<gh_stars>10-100
import os
import sys
import re
import shutil
from pathlib import Path
from app import emitter, logger, definitions, values, reader, synthesis, extractor
from app.utilities import error_exit


def read_conf(arg_list):
    emitter.normal("reading configuration values from arguments")
    if len(arg_list) > 0:
        for arg in arg_list:
            if definitions.ARG_DEBUG in arg:
                values.DEBUG = True
            elif definitions.ARG_CONF_FILE in arg:
                values.FILE_CONFIGURATION = str(arg).replace(definitions.ARG_CONF_FILE, '')
            elif definitions.ARG_DISABLE_DISTANCE_CAL in arg:
                values.IS_DISABLE_DISTANCE_CAL = True
            elif definitions.ARG_COLLECT_STAT in arg:
                values.CONF_COLLECT_STAT = True
            elif definitions.ARG_DIST_METRIC in arg:
                option = int(arg.replace(definitions.ARG_DIST_METRIC, ''))
                values.CONF_DISTANCE_METRIC = values.OPTIONS_DIST_METRIC[option]
            elif definitions.ARG_LOW_BOUND in arg:
                bound_value = int(arg.replace(definitions.ARG_LOW_BOUND, ''))
                values.CONF_LOW_BOUND = bound_value
            elif definitions.ARG_MAX_BOUND in arg:
                bound_value = int(arg.replace(definitions.ARG_MAX_BOUND, ''))
                values.CONF_MAX_BOUND = bound_value
            elif definitions.ARG_RANK_LIMIT in arg:
                values.CONF_RANK_LIMIT = int(arg.replace(definitions.ARG_RANK_LIMIT, ""))
            elif definitions.ARG_SELECTION_METHOD in arg:
                option = int(arg.replace(definitions.ARG_SELECTION_METHOD, ''))
                if option not in values.OPTIONS_SELECT_METHOD:
                    emitter.error("Invalid option for " + definitions.ARG_SELECTION_METHOD.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_SELECTION_STRATEGY = values.OPTIONS_SELECT_METHOD[option]
            elif definitions.ARG_OPERATION_MODE in arg:
                option = int(arg.replace(definitions.ARG_OPERATION_MODE, ''))
                if option not in values.OPTIONS_OPERATION_MODE:
                    emitter.error(
                        "Invalid option for " + definitions.ARG_OPERATION_MODE.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_OPERATION_MODE = values.OPTIONS_OPERATION_MODE[option]
            elif definitions.ARG_PATCH_TYPE in arg:
                option = int(arg.replace(definitions.ARG_PATCH_TYPE, ''))
                if option not in values.OPTIONS_PATCH_TYPE:
                    emitter.error("Invalid option for " + definitions.ARG_PATCH_TYPE.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_PATCH_TYPE = values.OPTIONS_PATCH_TYPE[option]
            elif definitions.ARG_REFINE_METHOD in arg:
                option = int(arg.replace(definitions.ARG_REFINE_METHOD, ''))
                if option not in values.OPTIONS_REFINE_METHOD:
                    emitter.error("Invalid option for " + definitions.ARG_REFINE_METHOD.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_REFINE_METHOD = values.OPTIONS_REFINE_METHOD[option]
            elif definitions.ARG_REDUCE_METHOD in arg:
                option = int(arg.replace(definitions.ARG_REDUCE_METHOD, ''))
                if option not in values.OPTIONS_REDUCE_METHOD:
                    emitter.error("Invalid option for " + definitions.ARG_REDUCE_METHOD.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_REDUCE_METHOD = values.OPTIONS_REDUCE_METHOD[option]
            elif definitions.ARG_SKIP_BUILD in arg:
                values.CONF_SKIP_BUILD = True
            elif definitions.ARG_TEST_SUITE_ID_LIST in arg:
                values.CONF_TEST_SUITE_ID_LIST = str(arg).replace(definitions.ARG_TEST_SUITE_ID_LIST, "").split(",")
            elif definitions.ARG_SEED_SUITE_ID_LIST in arg:
                values.CONF_SEED_SUITE_ID_LIST = str(arg).replace(definitions.ARG_SEED_SUITE_ID_LIST, "").split(",")
            elif definitions.ARG_ITERATION_COUNT in arg:
                values.CONF_ITERATION_LIMIT = int(arg.replace(definitions.ARG_ITERATION_COUNT, ""))
            elif definitions.ARG_COMP_ALL in arg:
                values.CONF_ALL_COMPS = True
            elif definitions.ARG_PRESERVE_BC in arg:
                values.CONF_PRESERVE_BC = True
            elif definitions.ARG_SKIP_GENERATION in arg:
                values.CONF_SKIP_GEN = True
            elif definitions.ARG_SKIP_TEST in arg:
                values.CONF_SKIP_TEST = True
            elif definitions.ARG_ONLY_GEN in arg:
                values.CONF_ONLY_GEN = True
            elif definitions.ARG_ONLY_TEST in arg:
                values.CONF_ONLY_TEST = True
            elif definitions.ARG_TIME_DURATION in arg:
                values.CONF_TIME_DURATION = int(arg.replace(definitions.ARG_TIME_DURATION, ""))
            elif definitions.ARG_PATCH_DIR in arg:
                values.CONF_PATCH_DIR = arg.replace(definitions.ARG_PATCH_DIR, "")
            elif definitions.ARG_CEGIS_TIME_SPLIT in arg:
                if ":" not in arg:
                    emitter.error("Invalid option for " + definitions.ARG_CEGIS_TIME_SPLIT.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                else:
                    time_split = arg.replace(definitions.ARG_CEGIS_TIME_SPLIT, "")
                    values.CONF_TIME_SPLIT = time_split
            elif arg in ["-help", "--help", "-h"]:
                emitter.emit_help()
                exit(0)
            else:
                emitter.error("Invalid argument: " + arg)
                emitter.emit_help()
                exit()
    else:
        emitter.emit_help()
        exit()


def read_conf_file():
    emitter.normal("reading configuration values form configuration file")
    emitter.note("\t[file] " + values.FILE_CONFIGURATION)
    logger.information(values.FILE_CONFIGURATION)
    if not os.path.exists(values.FILE_CONFIGURATION):
        emitter.error("[NOT FOUND] Configuration file " + values.FILE_CONFIGURATION)
        exit()
    if os.path.getsize(values.FILE_CONFIGURATION) == 0:
        emitter.error("[EMPTY] Configuration file " + values.FILE_CONFIGURATION)
        exit()
    with open(values.FILE_CONFIGURATION, 'r') as conf_file:
        configuration_list = [i.strip() for i in conf_file.readlines()]

