def insert_brand_model():
    config_file = r"D:\Users\Achelics\liu_project\mutil_device_recongition\handle_brand_information\database_config.ini"
    settion = "MyDataBase"
    db_config = Config(config_file, settion)

    url = db_config.get("url")
    user = db_config.get("user")
    pawd = db_config.get("pawd")
    database = db_config.get("database")

    try:
        # open the database
        conn = MySQLdb.connect(url, user, pawd, database)
        # Using the cursor() method to get the operate cursor.
        cursor = conn.cursor()
        for brand_model in __BRAND_MODEL_LIST:
            default_sql = "insert into iie_brand_model(brand, model, category) values('%s', '%s', '%s')" % \
                          (brand_model["Brand"], brand_model["Model"], brand_model["type"])
            cursor.execute(default_sql)
        # 获取所有结果
        conn.commit()
        # 关闭指针
        cursor.close()
        # 关闭数据库连接
        conn.close()
    except MySQLdb.Error, e:
        print("MySQL Error:%s" % str(e))
        print("插入数据库失败")
Exemplo n.º 2
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 def __init__(self, fullscreen, size, beamer_controller):
     #QtGui.QDialog.__init__(self)
     QtGui.QWidget.__init__(self)
     self.fullscreen = fullscreen
     self.beamer_controller = beamer_controller
     
     
     config = Config()
     self.screen = config.getBeamerScreen()
     
     if fullscreen:
         self.routeCanvasToSecondaryScreen()
     else:
         self.qsize = QtCore.QSize(size[0], size[1])
         self.qrect = QtCore.QRect(0, 0, size[0], size[1])
         self.setMinimumSize(self.qsize)
         self.setMaximumSize(self.qsize)
         self.resize(self.qsize)
     
     #self.setStyleSheet("QDialog { background-color: black; }")
     self.setStyleSheet("QWidget { background-color: black; }")
     
     self.layout = QtGui.QGridLayout()
     
     
     
     self.beam_data = None
Exemplo n.º 3
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def __init_brand_list():
    config_file = r"D:\Users\Achelics\liu_project\mutil_device_recongition\handle_brand_information\database_config.ini"
    settion = "MyDataBase"
    db_config = Config(config_file, settion)

    url = db_config.get("url")
    user = db_config.get("user")
    pawd = db_config.get("pawd")
    database = db_config.get("database")

    try:
        # open the database
        db = MySQLdb.connect(url, user, pawd, database)
        # Using the cursor() method to get the operate cursor.
        cursor = db.cursor()
        # SQL select by vulflag
        sql_default = "SELECT DISTINCT(en_name) FROM iie_brand ORDER BY LENGTH(en_name) DESC"
        # excute SQL sentence
        cursor.execute(sql_default)
        # Get the all record
        default_results = cursor.fetchall()
        for row in default_results:
            __BRAND_LIST.append(str(row[0]).upper())
        # 关闭数据库连接
        db.close()
    except MySQLdb.Error, e:
        print("MySQL Error:%s" % str(e))
Exemplo n.º 4
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def insert_brand():
    config_file = r"D:\Users\Achelics\liu_project\mutil_device_recongition\handle_brand_information\database_config.ini"
    settion = "MyDataBase"
    db_config = Config(config_file, settion)

    url = db_config.get("url")
    user = db_config.get("user")
    pawd = db_config.get("pawd")
    database = db_config.get("database")

    try:
        # open the database
        conn = MySQLdb.connect(url, user, pawd, database)
        # Using the cursor() method to get the operate cursor.
        cursor = conn.cursor()
        for brand_type in __RAW_BRAND_LIST:
            if str(brand_type[0]).strip().upper() not in __BRAND_LIST:
                print brand_type
                default_sql = "insert into iie_brand(en_name, product_type) values('%s', '%s')" % (
                    brand_type[0], brand_type[1])
                cursor.execute(default_sql)
        # 获取所有结果
        conn.commit()
        # 关闭指针
        cursor.close()
        # 关闭数据库连接
        conn.close()
    except MySQLdb.Error, e:
        print("MySQL Error:%s" % str(e))
Exemplo n.º 5
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 def getScreens(self):
     config = Config()
     main_screen = config.getProgramScreen()
     beamer_screen = config.getBeamerScreen()
     
     beamer_screen = self.checkForCorrectConfigScreenSettings(beamer_screen)
     
     return main_screen, beamer_screen
Exemplo n.º 6
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def main():
    # parse config
    config_file = sys.argv[1]
    config = Config(config_file)

    # setup logger
    setup_logging(config.working_dir)

    # encoding func
    encoding_func = ENCODING_METHOD_MAP[config.encoding_method]
    encoding_func2 = ENCODING_METHOD_MAP[config.encoding_method2]
    log_to_file('Encoding method2', config.encoding_method2)

    data_provider = []
    for p in range(config.base_model_count):
        temp_provider = DataProvider(encoding_func,
                                     encoding_func2,
                                     config.data_file,
                                     config.test_file,
                                     config.batch_size,
                                     max_len_hla=config.max_len_hla,
                                     max_len_pep=config.max_len_pep,
                                     model_count=config.model_count)
        data_provider.append(temp_provider)

    log_to_file('Traning samples', len(data_provider[0].train_samples[0]))
    log_to_file('Val samples', len(data_provider[0].validation_samples[0]))
    log_to_file('Traning steps', data_provider[0].train_steps())
    log_to_file('Val steps', data_provider[0].val_steps())
    log_to_file('Batch size', data_provider[0].batch_size)
    log_to_file('max_len_hla', data_provider[0].max_len_hla)
    log_to_file('max_len_pep', data_provider[0].max_len_pep)

    for p in range(config.base_model_count):
        train(config, data_provider[p], p)
Exemplo n.º 7
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def main():
    config = Config()

    print("Processing text for \'%s\'." % (config.text_file))
    data = preprocess.preprocess(config.text_file, 'infer', config)
    dataloader = dataprocess.load_infer(data, config)

