def __init__(self, libinfoFile, tablename=defaultTable, conf=None,
species=defaultSpecies, verbose=False, log=sys.stderr):
"create load_libinfo instance, connect to MySQL and check for existance of libinfo file"
# set attributes
self.verbose = verbose
self.log = log
self.file = libinfoFile
self.tablename = tablename
self.conf = None
self.species = species
self.__db = None # db connection
self.__cursor = None
# check libinfoFile
if not os.path.exists(self.file):
self.__inform("ERROR: library info file %s does not exist\n" % self.file)
raise Errors.ObjectInitError('load_libinfo', "library info file '%s' does not exist\n" % self.file)
# init configuration
if conf is not None and isinstance(conf, configuration.Configuration):
self.conf = conf
elif conf is not None and os.path.exists(conf):
self.conf = configuration.Configuration(filename=conf)
else:
self.conf = configuration.Configuration()
# check species
if not self.species in self.conf.getSpeciesList():
self.__inform("ERROR: species %s is not in configuration file %s\n" % (self.species, self.conf.configFile()))
raise Errors.ObjectInitError('load_libinfo', "species '%s' is not in configuration file %s\n" % (self.species, self.conf.configFile()))
# connect to MySQL
self.__connect()
def configuration(self, new_configuration):
"""Set configuration.
Parameters
----------
new_configuration : :class:`configuration:Configuration` or
string or 2-tuple
The attribute is set in one of the three following ways:
(i) an object of :class:`configuration:Configuration`;
(ii) a string with the name of the file to be read with
the configuration information; and (iii) a 2-tuple with
the name and the path to the file to be read.
Examples
--------
The following examples explain the ways to set the attribute:
>>> solver.configuration = Configuration(...)
>>> solver.configuration = 'myfile'
>>> solver.configuration = ('myfile', './folder/')
"""
if isinstance(new_configuration, tuple):
file_name, file_path = new_configuration
self._configuration = cfg.Configuration(import_filename=file_name,
import_filepath=file_path)
elif isinstance(new_configuration, str):
self._configuration = cfg.Configuration(
import_filename=new_configuration)
else:
self._configuration = cp.deepcopy(new_configuration)
def __init__(self, conf=None, log=sys.stderr):
"instanciate MakeMySQL class and read configuration"
# configuration
if conf is not None and isinstance(conf, configuration.Configuration):
self.conf = conf
elif conf is not None and os.path.exists(conf):
self.conf = configuration.Configuration(filename=conf)
else:
self.conf = configuration.Configuration()
# log
self.log = log
# store MySQL information
self.MySQL_info = {}
for species in self.conf.getSpeciesList():
self.MySQL_info[species] = {
"user": os.getlogin(),
"DB": self.conf[species]["Assembly"],
"PASSWORD": '',
"host": self.conf[species]["MySQLHost"],
"knownGene": self.conf[species]["knownGene"],
"mRNA": self.conf[species]["mRNA"],
"MetaTable": self.conf[species]["MetaTable"],
"Chromosomes": self.conf[species]["Chromosomes"].split(","),
}
self.db = None
self.cursor = None
self.currentspecies = None
def test_settings_save_load(self):
self.config = configuration.Configuration(self.path)
self.config.load()
element = configuration.createConfigurable(BasicConfig, self.config)
v = "New"
element.p2 = v
self.config.save()
self.config = configuration.Configuration(self.path)
self.config.load()
element = configuration.createConfigurable(BasicConfig, self.config)
self.assertEqual(element.p2, v)
def __init__(self, conf=None, replace=True, log=sys.stderr, gunzip=True):
if conf is not None and isinstance(conf, configuration.Configuration):
self.conf = conf
elif conf is not None and os.path.exists(conf):
self.conf = configuration.Configuration(filename=conf)
else:
self.conf = configuration.Configuration()
self.replace = bool(replace)
self.species = None
self.log = log
self.gunzip = gunzip
self.tablenames = {
} #format: self.tablenames[species][tablename] = dir_with_sql_and_data_files
def main():
# GLOBAL stuff
# detections=detect_by_gmm(frame)
config = configuration.Configuration()
test_img = cv2.imread('C:/Users/Public/Pictures/Sample Pictures/test.jpg')
# test NORMALIZE INPUT SHAPE
print("normalize_shape")
normalize_shape(test_img,config.input_shapes[3])
# test RELATIVE_to_absolute
print('relative_to_absolute')
relative_detections = [[70,170,40,105],[90,160,50,70]]
bb = [50, 300 , 20 , 340]
h_padding = 25
w_padding = 40
print(relative_to_absolute(relative_detections,bb,h_padding,w_padding))
# test SELECT model
print('select_model')
print(select_model(bb,config))
# test ABSOLUTE_to_relative
print('absolute_to_relative')
abs_cordinate = [70,350,40,415]
print(absolute_to_relative(abs_cordinate,bb))
def __init__(self, configfile=None):
'''
Initialization method of Choronzon. Reads the configuration,
instantiates objects of the vital classes, builds and
analyzes the first generation of chromosomes by reading
the initial population provided to the fuzzer.
