def __init__(self):
"""
Initiator class to load all necessary configurations, logger and HTTP client instances
"""
config_parser = ConfigParser()
self.config = config_parser.return_json(
path_to_config='TOREPLACE/config/example.json')
def load_from(config_meta):
with open(config_meta['path']) as f:
config = yaml.load(f)
parser = ConfigParser(config)
parser._create_directories()
task = Task.load_from(parser.task)
dataset = Dataset.load_from(parser.dataset)
model_config = config['model']
label_helper = Label.load_from(parser.label)
user = config['user']
# Set up logger
log_level = config_meta['log_level']
logger = logging.getLogger('label_app')
logger.setLevel(getattr(logging, log_level))
ch = logging.StreamHandler(sys.stdout)
ch.setFormatter(
logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s'))
logger.addHandler(ch)
return LabelApp(task, dataset, label_helper, user, model_config,
parser, logger)
def __init__(self, theConfigFilePath, theLogger=Logger()):
# parse config file
self.configParser = ConfigParser()
# self.configParser.parseFile(theConfigFilePath)
self.configParser.generateDirectories()
self.log = theLogger
# keytool path to parse apk's signature
self.keytoolPath = None
# sanddroid directories
self.mainDir = os.path.dirname(__file__)
self.appList = [] # list to store apk file - full path
self.runningApps = [] # list to store apk file which in being analyzed
self.runHeadless = False
self.emulatorStartPort = 5554
self.numThreads = 1
self.maxThreadRuntime = 600
# control running threads
self.threadLogFileList = [] # list to store thread log file path
self.numFinishedApps = 0 # number of analyzed apps
self.numRunningThreads = 0 # number of running threads
self.threadList = [] # list of threads, size=numThreads
self.threadActiveMask = [
] # bitmask to determine if thread is active, size=numThreads
self.avdsheartbeat = (0, 0, 0, 0) # list avds' times used in one cycle
self.avdheartbeat = 0
self.startTime = datetime.datetime.now()
def __init__(self, config_filepath):
"""
Class initializer.
Inputs:
config_filepath: (str) Configuration filepath.
"""
self.configparser = ConfigParser(config_filepath)
# read configuration file
self.filepath = self.configparser.getstr('filepath')
self.full_ontology_pkl = self.configparser.getstr('full_ontology_pkl')
self.candidate_ontology_pkl = self.configparser.getstr(
'candidate_ontology_pkl')
self.skeleton_and_entities_pkl = self.configparser.getstr(
'skeleton_and_entities_pkl')
self.overwrite_pkl = self.configparser.getbool('overwrite_pickle_flag')
self.outputFoodOn = self.configparser.getstr('outputFoodOn')
self.num_seeds = self.configparser.getint('num_seeds')
self.num_min_extracted_entities = self.configparser.getint(
'num_min_extracted_entities')
# generate pairs from csv file
self.pd_foodon_pairs = self.generate_pairs()
self.all_classes, self.all_entities = self.get_classes_and_entities()
self.foodon_graph, self.graph_dict, self.graph_dict_flip = self.generate_graph(
)
def __init__(self,
theApkObj,
theAvdName,
decompressDir,
runHeadless,
theLogger=Logger()):
Thread.__init__(self)
# configParser
self.configParser = ConfigParser()
self.apkObj = theApkObj
self.log = theLogger
self.curDir = os.path.dirname(__file__)
self.staticAnalyzer = None
self.dynamicAnalyzer = None
self.logcatAnalyzer = None
self.startTimeStr = None
self.endTimeStr = None
self.emulator = None
self.emulatorPort = 5554
self.avdName = theAvdName
self.runHeadless = runHeadless
self.decompressPath = decompressDir
self.logcatFile = None
self.session = None
self.cancelFlag = False # Flag for canceling run
def __init__(self, config_filepath):
"""
Class initializer.
Inputs:
config_filepath: (str) Configuration filepath.
"""
self.configparser = ConfigParser(config_filepath)
def __init__(self, config_file):
"""
Class initializer.
Inputs:
"""
self.configparser = ConfigParser(config_file)
self.epoch_callback = EpochCallback()
self.model = None
def load_from(config_path):
with open(config_path) as f:
config = yaml.load(f)
parser = ConfigParser(config)
parser._create_directories()
task = Task.load_from(parser.task)
dataset = Dataset.load_from(parser.dataset)
model_config = config['model']
label_helper = Label.load_from(parser.label)
user = config['user']
return LabelApp(task, dataset, label_helper, user, model_config,
parser)
def main(config_path, epochs=3):
# For pretraining, we do everything the same, except we replace the
# dataset:judgements_file with model:pretrain_file.
with open(config_path) as f:
config = yaml.load(f)
parser = ConfigParser(config)
parser.dataset['judgements_file'] = parser.model['pretrain_file']
task = Task.load_from(parser.task)
dataset = PretrainJSONDataset(parser.dataset)
model_config = config['model']
label_helper = Label.load_from(parser.label)
user = config['user']
label_app = LabelApp(task, dataset, label_helper, user, model_config,
parser)
label_app.trainer.load_existing()
label_app.trainer.train_epochs(epochs=epochs)
def __init__(self, module: str, cli: str):
self.current_env = os.environ.copy()
self.json_data = ConfigParser(
path="/home/vlad/infra/armature/armature/conf/modules.json"
).return_json()
self.module = module
self.cli = cli
self.module_data = self.json_data['modules'][module]
def main():
"""
Main function.
"""
# set log, parse args, and read configuration
args = parse_argument()
configparser = ConfigParser(args.config_file)
set_logging(configparser.getstr('logfile'))
# parse FoodOn
parse_foodon = ParseFoodOn(configparser.getstr('foodon_parse_config'))
classes_dict = parse_foodon.get_candidate_classes()
classes_dict_skeleton, candidate_entities = parse_foodon.get_seeded_skeleton(
classes_dict)
# run
scoring_manager = ScoringManager(classes_dict_skeleton, candidate_entities,
configparser.getstr('scoring_config'))
scoring_manager.run_iteration()
def main():
"""
Main function.
"""
# parse args
args = parse_argument()
# load main config file and set logging
main_config = ConfigParser(args.config_file)
set_logging(log_file=main_config.get_str('log_file'))
# initialize model manager object
model_manager = ModelManager()
# baseline / best classifiers
baseline_classifier = main_config.get_str('baseline')
best_classifier = main_config.get_str('classifier')
# plot PR curve and print confusion matrix
plot_pr_print_cm(baseline_classifier, best_classifier, main_config,
model_manager)
def main():
"""
Main function.
"""
# parse args
args = parse_argument()
# load main config file and set logging
main_config = ConfigParser(args.config_file)
set_logging(log_file=main_config.get_str('log_file'))
# initialize model manager object
model_manager = ModelManager()
# parse config
classifier = main_config.get_str('classifier')
pre_built_models_dir = os.path.join(main_config.get_str('pre_built_models_dir'), classifier)
num_classifiers = main_config.get_int('num_classifiers')
# we need to build the models first if they do not exist
if not dir_exists(pre_built_models_dir):
save_models(
classifier,
pre_built_models_dir,
main_config,
model_manager,
num_classifiers)
make_recommendation(
classifier,
pre_built_models_dir,
main_config,
model_manager,
num_classifiers)
def save_models(classifier,
pre_built_models_dir,
main_config,
model_manager,
num_classifiers):
log.info('Pre-built model directory specified for %s does not exist.', classifier)
log.info('Building models again.')
# create directory
create_dir(pre_built_models_dir)
# load config parsers
preprocess_config = ConfigParser(main_config.get_str('preprocess_config'))
classifier_config = ConfigParser(main_config.get_str('classifier_config'))
classifier_config.overwrite('classifier', classifier)
# perform preprocessing
X, y = model_manager.preprocess(preprocess_config, section=classifier)
# select subset of features if requested
selected_features = main_config.get_str_list('selected_features')
if selected_features:
log.info('Selecting subset of features: %s', selected_features)
X = X[selected_features]
# train multiple classifiers
for i in range(num_classifiers):
log.debug('Processing classifier %d/%s', i+1, num_classifiers)
cmanager = ClassifierManager(classifier_config)
clf = CalibratedClassifierCV(cmanager.get_classifier(), method='sigmoid', cv=5)
clf.fit(X, y)
save_pkl(
clf,
os.path.join(pre_built_models_dir, 'model_{}.pkl'.format(i)))
def main():
"""
Main function.