    for configuration in configuration_list:
        if definitions.CONF_PATH_PROJECT in configuration:
            values.CONF_PATH_PROJECT = configuration.replace(definitions.CONF_PATH_PROJECT, '')
        elif definitions.CONF_BINARY_PATH in configuration:
            values.CONF_PATH_PROGRAM = configuration.replace(definitions.CONF_BINARY_PATH, '')
        elif definitions.CONF_COMMAND_BUILD in configuration:
            values.CONF_COMMAND_BUILD = configuration.replace(definitions.CONF_COMMAND_BUILD, '')
        elif definitions.CONF_COMMAND_CONFIG in configuration:
            values.CONF_COMMAND_CONFIG = configuration.replace(definitions.CONF_COMMAND_CONFIG, '')
        elif definitions.CONF_RANK_LIMIT in configuration:
            values.CONF_RANK_LIMIT = int(configuration.replace(definitions.CONF_RANK_LIMIT, ''))
        elif definitions.CONF_GENERALIZED_SEED_INPUT in configuration:
            values.CONF_GENERALIZED_SEED_INPUT = str(configuration.replace(definitions.CONF_GENERALIZED_SEED_INPUT, ''))
        elif definitions.CONF_GENERALIZED_TEST_INPUT in configuration:
            values.CONF_GENERALIZED_TEST_INPUT = str(configuration.replace(definitions.CONF_GENERALIZED_TEST_INPUT, ''))
        elif definitions.CONF_SEED_FILE in configuration:
            seed_file_path = configuration.replace(definitions.CONF_SEED_FILE, '')
            if not os.path.isfile(seed_file_path):
                seed_file_path = values.CONF_PATH_PROJECT + "/" + seed_file_path
                if not os.path.isfile(seed_file_path):
                    error_exit("Seed file " + seed_file_path + " not found")
            values.CONF_SEED_FILE = seed_file_path
        elif definitions.CONF_TEST_INPUT_FILE in configuration:
            test_file_path = configuration.replace(definitions.CONF_TEST_INPUT_FILE, '')
            if not os.path.isfile(test_file_path):
                test_file_path = values.CONF_PATH_PROJECT + "/" + test_file_path
                if not os.path.isfile(test_file_path):
                    error_exit("Seed file " + test_file_path + " not found")
            values.CONF_TEST_INPUT_FILE = test_file_path
        elif definitions.CONF_SEED_DIR in configuration:
            seed_dir_path = configuration.replace(definitions.CONF_SEED_DIR, '')
            if not os.path.isdir(seed_dir_path):
                seed_dir_path = values.CONF_PATH_PROJECT + "/" + seed_dir_path
                if not os.path.isdir(seed_dir_path):
                    error_exit("Seed dir " + seed_dir_path + " not found")
            values.CONF_SEED_DIR = seed_dir_path
        elif definitions.CONF_TEST_OUTPUT_DIR in configuration:
            output_dir_path = configuration.replace(definitions.CONF_TEST_OUTPUT_DIR, '')
            if not os.path.isdir(output_dir_path):
                output_dir_path = values.CONF_PATH_PROJECT + "/" + output_dir_path
                if not os.path.isdir(output_dir_path):
                    error_exit("Seed dir " + output_dir_path + " not found")
            values.CONF_TEST_OUTPUT_DIR = output_dir_path
        elif definitions.CONF_TEST_INPUT_DIR in configuration:
            input_dir_path = configuration.replace(definitions.CONF_TEST_INPUT_DIR, '')
            if not os.path.isdir(input_dir_path):
                input_dir_path = values.CONF_PATH_PROJECT + "/" + input_dir_path
                if not os.path.isdir(input_dir_path):
                    error_exit("Seed dir " + input_dir_path + " not found")
            values.CONF_TEST_INPUT_DIR = input_dir_path
        elif definitions.CONF_TEST_OUTPUT_LIST in configuration:
            values.CONF_TEST_OUTPUT_LIST = configuration.replace(definitions.CONF_TEST_OUTPUT_LIST, '').split(",")
        elif definitions.CONF_TEST_INPUT_LIST in configuration:
             input_list = configuration.replace(definitions.CONF_TEST_INPUT_LIST, '').split("],[")
             processed_list = []
             for input in input_list:
                 processed_list.append(input.replace("[", "").replace("]", ""))
             values.CONF_TEST_INPUT_LIST = processed_list
        elif definitions.CONF_SEED_LIST in configuration:
            seed_list = configuration.replace(definitions.CONF_SEED_LIST, '').split("],[")
            processed_list = []
            for seed_input in seed_list:
                processed_list.append(seed_input.replace("[", "").replace("]", ""))
            values.CONF_SEED_LIST = processed_list
        elif definitions.CONF_PATH_SPECIFICATION in configuration:
            values.CONF_PATH_SPECIFICATION = configuration.replace(definitions.CONF_PATH_SPECIFICATION, '')
            assertion_file_path = values.CONF_PATH_PROJECT + "/" + values.CONF_PATH_SPECIFICATION
            values.SPECIFICATION_TXT = reader.collect_specification(assertion_file_path)
        elif definitions.CONF_CUSTOM_COMP_LIST in configuration:
            values.CONF_CUSTOM_COMP_LIST = configuration.replace(definitions.CONF_CUSTOM_COMP_LIST, '').split(",")
        elif definitions.CONF_GENERAL_COMP_LIST in configuration:
            values.CONF_GENERAL_COMP_LIST = configuration.replace(definitions.CONF_GENERAL_COMP_LIST, '').split(",")
        elif definitions.CONF_DEPTH_VALUE in configuration:
            values.CONF_DEPTH_VALUE = configuration.replace(definitions.CONF_DEPTH_VALUE, '')
        elif definitions.CONF_DIR_SRC in configuration:
            values.CONF_DIR_SRC = configuration.replace(definitions.CONF_DIR_SRC, '').replace("//", "/")
            if values.CONF_DIR_SRC:
                if values.CONF_DIR_SRC[-1] == "/":
                    values.CONF_DIR_SRC = values.CONF_DIR_SRC[:-1]
        elif definitions.CONF_LOC_BUG in configuration:
            values.CONF_LOC_BUG = configuration.replace(definitions.CONF_LOC_BUG, '')
        elif definitions.CONF_LOC_PATCH in configuration:
            values.CONF_LOC_PATCH = configuration.replace(definitions.CONF_LOC_PATCH, '')
        elif definitions.CONF_PATH_POC in configuration:
            values.CONF_PATH_POC = configuration.replace(definitions.CONF_PATH_POC, '')
            if not os.path.isfile(values.CONF_PATH_POC):
                poc_path = values.CONF_PATH_PROJECT + "/" + values.CONF_PATH_POC
                if os.path.isfile(poc_path):
                    values.CONF_PATH_POC = poc_path
                else:
                    error_exit("Test file " + values.CONF_PATH_POC + " not found")
        elif definitions.CONF_LOW_BOUND in configuration:
            values.CONF_LOW_BOUND = int(configuration.replace(definitions.CONF_LOW_BOUND, ''))
        elif definitions.CONF_MAX_BOUND in configuration:
            values.CONF_MAX_BOUND = int(configuration.replace(definitions.CONF_MAX_BOUND, ''))
        elif definitions.CONF_MAX_FORK in configuration:
            values.CONF_MAX_FORK = int(configuration.replace(definitions.CONF_MAX_FORK, ''))
        elif definitions.CONF_GEN_SEARCH_LIMIT in configuration:
            values.CONF_GEN_SEARCH_LIMIT = int(configuration.replace(definitions.CONF_GEN_SEARCH_LIMIT, ''))
        elif definitions.CONF_TAG_ID in configuration:
            values.CONF_TAG_ID = configuration.replace(definitions.CONF_TAG_ID, '')
        elif definitions.CONF_STATIC in configuration:
            conf_text = configuration.replace(definitions.CONF_STATIC, '')
            if "true" in str(conf_text).lower():
                values.CONF_STATIC = True
        elif definitions.CONF_IS_CRASH in configuration:
            conf_text = configuration.replace(definitions.CONF_IS_CRASH, '')
            if "true" in str(conf_text).lower():
                values.CONF_IS_CRASH = True
        elif definitions.CONF_GEN_SPECIAL_PATH in configuration:
            conf_text = configuration.replace(definitions.CONF_GEN_SPECIAL_PATH, '')
            if "false" in str(conf_text).lower():
                values.CONF_GEN_PATH_SPECIAL = False
        elif definitions.CONF_IS_CPP in configuration:
            conf_text = configuration.replace(definitions.CONF_IS_CPP, '')
            if "true" in str(conf_text).lower():
                values.CONF_IS_CPP = True
        elif definitions.CONF_PRESERVE_BC in configuration:
            conf_text = configuration.replace(definitions.CONF_PRESERVE_BC, '')
            if "true" in str(conf_text).lower():
                values.CONF_PRESERVE_BC = True
        elif definitions.CONF_FLAG_ASAN in configuration:
            values.CONF_FLAG_ASAN = configuration.replace(definitions.CONF_FLAG_ASAN, '')
        elif definitions.CONF_FLAGS_C in configuration:
            values.CONF_FLAGS_C = configuration.replace(definitions.CONF_FLAGS_C, '')
        elif definitions.CONF_FLAGS_CXX in configuration:
            values.CONF_FLAGS_CXX = configuration.replace(definitions.CONF_FLAGS_CXX, '')
        elif definitions.CONF_SELECTION_STRATEGY in configuration:
            values.CONF_SELECTION_STRATEGY = configuration.replace(definitions.CONF_SELECTION_STRATEGY, '')
            if values.CONF_SELECTION_STRATEGY not in values.OPTIONS_SELECT_METHOD:
                error_exit("Invalid configuration for " + definitions.CONF_SELECTION_STRATEGY)
        elif definitions.CONF_DISTANCE_METRIC in configuration:
            values.CONF_DISTANCE_METRIC = configuration.replace(definitions.CONF_DISTANCE_METRIC, '')
            if values.CONF_DISTANCE_METRIC not in values.OPTIONS_DIST_METRIC.values():
                error_exit("Invalid configuration for " + definitions.CONF_DISTANCE_METRIC)
        elif definitions.CONF_PATCH_TYPE in configuration:
            values.CONF_PATCH_TYPE = configuration.replace(definitions.CONF_PATCH_TYPE, '')
            if values.CONF_PATCH_TYPE not in values.OPTIONS_PATCH_TYPE.values():
                error_exit("Invalid configuration for " + definitions.CONF_PATCH_TYPE)
        elif definitions.CONF_OPERATION_MODE in configuration:
            values.CONF_OPERATION_MODE = configuration.replace(definitions.CONF_OPERATION_MODE, '')
            if values.CONF_OPERATION_MODE not in values.OPTIONS_OPERATION_MODE:
                error_exit("Invalid configuration for " + definitions.CONF_OPERATION_MODE)
        elif definitions.CONF_BUILD_FLAGS in configuration:
            values.CONF_BUILD_FLAGS = configuration.replace(definitions.CONF_BUILD_FLAGS, '')
        elif definitions.CONF_KLEE_FLAGS in configuration:
            values.CONF_KLEE_FLAGS = configuration.replace(definitions.CONF_KLEE_FLAGS, '')
        elif definitions.CONF_ITERATION_LIMIT in configuration:
            values.CONF_ITERATION_LIMIT = int(configuration.replace(definitions.CONF_ITERATION_LIMIT, ''))
        elif definitions.CONF_MAX_FLIPPINGS in configuration:
            values.CONF_MAX_FLIPPINGS = int(configuration.replace(definitions.CONF_MAX_FLIPPINGS, ''))
        elif definitions.CONF_STACK_SIZE in configuration:
            values.CONF_STACK_SIZE = int(configuration.replace(definitions.CONF_STACK_SIZE, ''))
        elif definitions.CONF_MASK_ARG in configuration:
            values.CONF_MASK_ARG = configuration.replace(definitions.CONF_MASK_ARG, '').split(",")
        elif definitions.CONF_TIMEOUT_SAT in configuration:
            values.CONF_TIMEOUT_SAT = int(configuration.replace(definitions.CONF_TIMEOUT_SAT, ''))
        elif definitions.CONF_TIMEOUT_CONCOLIC_RUN in configuration:
            values.CONF_TIMEOUT_CONCOLIC_RUN = int(configuration.replace(definitions.CONF_TIMEOUT_CONCOLIC_RUN, ''))
        elif definitions.CONF_TIMEOUT_CONCRETE_RUN in configuration:
            values.CONF_TIMEOUT_CONCRETE_RUN = int(configuration.replace(definitions.CONF_TIMEOUT_CONCRETE_RUN, ''))
        elif definitions.CONF_TEST_SUITE_ID_LIST in configuration:
            values.CONF_TEST_SUITE_ID_LIST = str(configuration).replace(definitions.CONF_TEST_SUITE_ID_LIST, "").split(",")
        elif definitions.CONF_SEED_SUITE_ID_LIST in configuration:
            values.CONF_SEED_SUITE_ID_LIST = str(configuration).replace(definitions.CONF_SEED_SUITE_ID_LIST, "").split(",")
        elif definitions.CONF_PATCH_DIR in configuration:
            values.CONF_PATCH_DIR = configuration.replace(definitions.CONF_PATCH_DIR, "")
        elif definitions.CONF_TEST_SUITE_CONFIG in configuration:
            config_path = configuration.replace(definitions.CONF_TEST_SUITE_CONFIG, "")
            config_path = values.CONF_PATH_PROJECT + "/" + config_path
            if os.path.isfile(config_path):
                values.CONF_TEST_SUITE_CONFIG = reader.read_json(config_path)
            else:
                error_exit("Test suite configuration file not found at " + str(config_path))
        elif definitions.CONF_SEED_SUITE_CONFIG in configuration:
            config_path = configuration.replace(definitions.CONF_SEED_SUITE_CONFIG, "")
            config_path = values.CONF_PATH_PROJECT + "/" + config_path
            if os.path.isfile(config_path):
                values.CONF_SEED_SUITE_CONFIG = reader.read_json(config_path)
            else:
                error_exit("Seed suite configuration file not found at " + str(config_path))
        elif definitions.CONF_TEST_BINARY_CONFIG_FILE in configuration:
            config_path = configuration.replace(definitions.CONF_TEST_BINARY_CONFIG_FILE, "")
            config_path = values.CONF_PATH_PROJECT + "/" + config_path
            if os.path.isfile(config_path):
                with open(config_path, "r") as conf_file:
                    values.CONF_TEST_BINARY_LIST = [x.strip().replace("\n", "") for x in conf_file.readlines()]
            else:
                error_exit("Test binary configuration file not found at " + str(config_path))
        elif definitions.CONF_SEED_BINARY_CONFIG_FILE in configuration:
            config_path = configuration.replace(definitions.CONF_SEED_BINARY_CONFIG_FILE, "")
            config_path = values.CONF_PATH_PROJECT + "/" + config_path
            if os.path.isfile(config_path):
                with open(config_path, "r") as conf_file:
                    values.CONF_SEED_BINARY_LIST = [x.strip().replace("\n", "") for x in conf_file.readlines()]
            else:
                error_exit("Test binary configuration file not found at " + str(config_path))