    G = Generator(config)
    G.load_state_dict(load_weights(config.checkpoint_file))
    G = set_device(G, config.device, config.use_cpu)
    G.eval()

    print("Generating spectrogram with \'%s\'." % (config.checkpoint_file))

    spec = []
    y_prev = torch.zeros(1, config.prev_length, config.fft_size // 2 + 1)
    for x in tqdm(dataloader, leave=False, ascii=True):
        x, y_prev = set_device((x, y_prev), config.device, config.use_cpu)

        y_gen = G(x, y_prev)
        y_gen = y_gen.squeeze(1)
        y_prev = y_gen[:, -config.prev_length:, :]
        spec.append(y_gen.data)

    print("Generating audio with Griffin-Lim algorithm.")
    spec = torch.cat(spec, dim=1).transpose(1, 2)  # T x D -> D x T
    wave = dsp.inv_spectrogram(spec, config)

    savename = config.checkpoint_file.replace('.pt', '_') + os.path.basename(
        config.text_file).replace('.txt', '.wav')
    dsp.save(savename, wave, config.sample_rate)

    print("Audio saved to \'%s\'." % (savename))
Exemplo n.º 8
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 def display(self, module="INIT", ioc="", message_type="DEBUG", string=""):
     exec('colorize = colors.%s' % message_type)
     config = Config.get_instance()
     if not config["debug"] and (message_type == "INFO"
                                 or message_type == "DEBUG"):
         pass
     else:
         if ioc != "":
             if len(ioc) >= 67:
                 ioc = '%s%s...' % (ioc[:64], colors.NORMAL)
             ioc_show = "{%s%s%s} " % (colors.INFO, ioc, colors.NORMAL)
         else:
             ioc_show = " "
         output = "[%s][%s%s%s]%s%s%s%s" % (
             module, colorize, message_type, colors.NORMAL, ioc_show,
             colors.BOLD, string, colors.NORMAL)
         if message_type == "FOUND":
             if not exists(config["log_found_file"]):
                 open(config["log_found_file"], 'a').close()
                 chmod(config["log_found_file"], 0o777)
             f = open(config["log_found_file"], 'a')
             f.write(
                 "%s%s\n" %
                 (datetime.now().strftime('[%d-%m-%Y %H:%M:%S]'), output))
             f.close()
         print(output)
Exemplo n.º 9
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    def allowedToSearch(self, status):
        config = Config.get_instance()
        """
            Input: "Online", "Onpremises"
        """
        if status == "Onpremises":
            '''
            here the modules claims to be related to an on premises service
            , i.e. being inside researcher nertwork, so we allow the lookup

            modules: misp, cuckoo
            '''
            return True
        elif status == "Online" and not config["offline"]:
            '''
            the modules claims to be online, and user _do not_ asked the
            lookup to be performed offline
            thus it is allowed to perform if online
            '''
            return True
        '''
        if none of previous case, lookup forbidden
        '''
        return False
        '''
Exemplo n.º 10
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def main():
    # parse config
    config_file = sys.argv[1]
    config = Config(config_file)

    # setup logger
    setup_logging(config.working_dir)

    # encoding func
    encoding_func = ENCODING_METHOD_MAP[config.encoding_method]
    encoding_func2= ENCODING_METHOD_MAP[config.encoding_method2]
    log_to_file('Encoding method2', config.encoding_method2)

    data_provider=[]
    for p in range(config.base_model_count):
        temp_provider = DataProvider(
             encoding_func,
             encoding_func2,
             config.data_file,
             config.test_file,
             config.batch_size,
             max_len_hla=config.max_len_hla,
             max_len_pep=config.max_len_pep,
             model_count=config.model_count
        )
        data_provider.append(temp_provider)
 
    log_to_file('max_len_hla', data_provider[0].max_len_hla)
    log_to_file('max_len_pep', data_provider[0].max_len_pep)
    
    test(config, data_provider[0])
Exemplo n.º 11
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 def __init__(self, iocs):
     config = Config.get_instance()
     if not exists(config["log_search_file"]):
         open(config["log_search_file"], 'a').close()
         chmod(config["log_search_file"], 0o777)
     f = open(config["log_search_file"], 'a')
     for ioc in iocs:
         f.write("%s %s\n" %
                 (datetime.now().strftime('[%d-%m-%Y %H:%M:%S]'), ioc))
     f.close()
Exemplo n.º 12
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def main():
    # parse config
    config_file = sys.argv[1]

    config = Config(config_file)
    folder = config_file.split('/')[0]
    encoding_func = ENCODING_METHOD_MAP[config.encoding_method]
    encoding_func2= ENCODING_METHOD_MAP[config.encoding_method2]
    data_provider = DataProvider(
        encoding_func,
        encoding_func2,
        config.data_file,
        config.test_file,
        config.batch_size,
        max_len_hla=config.max_len_hla,
        max_len_pep=config.max_len_pep,
        model_count=config.model_count
        )
    device = config.device
    models = config.model_count*config.base_model_count
    print(models)
    total_df=pd.DataFrame()
    for i in range(models):
    # load and prepare model
        path = folder + "/best_model_{}.pytorch".format(i)
        state_dict = torch.load(path)
        model = Model(config)
        model.load_state_dict(state_dict)
        model.to(device)
        model.eval()
        data_provider.new_epoch()