'''
# configuration is a singleton
self.configuration = configuration.Configuration(configfile)
self.campaign = campaign.Campaign(self.configuration['CampaignName'])
seedpath = self.campaign.copy_directory(
self.configuration['InitialPopulation'], name='seedfiles')
self.tracer = tracer.Tracer()
self.strategy = strategy.FuzzingStrategy()
self.population = world.Population(self.tracer.cache)
self.evaluator = evaluator.Evaluator(self.tracer.cache)
try:
self.sharedpath = self.campaign.create_shared_directory(
self.configuration['ChromosomeShared'])
except:
self.sharedpath = None
# Initialize factory for building chromosome
# and the proxy for computing the fitness.
chromosomes = chromosome.Factory.build(seedpath)
for chromo in chromosomes:
self.population.add_chromosome(chromo)
self.analyze()
def __init__(self, fake=False):
self.fake = fake
if self.fake:
self.table_name = "Fake" + self.table_name
self.ddb = ddb.DDB(self.table_name, [('channel_key', 'S')])
self.table = self.ddb.get_table()
self.configuration = configuration.Configuration()
def __init__(self, seed=1):
# configuration
self.seed = seed if isinstance(seed,(range,list)) else [seed]
self.cnf = cf.Configuration()
self.random = np.random
self.time = tm.strftime('%Y-%m-%d_%H-%M-%S')
self.cnf_name = '_'.join([self.cnf.learning_method, self.cnf.loss_function, 'lr='+str(self.cnf.learning_rate)])
def test_listDependencyGraph(self):
config = configuration.Configuration()
config.addClassifiers = ""
sourceKey = "repository:central"
topGavs = ['org.apache.ant:ant:1.8.0']
dependencies = {
'org.apache.ant:ant:pom:1.8.0': set(['']),
#'org.apache.ant:ant:jar:1.8.0': set(['']),
'org.apache.ant:ant-launcher:pom:1.8.0': set(['']),
'org.apache.ant:ant-launcher:jar:1.8.0': set(['']),
'org.apache.ant:ant-parent:pom:1.8.0': set(['']),
'org.apache:apache:pom:3': set(['']),
'org.apache:apache:pom:4': set(['']),
'xerces:xercesImpl:pom:2.9.0': set(['']),
'xerces:xercesImpl:jar:2.9.0': set(['']),
'xml-apis:xml-apis:pom:1.3.04': set(['']),
'xml-apis:xml-apis:jar:1.3.04': set(['']),
'xml-resolver:xml-resolver:pom:1.2': set(['']),
'xml-resolver:xml-resolver:jar:1.2': set([''])
}
expectedArtifacts = self._getExpectedArtifacts(self.indyUrl,
dependencies)
builder = artifact_list_builder.ArtifactListBuilder(config)
actualArtifacts = builder._listDependencyGraph(self.indyUrl, None,
sourceKey, topGavs)
self.assertEqualArtifactList(expectedArtifacts, actualArtifacts)
def __init__(self, notation, cam):
"""
Parses the passed notation and saves values into members.
@sfunc: Represents the function that returns the next given state.