    if not values.CONF_TAG_ID:
        emitter.error("[NOT FOUND] Tag ID ")
        exit()
    if values.CONF_DIR_SRC:
        if "/" != values.CONF_DIR_SRC[0]:
            values.CONF_DIR_SRC = values.CONF_PATH_PROJECT + "/" + values.CONF_DIR_SRC
    else:
        values.CONF_DIR_SRC = values.CONF_PATH_PROJECT

    if values.CONF_PATH_PROGRAM:
        if "/" != values.CONF_PATH_PROGRAM[0]:
            values.CONF_PATH_PROGRAM = values.CONF_DIR_SRC + "/" + values.CONF_PATH_PROGRAM


def load_component_list():
    emitter.normal("loading custom/general components")
    # base_list = ["equal.smt2", "not-equal.smt2", "less-than.smt2", "less-or-equal.smt2"]
    base_list = []
    if definitions.DIRECTORY_TESTS in values.CONF_PATH_PROJECT:
        base_list = []
    gen_comp_files = []
    os.chdir(definitions.DIRECTORY_COMPONENTS)
    if values.CONF_GENERAL_COMP_LIST and not values.CONF_ALL_COMPS:
        comp_list = list(set(values.CONF_GENERAL_COMP_LIST + base_list))
        for component_name in comp_list:
            gen_comp_files.append(Path(component_name))
            emitter.note("\tloading component: " + str(component_name))
    else:
        component_file_list = os.listdir(definitions.DIRECTORY_COMPONENTS)
        for comp_file in component_file_list:
            if ".smt2" in comp_file:
                if any(x in comp_file for x in ["logical-not", "post-decrement", "post-increment", "minus", "constant", "assignment", "sequence", "greater", "remainder"]):
                    continue
                gen_comp_files.append(Path(comp_file))
                emitter.note("\tloading component: " + str(comp_file))
    gen_comp_files = list(set(gen_comp_files))
    general_components = synthesis.load_components(gen_comp_files)

    proj_comp_files = []
    os.chdir(values.CONF_PATH_PROJECT)
    for component_name in values.CONF_CUSTOM_COMP_LIST:
        proj_comp_files.append(Path(component_name))
        emitter.note("\tloading component: " + str(component_name))
    project_components = synthesis.load_components(proj_comp_files)
    values.LIST_COMPONENTS = project_components + general_components
    values.COUNT_COMPONENTS = len(values.LIST_COMPONENTS)
    values.COUNT_COMPONENTS_CUS = len(project_components)
    values.COUNT_COMPONENTS_GEN = len(general_components)


def print_configuration():
    # emitter.note("\tconfiguration.is_crash:" + str(values.IS_CRASH))
    # assertion_formula = generator.generate_formula(values.SPECIFICATION_TXT[1])
    # emitter.configuration("\t[config] program specification:", values.SPECIFICATION_TXT[1])
    emitter.configuration("path generation limit", values.DEFAULT_GEN_SEARCH_LIMIT)
    emitter.configuration("synthesis max bound", values.DEFAULT_PATCH_UPPER_BOUND)
    emitter.configuration("synthesis low bound", values.DEFAULT_PATCH_LOWER_BOUND)
    emitter.configuration("stack size", sys.getrecursionlimit())
    emitter.configuration("refine strategy", values.DEFAULT_REFINE_METHOD)
    emitter.configuration("patch type", values.DEFAULT_PATCH_TYPE)
    emitter.configuration("repair method", values.DEFAULT_REDUCE_METHOD)
    emitter.configuration("timeout for CPR", values.DEFAULT_TIME_DURATION)
    emitter.configuration("timeout for sat", values.DEFAULT_TIMEOUT_SAT)
    emitter.configuration("timeout for klee", values.DEFAULT_TIMEOUT_KLEE_CONCOLIC)
    emitter.configuration("distance metric", values.DEFAULT_DISTANCE_METRIC)
    emitter.configuration("operation mode", values.DEFAULT_OPERATION_MODE)
    emitter.configuration("iteration limit", values.DEFAULT_ITERATION_LIMIT)
    emitter.configuration("collecting stats", str(values.DEFAULT_COLLECT_STAT))
    emitter.configuration("number of seeds", str(len(values.LIST_SEED_INPUT)))
    emitter.configuration("number of tests", str(len(values.LIST_TEST_INPUT)))
    emitter.configuration("list of seed ids", str(values.LIST_SEED_ID_LIST))
    emitter.configuration("list of test ids", str(values.LIST_TEST_ID_LIST))
    emitter.configuration("masked input arg id list", values.CONF_MASK_ARG)


def collect_test_list():
    emitter.normal("reading test configuration")
    if values.CONF_TEST_SUITE_CONFIG:
        for (test_id, bin_path, test_input, expected_output) in values.CONF_TEST_SUITE_CONFIG:
            if values.CONF_TEST_SUITE_ID_LIST:
                if str(test_id) not in values.CONF_TEST_SUITE_ID_LIST:
                    continue
            values.LIST_TEST_ID_LIST.add(str(test_id))
            bin_path = values.CONF_DIR_SRC + "/" + bin_path
            values.LIST_TEST_BINARY.append(bin_path)
            values.LIST_TEST_INPUT.append(test_input)
            values.LIST_TEST_OUTPUT.append(expected_output)

    else:
        if values.CONF_TEST_BINARY_LIST:
            for binary_path in values.CONF_TEST_BINARY_LIST:
                binary_path = values.CONF_DIR_SRC + "/" + binary_path
                values.LIST_TEST_BINARY.append(binary_path)

        if values.CONF_TEST_INPUT_LIST:
            for test_input in values.CONF_TEST_INPUT_LIST:
                values.LIST_TEST_INPUT.append(test_input)
        elif values.CONF_TEST_INPUT_FILE:
            with open(values.CONF_TEST_INPUT_FILE, "r") as in_file:
                content_lines = in_file.readlines()
                for content in content_lines:
                    test_input = content.strip().replace("\n", "")
                    if test_input.isspace():
                        continue
                    if "$POC_" in test_input:
                        test_input_file = test_input.split("$POC_")[1].split(" ")[0]
                        test_input_file_index = test_input_file
                        if values.CONF_GENERALIZED_TEST_INPUT:
                            test_input = values.CONF_GENERALIZED_TEST_INPUT.replace("$POC", test_input)
                        if test_input_file[0] != "/":
                            if values.CONF_SEED_DIR:
                                test_input_file = values.CONF_SEED_DIR + "/" + test_input_file
                            else:
                                test_input_file = values.CONF_DIR_SRC + "/" + test_input_file
                        values.LIST_TEST_FILES[test_input_file_index] = test_input_file
                    if test_input:
                        values.LIST_TEST_INPUT.append(test_input)
        else:
            error_exit("No test input is given (at least one is required)")

        if values.CONF_TEST_OUTPUT_LIST:
            for expected_output in values.CONF_TEST_OUTPUT_LIST:
                values.LIST_TEST_OUTPUT.append(expected_output)
        elif values.CONF_TEST_OUTPUT_DIR:
            expected_output_dir = values.CONF_TEST_OUTPUT_DIR
            file_list = [f for f in os.listdir(expected_output_dir) if
                         os.path.isfile(os.path.join(expected_output_dir, f))]
            for expected_output_file in file_list:
                if ".smt2" in expected_output_file:
                    expected_file_abs_path = expected_output_dir + "/" + expected_output_file
                    expected_file_rel_path = str(expected_file_abs_path).replace(values.CONF_PATH_PROJECT + "/", "")
                    values.LIST_TEST_OUTPUT.append(expected_file_rel_path)
        else:
            error_exit("No expected output is given (at least one is required)")

    if values.CONF_TEST_INPUT_DIR:
        test_file_dir = values.CONF_TEST_INPUT_DIR
        file_list = [f for f in os.listdir(test_file_dir) if os.path.isfile(os.path.join(test_file_dir, f))]
        for test_file in file_list:
            test_file_index = test_file
            # if "." in test_file:
            #     test_file_index = str(test_file).split(".")[0]
            test_abs_path = test_file_dir + "/" + test_file
            # if not values.CONF_PATH_POC:
            #     values.CONF_PATH_POC = test_abs_path
            values.LIST_TEST_FILES[test_file_index] = test_abs_path
    elif values.CONF_PATH_POC:
        test_file = values.CONF_PATH_POC
        test_file_index = test_file
        # if "." in test_file:
        #     test_file_index = str(test_file).split(".")[0]
        values.LIST_TEST_FILES[test_file_index] = values.CONF_PATH_POC


    test_input_list = values.LIST_TEST_INPUT
    concretized_test_input_list = []
    for arg_list_str in test_input_list:
        arg_list = extract_input_arg_list(arg_list_str)
        concretized_arg_list = []
        for arg in arg_list:
            if "$POC_" in arg:
                file_index = "_".join(str(arg).split("_")[1:])
                file_path = values.LIST_TEST_FILES[file_index]
                concretized_arg_list.append(file_path)
            elif "$POC" in arg:
                file_index = list(values.LIST_TEST_FILES.keys())[0]
                file_path = values.LIST_TEST_FILES[file_index]
                concretized_arg_list.append(file_path)
            else:
                concretized_arg_list.append(arg)
        concretized_arg_str = ",".join(concretized_arg_list)
        concretized_test_input_list.append(concretized_arg_str)
    values.LIST_TEST_INPUT = concretized_test_input_list