        for _ in range(data_provider.test_steps()):
            data = data_provider.batch_test()
            hla_a, hla_mask, hla_a2, hla_mask2, pep, pep_mask, pep2, pep_mask2, uid_list = data  
            temp_attn = {}
            temp_attn_hla = {}
            with torch.no_grad():
                 temp = model.encoder_peptide2.conv_0(pep2.to(device))
                 temp, att = model.encoder_peptide2.att_0(temp.to(device))

            for i in range(config.batch_size):
                temp_attn[uid_list[i].split('-')[3]]=att[i].tolist()

            temp_df=pd.DataFrame.from_dict(temp_attn,orient="index")

            total_df=pd.concat([total_df,temp_df])

    avg_= total_df.mean(axis=0)
    avg_= pd.DataFrame({'position':avg_.index+1, 'avg weight':avg_.values})  
    avg_.to_csv(folder + "/" + "attn_weight.csv",index=None)
Exemplo n.º 13
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def run():

    config = Config('configs.yaml')
    database = Database(config.database)

    controller = Controller()

    while True:
        controller.fill_wall_post_trigger(database)
        controller.fill_comment_trigger(database)

        controller.fill_wall_post_emotion(database)
        controller.fill_comment_emotion(database)

        sleep(60 * 60)
Exemplo n.º 14
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 def __init__(self, args):
     config = Config.get_instance()
     if not exists(config["log_search_file"]):
         open(config["log_search_file"], 'a').close()
         chmod(config["log_search_file"], 0o777)
     f = open(config["log_search_file"], 'a')
     if args.file == "False" :
         for ioc in args.observables :
             f.write("%s %s\n"%(datetime.now().strftime('[%d-%m-%Y %H:%M:%S]'), ioc))
         f.close()
     else :
         for file in args.observables :
             with open(file, "r") as f2 :
                 for ioc in f2.readlines():
                     f.write("%s %s\n" % (datetime.now().strftime('[%d-%m-%Y %H:%M:%S]'), ioc.strip('\n')))
         f.close()
Exemplo n.º 15
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class colors:
    config = Config.get_instance()
    if system() == "Windows" or config["terminal_color"] is False:
        DEBUG = ''
        INFO = ''
        FOUND = ''
        WARNING = ''
        ERROR = ''
        NORMAL = ''
        BOLD = ''
    else:
        DEBUG = '\033[95m'
        INFO = '\033[94m'
        FOUND = '\033[92m'
        WARNING = '\033[93m'
        ERROR = '\033[91m'
        NORMAL = '\033[0m'
        BOLD = '\033[1m'
Exemplo n.º 16
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 def __init__(self):
     QtGui.QMainWindow.__init__(self)
     
     self.setWindowTitle("musicbeamer")
     screen_rectangle = QtGui.QDesktopWidget().availableGeometry()
     sx, sy = screen_rectangle.getRect()[2], screen_rectangle.getRect()[3]
     #'for smaller displays, we want to use vertically all available space'
     #if sy <= 800:
     if platform.uname()[0] == "Windows":
         'on windows we has to deal with the taskbar manually'
         y = sy - 80
     else:
         'on linux .availableGeometry() did it already for us'
         y = sy
     #else:
     #    y = sy #* 0.61
     x = sx * 0.61
     self.resize(int(x), int(y))
     
     self.beamer_controller = BeamerController()
     
     self.addMenuBar()
     
     self.config = Config()
     screen = self.config.getProgramScreen()
     self.routeWindowToPrimaryScreen(screen)
     
     
     self.schedule = None
     self.preview = None
     
     self.layout = QtGui.QHBoxLayout()
     centralWidget = QtGui.QWidget()
     
     self.setCentralWidget(centralWidget)
     centralWidget.setLayout(self.layout)
     
     #self.addPreview()
     self.addSchedule()
     self.addPreview()
     
     self.setViewportSize(self.mainFrame().contentsSize())
Exemplo n.º 17
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def main():
    config = Config()
    config_basename = os.path.basename(config.configs[0])
    print("Configuration file: \'%s\'" % (config_basename))

    set_list = ['train', 'valid']
    file_list = {}

    # Creating Path for Features
    create_path(config.feature_path, action='overwrite', verbose=False)
    for set_type in set_list:
        path = os.path.join(config.feature_path, set_type)
        create_path(path, action='overwrite')

        list_file = set_type + '_list.txt'
        file_list[set_type] = read_file_list(
            os.path.join(config.dataset_path, list_file))

    # Extracting Features
    if config.num_proc > 1:
        if config.use_cpu is False:
            raise AssertionError("You can not use GPU with multiprocessing.")

        p = Pool(config.num_proc)
        for set_type in set_list:
            p.map(partial(preprocess, set_type=set_type, config=config),
                  file_list[set_type])
    else:
        for set_type in set_list:
            [
                preprocess(f, set_type=set_type, config=config)
                for f in file_list[set_type]
            ]