"""
# set log, parse args, and read configuration
set_logging()
args = parse_argument()
configparser = ConfigParser(args.config_file)
# load data to train with
sentence_column = configparser.getstr('sentence_column')
pd_data = pd.read_csv(configparser.getstr('input_filepath'), sep='\t')
pd_data.fillna('', inplace=True)
pd_data = pd_data[pd_data[sentence_column] != '']
# use specified column as sentences
sentences = pd_data[sentence_column].tolist()
sentences = [sentence.split() for sentence in sentences]
# init word2vec manager
w2vm = Word2VecManager(args.config_file)
# start training and load pre-training data if prompted
if configparser.getbool('pre_train'):
pretrained = configparser.getstr('pre_trained_vectors')
else:
pretrained = None
w2vm.train(sentences, pretrained=pretrained)
# save word embeddings and model
w2vm.save_model(configparser.getstr('model_saveto'))
w2vm.save_vectors(configparser.getstr('vectors_saveto'))
w2vm.save_loss(configparser.getstr('loss_saveto'))
def __init__(self, candidate_classes_info, candidate_entities,
scoring_config):
"""
Class initializer.
"""
# config parser
if isinstance(scoring_config, str):
scoring_config = ConfigParser(scoring_config)
# save arguments
self.candidate_classes_info = candidate_classes_info
self.candidate_entities = candidate_entities
# parse config file
self.alpha = scoring_config.getfloat('alpha')
self.num_mapping_per_iteration = scoring_config.getint(
'num_mapping_per_iteration')
self.initial_siblings_scores = scoring_config.getstr(
'initial_siblings_scores')
self.initial_parents_scores = scoring_config.getstr(
'initial_parents_scores')
self.pairs_filepath = scoring_config.getstr('pairs_filepath')
self.populated_filepath = scoring_config.getstr('populated_filepath')
self.preprocess_config_filepath = scoring_config.getstr(
'preprocess_config')
self.similarity_method = scoring_config.getstr('similarity_method')
log.debug('alpha: %f', self.alpha)
log.debug('num_mapping_per_iteration: %d',
self.num_mapping_per_iteration)
log.debug('initial_siblings_scores: %s', self.initial_siblings_scores)
log.debug('initial_parents_scores: %s', self.initial_parents_scores)
log.debug('pairs_filepath: %s', self.pairs_filepath)
log.debug('populated_filepath: %s', self.populated_filepath)
log.debug('similarity_method: %s', self.similarity_method)
# preprocess manager
self.fpm = FdcPreprocessManager(self.preprocess_config_filepath)
# number of candidate classes & entities
self.num_candidate_classes = len(self.candidate_classes_info)
self.num_candidate_entities = len(self.candidate_entities)
log.debug('Number of candidate classes: %d',
self.num_candidate_classes)
log.debug('Number of candidate entities: %d',
self.num_candidate_entities)
# extract the seeded entities to make complete list of entities
seed_entities = self._unpack_sublist(
[x[1] for _, x in self.candidate_classes_info.items()])
self.all_entity_labels = list(
set(self.candidate_entities + seed_entities))
# all labels of candidate class
self.candidate_classes_label = list(self.candidate_classes_info.keys())
# complete list of class labels
other_classes = self._unpack_sublist(
[x[0] for _, x in self.candidate_classes_info.items()], depth=2)
self.all_class_labels = list(
set(self.candidate_classes_label + other_classes))
# calculate embedding lookup table for class / entity labels
if 'we_' in self.similarity_method:
self.keyed_vectors = KeyedVectors.load_word2vec_format(
scoring_config.getstr('word_embeddings'))
# self.keyed_vectors.save('./output/glove_wiki_embeddings.bin')
# self.keyed_vectors = KeyedVectors.load('./output/glove_wiki_embeddings.bin')
self.pd_class_label_embeddings = self._calculate_label_embeddings(
self.all_class_labels)
self.pd_entity_label_embeddings = self._calculate_label_embeddings(
self.all_entity_labels)
# save_pkl(self.pd_class_label_embeddings, './output/pd_class_label_embeddings.pkl')
# save_pkl(self.pd_entity_label_embeddings, './output/pd_entity_label_embeddings.pkl')
# sys.exit()
# self.pd_class_label_embeddings = load_pkl('./output/pd_class_label_embeddings.pkl')
# self.pd_entity_label_embeddings = load_pkl('./output/pd_entity_label_embeddings.pkl')
# do initial calculation of the scores
self.pd_siblings_scores, self.pd_parents_scores = self._calculate_initial_scores(
)
print("==> Stitching frames to create final output videos")
stitch_videos(model_output_path, cfg.paths.frames, predictions_dict)
# Delete frame directories
for video in predictions_dict.keys():
directory_path = f"{model_output_path}/{video}"
shutil.rmtree(directory_path)
print("==> Generating confusion matrix")
metrics.compute_confusion_matrix(predictions_dict, classes,
model_output_path)
# Upload to AWS S3 only if bucket name is given in config
if cfg.bucket:
print("==> Creating zip file")
zip_videos(model_output_path, cfg.name)
print("==> Uploading to AWS S3")
response = upload_videos(model_output_path, cfg.name, cfg.bucket)
if response:
print(f"Output download link: {response}")
total_time = datetime.datetime.now() - start_time
print(f"Total time: {total_time.total_seconds()}")
if __name__ == "__main__":
cfg = ConfigParser().config
main(cfg)
def make_recommendation(classifier,
pre_built_models_dir,
main_config,
model_manager,
num_classifiers):
if not dir_exists(pre_built_models_dir):
raise RuntimeError('Pre-built model directory does not exist!')
log.info('Using pre-built model directory: %s', pre_built_models_dir)
# load config parsers
preprocess_config = ConfigParser(main_config.get_str('preprocess_recommender_config'))
classifier_config = ConfigParser(main_config.get_str('classifier_config'))
classifier_config.overwrite('classifier', classifier)
# perform preprocessing
X, y = model_manager.preprocess(preprocess_config, section=classifier, final_model=True)
# select subset of features if requested
selected_features = main_config.get_str_list('selected_features')
if selected_features:
log.info('Selecting subset of features: %s', selected_features)
X = X[selected_features]
def _revert_column(pd_data):
values = list(set(pd_data.tolist()))
replace_dict = {}
for value in values:
replace_dict[value] = list(filter(lambda a: a != value, values))[0]
return pd_data.replace(to_replace=replace_dict)
# get test data and its inverse for TRT column
X_inv = X.copy()
X_inv['TRT'] = _revert_column(X_inv['TRT'])
pos_trt_idx = (X['TRT'] == 1.0)
y_probs = []
y_probs_inv = []
for i in range(num_classifiers):
log.debug('Processing classifier %d/%s', i+1, num_classifiers)
classifier_filepath = os.path.join(pre_built_models_dir, 'model_{}.pkl'.format(i))
log.debug('Loading classifier: %s', classifier_filepath)
clf = load_pkl(classifier_filepath)
y_probs.append(clf.predict_proba(X)[:, 1])
y_probs_inv.append(clf.predict_proba(X_inv)[:, 1])
y_probs = pd.DataFrame(y_probs).T
y_probs.index = X.index
y_probs_inv = pd.DataFrame(y_probs_inv).T
y_probs_inv.index = X.index
# make recommendation
y_probs_avg = y_probs.mean(axis=1)
y_probs_inv_avg = y_probs_inv.mean(axis=1)
y_probs_avg_diff = y_probs_avg - y_probs_inv_avg
inv_minus_pos = y_probs_inv_avg - y_probs_avg
y_probs_avg_diff[~pos_trt_idx] = inv_minus_pos[~pos_trt_idx]
pval = pd.Series(index=X.index)
for index, _ in pval.items():
_, pval[index] = ttest_rel(y_probs.loc[index], y_probs_inv.loc[index])
# calculate y_probs_trt / right now it's y_probs ################
pd_concat = pd.concat(
[pos_trt_idx, y_probs_avg, y_probs_inv_avg, y_probs_avg_diff, pval], axis=1)
pd_concat.columns = ['pos_trt', 'y_probs_avg', 'y_probs_inv_avg', 'y_probs_avg_diff', 'pval']
print(pd_concat)
# -*- coding: utf-8 -*-
from db.db_worker import DBWorker
from db.sql_requests import SQLRequests
from utils.config_parser import ConfigParser
from utils.settings_parser import SettingsParser
import logging
if __name__ == "__main__":
config = ConfigParser().get_config_settings()
settings = SettingsParser().get_test_settings()
logging.basicConfig(filename=config['log_filename'],
level=logging.INFO,
format=config['log_format'])
logger = logging.getLogger()
db_worker = DBWorker(config['host'], config['user'], config['password'],
config['database'])
sql_request = SQLRequests(db_worker, settings)
try:
db_worker.connect()
logger.info('Шаг 1')
sql_request.get_min_working_time()
logger.info('-' * 200)
logger.info('Шаг 2')
def main():
"""
Main function.