def collect_seed_list():
    emitter.normal("reading seed information")
    if values.CONF_SEED_SUITE_CONFIG:
        for (seed_id, bin_path, test_input) in values.CONF_SEED_SUITE_CONFIG:
            if values.CONF_SEED_SUITE_ID_LIST:
                if str(seed_id) not in values.CONF_SEED_SUITE_ID_LIST:
                    continue
            values.LIST_SEED_ID_LIST.add(str(seed_id))
            bin_path = values.CONF_DIR_SRC + "/" + bin_path
            values.LIST_SEED_BINARY.append(bin_path)
            values.LIST_SEED_INPUT.append((seed_id, test_input))
    else:
        if values.CONF_SEED_BINARY_LIST:
            for binary_path in values.CONF_SEED_BINARY_LIST:
                binary_path = values.CONF_DIR_SRC + "/" + binary_path
                values.LIST_SEED_BINARY.append(binary_path)
        if values.CONF_SEED_LIST:
            for seed_input in values.CONF_SEED_LIST:
                values.LIST_SEED_INPUT.append(seed_input)
        elif values.CONF_SEED_FILE:
            with open(values.CONF_SEED_FILE, "r") as in_file:
                content_lines = in_file.readlines()
                seed_id = 0
                for content in content_lines:
                    seed_id = seed_id + 1
                    seed_input = content.strip().replace("\n", "")
                    if values.CONF_SEED_SUITE_ID_LIST:
                        if str(seed_id) not in values.CONF_SEED_SUITE_ID_LIST:
                            continue
                    if seed_input.isspace():
                        continue
                    if "$POC_" in seed_input:
                        seed_input_file = seed_input.split("$POC_")[1].split(" ")[0]
                        seed_input_file_index = seed_input_file
                        if values.CONF_GENERALIZED_SEED_INPUT:
                            seed_input = values.CONF_GENERALIZED_SEED_INPUT.replace("$POC", seed_input)
                        if seed_input_file[0] != "/":
                            if values.CONF_SEED_DIR:
                                seed_input_file = values.CONF_SEED_DIR + "/" + seed_input_file
                            else:
                                seed_input_file = values.CONF_DIR_SRC + "/" + seed_input_file
                        values.LIST_SEED_FILES[seed_input_file_index] = seed_input_file
                    if seed_input:
                        values.LIST_SEED_INPUT.append((seed_id, seed_input))
    if values.CONF_SEED_DIR:
        seed_dir = values.CONF_SEED_DIR
        file_list = [f for f in os.listdir(seed_dir) if os.path.isfile(os.path.join(seed_dir, f))]
        for seed_file in file_list:
            seed_file_index = seed_file
            seed_abs_path = seed_dir + "/" + seed_file
            values.LIST_SEED_FILES[seed_file_index] = seed_abs_path

    if values.LIST_SEED_INPUT:
        seed_index = 0
        for seed in values.LIST_SEED_INPUT:
            if isinstance(seed, tuple):
                seed_id, seed_arg_list_str = seed
            else:
                seed_arg_list_str = seed
                seed_id = values.LIST_SEED_INPUT.index(seed) + 1
            arg_list = extract_input_arg_list(seed_arg_list_str)
            concretized_arg_list = []
            for arg in arg_list:
                if "$POC_" in arg:
                    file_index = "_".join(str(arg).split("_")[1:])
                    if file_index not in values.LIST_SEED_FILES:
                        continue
                    file_path = values.LIST_SEED_FILES[file_index]
                    concretized_arg_list.append(file_path)
                elif "$POC" in arg:
                    file_index = list(values.LIST_TEST_FILES.keys())[0]
                    file_path = values.LIST_TEST_FILES[file_index]
                    concretized_arg_list.append(file_path)
                else:
                    concretized_arg_list.append(arg)
            concretized_arg_str = ",".join(concretized_arg_list)
            values.LIST_TEST_INPUT.append(concretized_arg_str)
            if values.LIST_SEED_BINARY:
                values.LIST_TEST_BINARY.append(values.LIST_SEED_BINARY[seed_index])
            seed_index = seed_index + 1


def collect_var_mapping():
    emitter.normal("updating mapping for program variables")
    patch_loc = values.CONF_LOC_PATCH
    source_file_path, line_number = patch_loc.split(":")
    with open(source_file_path, 'r') as source_file:
        content = source_file.readlines()
        patch_line = content[int(line_number) - 1]
        trident_call_str = re.findall("trident_choice\((.+?)\)[\),\s,;]", patch_line)[0]
        patch_type = trident_call_str.split(",")[1]
        if patch_type == "bool":
            values.IS_PATCH_BOOL = True
        prog_var_list = re.findall("{(.+?)}", trident_call_str)[0].split(",")
        comp_name_list = re.findall("{(.+?)}", trident_call_str)[1].split(",")
        for i in range (0, len(prog_var_list)):
            values.MAP_PROG_VAR[comp_name_list[i].strip().replace("\"", "").replace("\'", "")] = prog_var_list[i]
    # print(values.MAP_PROG_VAR)


def update_configuration():
    emitter.normal("updating configuration values")
    klee_last_dir = values.KLEE_LAST_DIR
    values.FILE_PPC_LOG = klee_last_dir + "/ppc.log"
    values.FILE_EXPR_LOG = klee_last_dir + "/expr.log"
    values.FILE_TRACE_LOG = klee_last_dir + "/trace.log"
    values.FILE_MESSAGE_LOG = klee_last_dir + "/messages.txt"
    definitions.DIRECTORY_OUTPUT = definitions.DIRECTORY_OUTPUT_BASE + "/" + values.CONF_TAG_ID
    definitions.DIRECTORY_LOG = definitions.DIRECTORY_LOG_BASE + "/" + values.CONF_TAG_ID

    if os.path.isdir(definitions.DIRECTORY_OUTPUT):
        shutil.rmtree(definitions.DIRECTORY_OUTPUT)
    os.mkdir(definitions.DIRECTORY_OUTPUT)

    if os.path.isdir(definitions.DIRECTORY_LOG):
        shutil.rmtree(definitions.DIRECTORY_LOG)
    os.mkdir(definitions.DIRECTORY_LOG)
    if values.CONF_PATCH_DIR:
        if os.path.isdir(values.CONF_PATCH_DIR):
            values.DEFAULT_PATCH_DIR = values.CONF_PATCH_DIR
    if values.CONF_MAX_BOUND:
        values.DEFAULT_PATCH_UPPER_BOUND = values.CONF_MAX_BOUND
    if values.CONF_LOW_BOUND:
        values.DEFAULT_PATCH_LOWER_BOUND = values.CONF_LOW_BOUND
    if values.CONF_MAX_FORK:
        values.DEFAULT_MAX_FORK = values.CONF_MAX_FORK
    if values.CONF_GEN_SEARCH_LIMIT:
        values.DEFAULT_GEN_SEARCH_LIMIT = values.CONF_GEN_SEARCH_LIMIT
    if values.CONF_ITERATION_LIMIT >= 0:
        values.DEFAULT_ITERATION_LIMIT = values.CONF_ITERATION_LIMIT
    if values.CONF_STACK_SIZE:
        values.DEFAULT_STACK_SIZE = values.CONF_STACK_SIZE
    # if values.CONF_IS_CRASH:
    #     values.IS_CRASH = values.CONF_IS_CRASH
    if values.CONF_GEN_PATH_SPECIAL is not None:
        values.DEFAULT_GEN_SPECIAL_PATH = values.CONF_GEN_PATH_SPECIAL
    if values.CONF_TIME_DURATION:
        values.DEFAULT_TIME_DURATION = values.CONF_TIME_DURATION
    if values.CONF_TIMEOUT_SAT:
        values.DEFAULT_TIMEOUT_SAT = values.CONF_TIMEOUT_SAT
    if values.CONF_TIMEOUT_CONCOLIC_RUN:
        values.DEFAULT_TIMEOUT_KLEE_CONCOLIC = values.CONF_TIMEOUT_CONCOLIC_RUN
    if values.CONF_TIMEOUT_CONCRETE_RUN:
        values.DEFAULT_TIMEOUT_KLEE_CONCRETE = values.CONF_TIMEOUT_CONCRETE_RUN
    if values.CONF_RANK_LIMIT:
        values.DEFAULT_PATCH_RANK_LIMIT = values.CONF_RANK_LIMIT
    if values.CONF_SELECTION_STRATEGY:
        values.DEFAULT_SELECTION_STRATEGY = values.CONF_SELECTION_STRATEGY
    if values.CONF_DISTANCE_METRIC:
        values.DEFAULT_DISTANCE_METRIC = values.CONF_DISTANCE_METRIC
    if values.CONF_PATCH_TYPE:
        values.DEFAULT_PATCH_TYPE = values.CONF_PATCH_TYPE
    if values.CONF_REFINE_METHOD:
        values.DEFAULT_REFINE_METHOD = values.CONF_REFINE_METHOD
    if values.CONF_OPERATION_MODE:
        values.DEFAULT_OPERATION_MODE = values.CONF_OPERATION_MODE
    if values.CONF_REDUCE_METHOD:
        values.DEFAULT_REDUCE_METHOD = values.CONF_REDUCE_METHOD
    if values.DEFAULT_REDUCE_METHOD == "cegis":
        values.DEFAULT_PATCH_TYPE = values.OPTIONS_PATCH_TYPE[0]
    if values.CONF_COLLECT_STAT:
        values.DEFAULT_COLLECT_STAT = True
    if values.CONF_TIME_SPLIT:
        explore, refine = values.CONF_TIME_SPLIT.split(":")
        total = int(explore) + int(refine)
        values.CONF_TIME_CEGIS_EXPLORE = (int(explore) / total) * values.DEFAULT_TIME_DURATION
        values.CONF_TIME_CEGIS_REFINE = (int(refine) / total) * values.DEFAULT_TIME_DURATION
    sys.setrecursionlimit(values.DEFAULT_STACK_SIZE)


def extract_input_arg_list(argument_str):
    if "," not in argument_str:
        argument_list = str(argument_str).split(" ")
    else:
        # argument_str = argument_str.replace("[", "").replace("]", "")
        argument_list = str(argument_str).split(",")
    return argument_list
import os
import sys
import re
import shutil
from pathlib import Path
from app import emitter, logger, definitions, values, reader, synthesis, extractor
from app.utilities import error_exit