    # Creating Files Indices
    for set_type in set_list:
        path = os.path.join(config.feature_path, set_type)
        file_indices = make_indices(path)
        torch.save(file_indices,
                   os.path.join(config.feature_path, set_type + '_indices.pt'))

    print("Feature saved to \'%s\'." % (config.feature_path))
Exemplo n.º 18
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 def __init__(self, parentQScrollArea, beamer_screen):
     QtWidgets.QWidget.__init__(self)
     
     self.parentQScrollArea = parentQScrollArea
     
     self.layout = QtWidgets.QGridLayout()
     self.setLayout(self.layout)
     
     self.current_id = None
     
     self.setStyleSheet('QWidget { background-color: yellow; }')
     
     self.config = Config()
     #self.screen = self.config.getBeamerScreen()
     self.screen = beamer_screen
     self.column_count = self.config.getPreviewColumnCount()
     
     #self.aspect_ratio = self.getBeamerWindowAspect()
     
     self.canvas = None
Exemplo n.º 19
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    def __init__(self, module_name, url, filename, search_method):
        self.config = Config.get_instance()
        self.module_name = module_name
        self.url = url
        self.filename = self.new_filename = filename
        self.temp_folder = "%s%s/" % (self.config["temporary_cache_path"],
                                      self.module_name)
        position = 0
        filename_copy = self.filename
        if not self.filename.isalnum():
            filename_copy = self.filename.replace("_", "")
            for pos, char in enumerate(filename_copy):
                if not char.isalnum() and char != '.':
                    position = pos
        self.new_filename = filename_copy[position:]
        self.temp_file = "%s%s" % (self.temp_folder, self.new_filename)

        self.createModuleFolder()
        if self.checkIfUpdate():
            if mod.allowedToSearch(search_method):
                self.downloadFile()
        self.content = self.getContent()
Exemplo n.º 20
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    def create_experiment_info(self):
        # create subject data directory
        data_dir = 'data/{}/'.format(self.subject_number.get())
        if not os.path.exists(data_dir):
            os.makedirs(data_dir)
        else:
            files = glob.glob(data_dir + '*')
            [os.remove(f) for f in files]

        # create config object
        config = Config(config_filename=self.config_filename.get())

        # create trial list and save to csv
        config.save_trial_list(path=data_dir)

        print "Trial list created as {}.".format(data_dir + 'trials.csv')

        # create experiment info and save to txt
        config.save_experiment_info(glove_hand=self.hand.get(), path=data_dir)

        print "Experiment info created as {}.".format(data_dir + 'exp_info.txt')
Exemplo n.º 21
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def main():
    config = Config()
    config_basename = os.path.basename(config.configs[0])
    print("Configuration file: \'%s\'" % (config_basename))

    checkpoint_path = create_path(config.checkpoint_path,
                                  action=config.checkpoint_path_action)
    config.save(os.path.join(checkpoint_path, config_basename))
    logger = Logger(os.path.join(checkpoint_path, 'log'))

    dataloader = dataprocess.load_train(config)
    step_size = config.step_epoch * len(dataloader.train)

    G = Generator(config)
    D = Discriminator(config)
    G, D = set_device((G, D), config.device, config.use_cpu)

    criterionL1 = nn.L1Loss()
    optimizerG = torch.optim.Adam(G.parameters(),
                                  lr=config.learn_rate,
                                  betas=config.betas,
                                  weight_decay=config.weight_decay)
    optimizerD = torch.optim.Adam(D.parameters(),
                                  lr=config.learn_rate,
                                  betas=config.betas,
                                  weight_decay=config.weight_decay)
    schedulerG = StepLR(optimizerG,
                        step_size=step_size,
                        gamma=config.decay_factor)
    schedulerD = StepLR(optimizerD,
                        step_size=step_size,
                        gamma=config.decay_factor)

    k = 0.0
    M = AverageMeter()
    lossG_train = AverageMeter()
    lossG_valid = AverageMeter()
    lossD_train = AverageMeter()

    print('Training start')
    for epoch in range(config.stop_epoch + 1):
        # Training Loop
        G.train()
        D.train()
        for batch in tqdm(dataloader.train, leave=False, ascii=True):
            x, y_prev, y = set_device(batch, config.device, config.use_cpu)
            y = y.unsqueeze(1)

            optimizerG.zero_grad()
            y_gen = G(x, y_prev)
            lossL1 = criterionL1(y_gen, y)
            loss_advG = criterionAdv(D, y_gen)
            lossG = lossL1 + loss_advG
            lossG.backward()
            optimizerG.step()
            schedulerG.step()

            optimizerD.zero_grad()
            loss_real = criterionAdv(D, y)
            loss_fake = criterionAdv(D, y_gen.detach())
            loss_advD = loss_real - k * loss_fake
            loss_advD.backward()
            optimizerD.step()
            schedulerD.step()

            diff = torch.mean(config.gamma * loss_real - loss_fake)
            k = k + config.lambda_k * diff.item()
            k = min(max(k, 0), 1)

            measure = (loss_real + torch.abs(diff)).data
            M.step(measure, y.size(0))

            logger.log_train(lossL1, loss_advG, lossG, loss_real, loss_fake,
                             loss_advD, M.avg, k, lossG_train.steps)
            lossG_train.step(lossG.item(), y.size(0))
            lossD_train.step(loss_advD.item(), y.size(0))

