]}