def read_conf(arg_list):
    emitter.normal("reading configuration values from arguments")
    if len(arg_list) > 0:
        for arg in arg_list:
            if definitions.ARG_DEBUG in arg:
                values.DEBUG = True
            elif definitions.ARG_CONF_FILE in arg:
                values.FILE_CONFIGURATION = str(arg).replace(definitions.ARG_CONF_FILE, '')
            elif definitions.ARG_DISABLE_DISTANCE_CAL in arg:
                values.IS_DISABLE_DISTANCE_CAL = True
            elif definitions.ARG_COLLECT_STAT in arg:
                values.CONF_COLLECT_STAT = True
            elif definitions.ARG_DIST_METRIC in arg:
                option = int(arg.replace(definitions.ARG_DIST_METRIC, ''))
                values.CONF_DISTANCE_METRIC = values.OPTIONS_DIST_METRIC[option]
            elif definitions.ARG_LOW_BOUND in arg:
                bound_value = int(arg.replace(definitions.ARG_LOW_BOUND, ''))
                values.CONF_LOW_BOUND = bound_value
            elif definitions.ARG_MAX_BOUND in arg:
                bound_value = int(arg.replace(definitions.ARG_MAX_BOUND, ''))
                values.CONF_MAX_BOUND = bound_value
            elif definitions.ARG_RANK_LIMIT in arg:
                values.CONF_RANK_LIMIT = int(arg.replace(definitions.ARG_RANK_LIMIT, ""))
            elif definitions.ARG_SELECTION_METHOD in arg:
                option = int(arg.replace(definitions.ARG_SELECTION_METHOD, ''))
                if option not in values.OPTIONS_SELECT_METHOD:
                    emitter.error("Invalid option for " + definitions.ARG_SELECTION_METHOD.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_SELECTION_STRATEGY = values.OPTIONS_SELECT_METHOD[option]
            elif definitions.ARG_OPERATION_MODE in arg:
                option = int(arg.replace(definitions.ARG_OPERATION_MODE, ''))
                if option not in values.OPTIONS_OPERATION_MODE:
                    emitter.error(
                        "Invalid option for " + definitions.ARG_OPERATION_MODE.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_OPERATION_MODE = values.OPTIONS_OPERATION_MODE[option]
            elif definitions.ARG_PATCH_TYPE in arg:
                option = int(arg.replace(definitions.ARG_PATCH_TYPE, ''))
                if option not in values.OPTIONS_PATCH_TYPE:
                    emitter.error("Invalid option for " + definitions.ARG_PATCH_TYPE.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_PATCH_TYPE = values.OPTIONS_PATCH_TYPE[option]
            elif definitions.ARG_REFINE_METHOD in arg:
                option = int(arg.replace(definitions.ARG_REFINE_METHOD, ''))
                if option not in values.OPTIONS_REFINE_METHOD:
                    emitter.error("Invalid option for " + definitions.ARG_REFINE_METHOD.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_REFINE_METHOD = values.OPTIONS_REFINE_METHOD[option]
            elif definitions.ARG_REDUCE_METHOD in arg:
                option = int(arg.replace(definitions.ARG_REDUCE_METHOD, ''))
                if option not in values.OPTIONS_REDUCE_METHOD:
                    emitter.error("Invalid option for " + definitions.ARG_REDUCE_METHOD.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                values.CONF_REDUCE_METHOD = values.OPTIONS_REDUCE_METHOD[option]
            elif definitions.ARG_SKIP_BUILD in arg:
                values.CONF_SKIP_BUILD = True
            elif definitions.ARG_TEST_SUITE_ID_LIST in arg:
                values.CONF_TEST_SUITE_ID_LIST = str(arg).replace(definitions.ARG_TEST_SUITE_ID_LIST, "").split(",")
            elif definitions.ARG_SEED_SUITE_ID_LIST in arg:
                values.CONF_SEED_SUITE_ID_LIST = str(arg).replace(definitions.ARG_SEED_SUITE_ID_LIST, "").split(",")
            elif definitions.ARG_ITERATION_COUNT in arg:
                values.CONF_ITERATION_LIMIT = int(arg.replace(definitions.ARG_ITERATION_COUNT, ""))
            elif definitions.ARG_COMP_ALL in arg:
                values.CONF_ALL_COMPS = True
            elif definitions.ARG_PRESERVE_BC in arg:
                values.CONF_PRESERVE_BC = True
            elif definitions.ARG_SKIP_GENERATION in arg:
                values.CONF_SKIP_GEN = True
            elif definitions.ARG_SKIP_TEST in arg:
                values.CONF_SKIP_TEST = True
            elif definitions.ARG_ONLY_GEN in arg:
                values.CONF_ONLY_GEN = True
            elif definitions.ARG_ONLY_TEST in arg:
                values.CONF_ONLY_TEST = True
            elif definitions.ARG_TIME_DURATION in arg:
                values.CONF_TIME_DURATION = int(arg.replace(definitions.ARG_TIME_DURATION, ""))
            elif definitions.ARG_PATCH_DIR in arg:
                values.CONF_PATCH_DIR = arg.replace(definitions.ARG_PATCH_DIR, "")
            elif definitions.ARG_CEGIS_TIME_SPLIT in arg:
                if ":" not in arg:
                    emitter.error("Invalid option for " + definitions.ARG_CEGIS_TIME_SPLIT.replace("=", "") + " : " + arg)
                    emitter.emit_help()
                    exit()
                else:
                    time_split = arg.replace(definitions.ARG_CEGIS_TIME_SPLIT, "")
                    values.CONF_TIME_SPLIT = time_split
            elif arg in ["-help", "--help", "-h"]:
                emitter.emit_help()
                exit(0)
            else:
                emitter.error("Invalid argument: " + arg)
                emitter.emit_help()
                exit()
    else:
        emitter.emit_help()
        exit()


def read_conf_file():
    emitter.normal("reading configuration values form configuration file")
    emitter.note("\t[file] " + values.FILE_CONFIGURATION)
    logger.information(values.FILE_CONFIGURATION)
    if not os.path.exists(values.FILE_CONFIGURATION):
        emitter.error("[NOT FOUND] Configuration file " + values.FILE_CONFIGURATION)
        exit()
    if os.path.getsize(values.FILE_CONFIGURATION) == 0:
        emitter.error("[EMPTY] Configuration file " + values.FILE_CONFIGURATION)
        exit()
    with open(values.FILE_CONFIGURATION, 'r') as conf_file:
        configuration_list = [i.strip() for i in conf_file.readlines()]