        # Validation Loop
        G.eval()
        D.eval()
        for batch in tqdm(dataloader.valid, leave=False, ascii=True):
            x, y_prev, y = set_device(batch, config.device, config.use_cpu)
            y = y.unsqueeze(1)

            y_gen = G(x, y_prev)
            lossL1 = criterionL1(y_gen, y)
            loss_advG = criterionAdv(D, y_gen)
            lossG = lossL1 + loss_advG

            logger.log_valid(lossL1, loss_advG, lossG, lossG_valid.steps)
            lossG_valid.step(lossG.item(), y.size(0))

        for param_group in optimizerG.param_groups:
            learn_rate = param_group['lr']

        print(
            "[Epoch %d/%d] [loss G train: %.5f] [loss G valid: %.5f] [loss D train: %.5f] [lr: %.6f]"
            % (epoch, config.stop_epoch, lossG_train.avg, lossG_valid.avg,
               lossD_train.avg, learn_rate))

        lossG_train.reset()
        lossG_valid.reset()
        lossD_train.reset()

        savename = os.path.join(checkpoint_path, 'latest_')
        save_checkpoint(savename + 'G.pt', G, optimizerG, learn_rate,
                        lossG_train.steps)
        save_checkpoint(savename + 'D.pt', D, optimizerD, learn_rate,
                        lossD_train.steps)
        if epoch % config.save_epoch == 0:
            savename = os.path.join(checkpoint_path,
                                    'epoch' + str(epoch) + '_')
            save_checkpoint(savename + 'G.pt', G, optimizerG, learn_rate,
                            lossG_train.steps)
            save_checkpoint(savename + 'D.pt', D, optimizerD, learn_rate,
                            lossD_train.steps)

    print('Training finished')
Exemplo n.º 22
0
from time import sleep

from src.controller import Controller
from src.database import Database
from config_parser import Config

config = Config('configs.yaml')
database = Database(config.database)

controller = Controller()

while True:
    controller.fill_trigger(database)
    controller.fill_emotion(database)
    print("Update completed")
    sleep(60 * 60)
Exemplo n.º 23
0
def run():

    config = Config('configs.yaml')

    vk = VK(config.vk)
    database = Database(config.database)
    controller = Controller(config.controller)
    group_urls_path = 'data/vk/group_short_url.txt'

    n = 0

    while True:

        offset = n * 100

        for url in get_data(group_urls_path):

            group_info = controller.get_group_info(vk, url)
            group_id = group_info[0]['id']

            try:

                wall_posts = controller.get_target_post(
                    vk, group_id, offset, url)

                for post in wall_posts:

                    post['Text'] = ' '.join(
                        list(filter(None, re.split('\W|\d', post['Text']))))
                    post['PublishDateTime'] = handle_date(
                        post['PublishDateTime'])

                    controller.save_data_to_bd(bd=database,
                                               table='WallPost',
                                               target_object=post)

                for post in wall_posts:

                    comments = controller.get_target_comments(
                        vk, group_id, post_id=post['OuterId'], offset=0)

                    for comment in comments:

                        comment['Text'] = ' '.join(
                            list(
                                filter(None, re.split('\W|\d',
                                                      comment['Text']))))
                        comment['PublishDateTime'] = handle_date(
                            comment['PublishDateTime'])

                        controller.save_data_to_bd(bd=database,
                                                   table='Comment',
                                                   target_object=comment)

                    for comment in comments:

                        user = controller.get_target_user(
                            vk, comment['OuterId'])

                        controller.save_data_to_bd(bd=database,
                                                   table='SocialNetworkUser',
                                                   target_object=user)

            except Exception as e:
                print(e)

        n += 1
Exemplo n.º 24
0
def main():

    config = Config("dup_0/config.json")

    # get HLA and peptide
    HLA = sys.argv[1]
    peptide = sys.argv[2]
    if len(peptide) > 15:
        print("please input the peptide shorter than 16 amino acids.")
        return

    hla_seq = 0
    # get the sequence of HLA
    hla_path = os.path.join(BASE_DIR, '..', 'dataset',
                            'mhc_i_protein_seq2.txt')
    with open(hla_path, 'r') as in_file:
        for line_num, line in enumerate(in_file):
            if line_num == 0:
                continue

            info = line.strip('\n').split(' ')
            if info[0] != HLA:
                continue
            hla_seq = info[1]
            break
    if hla_seq == 0:
        print("The HLA is not included  in the dataset.")
        return

    # encode the sequences

    encoding_func = ENCODING_METHOD_MAP["one_hot"]
    encoding_func2 = ENCODING_METHOD_MAP["blosum"]

    hla, hla_mask = encoding_func(hla_seq, 385)
    hla = torch.reshape(hla, (1, hla.size(0), hla.size(1)))

    pep, pep_mask = encoding_func(peptide, 15)
    pep = torch.reshape(pep, (1, pep.size(0), pep.size(1)))

    hla2, hla_mask2 = encoding_func2(hla_seq, 385)
    hla2 = torch.reshape(hla2, (1, hla2.size(0), hla2.size(1)))
    pep2, pep_mask2 = encoding_func2(peptide, 15)
    pep2 = torch.reshape(pep2, (1, pep2.size(0), pep2.size(1)))