"""
# parse args
args = parse_argument()
# load main config file and set logging
main_config = ConfigParser(args.config_file)
set_logging(log_file=main_config.get_str('log_file'))
# initialize model manager object
model_manager = ModelManager()
# perform analysis on these classifiers
classifiers = main_config.get_str_list('classifier')
# do prediction
classifiers_ys = {}
for classifier in classifiers:
log.info('Running model for classifier \'%s\'', classifier)
# load config parsers
preprocess_config = ConfigParser(
main_config.get_str('preprocess_config'))
classifier_config = ConfigParser(
main_config.get_str('classifier_config'))
# perform preprocessing
X, y = model_manager.preprocess(preprocess_config, section=classifier)
# run classification model
classifier_config.overwrite('classifier', classifier)
X = model_manager.feature_selector(X, y, classifier_config)
score_avg, score_std, ys = model_manager.run_model_cv(
X, y, 'f1', classifier_config)
classifiers_ys[classifier] = ys
# plot PR curve
fig = plt.figure()
lines = []
labels = []
for classifier, ys in classifiers_ys.items():
y_trues, y_preds, y_probs = ys
y_probs_1 = tuple(y_prob[1].to_numpy() for y_prob in y_probs)
line, label = plot_pr(y_trues, y_probs_1, classifier)
lines.append(line)
labels.append(label)
plt.xlabel('Recall')
plt.ylabel('Precision')
plt.title('PR Curve')
plt.legend(lines, labels, loc='lower right', prop={'size': 8})
save_figure(
fig,
os.path.join(main_config.get_str('visualization_dir'), 'pr_curve.png'))
# plot ROC curve
fig = plt.figure()
lines = []
labels = []
for classifier, ys in classifiers_ys.items():
y_trues, y_preds, y_probs = ys
y_probs_1 = tuple(y_prob[1].to_numpy() for y_prob in y_probs)
line, label = plot_roc(y_trues, y_probs_1, classifier)
lines.append(line)
labels.append(label)
# plt.plot([0, 1], [0, 1], color='k', linestyle='--')
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.05])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('ROC Curve')
plt.legend(lines, labels, loc='lower right', prop={'size': 8})
save_figure(
fig,
os.path.join(main_config.get_str('visualization_dir'),
'roc_curve.png'))
def main():
"""
Main function.
"""
# parse args
args = parse_argument()
# load main config file and set logging
main_config = ConfigParser(args.config_file)
set_logging(log_file=main_config.get_str('log_file'))
# initialize model manager object
model_manager = ModelManager()
# run models for all possible combination of preprocessing
scale_modes = main_config.get_str_list('scale_mode')
mvi_modes = main_config.get_str_list('mvi_mode')
outlier_modes = main_config.get_str_list('outlier_mode')
classifiers = main_config.get_str_list('classifier')
classifier_score_dict = {classifier: 0 for classifier in classifiers}
classifier_best_combination_dict = {
classifier: None
for classifier in classifiers
}
all_combinations = [scale_modes, mvi_modes, outlier_modes, classifiers]
all_combinations = list(itertools.product(*all_combinations))
failed_combinations = []
for idx, combination in enumerate(all_combinations):
# unpack the tuple
scale_mode = combination[0]
mvi_mode = combination[1]
outlier_mode = combination[2]
classifier = combination[3]
# log current combination
combination_str_joined = ', '.join(list(combination))
log.info('Running grid search %d/%d: (%s)', idx + 1,
len(all_combinations), combination_str_joined)
# some classifiers must use minmax scaler
if classifier in ['MultinomialNB', 'CategoricalNB'
] and scale_mode != 'minmax':
log.info('Skipping this combination...')
continue
# overwrite the config file using the current combination
preprocess_config = ConfigParser(
main_config.get_str('preprocess_config'))
classifier_config = ConfigParser(
main_config.get_str('classifier_config'))
preprocess_config.overwrite('scale_mode', scale_mode)
preprocess_config.overwrite('mvi_mode', mvi_mode)
preprocess_config.overwrite('outlier_mode', outlier_mode)
classifier_config.overwrite('classifier', classifier)
# perform preprocessing
X, y = model_manager.preprocess(preprocess_config)
# run classification model
try:
score = model_manager.grid_search(
X, y, main_config.get_str('optimize_scoring'),
classifier_config,
main_config.get_str('updated_classifier_config'))
except (IndexError, ValueError) as e:
failed_combinations.append(combination_str_joined)
log.error(e)
continue
# update the best preprocessing combination
if classifier_score_dict[classifier] < score:
classifier_score_dict[classifier] = score
classifier_best_combination_dict[
classifier] = combination_str_joined
log.info('Best %s score for each classifier: %s',
main_config.get_str('optimize_scoring'), classifier_score_dict)
log.info(
'Preprocessing combination of the best %s score for each classifier: %s',
main_config.get_str('optimize_scoring'),
classifier_best_combination_dict)
log.info('%d failed combinations: %s', len(failed_combinations),
failed_combinations)
import click
from modules.executor import Executor
from utils.config_parser import ConfigParser
json_data = ConfigParser(
path="/home/vlad/infra/armature/armature/conf/modules.json").return_json()
MODULE = "packer"
@click.group()
def cli():
pass
@cli.command()
def prepare_template():
"""Validate configuration file"""
click.echo('prepare_template')
with Executor(module=MODULE, cli="prepare_template") as cli_executor:
cli_executor.run(cli="prepare_template", use_docker_run_wrapper=True)
@cli.command()
def validate_template():
"""Validate configuration file"""
click.echo('validate_template')
with Executor(module=MODULE, cli="validate_template") as cli_executor:
cli_executor.run(cli="validate_template", use_docker_run_wrapper=True)
class FdcPreprocessManager:
"""
Class for preprocessing the FDC data.
"""
def __init__(self, config_filepath):
"""
Class initializer.
Inputs:
config_filepath: (str) Configuration filepath.
"""
self.configparser = ConfigParser(config_filepath)
def _load_synonym_map(self, section='filter'):
pd_map = pd.read_csv(self.configparser.getstr('synonym_map', section),
sep='\t',
index_col='from')
return pd_map['to'].to_dict()
def _map_synonyms(self, text, table):
regex_str = '|'.join(r'\b%s\b' % re.escape(s) for s in table)
return re.sub(regex_str, lambda x: table[x.group(0)], text)
def _generate_custom_stopwords(self, section='filter'):
"""
(Private) Generate custom stopwords by adding or removing
user specified stopwords to the gensim's default stopwords.
Inputs:
section: (str, optional) Section name of the .ini file.
Returns:
(frozenset) New updated stopwords.
"""
my_stopwords = list(gpp.STOPWORDS)
# stopwords to add
to_add_filename = self.configparser.getstr('stopwords_to_add', section)
with open(to_add_filename, 'r') as file:
to_add_list = file.read().splitlines()
if len(to_add_list) > 0:
log.info('Adding custom stopwords %s', to_add_list)
else:
log.info('Not adding any custom stopwords')
# stopwords to remove
to_remove_filename = self.configparser.getstr('stopwords_to_remove',
section)
with open(to_remove_filename, 'r') as file:
to_remove_list = file.read().splitlines()
if len(to_remove_list) > 0:
log.info('Removing stopwords %s', to_remove_list)
else:
log.info('Not removing any custom stopword')
# add and remove stopwords
my_stopwords.extend(to_add_list)
my_stopwords = [x for x in my_stopwords if x not in to_remove_list]
return frozenset(my_stopwords)
def _custom_remove_stopwords(self, s, stopwords):
"""
(Private) Custom remove stopwords function.
Inputs:
s: (str) String to process.
stopwords: (frozenset) Custom stopwords.
Returns:
(str) Preprocessed string with stopwords removed.
"""
s = gensim_utils.to_unicode(s)
return " ".join(w for w in s.split() if w not in stopwords)
def _custom_lemmatize(self, text):
result = gensim_utils.lemmatize(text)
result = b' '.join(result).decode('utf-8')
result = re.sub(r'/[^\s]+', '', result)
return result
def _build_custom_filter_list(self, section='filter'):
"""
(Private) Build list of filters based on the configuration file
that will be applied by gpp.preprocess_string().