    for configuration in configuration_list:
        if definitions.CONF_PATH_PROJECT in configuration:
            values.CONF_PATH_PROJECT = configuration.replace(definitions.CONF_PATH_PROJECT, '')
        elif definitions.CONF_BINARY_PATH in configuration:
            values.CONF_PATH_PROGRAM = configuration.replace(definitions.CONF_BINARY_PATH, '')
        elif definitions.CONF_COMMAND_BUILD in configuration:
            values.CONF_COMMAND_BUILD = configuration.replace(definitions.CONF_COMMAND_BUILD, '')
        elif definitions.CONF_COMMAND_CONFIG in configuration:
            values.CONF_COMMAND_CONFIG = configuration.replace(definitions.CONF_COMMAND_CONFIG, '')
        elif definitions.CONF_RANK_LIMIT in configuration:
            values.CONF_RANK_LIMIT = int(configuration.replace(definitions.CONF_RANK_LIMIT, ''))
        elif definitions.CONF_GENERALIZED_SEED_INPUT in configuration:
            values.CONF_GENERALIZED_SEED_INPUT = str(configuration.replace(definitions.CONF_GENERALIZED_SEED_INPUT, ''))
        elif definitions.CONF_GENERALIZED_TEST_INPUT in configuration:
            values.CONF_GENERALIZED_TEST_INPUT = str(configuration.replace(definitions.CONF_GENERALIZED_TEST_INPUT, ''))
        elif definitions.CONF_SEED_FILE in configuration:
            seed_file_path = configuration.replace(definitions.CONF_SEED_FILE, '')
            if not os.path.isfile(seed_file_path):
                seed_file_path = values.CONF_PATH_PROJECT + "/" + seed_file_path
                if not os.path.isfile(seed_file_path):
                    error_exit("Seed file " + seed_file_path + " not found")
            values.CONF_SEED_FILE = seed_file_path
        elif definitions.CONF_TEST_INPUT_FILE in configuration:
            test_file_path = configuration.replace(definitions.CONF_TEST_INPUT_FILE, '')
            if not os.path.isfile(test_file_path):
                test_file_path = values.CONF_PATH_PROJECT + "/" + test_file_path
                if not os.path.isfile(test_file_path):
                    error_exit("Seed file " + test_file_path + " not found")
            values.CONF_TEST_INPUT_FILE = test_file_path
        elif definitions.CONF_SEED_DIR in configuration:
            seed_dir_path = configuration.replace(definitions.CONF_SEED_DIR, '')
            if not os.path.isdir(seed_dir_path):
                seed_dir_path = values.CONF_PATH_PROJECT + "/" + seed_dir_path
                if not os.path.isdir(seed_dir_path):
                    error_exit("Seed dir " + seed_dir_path + " not found")
            values.CONF_SEED_DIR = seed_dir_path
        elif definitions.CONF_TEST_OUTPUT_DIR in configuration:
            output_dir_path = configuration.replace(definitions.CONF_TEST_OUTPUT_DIR, '')
            if not os.path.isdir(output_dir_path):
                output_dir_path = values.CONF_PATH_PROJECT + "/" + output_dir_path
                if not os.path.isdir(output_dir_path):
                    error_exit("Seed dir " + output_dir_path + " not found")
            values.CONF_TEST_OUTPUT_DIR = output_dir_path
        elif definitions.CONF_TEST_INPUT_DIR in configuration:
            input_dir_path = configuration.replace(definitions.CONF_TEST_INPUT_DIR, '')
            if not os.path.isdir(input_dir_path):
                input_dir_path = values.CONF_PATH_PROJECT + "/" + input_dir_path
                if not os.path.isdir(input_dir_path):
                    error_exit("Seed dir " + input_dir_path + " not found")
            values.CONF_TEST_INPUT_DIR = input_dir_path
        elif definitions.CONF_TEST_OUTPUT_LIST in configuration:
            values.CONF_TEST_OUTPUT_LIST = configuration.replace(definitions.CONF_TEST_OUTPUT_LIST, '').split(",")
        elif definitions.CONF_TEST_INPUT_LIST in configuration:
             input_list = configuration.replace(definitions.CONF_TEST_INPUT_LIST, '').split("],[")
             processed_list = []
             for input in input_list:
                 processed_list.append(input.replace("[", "").replace("]", ""))
             values.CONF_TEST_INPUT_LIST = processed_list
        elif definitions.CONF_SEED_LIST in configuration:
            seed_list = configuration.replace(definitions.CONF_SEED_LIST, '').split("],[")
            processed_list = []
            for seed_input in seed_list:
                processed_list.append(seed_input.replace("[", "").replace("]", ""))
            values.CONF_SEED_LIST = processed_list
        elif definitions.CONF_PATH_SPECIFICATION in configuration:
            values.CONF_PATH_SPECIFICATION = configuration.replace(definitions.CONF_PATH_SPECIFICATION, '')
            assertion_file_path = values.CONF_PATH_PROJECT + "/" + values.CONF_PATH_SPECIFICATION
            values.SPECIFICATION_TXT = reader.collect_specification(assertion_file_path)
        elif definitions.CONF_CUSTOM_COMP_LIST in configuration:
            values.CONF_CUSTOM_COMP_LIST = configuration.replace(definitions.CONF_CUSTOM_COMP_LIST, '').split(",")
        elif definitions.CONF_GENERAL_COMP_LIST in configuration:
            values.CONF_GENERAL_COMP_LIST = configuration.replace(definitions.CONF_GENERAL_COMP_LIST, '').split(",")
        elif definitions.CONF_DEPTH_VALUE in configuration:
            values.CONF_DEPTH_VALUE = configuration.replace(definitions.CONF_DEPTH_VALUE, '')
        elif definitions.CONF_DIR_SRC in configuration:
            values.CONF_DIR_SRC = configuration.replace(definitions.CONF_DIR_SRC, '').replace("//", "/")
            if values.CONF_DIR_SRC:
                if values.CONF_DIR_SRC[-1] == "/":
                    values.CONF_DIR_SRC = values.CONF_DIR_SRC[:-1]
        elif definitions.CONF_LOC_BUG in configuration:
            values.CONF_LOC_BUG = configuration.replace(definitions.CONF_LOC_BUG, '')
        elif definitions.CONF_LOC_PATCH in configuration:
            values.CONF_LOC_PATCH = configuration.replace(definitions.CONF_LOC_PATCH, '')
        elif definitions.CONF_PATH_POC in configuration:
            values.CONF_PATH_POC = configuration.replace(definitions.CONF_PATH_POC, '')
            if not os.path.isfile(values.CONF_PATH_POC):
                poc_path = values.CONF_PATH_PROJECT + "/" + values.CONF_PATH_POC
                if os.path.isfile(poc_path):
                    values.CONF_PATH_POC = poc_path
                else:
                    error_exit("Test file " + values.CONF_PATH_POC + " not found")
        elif definitions.CONF_LOW_BOUND in configuration:
            values.CONF_LOW_BOUND = int(configuration.replace(definitions.CONF_LOW_BOUND, ''))
        elif definitions.CONF_MAX_BOUND in configuration:
            values.CONF_MAX_BOUND = int(configuration.replace(definitions.CONF_MAX_BOUND, ''))
        elif definitions.CONF_MAX_FORK in configuration:
            values.CONF_MAX_FORK = int(configuration.replace(definitions.CONF_MAX_FORK, ''))
        elif definitions.CONF_GEN_SEARCH_LIMIT in configuration:
            values.CONF_GEN_SEARCH_LIMIT = int(configuration.replace(definitions.CONF_GEN_SEARCH_LIMIT, ''))
        elif definitions.CONF_TAG_ID in configuration:
            values.CONF_TAG_ID = configuration.replace(definitions.CONF_TAG_ID, '')
        elif definitions.CONF_STATIC in configuration:
            conf_text = configuration.replace(definitions.CONF_STATIC, '')
            if "true" in str(conf_text).lower():
                values.CONF_STATIC = True
        elif definitions.CONF_IS_CRASH in configuration:
            conf_text = configuration.replace(definitions.CONF_IS_CRASH, '')
            if "true" in str(conf_text).lower():
                values.CONF_IS_CRASH = True
        elif definitions.CONF_GEN_SPECIAL_PATH in configuration:
            conf_text = configuration.replace(definitions.CONF_GEN_SPECIAL_PATH, '')
            if "false" in str(conf_text).lower():
                values.CONF_GEN_PATH_SPECIAL = False
        elif definitions.CONF_IS_CPP in configuration:
            conf_text = configuration.replace(definitions.CONF_IS_CPP, '')
            if "true" in str(conf_text).lower():
                values.CONF_IS_CPP = True
        elif definitions.CONF_PRESERVE_BC in configuration:
            conf_text = configuration.replace(definitions.CONF_PRESERVE_BC, '')
            if "true" in str(conf_text).lower():
                values.CONF_PRESERVE_BC = True
        elif definitions.CONF_FLAG_ASAN in configuration:
            values.CONF_FLAG_ASAN = configuration.replace(definitions.CONF_FLAG_ASAN, '')
        elif definitions.CONF_FLAGS_C in configuration:
            values.CONF_FLAGS_C = configuration.replace(definitions.CONF_FLAGS_C, '')
        elif definitions.CONF_FLAGS_CXX in configuration:
            values.CONF_FLAGS_CXX = configuration.replace(definitions.CONF_FLAGS_CXX, '')
        elif definitions.CONF_SELECTION_STRATEGY in configuration:
            values.CONF_SELECTION_STRATEGY = configuration.replace(definitions.CONF_SELECTION_STRATEGY, '')
            if values.CONF_SELECTION_STRATEGY not in values.OPTIONS_SELECT_METHOD:
                error_exit("Invalid configuration for " + definitions.CONF_SELECTION_STRATEGY)
        elif definitions.CONF_DISTANCE_METRIC in configuration:
            values.CONF_DISTANCE_METRIC = configuration.replace(definitions.CONF_DISTANCE_METRIC, '')
            if values.CONF_DISTANCE_METRIC not in values.OPTIONS_DIST_METRIC.values():
                error_exit("Invalid configuration for " + definitions.CONF_DISTANCE_METRIC)
        elif definitions.CONF_PATCH_TYPE in configuration:
            values.CONF_PATCH_TYPE = configuration.replace(definitions.CONF_PATCH_TYPE, '')
            if values.CONF_PATCH_TYPE not in values.OPTIONS_PATCH_TYPE.values():
                error_exit("Invalid configuration for " + definitions.CONF_PATCH_TYPE)
        elif definitions.CONF_OPERATION_MODE in configuration:
            values.CONF_OPERATION_MODE = configuration.replace(definitions.CONF_OPERATION_MODE, '')
            if values.CONF_OPERATION_MODE not in values.OPTIONS_OPERATION_MODE:
                error_exit("Invalid configuration for " + definitions.CONF_OPERATION_MODE)
        elif definitions.CONF_BUILD_FLAGS in configuration:
            values.CONF_BUILD_FLAGS = configuration.replace(definitions.CONF_BUILD_FLAGS, '')
        elif definitions.CONF_KLEE_FLAGS in configuration:
            values.CONF_KLEE_FLAGS = configuration.replace(definitions.CONF_KLEE_FLAGS, '')
        elif definitions.CONF_ITERATION_LIMIT in configuration:
            values.CONF_ITERATION_LIMIT = int(configuration.replace(definitions.CONF_ITERATION_LIMIT, ''))
        elif definitions.CONF_MAX_FLIPPINGS in configuration:
            values.CONF_MAX_FLIPPINGS = int(configuration.replace(definitions.CONF_MAX_FLIPPINGS, ''))
        elif definitions.CONF_STACK_SIZE in configuration:
            values.CONF_STACK_SIZE = int(configuration.replace(definitions.CONF_STACK_SIZE, ''))
        elif definitions.CONF_MASK_ARG in configuration:
            values.CONF_MASK_ARG = configuration.replace(definitions.CONF_MASK_ARG, '').split(",")
        elif definitions.CONF_TIMEOUT_SAT in configuration:
            values.CONF_TIMEOUT_SAT = int(configuration.replace(definitions.CONF_TIMEOUT_SAT, ''))
        elif definitions.CONF_TIMEOUT_CONCOLIC_RUN in configuration:
            values.CONF_TIMEOUT_CONCOLIC_RUN = int(configuration.replace(definitions.CONF_TIMEOUT_CONCOLIC_RUN, ''))
        elif definitions.CONF_TIMEOUT_CONCRETE_RUN in configuration:
            values.CONF_TIMEOUT_CONCRETE_RUN = int(configuration.replace(definitions.CONF_TIMEOUT_CONCRETE_RUN, ''))
        elif definitions.CONF_TEST_SUITE_ID_LIST in configuration:
            values.CONF_TEST_SUITE_ID_LIST = str(configuration).replace(definitions.CONF_TEST_SUITE_ID_LIST, "").split(",")
        elif definitions.CONF_SEED_SUITE_ID_LIST in configuration:
            values.CONF_SEED_SUITE_ID_LIST = str(configuration).replace(definitions.CONF_SEED_SUITE_ID_LIST, "").split(",")
        elif definitions.CONF_PATCH_DIR in configuration:
            values.CONF_PATCH_DIR = configuration.replace(definitions.CONF_PATCH_DIR, "")
        elif definitions.CONF_TEST_SUITE_CONFIG in configuration:
            config_path = configuration.replace(definitions.CONF_TEST_SUITE_CONFIG, "")
            config_path = values.CONF_PATH_PROJECT + "/" + config_path
            if os.path.isfile(config_path):
                values.CONF_TEST_SUITE_CONFIG = reader.read_json(config_path)
            else:
                error_exit("Test suite configuration file not found at " + str(config_path))
        elif definitions.CONF_SEED_SUITE_CONFIG in configuration:
            config_path = configuration.replace(definitions.CONF_SEED_SUITE_CONFIG, "")
            config_path = values.CONF_PATH_PROJECT + "/" + config_path
            if os.path.isfile(config_path):
                values.CONF_SEED_SUITE_CONFIG = reader.read_json(config_path)
            else:
                error_exit("Seed suite configuration file not found at " + str(config_path))
        elif definitions.CONF_TEST_BINARY_CONFIG_FILE in configuration:
            config_path = configuration.replace(definitions.CONF_TEST_BINARY_CONFIG_FILE, "")
            config_path = values.CONF_PATH_PROJECT + "/" + config_path
            if os.path.isfile(config_path):
                with open(config_path, "r") as conf_file:
                    values.CONF_TEST_BINARY_LIST = [x.strip().replace("\n", "") for x in conf_file.readlines()]
            else:
                error_exit("Test binary configuration file not found at " + str(config_path))
        elif definitions.CONF_SEED_BINARY_CONFIG_FILE in configuration:
            config_path = configuration.replace(definitions.CONF_SEED_BINARY_CONFIG_FILE, "")
            config_path = values.CONF_PATH_PROJECT + "/" + config_path
            if os.path.isfile(config_path):
                with open(config_path, "r") as conf_file:
                    values.CONF_SEED_BINARY_LIST = [x.strip().replace("\n", "") for x in conf_file.readlines()]
            else:
                error_exit("Test binary configuration file not found at " + str(config_path))