@ruleset: A created ruleset that matches always
@offsets: Represents the Moore neighborhood corresponding to the given CAM
"""
self.sfunc = None
self.offsets = c.Configuration.moore(cam.master)
self.ruleset = r.Ruleset(r.Ruleset.Method.ALWAYS_PASS)
if re.match(CAMParser.MCELL_FORMAT, notation):
x, y = notation.split('/')
if all(map(self._numasc, [x, y])):
self.sfunc = self._mcell(x, y)
else:
raise ValueError("Non-ascending values in MCELL format")
elif re.match(CAMParser.RLE_FORMAT, notation):
B, S = map(lambda x: x[1:], notation.split('/'))
if all(map(self._numasc, [B, S])):
self.sfunc = self._mcell(S, B)
else:
raise ValueError("Non-ascending values in RLE format")
else:
raise ValueError("No supported format passed to parser.")
# Add configuration to given CAM
config = c.Configuration(self.sfunc, plane=cam.master, offsets=self.offsets)
self.ruleset.configurations.append(config)
def reset(self):
self.unsubscribe_all()
# make conf
self.conf = configuration.Configuration(self.aircraft)
self.settings = []
for sc in self.conf.settings:
for s in sc['settings']:
if not ((s['has_key']('settingsapp')
and s['settingsapp'] == "ignore")):
self.settings.append(s)
# if setting doesn't have guipage, set guipage to "unsorted"
for s in self.settings:
if not s['has_key']('guipage'):
s['guipage'] = 'unsorted'
self.settings.sort(key=lambda x: x['guipage'])
# group settings by guipage and add to notebook
self.notebook = wx.Notebook(self)
self.guipages = {}
from itertools import groupby
for guipage_name, g in groupby(self.settings, lambda s: s['guipage']):
self.guipages[guipage_name] = GuiPage(self.notebook, self.lc,
list(g), self.lc_event)
self.notebook.AddPage(self.guipages[guipage_name], guipage_name)
def test_handleGetConfigCommand(self):
self.backend.storage = MockStorage(test=self)
self.backend.BL4PAddress = 'BL4PAddress'
MS = MockStorage(test=self)
MS.configuration['bl4p.apiKey'] = 'foo'
MS.configuration['bl4p.apiSecret'] = 'bar'
self.backend.configuration = configuration.Configuration(MS)
cmd = Mock()
cmd.commandID = 42
self.backend.handleGetConfigCommand(cmd)
self.assertEqual(self.outgoingMessages,
[messages.PluginCommandResult(
commandID=42,
result=\
{
'values':
{
'bl4p.url' : '',
'bl4p.apiKey' : 'foo',
'bl4p.apiSecret' : 'bar',
'bl4p.signingPrivateKey': '',
}
}
)])
def convert_osm_to_roadgraph(filename, network_type, options):
configuration = config.Configuration(network_type)
r_index = filename.rfind(".")
out_file = filename[:r_index]
print("selected network type: {}".format(configuration.network_type))
print("accepted highway tags: {}".format(configuration.accepted_highways))
print("opening file: {}".format(filename))
nodes, ways = osm.read_osm.read_file(filename, configuration)
osm.sanitize_input.sanitize_input(ways, nodes)
graph = graphfactory.build_graph_from_osm(nodes, ways)
if not options.lcc:
graph = algorithms.computeLCCGraph(graph)
output.write_to_file(graph, out_file, configuration.get_file_extension())
if options.contract:
contracted_graph = contract.contract(graph)
output.write_to_file(contracted_graph, out_file,
"{}c".format(configuration.get_file_extension()))
def convert_osm_to_roadgraph(filename, network_type, options):
configuration = config.Configuration(network_type)
r_index = filename.rfind(".")