Inputs:
section: (str, optional) Section name of the .ini file.
Returns:
custom_filters: (list) List of functions.
"""
custom_filters = []
if self.configparser.getbool('lower', section):
log.debug('Converting to lower cases')
custom_filters.append(lambda x: x.lower())
if self.configparser.getbool('map_synonym', section):
log.debug('Mapping synonym')
map_table = self._load_synonym_map(section)
custom_filters.append(lambda x: self._map_synonyms(x, map_table))
if self.configparser.getbool('strip_punctuation', section):
log.debug('Stripping punctuation')
custom_filters.append(gpp.strip_punctuation)
if self.configparser.getbool('strip_multiple_whitespaces', section):
log.debug('Stripping multiple whitespaces')
custom_filters.append(gpp.strip_multiple_whitespaces)
if self.configparser.getbool('strip_numeric', section):
log.debug('Stripping numeric')
custom_filters.append(gpp.strip_numeric)
if self.configparser.getbool('remove_stopwords', section):
log.debug('Removing stopwords')
stopwords = self._generate_custom_stopwords(section)
custom_filters.append(
lambda x: self._custom_remove_stopwords(x, stopwords))
if self.configparser.getbool('strip_short', section):
minsize = self.configparser.getint('strip_short_minsize', section)
log.debug('Stripping words shorter than %d', minsize)
custom_filters.append(
lambda x: gpp.strip_short(x, minsize=minsize))
if self.configparser.getbool('lemmatize', section):
log.debug('Lemmatizing text')
custom_filters.append(self._custom_lemmatize)
return custom_filters
def _generate_phrase(self, pd_data, load_model=False, section='phrase'):
"""
(Private) Generate phrase using the gensim Phrase detection module.
Inputs:
pd_data: (pd.Series) Data which will be used to generate phase.
section: (str, optional) Section name of the .ini file.
Returns:
pd_data: (pd.Series) Input data but using phrases.
"""
if not self.configparser.getbool('generate_phrase', section):
log.info('Skipping phrase generation...')
return pd_data
if load_model:
model_filepath = self.configparser.getstr('phrase_model', section)
model = Phraser.load(model_filepath)
# apply phrase model
log.info('Applying loaded phrase model...')
pd_data = pd_data.apply(lambda x: model[x], convert_dtype=False)
else:
log.info('Generating new phrases...')
# this is our training data
sentences = pd_data.tolist()
# detect phrases using the configuration
model = Phrases(
sentences,
min_count=self.configparser.getint('min_count', section),
threshold=self.configparser.getfloat('threshold', section),
max_vocab_size=self.configparser.getint(
'max_vocab_size', section),
progress_per=self.configparser.getint('progress_per', section),
scoring=self.configparser.getstr('scoring', section))
# apply trained model to generate phrase
log.info('Applying phrase model...')
pd_data = pd_data.apply(lambda x: model[x], convert_dtype=False)
# save phrase model
model_filepath = self.configparser.getstr('phrase_model', section)
log.info('Saving phrase model to \'%s\'...', model_filepath)
model.save(model_filepath)
# dump phrase and its score as text
phrase_score_list = []
for phrase, score in model.export_phrases(sentences):
phrase_score_list.append([phrase.decode('utf-8'), score])
pd_phrase_score = pd.DataFrame(phrase_score_list,
columns=['phrase', 'score'])
pd_phrase_score.drop_duplicates(subset='phrase', inplace=True)
export_filepath = self.configparser.getstr('phrase_dump_filename',
section)
log.info('Dumping phrases to \'%s\'...', export_filepath)
pd_phrase_score.to_csv(export_filepath, sep='\t', index=False)
return pd_data
def preprocess_column(self, pd_data, load_model=False):
"""
Preprocess specified column.
Inputs:
pd_data: (pd.Series) Input data to preprocess.
Returns:
pd_data: (pd.Series) Preprocess data.
"""
# preprocess using set of filters
custom_filters = self._build_custom_filter_list()
log.info('Applying preprocess filters to the %s...', pd_data.name)
pd_data = pd_data.apply(
lambda x: gpp.preprocess_string(x, custom_filters),
convert_dtype=False)
# generate phrase based on the configuration
pd_data = self._generate_phrase(pd_data, load_model=load_model)
# join the list of words into space delimited string
pd_data = pd_data.apply(lambda x: ' '.join(x))
return pd_data
def get_vocabs(self, pd_data):
log.info('Getting all vocabs...')
vocabs = []
for row in pd_data.tolist():
vocabs.extend(row.split(' '))
vocabs = list(set(vocabs))
vocabs = sorted(vocabs, key=str.lower)
log.info('Got %d unique vocabularies', len(vocabs))
return vocabs
def __init__(self, config_filepath):
configparser = ConfigParser(config_filepath)
gt_ontology_filename = configparser.getstr('gt_entitymapping')
self.gt_ontology = load_pkl(gt_ontology_filename)
class Word2VecManager():
"""
"""
def __init__(self, config_file):
"""
Class initializer.
Inputs:
"""
self.configparser = ConfigParser(config_file)
self.epoch_callback = EpochCallback()
self.model = None
def train(self, sentences, pretrained=None):
self.model = Word2Vec(
size=self.configparser.getint('size'),
window=self.configparser.getint('window'),
min_count=self.configparser.getint('min_count'),
workers=self.configparser.getint('workers'),
callbacks=[self.epoch_callback])
log.info('Building vocabularies...')
self.model.build_vocab(sentences)
total_examples = self.model.corpus_count
if pretrained:
original_vocabs = self.model.wv.vocab.keys()
pretrained_vocabs = KeyedVectors.load_word2vec_format(pretrained).vocab.keys()
common_vocabs = list(set(original_vocabs) & set(pretrained_vocabs))
log.info('Intersecting %d common vocabularies for transfer learning', len(common_vocabs))
if self.configparser.getbool('pre_train_update_vocab'):
log.info('Updating vocabularies using vocabs from pre-trained data')
self.model.build_vocab([list(pretrained_vocabs)], update=True, min_count=1)
self.model.intersect_word2vec_format(pretrained, lockf=1.0)
self.model.train(
sentences,
total_examples=total_examples,
epochs=self.configparser.getint('epochs'),
compute_loss=True)
def save_model(self, filepath):
assert self.model is not None
log.info('Saving model to %s...', filepath)
self.model.save(filepath)
def save_vectors(self, filepath):
assert self.model is not None
log.info('Saving word embeddings to %s...', filepath)
self.model.wv.save_word2vec_format(filepath)
def save_loss(self, filepath):
assert self.model is not None
# sorted by key, return a list of tuples
lists = sorted(self.epoch_callback.loss.items())
# unpack a list of pairs into two tuples
x, y = zip(*lists)
plt.plot(x, y)
plt.xlabel('Epoch')
plt.ylabel('Loss')
plt.savefig(filepath)
class SandDroid():
def __init__(self, theConfigFilePath, theLogger=Logger()):
# parse config file
self.configParser = ConfigParser()
# self.configParser.parseFile(theConfigFilePath)
self.configParser.generateDirectories()
self.log = theLogger
# keytool path to parse apk's signature
self.keytoolPath = None
# sanddroid directories
self.mainDir = os.path.dirname(__file__)
self.appList = [] # list to store apk file - full path
self.runningApps = [] # list to store apk file which in being analyzed
self.runHeadless = False
self.emulatorStartPort = 5554
self.numThreads = 1
self.maxThreadRuntime = 600
# control running threads
self.threadLogFileList = [] # list to store thread log file path
self.numFinishedApps = 0 # number of analyzed apps
self.numRunningThreads = 0 # number of running threads
self.threadList = [] # list of threads, size=numThreads
self.threadActiveMask = [
] # bitmask to determine if thread is active, size=numThreads
self.avdsheartbeat = (0, 0, 0, 0) # list avds' times used in one cycle
self.avdheartbeat = 0
self.startTime = datetime.datetime.now()
# ================================================================================
# Helpers
# ================================================================================
def __isConfigValid(self):
# check configure
javaHome = os.environ.get('JAVA_HOME')
if not javaHome:
self.log.error('Java environment not detected')
return False
else:
keytoolPath = os.path.join(javaHome, 'bin', 'keytool')
if not os.path.exists(keytoolPath):
self.log.error('Java keytool no exist')
return False
else:
self.keytoolPath = keytoolPath
for desc, directory in self.configParser.getDirectoies().items():
if not directory or not os.path.exists(directory):
self.log.error('%s doesn\'t exist!' % desc)
return False
if (not self.configParser.getDbUsr()) and (not self.configParser.getDbHost()) and (
not self.configParser.getDbPort()) \
and (not self.configParser.getDbPswd()) and (not self.configParser.getDbName()):
return False
return True
def _getLogDir(self):
"""
Get log directory
"""
logRootDir = self.configParser.getLogDir()
logDir = '%s/%s-%s' % (logRootDir, Utils.getDateAsString(
self.startTime), Utils.getTimeAsString(self.startTime))
return logDir
def _createLogDir(self, logDir):
"""
Create log directory
"""
if not os.path.exists(logDir):
try:
os.makedirs(logDir)
except OSError, e:
print e
class ParseFoodOn:
"""
Class for parsing FoodOn.