    if not values.CONF_TAG_ID:
        emitter.error("[NOT FOUND] Tag ID ")
        exit()
    if values.CONF_DIR_SRC:
        if "/" != values.CONF_DIR_SRC[0]:
            values.CONF_DIR_SRC = values.CONF_PATH_PROJECT + "/" + values.CONF_DIR_SRC
    else:
        values.CONF_DIR_SRC = values.CONF_PATH_PROJECT

    if values.CONF_PATH_PROGRAM:
        if "/" != values.CONF_PATH_PROGRAM[0]:
            values.CONF_PATH_PROGRAM = values.CONF_DIR_SRC + "/" + values.CONF_PATH_PROGRAM


def load_component_list():
    emitter.normal("loading custom/general components")
    # base_list = ["equal.smt2", "not-equal.smt2", "less-than.smt2", "less-or-equal.smt2"]
    base_list = []
    if definitions.DIRECTORY_TESTS in values.CONF_PATH_PROJECT:
        base_list = []
    gen_comp_files = []
    os.chdir(definitions.DIRECTORY_COMPONENTS)
    if values.CONF_GENERAL_COMP_LIST and not values.CONF_ALL_COMPS:
        comp_list = list(set(values.CONF_GENERAL_COMP_LIST + base_list))
        for component_name in comp_list:
            gen_comp_files.append(Path(component_name))
            emitter.note("\tloading component: " + str(component_name))
    else:
        component_file_list = os.listdir(definitions.DIRECTORY_COMPONENTS)
        for comp_file in component_file_list:
            if ".smt2" in comp_file:
                if any(x in comp_file for x in ["logical-not", "post-decrement", "post-increment", "minus", "constant", "assignment", "sequence", "greater", "remainder"]):
                    continue
                gen_comp_files.append(Path(comp_file))
                emitter.note("\tloading component: " + str(comp_file))
    gen_comp_files = list(set(gen_comp_files))
    general_components = synthesis.load_components(gen_comp_files)

    proj_comp_files = []
    os.chdir(values.CONF_PATH_PROJECT)
    for component_name in values.CONF_CUSTOM_COMP_LIST:
        proj_comp_files.append(Path(component_name))
        emitter.note("\tloading component: " + str(component_name))
    project_components = synthesis.load_components(proj_comp_files)
    values.LIST_COMPONENTS = project_components + general_components
    values.COUNT_COMPONENTS = len(values.LIST_COMPONENTS)
    values.COUNT_COMPONENTS_CUS = len(project_components)
    values.COUNT_COMPONENTS_GEN = len(general_components)


def print_configuration():
    # emitter.note("\tconfiguration.is_crash:" + str(values.IS_CRASH))
    # assertion_formula = generator.generate_formula(values.SPECIFICATION_TXT[1])
    # emitter.configuration("\t[config] program specification:", values.SPECIFICATION_TXT[1])
    emitter.configuration("path generation limit", values.DEFAULT_GEN_SEARCH_LIMIT)
    emitter.configuration("synthesis max bound", values.DEFAULT_PATCH_UPPER_BOUND)
    emitter.configuration("synthesis low bound", values.DEFAULT_PATCH_LOWER_BOUND)
    emitter.configuration("stack size", sys.getrecursionlimit())
    emitter.configuration("refine strategy", values.DEFAULT_REFINE_METHOD)
    emitter.configuration("patch type", values.DEFAULT_PATCH_TYPE)
    emitter.configuration("repair method", values.DEFAULT_REDUCE_METHOD)
    emitter.configuration("timeout for CPR", values.DEFAULT_TIME_DURATION)
    emitter.configuration("timeout for sat", values.DEFAULT_TIMEOUT_SAT)
    emitter.configuration("timeout for klee", values.DEFAULT_TIMEOUT_KLEE_CONCOLIC)
    emitter.configuration("distance metric", values.DEFAULT_DISTANCE_METRIC)
    emitter.configuration("operation mode", values.DEFAULT_OPERATION_MODE)
    emitter.configuration("iteration limit", values.DEFAULT_ITERATION_LIMIT)
    emitter.configuration("collecting stats", str(values.DEFAULT_COLLECT_STAT))
    emitter.configuration("number of seeds", str(len(values.LIST_SEED_INPUT)))
    emitter.configuration("number of tests", str(len(values.LIST_TEST_INPUT)))
    emitter.configuration("list of seed ids", str(values.LIST_SEED_ID_LIST))
    emitter.configuration("list of test ids", str(values.LIST_TEST_ID_LIST))
    emitter.configuration("masked input arg id list", values.CONF_MASK_ARG)


def collect_test_list():
    emitter.normal("reading test configuration")
    if values.CONF_TEST_SUITE_CONFIG:
        for (test_id, bin_path, test_input, expected_output) in values.CONF_TEST_SUITE_CONFIG:
            if values.CONF_TEST_SUITE_ID_LIST:
                if str(test_id) not in values.CONF_TEST_SUITE_ID_LIST:
                    continue
            values.LIST_TEST_ID_LIST.add(str(test_id))
            bin_path = values.CONF_DIR_SRC + "/" + bin_path
            values.LIST_TEST_BINARY.append(bin_path)
            values.LIST_TEST_INPUT.append(test_input)
            values.LIST_TEST_OUTPUT.append(expected_output)

    else:
        if values.CONF_TEST_BINARY_LIST:
            for binary_path in values.CONF_TEST_BINARY_LIST:
                binary_path = values.CONF_DIR_SRC + "/" + binary_path
                values.LIST_TEST_BINARY.append(binary_path)

        if values.CONF_TEST_INPUT_LIST:
            for test_input in values.CONF_TEST_INPUT_LIST:
                values.LIST_TEST_INPUT.append(test_input)
        elif values.CONF_TEST_INPUT_FILE:
            with open(values.CONF_TEST_INPUT_FILE, "r") as in_file:
                content_lines = in_file.readlines()
                for content in content_lines:
                    test_input = content.strip().replace("\n", "")
                    if test_input.isspace():
                        continue
                    if "$POC_" in test_input:
                        test_input_file = test_input.split("$POC_")[1].split(" ")[0]
                        test_input_file_index = test_input_file
                        if values.CONF_GENERALIZED_TEST_INPUT:
                            test_input = values.CONF_GENERALIZED_TEST_INPUT.replace("$POC", test_input)
                        if test_input_file[0] != "/":
                            if values.CONF_SEED_DIR:
                                test_input_file = values.CONF_SEED_DIR + "/" + test_input_file
                            else:
                                test_input_file = values.CONF_DIR_SRC + "/" + test_input_file
                        values.LIST_TEST_FILES[test_input_file_index] = test_input_file
                    if test_input:
                        values.LIST_TEST_INPUT.append(test_input)
        else:
            error_exit("No test input is given (at least one is required)")

        if values.CONF_TEST_OUTPUT_LIST:
            for expected_output in values.CONF_TEST_OUTPUT_LIST:
                values.LIST_TEST_OUTPUT.append(expected_output)
        elif values.CONF_TEST_OUTPUT_DIR:
            expected_output_dir = values.CONF_TEST_OUTPUT_DIR
            file_list = [f for f in os.listdir(expected_output_dir) if
                         os.path.isfile(os.path.join(expected_output_dir, f))]
            for expected_output_file in file_list:
                if ".smt2" in expected_output_file:
                    expected_file_abs_path = expected_output_dir + "/" + expected_output_file
                    expected_file_rel_path = str(expected_file_abs_path).replace(values.CONF_PATH_PROJECT + "/", "")
                    values.LIST_TEST_OUTPUT.append(expected_file_rel_path)
        else:
            error_exit("No expected output is given (at least one is required)")

    if values.CONF_TEST_INPUT_DIR:
        test_file_dir = values.CONF_TEST_INPUT_DIR
        file_list = [f for f in os.listdir(test_file_dir) if os.path.isfile(os.path.join(test_file_dir, f))]
        for test_file in file_list:
            test_file_index = test_file
            # if "." in test_file:
            #     test_file_index = str(test_file).split(".")[0]
            test_abs_path = test_file_dir + "/" + test_file
            # if not values.CONF_PATH_POC:
            #     values.CONF_PATH_POC = test_abs_path
            values.LIST_TEST_FILES[test_file_index] = test_abs_path
    elif values.CONF_PATH_POC:
        test_file = values.CONF_PATH_POC
        test_file_index = test_file
        # if "." in test_file:
        #     test_file_index = str(test_file).split(".")[0]
        values.LIST_TEST_FILES[test_file_index] = values.CONF_PATH_POC


    test_input_list = values.LIST_TEST_INPUT
    concretized_test_input_list = []
    for arg_list_str in test_input_list:
        arg_list = extract_input_arg_list(arg_list_str)
        concretized_arg_list = []
        for arg in arg_list:
            if "$POC_" in arg:
                file_index = "_".join(str(arg).split("_")[1:])
                file_path = values.LIST_TEST_FILES[file_index]
                concretized_arg_list.append(file_path)
            elif "$POC" in arg:
                file_index = list(values.LIST_TEST_FILES.keys())[0]
                file_path = values.LIST_TEST_FILES[file_index]
                concretized_arg_list.append(file_path)
            else:
                concretized_arg_list.append(arg)
        concretized_arg_str = ",".join(concretized_arg_list)
        concretized_test_input_list.append(concretized_arg_str)
    values.LIST_TEST_INPUT = concretized_test_input_list