    # load model
    device = config.device

    temp_list = []
    for p in range(config.base_model_count):
        for k in range(config.model_count):
            state_dict = torch.load(
                config.model_save_path(p * config.model_count + k))
            model = Model(config)
            model.load_state_dict(state_dict)
            model.to(device)
            model.eval()
            with torch.no_grad():
                pred_ic50 = model(hla.to(device), hla_mask.to(device),
                                  hla2.to(device), hla_mask2.to(device),
                                  pep.to(device), pep_mask.to(device),
                                  pep2.to(device), pep_mask2.to(device))
                pred_ic50 = math.pow(50000, 1 - pred_ic50)

            temp_list.append(pred_ic50)

    pred_ic50 = sum(temp_list) / len(temp_list)

    print("the predicted IC50 value is : {}".format(pred_ic50))
Exemplo n.º 25
0
class PreviewArea(QtWidgets.QWidget):
    def __init__(self, parentQScrollArea, beamer_screen):
        QtWidgets.QWidget.__init__(self)
        
        self.parentQScrollArea = parentQScrollArea
        
        self.layout = QtWidgets.QGridLayout()
        self.setLayout(self.layout)
        
        self.current_id = None
        
        self.setStyleSheet('QWidget { background-color: yellow; }')
        
        self.config = Config()
        #self.screen = self.config.getBeamerScreen()
        self.screen = beamer_screen
        self.column_count = self.config.getPreviewColumnCount()
        
        #self.aspect_ratio = self.getBeamerWindowAspect()
        
        self.canvas = None
        
        #self.alertAlreadyShown = False
        
#        print("##########")
#        print(self.width(), self.height())
#        print(self.sizeHint())
#        print(self.size())
#        print("##########")

#        images_list = ["./testimages/facepalm0.jpg",
#                       "./testimages/facepalm00.jpg",
#                       "./testimages/facepalm1.jpg",
#                       "./testimages/facepalm2.jpg",
#                       "./testimages/facepalm3.jpg"]
        #self.showPreviewWithoutWindow()
        
        #self.generatePreviewsForImagePathList(images_list)
        
    #def showPreviewWithoutWindow(self):
        #label = ClickLabel(self)
        #label.resize(QtCore.QSize(PREVIEW_WIDTH, PREVIEW_HEIGHT))
        ##label.setGeometry(QtCore.QRect(0, 0, 400, 400))
        
        #label.setStyleSheet('QLabel { background-color: red; }')
        
        #self.canvas = Canvas()
        ##self.canvas.showImage("./testimages/facepalm0.jpg")
        #pixmap = QtGui.QPixmap("./testimages/facepalm0.jpg")
        
        #self.canvas.showImage(pixmap)
        ##self.canvas.routeCanvasToScreen()
        #preview_pixmap = QtGui.QPixmap(self.generatePreview())
        #pixmap_scaled = preview_pixmap.scaled(label.size(), QtCore.Qt.KeepAspectRatio)
        
        #label.setPixmap(pixmap_scaled)
        #label.clicked.connect(lambda: self.imageToCanvas(pixmap))
        
        #self.layout.addWidget(label, 0, 0)
        
        #self.destroyBeamerWindow()
    
    def generatePreviewsForImagePathList(self, image_path_list):
        self.images_list = image_path_list
        
        preview_pixmap_list = []
        
        for image in image_path_list:
            pixmap = QtGui.QPixmap(image)
            
            self.canvas = Canvas(self.screen)
            self.canvas.showImage(pixmap)
            
            preview_pixmap = QtGui.QPixmap()
            preview_pixmap = QtGui.QPixmap(self.generatePreview())
            preview_pixmap_list.append(preview_pixmap)
            
        self.showPreviews(preview_pixmap_list, image_path_list)
        
    def showPreviews(self, preview_pixmap_list, images_list):
        label_list = []
        for i, pixmap in enumerate(preview_pixmap_list):
            label = ClickLabel(self)
            
            #preview_width = PREVIEW_WIDTH
            #preview_width = self.parentQScrollArea.viewportSize().width()
            preview_width = self.parentQScrollArea.viewport().width()
            preview_height = PREVIEW_HEIGHT
            label.resize(QtCore.QSize(preview_width, preview_height))
            
            pixmap_scaled = pixmap.scaled(label.size(), QtCore.Qt.KeepAspectRatio)
            
            label.setPixmap(pixmap_scaled)
            label.setPixmapPath(images_list[i])
            label.name_id = i
            original_pixmap = QtGui.QPixmap(images_list[i])
            #label.clicked.connect(lambda: self.imageToCanvas(original_pixmap))
            label.clicked.connect(self.imageToCanvas)
            
            label_list.append(label)
            
        for i, label in enumerate(label_list):
            x = int(i / self.column_count)
            y = i % self.column_count
            self.layout.addWidget(label, x, y)
    
    def generatePreview(self):
        return self.canvas.getPreviewImage()
    
    def imageToCanvas(self, id):
        self.current_id = id
        print("CURRENT ID: ", id)
        
        pixmap = QtGui.QPixmap(self.images_list[id])
    
        self.canvas = Canvas(self.screen)
        #self.canvas.setScreen(self.config.getBeamerScreen())
        self.canvas.showImage(pixmap)
        self.canvas.routeCanvasToScreen()
        
        self.connectCanvas()
        
    def destroyBeamerWindow(self):
        self.canvas.destroy(True, True)
        self.canvas = None
        
    def connectCanvas(self):
        self.canvas.beam_prev.connect(self.beamPrev)
        self.canvas.beam_next.connect(self.beamNext)
    
    def closeEvent(self, event):
        self.destroyBeamerWindow()
        
    def beamNext(self):
        next_id = self.current_id + 1
        if next_id >= len(self.images_list):
            next_id = len(self.images_list)-1
        self.imageToCanvas(next_id)
        