"""
def __init__(self, config_filepath):
"""
Class initializer.
Inputs:
config_filepath: (str) Configuration filepath.
"""
self.configparser = ConfigParser(config_filepath)
# read configuration file
self.filepath = self.configparser.getstr('filepath')
self.full_ontology_pkl = self.configparser.getstr('full_ontology_pkl')
self.candidate_ontology_pkl = self.configparser.getstr(
'candidate_ontology_pkl')
self.skeleton_and_entities_pkl = self.configparser.getstr(
'skeleton_and_entities_pkl')
self.overwrite_pkl = self.configparser.getbool('overwrite_pickle_flag')
self.outputFoodOn = self.configparser.getstr('outputFoodOn')
self.num_seeds = self.configparser.getint('num_seeds')
self.num_min_extracted_entities = self.configparser.getint(
'num_min_extracted_entities')
# generate pairs from csv file
self.pd_foodon_pairs = self.generate_pairs()
self.all_classes, self.all_entities = self.get_classes_and_entities()
self.foodon_graph, self.graph_dict, self.graph_dict_flip = self.generate_graph(
)
def generate_graph(self):
graph_dict = {k: v for v, k in enumerate(self.all_classes)}
graph_dict_flip = {v: k for v, k in enumerate(self.all_classes)}
G = nx.DiGraph()
for _, row in self.pd_foodon_pairs.iterrows():
if row['Parent'] in self.all_classes and row[
'Child'] in self.all_classes:
node_from = graph_dict[row['Parent']]
node_to = graph_dict[row['Child']]
G.add_edge(node_from, node_to)
return G, graph_dict, graph_dict_flip
def get_classes_and_entities(self):
all_classes = self.pd_foodon_pairs['Parent'].tolist()
all_classes = list(set(all_classes))
all_classes.sort()
log.debug('Found %d classes.', len(all_classes))
child = self.pd_foodon_pairs['Child'].tolist()
child = list(set(child))
child.sort()
all_entities = [c for c in child if c not in all_classes]
log.debug('Found %d entities.', len(all_entities))
return all_classes, all_entities
def generate_pairs(self):
log.info('Generating pairs of FoodOn.')
if file_exists(self.outputFoodOn) and not self.overwrite_pkl:
log.info('Using pre-generated pairs file.')
return pd.read_csv(self.outputFoodOn, sep='\t')
# 1.Read specified columns from FoodON.csv file
foodon = pd.read_csv(
self.filepath, usecols=['Class ID', 'Parents', 'Preferred Label'])
# 2.Create dictionary of URI and ClassLabel
labels_tmp = foodon[["Class ID", "Preferred Label"]].copy()
self.labels = labels_tmp.set_index(
'Class ID')['Preferred Label'].to_dict()
# 3.Create data frame with columns - child and all its' parents
foodonOrigDF = (foodon[[
"Class ID", "Parents"
]].copy()).rename(columns={'Class ID': 'Child'})
# 4.Split above DF into pairs of Child-Parent
pairs = []
for _, row in foodonOrigDF.iterrows():
parents = str(row['Parents'])
parentList = parents.split("|")
for pClass in parentList:
child = str(row['Child'])
pairs.append([child, pClass])
foodonDF = pd.DataFrame(pairs, columns=['Child', 'Parent'])
foodonDF = self.filter_ontology(
foodonDF, 'http://purl.obolibrary.org/obo/FOODON_00001872')
foodonDF = self.get_subtree(
foodonDF, 'http://purl.obolibrary.org/obo/FOODON_00001002')
# In foodonDF, replace URI by label
for idx, pair in foodonDF.iterrows():
pair['Child'] = self.labels[pair['Child']]
if pair['Parent'] in self.labels:
pair['Parent'] = self.labels[pair['Parent']]
foodonDF.drop_duplicates(inplace=True, ignore_index=True)
foodonDF.to_csv(self.outputFoodOn, sep='\t', index=False)
return foodonDF
def filter_ontology(self, dfObj, classname):
# Remove class and its children from the ontology.
# Works only if the children are leaf nodes.
indexNames = dfObj[dfObj['Parent'] == classname].index
dfObj.drop(indexNames, inplace=True)
indexNames = dfObj[dfObj['Child'] == classname].index
dfObj.drop(indexNames, inplace=True)
return dfObj
def get_subtree(self, df, rootclass):
subtreeDF, nextlevelclasses = self.traverse_next_level(
df, ['http://purl.obolibrary.org/obo/FOODON_00001002'])
while (len(nextlevelclasses) > 0):
pairsDF, nextlevelclasses = self.traverse_next_level(
df, nextlevelclasses)
subtreeDF = pd.concat([subtreeDF, pairsDF], ignore_index=True)
return subtreeDF
def traverse_next_level(self, df, classnames):
nextlevel = []
subtree_pairs = []
for parent in classnames:
selectedPairs = df[df['Parent'] == parent]
for idex, pair in selectedPairs.iterrows():
subtree_pairs.append([pair['Child'], pair['Parent']])
ifparent = df[df['Parent'] ==
pair['Child']] # Check if it is a leaf node
if ifparent.empty != True:
nextlevel.append(pair['Child'])
subtreeDF = pd.DataFrame(subtree_pairs, columns=['Child', 'Parent'])
return (subtreeDF, nextlevel)
def get_all_classes_dict(self):
"""
Get all candidate classes.
"""
log.info('Generating dictionary of all classes.')
if file_exists(self.full_ontology_pkl) and not self.overwrite_pkl:
log.info('Using pre-generated full classes dictionary file.')
return load_pkl(self.full_ontology_pkl)
full_classes_dict = {}
for class_label in self.all_classes:
pd_match = self.pd_foodon_pairs[self.pd_foodon_pairs['Parent'] ==
class_label]
children = pd_match['Child'].tolist()
children_entities = [c for c in children if c in self.all_entities]
node_from = self.graph_dict['foodon product type']
node_to = self.graph_dict[class_label]
paths = []
if class_label == 'foodon product type':
paths.append(tuple(['foodon product type']))
else:
for path in nx.all_simple_paths(self.foodon_graph,
source=node_from,
target=node_to):
translated_path = [self.graph_dict_flip[p] for p in path]
paths.append(tuple(translated_path[::-1]))
full_classes_dict[class_label] = (paths, children_entities)
save_pkl(full_classes_dict, self.full_ontology_pkl)
return full_classes_dict
def get_candidate_classes(self):
"""
Get all candidate classes.