def collect_seed_list():
    emitter.normal("reading seed information")
    if values.CONF_SEED_SUITE_CONFIG:
        for (seed_id, bin_path, test_input) in values.CONF_SEED_SUITE_CONFIG:
            if values.CONF_SEED_SUITE_ID_LIST:
                if str(seed_id) not in values.CONF_SEED_SUITE_ID_LIST:
                    continue
            values.LIST_SEED_ID_LIST.add(str(seed_id))
            bin_path = values.CONF_DIR_SRC + "/" + bin_path
            values.LIST_SEED_BINARY.append(bin_path)
            values.LIST_SEED_INPUT.append((seed_id, test_input))
    else:
        if values.CONF_SEED_BINARY_LIST:
            for binary_path in values.CONF_SEED_BINARY_LIST:
                binary_path = values.CONF_DIR_SRC + "/" + binary_path
                values.LIST_SEED_BINARY.append(binary_path)
        if values.CONF_SEED_LIST:
            for seed_input in values.CONF_SEED_LIST:
                values.LIST_SEED_INPUT.append(seed_input)
        elif values.CONF_SEED_FILE:
            with open(values.CONF_SEED_FILE, "r") as in_file:
                content_lines = in_file.readlines()
                seed_id = 0
                for content in content_lines:
                    seed_id = seed_id + 1
                    seed_input = content.strip().replace("\n", "")
                    if values.CONF_SEED_SUITE_ID_LIST:
                        if str(seed_id) not in values.CONF_SEED_SUITE_ID_LIST:
                            continue
                    if seed_input.isspace():
                        continue
                    if "$POC_" in seed_input:
                        seed_input_file = seed_input.split("$POC_")[1].split(" ")[0]
                        seed_input_file_index = seed_input_file
                        if values.CONF_GENERALIZED_SEED_INPUT:
                            seed_input = values.CONF_GENERALIZED_SEED_INPUT.replace("$POC", seed_input)
                        if seed_input_file[0] != "/":
                            if values.CONF_SEED_DIR:
                                seed_input_file = values.CONF_SEED_DIR + "/" + seed_input_file
                            else:
                                seed_input_file = values.CONF_DIR_SRC + "/" + seed_input_file
                        values.LIST_SEED_FILES[seed_input_file_index] = seed_input_file
                    if seed_input:
                        values.LIST_SEED_INPUT.append((seed_id, seed_input))
    if values.CONF_SEED_DIR:
        seed_dir = values.CONF_SEED_DIR
        file_list = [f for f in os.listdir(seed_dir) if os.path.isfile(os.path.join(seed_dir, f))]
        for seed_file in file_list:
            seed_file_index = seed_file
            seed_abs_path = seed_dir + "/" + seed_file
            values.LIST_SEED_FILES[seed_file_index] = seed_abs_path

    if values.LIST_SEED_INPUT:
        seed_index = 0
        for seed in values.LIST_SEED_INPUT:
            if isinstance(seed, tuple):
                seed_id, seed_arg_list_str = seed
            else:
                seed_arg_list_str = seed
                seed_id = values.LIST_SEED_INPUT.index(seed) + 1
            arg_list = extract_input_arg_list(seed_arg_list_str)
            concretized_arg_list = []
            for arg in arg_list:
                if "$POC_" in arg:
                    file_index = "_".join(str(arg).split("_")[1:])
                    if file_index not in values.LIST_SEED_FILES:
                        continue
                    file_path = values.LIST_SEED_FILES[file_index]
                    concretized_arg_list.append(file_path)
                elif "$POC" in arg:
                    file_index = list(values.LIST_TEST_FILES.keys())[0]
                    file_path = values.LIST_TEST_FILES[file_index]
                    concretized_arg_list.append(file_path)
                else:
                    concretized_arg_list.append(arg)
            concretized_arg_str = ",".join(concretized_arg_list)
            values.LIST_TEST_INPUT.append(concretized_arg_str)
            if values.LIST_SEED_BINARY:
                values.LIST_TEST_BINARY.append(values.LIST_SEED_BINARY[seed_index])
            seed_index = seed_index + 1


def collect_var_mapping():
    emitter.normal("updating mapping for program variables")
    patch_loc = values.CONF_LOC_PATCH
    source_file_path, line_number = patch_loc.split(":")
    with open(source_file_path, 'r') as source_file:
        content = source_file.readlines()
        patch_line = content[int(line_number) - 1]
        trident_call_str = re.findall("trident_choice\((.+?)\)[\),\s,;]", patch_line)[0]
        patch_type = trident_call_str.split(",")[1]
        if patch_type == "bool":
            values.IS_PATCH_BOOL = True
        prog_var_list = re.findall("{(.+?)}", trident_call_str)[0].split(",")
        comp_name_list = re.findall("{(.+?)}", trident_call_str)[1].split(",")
        for i in range (0, len(prog_var_list)):
            values.MAP_PROG_VAR[comp_name_list[i].strip().replace("\"", "").replace("\'", "")] = prog_var_list[i]
    # print(values.MAP_PROG_VAR)


def update_configuration():
    emitter.normal("updating configuration values")
    klee_last_dir = values.KLEE_LAST_DIR
    values.FILE_PPC_LOG = klee_last_dir + "/ppc.log"
    values.FILE_EXPR_LOG = klee_last_dir + "/expr.log"
    values.FILE_TRACE_LOG = klee_last_dir + "/trace.log"
    values.FILE_MESSAGE_LOG = klee_last_dir + "/messages.txt"
    definitions.DIRECTORY_OUTPUT = definitions.DIRECTORY_OUTPUT_BASE + "/" + values.CONF_TAG_ID
    definitions.DIRECTORY_LOG = definitions.DIRECTORY_LOG_BASE + "/" + values.CONF_TAG_ID

    if os.path.isdir(definitions.DIRECTORY_OUTPUT):
        shutil.rmtree(definitions.DIRECTORY_OUTPUT)
    os.mkdir(definitions.DIRECTORY_OUTPUT)

    if os.path.isdir(definitions.DIRECTORY_LOG):
        shutil.rmtree(definitions.DIRECTORY_LOG)
    os.mkdir(definitions.DIRECTORY_LOG)
    if values.CONF_PATCH_DIR:
        if os.path.isdir(values.CONF_PATCH_DIR):
            values.DEFAULT_PATCH_DIR = values.CONF_PATCH_DIR
    if values.CONF_MAX_BOUND:
        values.DEFAULT_PATCH_UPPER_BOUND = values.CONF_MAX_BOUND
    if values.CONF_LOW_BOUND:
        values.DEFAULT_PATCH_LOWER_BOUND = values.CONF_LOW_BOUND
    if values.CONF_MAX_FORK:
        values.DEFAULT_MAX_FORK = values.CONF_MAX_FORK
    if values.CONF_GEN_SEARCH_LIMIT:
        values.DEFAULT_GEN_SEARCH_LIMIT = values.CONF_GEN_SEARCH_LIMIT
    if values.CONF_ITERATION_LIMIT >= 0:
        values.DEFAULT_ITERATION_LIMIT = values.CONF_ITERATION_LIMIT
    if values.CONF_STACK_SIZE:
        values.DEFAULT_STACK_SIZE = values.CONF_STACK_SIZE
    # if values.CONF_IS_CRASH:
    #     values.IS_CRASH = values.CONF_IS_CRASH
    if values.CONF_GEN_PATH_SPECIAL is not None:
        values.DEFAULT_GEN_SPECIAL_PATH = values.CONF_GEN_PATH_SPECIAL
    if values.CONF_TIME_DURATION:
        values.DEFAULT_TIME_DURATION = values.CONF_TIME_DURATION
    if values.CONF_TIMEOUT_SAT:
        values.DEFAULT_TIMEOUT_SAT = values.CONF_TIMEOUT_SAT
    if values.CONF_TIMEOUT_CONCOLIC_RUN:
        values.DEFAULT_TIMEOUT_KLEE_CONCOLIC = values.CONF_TIMEOUT_CONCOLIC_RUN
    if values.CONF_TIMEOUT_CONCRETE_RUN:
        values.DEFAULT_TIMEOUT_KLEE_CONCRETE = values.CONF_TIMEOUT_CONCRETE_RUN
    if values.CONF_RANK_LIMIT:
        values.DEFAULT_PATCH_RANK_LIMIT = values.CONF_RANK_LIMIT
    if values.CONF_SELECTION_STRATEGY:
        values.DEFAULT_SELECTION_STRATEGY = values.CONF_SELECTION_STRATEGY
    if values.CONF_DISTANCE_METRIC:
        values.DEFAULT_DISTANCE_METRIC = values.CONF_DISTANCE_METRIC
    if values.CONF_PATCH_TYPE:
        values.DEFAULT_PATCH_TYPE = values.CONF_PATCH_TYPE
    if values.CONF_REFINE_METHOD:
        values.DEFAULT_REFINE_METHOD = values.CONF_REFINE_METHOD
    if values.CONF_OPERATION_MODE:
        values.DEFAULT_OPERATION_MODE = values.CONF_OPERATION_MODE
    if values.CONF_REDUCE_METHOD:
        values.DEFAULT_REDUCE_METHOD = values.CONF_REDUCE_METHOD
    if values.DEFAULT_REDUCE_METHOD == "cegis":
        values.DEFAULT_PATCH_TYPE = values.OPTIONS_PATCH_TYPE[0]
    if values.CONF_COLLECT_STAT:
        values.DEFAULT_COLLECT_STAT = True
    if values.CONF_TIME_SPLIT:
        explore, refine = values.CONF_TIME_SPLIT.split(":")
        total = int(explore) + int(refine)
        values.CONF_TIME_CEGIS_EXPLORE = (int(explore) / total) * values.DEFAULT_TIME_DURATION
        values.CONF_TIME_CEGIS_REFINE = (int(refine) / total) * values.DEFAULT_TIME_DURATION
    sys.setrecursionlimit(values.DEFAULT_STACK_SIZE)


def extract_input_arg_list(argument_str):
    if "," not in argument_str:
        argument_list = str(argument_str).split(" ")
    else:
        # argument_str = argument_str.replace("[", "").replace("]", "")
        argument_list = str(argument_str).split(",")
    return argument_list
# base_list = ["equal.smt2", "not-equal.smt2", "less-than.smt2", "less-or-equal.smt2"] # emitter.note("\tconfiguration.is_crash:" + str(values.IS_CRASH)) # assertion_formula = generator.generate_formula(values.SPECIFICATION_TXT[1]) # emitter.configuration("\t[config] program specification:", values.SPECIFICATION_TXT[1]) # if "." in test_file: #     test_file_index = str(test_file).split(".")[0] # if not values.CONF_PATH_POC: #     values.CONF_PATH_POC = test_abs_path # if "." in test_file: #     test_file_index = str(test_file).split(".")[0] # print(values.MAP_PROG_VAR) # if values.CONF_IS_CRASH: #     values.IS_CRASH = values.CONF_IS_CRASH # argument_str = argument_str.replace("[", "").replace("]", "")