    def beamPrev(self):
        next_id = self.current_id - 1
        if next_id < 0:
            next_id = 0
        self.imageToCanvas(next_id)
        
    def keyPressEvent(self, e):
        if e.key() == QtCore.Qt.Key_Escape:
            self.destroyBeamerWindow()
        elif e.key() == QtCore.Qt.Key_Left:
            self.beamPrev()
        elif e.key() == QtCore.Qt.Key_Right:
            self.beamNext()
Exemplo n.º 26
0
import os
import sys
from github import Github
import argparse
from envdefault import EnvDefault
import checks
from config_parser import Config
import openpyxl

config = Config("config.yml")
row = 1


def parse_arguments():
    """
    Parse them args
    """
    parser = argparse.ArgumentParser()
    parser.add_argument(
        '-t',
        '--token',
        action=EnvDefault,
        envvar='GIT_API_TOKEN',
        help="GitHub token: set using -t or setting env var 'GIT_API_TOKEN'")
    parser.add_argument('-e',
                        '--enterprise',
                        action='store_true',
                        help="Enable Github Enterprise")
    org_repo_group = parser.add_mutually_exclusive_group(required=True)
    org_repo_group.add_argument('-o',
                                '--organization',
Exemplo n.º 27
0
 def __init__(self, enviornment=None):
     self.__config_obj = Config(enviornment)
     self.__oracle_runner = OracleRunner(self.__config_obj.db_user,
                                         self.__config_obj.db_password,
                                         self.__config_obj.db_sid, False,
                                         self.__config_obj.log_path)
Exemplo n.º 28
0
from config_parser import Config
import json
import viz
import vizact
import numpy as np
from vis_env import Room, BaseballGlove
from stimuli import Ball

config_filename = 'config/home.py'

config = Config(config_filename)
config.save_experiment_info(path='figures/')

# read experiment info (config dict)
with open('figures/exp_info.txt') as info_file:
    config = json.load(info_file)

room = Room(config)

#ball = Ball(room, size=0.15, position=[0,1.8,4], color=[1, 1, 1])
#ball.setContrastMode('constant_dark')
glove = viz.addChild('pole.wrl')


def rotate_glove():
    direction = glove.getMatrix().getForward()
    print direction
    print glove.getQuat()
    #direction[0] = -direction[0]
    #glove.lookAt(direction, viz.REL_LOCAL)
    #print glove.getMatrix().getForward()
Exemplo n.º 29
0
"""This module contains functions for work with database."""
import time

from db_pool import DBPool
from config_parser import Config

conf_parser = Config()
CONFIGS = conf_parser.get_config()

DB_POOL = DBPool({'user': CONFIGS['db.user'],
                  'passwd': CONFIGS['db.passwd'],
                  'db_name': CONFIGS['db.db_name'],
                  'ttl': int(CONFIGS['db_pool.ttl'])},
                 pool_size=int(CONFIGS['db_pool.pool_size']))


def log(msg):
    """Inserts log into db.

    This function takes log message and writes it to database.

    :Parameters:
        - `msg`: log message to write into database.
    """
    with DB_POOL.connection() as conn:
        cursor = conn.cursor()
        query = """INSERT INTO `log` (event, time)
                   VALUES (%s, %s);
                """
        cursor.execute(query, (msg, str(int(time.time()))))
        conn.commit()
Exemplo n.º 30
0
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.

import os
from platform import system
from re import findall

from requests import get

from config_parser import Config
from lib.io import module as mod

cfg = Config.get_instance()
if system() != "Windows":
    import requests_cache
    requests_cache.install_cache('%sBTG' % cfg["sqlite_path"])


class Malekal:
    """
        This module allow you to search IOC in Malekal website (HTTP Requests)
        or local directory specified in BTG configuration file.
    """
    def __init__(self, ioc, type, config):
        self.config = config
        self.module_name = __name__.split(".")[1]
        if "malekal_local" in self.config and "malekal_remote" in self.config:
            if self.config[
Exemplo n.º 31
0
class Songbeamer(QtGui.QMainWindow):
    def __init__(self):
        QtGui.QMainWindow.__init__(self)
        
        self.setWindowTitle("musicbeamer")
        screen_rectangle = QtGui.QDesktopWidget().availableGeometry()
        sx, sy = screen_rectangle.getRect()[2], screen_rectangle.getRect()[3]
        #'for smaller displays, we want to use vertically all available space'
        #if sy <= 800:
        if platform.uname()[0] == "Windows":
            'on windows we has to deal with the taskbar manually'
            y = sy - 80
        else:
            'on linux .availableGeometry() did it already for us'
            y = sy
        #else:
        #    y = sy #* 0.61
        x = sx * 0.61
        self.resize(int(x), int(y))
        
        self.beamer_controller = BeamerController()
        
        self.addMenuBar()
        
        self.config = Config()
        screen = self.config.getProgramScreen()
        self.routeWindowToPrimaryScreen(screen)
        
        
        self.schedule = None
        self.preview = None
        
        self.layout = QtGui.QHBoxLayout()
        centralWidget = QtGui.QWidget()
        
        self.setCentralWidget(centralWidget)
        centralWidget.setLayout(self.layout)
        