"""
log.info('Generating dictionary of candidate classes.')
if file_exists(self.candidate_ontology_pkl) and not self.overwrite_pkl:
log.info(
'Using pre-generated candidate classes dictionary file: %s',
self.candidate_ontology_pkl)
return load_pkl(self.candidate_ontology_pkl)
candidate_classes_dict = {}
for class_label in self.all_classes:
pd_match = self.pd_foodon_pairs[self.pd_foodon_pairs['Parent'] ==
class_label]
children = pd_match['Child'].tolist()
children_entities = [c for c in children if c in self.all_entities]
if len(children_entities) > 0:
node_from = self.graph_dict['foodon product type']
node_to = self.graph_dict[class_label]
paths = []
if class_label == 'foodon product type':
paths.append(tuple(['foodon product type']))
else:
for path in nx.all_simple_paths(self.foodon_graph,
source=node_from,
target=node_to):
translated_path = [
self.graph_dict_flip[p] for p in path
]
paths.append(tuple(translated_path[::-1]))
candidate_classes_dict[class_label] = (paths,
children_entities)
log.info('Found %d candidate classes out of %d all classes.',
len(candidate_classes_dict.keys()), len(self.all_classes))
save_pkl(candidate_classes_dict, self.candidate_ontology_pkl)
return candidate_classes_dict
def get_seeded_skeleton(self, candidate_classes_dict):
log.info('Generating dictionary of skeleton candidate classes.')
if file_exists(
self.skeleton_and_entities_pkl) and not self.overwrite_pkl:
log.info('Using pickled skeleton file: %s',
self.skeleton_and_entities_pkl)
return load_pkl(self.skeleton_and_entities_pkl)
skeleton_candidate_classes_dict = {}
candidate_entities = []
for candidate_class in candidate_classes_dict.keys():
entities = candidate_classes_dict[candidate_class][1]
if len(entities) <= self.num_seeds:
temp_num_seeds = len(
entities) - self.num_min_extracted_entities
if temp_num_seeds > 0:
seeds = random.sample(entities, temp_num_seeds)
candidate_entities.extend(list(set(entities) - set(seeds)))
else:
seeds = entities.copy()
else:
seeds = random.sample(entities, self.num_seeds)
candidate_entities.extend(list(set(entities) - set(seeds)))
skeleton_candidate_classes_dict[candidate_class] = (
candidate_classes_dict[candidate_class][0], seeds)
candidate_entities = list(set(candidate_entities))
candidate_entities.sort()
log.info(
'Found %d candidate entities to populate out of %d all entities.',
len(candidate_entities), len(self.all_entities))
return_value = (skeleton_candidate_classes_dict, candidate_entities)
save_pkl(return_value, self.skeleton_and_entities_pkl)
return return_value
def main():
"""
Main function.
"""
# set log, parse args, and read configuration
set_logging(log_level=log.INFO)
args = parse_argument()
configparser = ConfigParser(args.config_file)
# need to apply preprocessing
fpm = FdcPreprocessManager(configparser.getstr('preprocess_config'))
# read FoodOn vocabs
labels = []
pd_foodon_pairs = pd.read_csv('./data/FoodOn/foodonpairs.txt', sep='\t')
labels.extend(pd_foodon_pairs['Parent'].tolist())
labels.extend(pd_foodon_pairs['Child'].tolist())
labels = list(set(labels))
log.info('Number of unique labels: %d', len(labels))
processed_labels = fpm.preprocess_column(pd.Series(labels),
load_model=True).tolist()
queries = processed_labels.copy()
for processed_label in processed_labels:
queries.extend(processed_label.split())
queries = list(set(queries))
# get summaries of the wikipedia entry
wm = WikipediaManager()
# check if we're gonna reuse the previous results
if configparser.getbool('reuse_previous'):
prev_summary = configparser.getstr('prev_summaries_filepath')
prev_failed = configparser.getstr('prev_failed_filepath')
else:
prev_summary = None
prev_failed = None
pd_summary, pd_failed = wm.get_summary(queries,
prev_summary=prev_summary,
prev_failed=prev_failed)
# save results
log.info('Saving successfully pulled wiki summaries to %s',
configparser.getstr('summaries_filepath'))
pd_summary.to_csv(configparser.getstr('summaries_filepath'),
sep='\t',
index=False)
log.info('Saving failed wiki queries to %s',
configparser.getstr('failed_filepath'))
pd_failed.to_csv(configparser.getstr('failed_filepath'),
sep='\t',
index=False)
# preprocess columns
pd_summary['summary_preprocessed'] = fpm.preprocess_column(
pd_summary['summary'], load_model=True)
output_filepath = configparser.getstr('preprocessed_output')
log.info('Saving preprocessed wikipedia data to %s...', output_filepath)
pd_summary.to_csv(output_filepath, sep='\t', index=False)
def plot_pr_print_cm(baseline_classifier, best_classifier, main_config,
model_manager):
classifiers_ys = {}
for classifier in [baseline_classifier, best_classifier]:
log.info('Running model for classifier \'%s\'', classifier)
# load config parsers
preprocess_config = ConfigParser(
main_config.get_str('preprocess_config'))
classifier_config = ConfigParser(
main_config.get_str('classifier_config'))
# perform preprocessing
X, y = model_manager.preprocess(preprocess_config, section=classifier)
# select subset of features if requested
selected_features = main_config.get_str_list('selected_features')
if selected_features:
log.info('Selecting subset of features: %s', selected_features)
X = X[selected_features]
# run classification model
classifier_config.overwrite('classifier', classifier)
score_avg, score_std, ys = model_manager.run_model_cv(
X, y, 'f1', classifier_config)
classifiers_ys[classifier] = ys
# confusion matrix
(y_trues, y_preds, y_probs) = classifiers_ys[best_classifier]
tn = []
fp = []
fn = []
tp = []
pred_pos = []
pred_neg = []
known_pos = []
known_neg = []
f1 = []
precision = []
recall = []
specificity = []
npv = []
fdr = []
accuracy = []
for fold in range(len(y_trues)):
cm_result = confusion_matrix(y_trues[fold], y_preds[fold]).ravel()
tn.append(cm_result[0])
fp.append(cm_result[1])
fn.append(cm_result[2])
tp.append(cm_result[3])
pred_pos.append(cm_result[3] + cm_result[1])
pred_neg.append(cm_result[2] + cm_result[0])
known_pos.append(cm_result[3] + cm_result[2])
known_neg.append(cm_result[1] + cm_result[0])
f1.append(f1_score(y_trues[fold], y_preds[fold]))
precision.append(
precision_score(y_trues[fold], y_preds[fold], average='binary'))
recall.append(
recall_score(y_trues[fold], y_preds[fold], average='binary'))
specificity.append(cm_result[0] / (cm_result[0] + cm_result[1]))
npv.append(cm_result[0] / (cm_result[0] + cm_result[2]))
fdr.append(cm_result[1] / (cm_result[1] + cm_result[3]))
accuracy.append(accuracy_score(y_trues[fold], y_preds[fold]))
tn_mean = np.mean(tn)
fp_mean = np.mean(fp)
fn_mean = np.mean(fn)
tp_mean = np.mean(tp)
pred_pos_mean = np.mean(pred_pos)
pred_neg_mean = np.mean(pred_neg)
known_pos_mean = np.mean(known_pos)
known_neg_mean = np.mean(known_neg)
f1_mean = np.mean(f1)
precision_mean = np.mean(precision)
recall_mean = np.mean(recall)
specificity_mean = np.mean(specificity)
npv_mean = np.mean(npv)
fdr_mean = np.mean(fdr)
accuracy_mean = np.mean(accuracy)
tn_std = np.std(tn)
fp_std = np.std(fp)
fn_std = np.std(fn)
tp_std = np.std(tp)
pred_pos_std = np.std(pred_pos)
pred_neg_std = np.std(pred_neg)
known_pos_std = np.std(known_pos)
known_neg_std = np.std(known_neg)
f1_std = np.std(f1)
precision_std = np.std(precision)
recall_std = np.std(recall)
specificity_std = np.std(specificity)
npv_std = np.std(npv)
fdr_std = np.std(fdr)
accuracy_std = np.std(accuracy)
log.info(
'Confusion matrix (tp, fp, fn, tn): (%.2f±%.2f, %.2f±%.2f, %.2f±%.2f, %.2f±%.2f)',
tp_mean, tp_std, fp_mean, fp_std, fn_mean, fn_std, tn_mean, tn_std)
log.info('pred pos: %.2f±%.2f', pred_pos_mean, pred_pos_std)
log.info('pred neg: %.2f±%.2f', pred_neg_mean, pred_neg_std)
log.info('known pos: %.2f±%.2f', known_pos_mean, known_pos_std)
log.info('known neg: %.2f±%.2f', known_neg_mean, known_neg_std)