out_file = filename[:r_index]
print(f"selected network type: {configuration.network_type}")
print(f"accepted highway tags: {configuration.accepted_highways}")
print(f"opening file: {filename}")
nodes, ways = osm.read_osm.read_file(filename, configuration)
osm.sanitize_input.sanitize_input(ways, nodes)
graph = graphfactory.build_graph_from_osm(nodes, ways)
if not options.lcc:
graph = algorithms.computeLCCGraph(graph)
output.write_to_file(graph, out_file, configuration.get_file_extension())
if options.networkx_output:
nx_graph = convert_graph.convert_to_networkx(graph)
output.write_nx_to_file(nx_graph, f"{out_file}.json")
if options.contract:
contracted_graph = contract_graph.ContractGraph(graph).contract()
output.write_to_file(contracted_graph, out_file,
f"{configuration.get_file_extension()}c")
if options.networkx_output:
nx_graph = convert_graph.convert_to_networkx(contracted_graph)
output.write_nx_to_file(nx_graph, f"{out_file}_contracted.json")
def load_config(self, config_file, raise_exception=False):
try:
config_from_yaml = yaml.load(open(config_file, 'r'))
config = configuration.Configuration(config_from_yaml)
for module_name in config.plugins:
action_module = '%s.actions' % module_name
importlib.import_module(action_module)
self.validate_config(config)
self.config_filename = config_file
self.config_mtime = os.stat(config_file).st_mtime
# move clients from old config if they have the same connection
if self.config is not None:
for gerrit_name in config.gerrits:
client = config.gerrits[gerrit_name]['client']
old_client = self.config.gerrits[gerrit_name]['client']
if old_client == client:
logging.debug('Reusing client for %s' % gerrit_name)
config.gerrits[gerrit_name]['client'] = old_client
self.config.gerrits[gerrit_name]['client'] = None
self.config.close_clients()
self.config = config
except Exception as e:
logging.error('Could not load configuration file, '
'encountered errors : ' + e.message)
if raise_exception:
raise e
def __init__(self, master=None, name='root'):
tk.Frame.__init__(self, master, name=name)
self.grid(sticky=tk.N + tk.S + tk.E + tk.W)
self.path = os.path.dirname(os.path.abspath(__file__))
self.config = configuration.Configuration('cosmexo', 'config')
self.createWidgets()
self.db = None
def __init__(self, db: asyncpg.pool.Pool):
intents: discord.Intents = discord.Intents.none()
intents.guilds = True
intents.guild_messages = True
intents.members = True
super().__init__(
command_prefix='!reg ',
activity=discord.Game('type "!reg help" for help'),
description=
'Hello, I\'m Reg. I help with managing this server. Contact Alpatron if I go haywire. My commands are:',
intents=intents)
self.db = db
import configuration #This is to prevent circular dependency errors. Come to think about it, cogs are circularly dependent! All cogs must know about the bot, and the bot needs to know about cogs!
self.add_cog(configuration.Configuration(self))
import configurationCommands
self.add_cog(
configurationCommands.ConfigurationCommands(
self, self.get_cog('Configuration')))
import adminCommands
self.add_cog(
adminCommands.AdminCommands(self, self.get_cog('Configuration')))
import userCommands
self.add_cog(
userCommands.UserCommands(self, self.get_cog('Configuration')))
self.http_session = aiohttp.ClientSession()
print("Reg Bot ready!")
def test_listDependencies_recursive(self):
config = configuration.Configuration()
config.addClassifiers = "__all__"
repoUrls = ['http://repo.maven.apache.org/maven2/']
gavs = ['com.sun.faces:jsf-api:2.0.11', 'org.apache.ant:ant:1.8.0']
dependencies = {
'junit:junit:pom:3.8.2':
set(['']),
'junit:junit:jar:3.8.2':
set(['', 'sources', 'javadoc']),
'xerces:xercesImpl:pom:2.9.0':
set(['']),
'xerces:xercesImpl:jar:2.9.0':
set(['']),
'xml-apis:xml-apis:pom:1.3.04':
set(['']),
'xml-apis:xml-apis:jar:1.3.04':
set(['', 'source', 'sources']),
'javax.el:javax.el-api:pom:2.2.1':
set(['']),
'javax.el:javax.el-api:jar:2.2.1':
set(['', 'sources', 'javadoc']),
'xml-resolver:xml-resolver:pom:1.2':
set(['']),