        #self.addPreview()
        self.addSchedule()
        self.addPreview()
        
        self.setViewportSize(self.mainFrame().contentsSize())
        
    def addMenuBar(self):
        menubar = self.menuBar()
        
        file = menubar.addMenu('&File')
        
        schedule = QtGui.QAction(QtGui.QIcon("icons/exit.png"), "Neuer Ablaufplan", self)
        schedule.setShortcut("Ctrl+N")
        schedule.setStatusTip("Neuer Ablaufplan")
        self.connect(schedule, QtCore.SIGNAL("triggered()"), self.addSchedule)
        file.addAction(schedule)
        
        exit = QtGui.QAction(QtGui.QIcon('icons/exit.png'), 'Exit', self)
        exit.setShortcut('Ctrl+Q')
        exit.setStatusTip('Exit application')
        self.connect(exit, QtCore.SIGNAL('triggered()'), QtCore.SLOT('close()'))
        file.addAction(exit)
        
        
        edit = menubar.addMenu("&Bearbeiten")
        
        
        insert = menubar.addMenu("&Einfügen")
        
        song = QtGui.QAction(QtGui.QIcon("icons/exit.png"), "Lied einfügen", self)
        song.setShortcut("Ctrl+I")
        song.setStatusTip("Neues Lied in Ablauf einfügen")
        self.connect(song, QtCore.SIGNAL("triggered()"), self.newSong)
        insert.addAction(song)
        
        
        presentation = menubar.addMenu("&Präsentation")
        
        black = QtGui.QAction(QtGui.QIcon("icons/exit.png"), "black", self)
        black.setShortcut("Ctrl+B")
        black.setStatusTip("Leinwand schwarz")
        self.connect(black, QtCore.SIGNAL("triggered()"), self.beamer_controller.blackBeamerWindow)
        presentation.addAction(black)
        
        desktop = QtGui.QAction(QtGui.QIcon("icons/exit.png"), "desktop", self)
        desktop.setStatusTip("Präsentationsfenster schließen")
        self.connect(desktop, QtCore.SIGNAL("triggered()"), self.beamer_controller.closeBeamerWindow)
        presentation.addAction(desktop)
        
        web = QtGui.QAction(QtGui.QIcon("icons/exit.png"), "text", self)
        web.setStatusTip("Zeigt einen Text")
        self.connect(web, QtCore.SIGNAL("triggered()"), lambda: self.beamer_controller.newBeamerWebWindow(None))
        presentation.addAction(web)
        
        image = QtGui.QAction(QtGui.QIcon("icons/exit.png"), "image", self)
        image.setStatusTip("Zeigt einige Bilder")
        self.connect(image, QtCore.SIGNAL("triggered()"), lambda: self.beamer_controller.newBeamerImageWindow(None))
        presentation.addAction(image)
        
        
    def routeWindowToPrimaryScreen(self, screen):
        desktop = QtGui.QApplication.desktop()
        screen_rect = desktop.screenGeometry(int(screen))
        
        self.move(screen_rect.left(), screen_rect.top())
        

    
    def resetSchedule(self):
        pass
    
    def addSchedule(self):
        #self.newPreview()
        #scroll_area_preview = self.addPreview()
        
        self.schedule = Schedule(self.preview)
        #self.schedule.setGeometry(0, 0, 300, 400)
        
        scroll_layout = QtGui.QVBoxLayout()
        scroll_layout.addWidget(self.schedule)
        scroll_layout.setAlignment(QtCore.Qt.AlignTop)
        
        scroll_widget = QtGui.QWidget()
        #scroll_widget = Schedule("bla")
        #self.schedule = scroll_widget
        scroll_widget.setLayout(scroll_layout)
        
        scroll_area = QtGui.QScrollArea()
        scroll_area.setWidgetResizable(True)
        scroll_area.setFixedWidth( SCHEDULE_WIDTH )
        scroll_area.setWidget(scroll_widget)
        
        self.layout.setAlignment(QtCore.Qt.AlignLeft)
        self.layout.addWidget(scroll_area)
        #self.layout.addWidget(scroll_area_preview)
        
        
    def addPreview(self):
        self.preview = Preview(self.beamer_controller)
        
        scroll_layout = QtGui.QVBoxLayout()
        scroll_layout.addWidget(self.preview)
        
        scroll_widget = QtGui.QWidget()
        scroll_widget.setLayout(scroll_layout)
        
        scroll_area = QtGui.QScrollArea()
        scroll_area.setWidgetResizable(False)
        #scroll_area.setFixedWidth( self.y() - SCHEDULE_WIDTH )
        #scroll_area.setFixedWidth(1000)
        #scroll_area.setFixedHeight(2000)
        scroll_area.setWidget(scroll_widget)
        
        self.layout.addWidget(scroll_area)
        
        #self.connect(schedule, QtCore.SIGNAL("triggered()"), self.addSchedule)
        
        print("scroll area")
        print(scroll_area.size())
        
    def newSong(self):
        self.schedule.addButton()
Exemplo n.º 32
0
            cursor = connection.cursor()
            cursor.execute(sql_select_Query)
            records = cursor.fetchall()

            print("Total number of rows in Laptop is: ", cursor.rowcount)

            print("\nPrinting each laptop record")

            if db_name == "TriggerWord":
                return self.get_trigger_word_list(records)
            if db_name == "WallPost":
                return self.get_wall_post_list(records)
            if db_name == 'Comment':
                return self.get_comment_list(records)


        except Error as e:
            print("Error reading data from MySQL table", e)
        finally:
            if (connection.is_connected()):
                connection.close()
                cursor.close()
                print("MySQL connection is closed")


if __name__ == "__main__":
    from config_parser import Config
    config = Config("../configs.yaml")
    db = Database(config.database)
    L = db.select('WallPost')
    print(L)