log.info('F1: %.2f±%.2f', f1_mean, f1_std)
log.info('Precision: %.2f±%.2f', precision_mean, precision_std)
log.info('Recall: %.2f±%.2f', recall_mean, recall_std)
log.info('Specificity: %.2f±%.2f', specificity_mean, specificity_std)
log.info('Npv: %.2f±%.2f', npv_mean, npv_std)
log.info('Fdr: %.2f±%.2f', fdr_mean, fdr_std)
log.info('Accuracy: %.2f±%.2f', accuracy_mean, accuracy_std)
# plot PR curve
fig = plt.figure()
lines = []
labels = []
for classifier, ys in classifiers_ys.items():
y_trues, y_preds, y_probs = ys
if classifier == best_classifier:
num_folds = len(y_trues)
precision = 0
recall = 0
for fold in range(num_folds):
precision += precision_score(y_trues[fold],
y_preds[fold],
average='binary')
recall += recall_score(y_trues[fold],
y_preds[fold],
average='binary')
precision /= num_folds
recall /= num_folds
arrowprops = {'arrowstyle': '->'}
plt.scatter(recall, precision, s=30, marker='x', c='k', zorder=3)
plt.annotate('Operational point', (recall, precision),
(recall - 0.05, precision + 0.05),
arrowprops=arrowprops)
y_probs_1 = tuple(y_prob[1].to_numpy() for y_prob in y_probs)
line, label = plot_pr(y_trues, y_probs_1, classifier)
lines.append(line)
labels.append(label)
plt.xlabel('Recall')
plt.ylabel('Precision')
plt.title('Best model ({}) PR curve'.format(best_classifier))
plt.legend(lines, labels, loc='upper right', prop={'size': 10})
save_figure(fig, main_config.get_str('pr_curve'))
class RunnerThread(Thread):
def __createXml(self):
doc = xml.dom.minidom.Document()
root = doc.createElement('static_info')
doc.appendChild(root)
ltime = doc.createElement('datetime')
timeStr = time.strftime('%Y-%m-%d: %H:%M:%S',
time.localtime(time.time()))
ltime.appendChild(doc.createTextNode(str(timeStr)))
root.appendChild(ltime)
basicInfo = doc.createElement('basicInfo')
staticPojo = self.staticAnalyzer
if staticPojo.basicInfo is not None and staticPojo.basicInfo is not {}:
if staticPojo.basicInfo['VersionCode'] is not None:
versionCode = doc.createElement('VersionCode')
versionCode.appendChild(
doc.createTextNode(str(
staticPojo.basicInfo['VersionCode'])))
basicInfo.appendChild(versionCode)
else:
versionCode = doc.createElement('VersionCode')
versionCode.appendChild(doc.createTextNode('None'))
basicInfo.appendChild(versionCode)
if staticPojo.basicInfo['FileName'] is not None:
versionCode = doc.createElement('FileName')
versionCode.appendChild(
doc.createTextNode(str(staticPojo.basicInfo['FileName'])))
basicInfo.appendChild(versionCode)
else:
versionCode = doc.createElement('FileName')
versionCode.appendChild(doc.createTextNode('FileName'))
basicInfo.appendChild(versionCode)
if staticPojo.basicInfo['FileMD5'] is not None:
versionCode = doc.createElement('FileMD5')
versionCode.appendChild(
doc.createTextNode(str(staticPojo.basicInfo['FileMD5'])))
basicInfo.appendChild(versionCode)
else:
versionCode = doc.createElement('FileMD5')
versionCode.appendChild(doc.createTextNode('None'))
basicInfo.appendChild(versionCode)
if staticPojo.basicInfo['FileSize'] is not None:
versionCode = doc.createElement('FileSize')
versionCode.appendChild(
doc.createTextNode(str(staticPojo.basicInfo['FileSize'])))
basicInfo.appendChild(versionCode)
else:
versionCode = doc.createElement('Filesize')
versionCode.appendChild(doc.createTextNode('None'))
basicInfo.appendChild(versionCode)
if staticPojo.basicInfo['Package'] is not None:
versionCode = doc.createElement('Package')
versionCode.appendChild(
doc.createTextNode(str(staticPojo.basicInfo['Package'])))
basicInfo.appendChild(versionCode)
else:
versionCode = doc.createElement('Package')
versionCode.appendChild(doc.createTextNode('None'))
basicInfo.appendChild(versionCode)
if staticPojo.basicInfo['MinSDK'] is not None:
versionCode = doc.createElement('MinSDK')
versionCode.appendChild(
doc.createTextNode(str(staticPojo.basicInfo['MinSDK'])))
basicInfo.appendChild(versionCode)
else:
versionCode = doc.createElement('MinSDK')
versionCode.appendChild(doc.createTextNode('None'))
basicInfo.appendChild(versionCode)
if staticPojo.basicInfo['TargetSDK'] is not None:
versionCode = doc.createElement('TargetSDK')
versionCode.appendChild(
doc.createTextNode(str(staticPojo.basicInfo['TargetSDK'])))
basicInfo.appendChild(versionCode)
else:
versionCode = doc.createElement('TargetSDK')
versionCode.appendChild(doc.createTextNode('None'))
basicInfo.appendChild(versionCode)
if staticPojo.basicInfo['Cert'] is not None:
versionCode = doc.createElement('Cert')
versionCode.appendChild(
doc.createTextNode(str(staticPojo.basicInfo['Cert'])))
basicInfo.appendChild(versionCode)
else:
versionCode = doc.createElement('Cert')
versionCode.appendChild(doc.createTextNode('None'))
basicInfo.appendChild(versionCode)
root.appendChild(basicInfo)
isRepackaged = doc.createElement('isRepackaged')
if staticPojo.isRepackaged is False:
isRepackaged.appendChild(doc.createTextNode('0'))
else:
isRepackaged.appendChild(doc.createTextNode('1'))
root.appendChild(isRepackaged)
isRepackaged = doc.createElement('malware')
if staticPojo.malware is not None:
isRepackaged.appendChild(doc.createTextNode(staticPojo.malware))
else:
isRepackaged.appendChild(doc.createTextNode('0'))
root.appendChild(isRepackaged)
isRepackaged = doc.createElement('riskValue')
isRepackaged.appendChild(doc.createTextNode(str(staticPojo.riskValue)))
root.appendChild(isRepackaged)
sensitiveAPIs = doc.createElement('sensitiveAPIs')
if staticPojo.sensitiveAPIs is not None and staticPojo.sensitiveAPIs is not {}:
for key, value in staticPojo.sensitiveAPIs.items():
sensitiveAPI = doc.createElement('sensitiveAPI')
keyName = doc.createElement('name')
keyName.appendChild(doc.createTextNode(str(key)))
sensitiveAPI.appendChild(keyName)
desc = doc.createElement('desc')
desc.appendChild(doc.createTextNode(str(value)))
sensitiveAPI.appendChild(desc)
sensitiveAPIs.appendChild(sensitiveAPI)
root.appendChild(sensitiveAPIs)
sensitiveAPIs = doc.createElement('sensitiveStrs')
if staticPojo.sensitiveStrs is not None and staticPojo.sensitiveStrs is not {}:
for key, value in staticPojo.sensitiveStrs.items():
sensitiveAPI = doc.createElement('sensitiveStr')
keyName = doc.createElement('name')
keyName.appendChild(doc.createTextNode(str(key)))
sensitiveAPI.appendChild(keyName)
desc = doc.createElement('desc')
desc.appendChild(doc.createTextNode(str(value)))
sensitiveAPI.appendChild(desc)
sensitiveAPIs.appendChild(sensitiveAPI)
root.appendChild(sensitiveAPIs)
sensitiveAPIs = doc.createElement('sensitiveFiles')
if staticPojo.sensitiveFiles is not None and staticPojo.sensitiveFiles is not {}:
for key, value in staticPojo.sensitiveFiles.items():
sensitiveAPI = doc.createElement('sensitiveFile')
keyName = doc.createElement('name')
keyName.appendChild(doc.createTextNode(str(key)))
sensitiveAPI.appendChild(keyName)
desc = doc.createElement('type')
desc.appendChild(doc.createTextNode(str(value)))
sensitiveAPI.appendChild(desc)
sensitiveAPIs.appendChild(sensitiveAPI)
root.appendChild(sensitiveAPIs)
sensitiveAPIs = doc.createElement('sensitiveCodes')
if staticPojo.sensitiveCodes is not None and staticPojo.sensitiveCodes is not {}:
for key, value in staticPojo.sensitiveCodes.items():
sensitiveAPI = doc.createElement('sensitiveCode')
keyName = doc.createElement('name')
keyName.appendChild(doc.createTextNode(str(key)))
sensitiveAPI.appendChild(keyName)
desc = doc.createElement('desc')
desc.appendChild(doc.createTextNode(str(value)))
sensitiveAPI.appendChild(desc)
sensitiveAPIs.appendChild(sensitiveAPI)
root.appendChild(sensitiveAPIs)
urls_static = doc.createElement('urls')
if staticPojo.urls is not None and staticPojo.urls is not []:
for item in staticPojo.urls:
url_static = doc.createElement('url')
url_static.appendChild(doc.createTextNode(str(item)))
urls_static.appendChild(url_static)
root.appendChild(urls_static)
sensitiveAPIs = doc.createElement('permissions')
if staticPojo.permissions is not None and staticPojo.permissions is not {}:
for key, value in staticPojo.permissions.items():
sensitiveAPI = doc.createElement('permission')
keyName = doc.createElement('name')
keyName.appendChild(doc.createTextNode(str(key)))
sensitiveAPI.appendChild(keyName)
desc = doc.createElement('desc')
desc.appendChild(doc.createTextNode(str(value)))
sensitiveAPI.appendChild(desc)
sensitiveAPIs.appendChild(sensitiveAPI)
root.appendChild(sensitiveAPIs)
mainActivity = doc.createElement('mainActivity')
if staticPojo.mainActivity is not None and staticPojo.mainActivity is not {}:
mainActivity.appendChild(
doc.createTextNode(str(staticPojo.mainActivity)))
root.appendChild(mainActivity)
activities = doc.createElement('activities')
if staticPojo.activities is not None and staticPojo.activities is not {}:
for value in staticPojo.activities:
activity = doc.createElement('activity')
activity.appendChild(doc.createTextNode(str(value)))
activities.appendChild(activity)
root.appendChild(activities)
services = doc.createElement('services')
if staticPojo.services is not None and staticPojo.services is not {}:
for value in staticPojo.services:
service = doc.createElement('service')
service.appendChild(doc.createTextNode(str(value)))
services.appendChild(service)
root.appendChild(services)
receivers = doc.createElement('receivers')
if staticPojo.receivers is not None and staticPojo.receivers is not {}:
for value in staticPojo.receivers:
receiver = doc.createElement('receiver')
receiver.appendChild(doc.createTextNode(str(value)))
receivers.appendChild(receiver)
root.appendChild(receivers)
providers = doc.createElement('provicers')
if staticPojo.providers is not None and staticPojo.providers is not {}:
for value in staticPojo.providers:
provider = doc.createElement('provicer')
provider.appendChild(doc.createTextNode(str(value)))
providers.appendChild(provider)
root.appendChild(providers)
exposedActivities = doc.createElement('exposedActivities')
if staticPojo.exposedActivities is not None and staticPojo.exposedActivities is not {}:
for value in staticPojo.exposedActivities:
exposedActivity = doc.createElement('exposedActivity')
exposedActivity.appendChild(doc.createTextNode(str(value)))
exposedActivities.appendChild(exposedActivity)
root.appendChild(exposedActivities)
exposedServices = doc.createElement('exposedServices')
if staticPojo.exposedServices is not None and staticPojo.exposedServices is not {}:
for value in staticPojo.exposedServices:
exposedService = doc.createElement('exposedService')
exposedService.appendChild(doc.createTextNode(str(value)))
exposedServices.appendChild(exposedService)
root.appendChild(exposedServices)
exposedReceivers = doc.createElement('exposedReceivers')
if staticPojo.exposedReceivers is not None and staticPojo.exposedReceivers is not {}:
for value in staticPojo.exposedReceivers:
exposedReceiver = doc.createElement('exposedReceiver')
exposedReceiver.appendChild(doc.createTextNode(str(value)))
exposedReceivers.appendChild(exposedReceiver)
root.appendChild(exposedReceivers)
classifyInfo = doc.createElement('classifyInfo')
if staticPojo.classifyInfo is not None and staticPojo.classifyInfo is not {}:
classifyInfo.appendChild(
doc.createTextNode(str(staticPojo.classifyInfo)))
root.appendChild(classifyInfo)
xmlFilename = '/home/mindmac/workspace/SandDroidIIE/staticAnaReports/' + staticPojo.basicInfo[
'FileMD5'] + '.xml'
xmlFile = open(xmlFilename, 'w')
doc.writexml(xmlFile,
indent='\t',
addindent='\t',
newl='\n',
encoding="utf-8")
def __init__(self,
theApkObj,
theAvdName,
decompressDir,
runHeadless,
theLogger=Logger()):
Thread.__init__(self)
# configParser
self.configParser = ConfigParser()
self.apkObj = theApkObj
self.log = theLogger
self.curDir = os.path.dirname(__file__)
self.staticAnalyzer = None
self.dynamicAnalyzer = None
self.logcatAnalyzer = None
self.startTimeStr = None
self.endTimeStr = None
self.emulator = None
self.emulatorPort = 5554
self.avdName = theAvdName
self.runHeadless = runHeadless
self.decompressPath = decompressDir
self.logcatFile = None
self.session = None
self.cancelFlag = False # Flag for canceling run
def checkForCancelation(self):
"""
Checks for the cancelation flag sent from the main program.
If cancel flag is set, abort execution by raising KeyboardInterrupt.
"""
if self.cancelFlag:
self.log.info('Cancelation flag found, abort thread')
traceback.print_stack(file=self.log.log)
raise KeyboardInterrupt
def __getLogcatFilePath(self):
"""
Generates logcat file name
"""
return os.path.join(self.decompressPath, 'logcat.log')
def getLogger(self):
return self.log
def staticAnalyze(self):
"""
Static Analysis
"""
# Static Analyzer
self.staticAnalyzer = StaticAnalyzer(self.apkObj, self.decompressPath,
self.curDir, self.log)
# Init
self.log.info('Initialization...')
self.staticAnalyzer.initEnv()
# Parse smali files
self.log.info('Parse smali files to get methods, urls...')
self.staticAnalyzer.parseSmali()
# APK basic information
self.log.info('Get APK\'s basic information')
self.staticAnalyzer.getBasicInfo()
# APK permissions used
self.log.info('Get APK\'s used permissions')
self.staticAnalyzer.getPermissions()
# APK components used
self.log.info('Get APK\'s used components')
self.staticAnalyzer.getComponents()
# APK components exposed
self.log.info('Get APK\'s exposed components')
self.staticAnalyzer.getExposedComps()
# APK classifier
self.log.info('Get APK\'s classifier information')
self.staticAnalyzer.classifyByPermission()
# APK fuzzy risk value
self.log.info('Get APK\'s fuzzy risk score')
self.staticAnalyzer.getRisk()
# APK gexf graph
self.log.info('Get APK\'s gexf graph', setTime=True)
#gexfOutFile = os.path.join(self.decompressPath, '%s.gexf' % self.apkObj.getMd5Hash().upper())
#self.staticAnalyzer.getGexf(gexfOutFile)
# APK Malware detection
self.log.info('Get APK\'s malicious information', setTime=True)
self.staticAnalyzer.getMal()
# APK repackaged
self.log.info('Check APK if repackaged', setTime=True)
self.staticAnalyzer.checkRepackage(self.session)
def dynamicAnalyze(self):
"""
Dynamic Anlysis
"""
cur_dir = os.path.dirname(__file__)
imageDir = os.path.join(cur_dir, 'resources', 'images')
pcapFile = os.path.join(self.decompressPath,
'%s.pcap' % self.apkObj.getMd5Hash().upper())
self.dynamicAnalyzer = DynamicAnalyzer(self.decompressPath,
self.avdName, self.curDir,
self.log)
self.emulator = EmulatorClient(
theSdkPath=self.configParser.getAndroidSdkDir(),
thePort=self.emulatorPort,
theImageDir=imageDir,
thePcapFile=pcapFile,
theRunHeadless=self.runHeadless,
theAvdName=self.avdName,
theLogger=self.log)
self.checkForCancelation()
# Start emulator
self.log.info('Start emulator', setTime=True)
self.emulator.start()
# Run app
isFinishedRunnig = self.dynamicAnalyzer.runApp(self.emulator,
self.apkObj)
# Store logcat file
if isFinishedRunnig:
self.log.info('Store logcat file')
self.emulator.stopLogcatRedirect()
self.emulator.storeLogcatRedirectFile(
self.dynamicAnalyzer.logcatRedirectFile, self.logcatFile)
else:
self.log.error('Run app failed!')
def killEmulator(self):
if not self.emulator:
self.emulator.shutDown()
def logcatAnalyze(self, logcatFile):
"""
Analyze logcat file
"""
try:
if not os.path.exists(logcatFile):
self.log.info('Logcat file %s doesn\'t exist!' % logcatFile)
return
else:
# Build self.logcatAnalyzer
self.logcatAnalyzer = LogcatAnalyzer(theLogger=self.log)
self.logcatAnalyzer.setLogFile(logcatFile)
self.logcatAnalyzer.extractLogEntries()
except EmulatorClientError, ecErr:
self.runnerThread.result['errorList'].append(ecErr)