'xml-resolver:xml-resolver:jar:1.2':
set(['', 'sources']),
'javax.servlet:servlet-api:pom:2.5':
set(['']),
'javax.servlet:servlet-api:jar:2.5':
set(['', 'sources']),
'javax.servlet.jsp:jsp-api:pom:2.1':
set(['']),
'javax.servlet.jsp:jsp-api:jar:2.1':
set(['', 'sources']),
'org.apache.ant:ant-launcher:pom:1.8.0':
set(['']),
'org.apache.ant:ant-launcher:jar:1.8.0':
set(['']),
'javax.servlet.jsp.jstl:jstl-api:pom:1.2':
set(['']),
'javax.servlet.jsp.jstl:jstl-api:jar:1.2':
set(['', 'sources', 'javadoc']),
'javax.servlet:javax.servlet-api:pom:3.0.1':
set(['']),
'javax.servlet:javax.servlet-api:jar:3.0.1':
set(['', 'sources', 'javadoc']),
'javax.servlet.jsp:javax.servlet.jsp-api:pom:2.2.1':
set(['']),
'javax.servlet.jsp:javax.servlet.jsp-api:jar:2.2.1':
set(['', 'sources', 'javadoc'])
}
expectedArtifacts = self._getExpectedArtifacts(repoUrls[0],
dependencies)
builder = artifact_list_builder.ArtifactListBuilder(config)
actualArtifacts = builder._listDependencies(repoUrls, gavs, True, None,
False)
self.assertEqualArtifactList(expectedArtifacts, actualArtifacts)
def elaborate_data(elaborate, config, invariants):
print("==== Starting data elaboration ====")
# extract the input file name
input_file = do_manual_substitution(elaborate.input_file.currValue(),
config)
print("\t*** The skeleton for input files is: %s ***" % input_file)
dir_skel = os.path.dirname(input_file)
file_skel = os.path.basename(input_file)
# create an iterator through all the directories spawned by this benchmark
dc = configuration.Configuration()
for param_name in extract_parameters(dir_skel):
dc += config.parameters[param_name]
fc = configuration.Configuration()
for param_name in extract_parameters(file_skel):
fc += config.parameters[param_name]
# now iterate through all the directories
for it in iterator.ConfigIterator(dc, invariants):
# for each directory we list the files and look for files which have been generated by the benchmark
curr_dir = dir_skel.format(**it.parameters)
print("\t*** Looking up directory: %s ***" % curr_dir)
for file in os.listdir(curr_dir):
if not file.startswith('~'):
# skip raw files
continue
print("\t\t-> Opening file:", file)
p = re.compile('-{0,1}[a-zA-Z0-9]+')
file_name_vals = [
config_parse.convert(x.group())
for x in p.finditer(os.path.splitext(file)[0])
]
# check number of arguments in file name
if len(file_name_vals) != len(fc):
print(
'\t\t\t# Wrong number of elements in file name: found %d expected %d #, skipping file!'
% (len(file_name_vals), len(fc)))
continue
# if the number of args is correct we now set the configuration values
i = 0
for param_name in fc.parameter_keys():
fc.parameters[param_name].setValue(file_name_vals[i])
i += 1
def scheduled_job():
c = configuration.Configuration()
p = async_html_parser.HtmlParser(c)
m = mail_sender.MailSender(c)
m.send_zip(p.process_async())
def __init__(self, fake=False):
self.fake = fake
if fake:
self.table_name = self.fake_table_name
self.ddb = ddb.DDB(self.table_name, [('id', 'S')])
self.table = self.ddb.get_table()
self.users = {}
self.userhash = userhash.UserHash(fake=fake)
self.configuration = configuration.Configuration(fake=fake)
self.modified = {}
def main():
#make a list of algorithms
functions = []
for algorithm in att.ALGORITHMS:
functions.append(getattr(conf.Configuration(), algorithm))
#execute each configuration
with Pool(processes=att.THREADS) as p:
p.starmap(call_function, zip(functions))
def setUp(self) -> None:
self.configurationService = configuration.Configuration()
# reads and parses initial configuration file
with open(
self.configurationService.
shared_memory_manager_dict["config_file"], "r") as f:
raw = f.read()
self.configurationService.shared_memory_manager_dict[
"config_data"], _flag, _error = configuration.parse(raw,
yaml=True)
def draw_gap(file_name):
cfg = configuration.Configuration(file_name=file_name)
gap, a, b = max_backwards(cfg.path.points)
path = cfg.path.points
movie = Movie()
movie.background([(cfg, "black")])
movie.background([(circle.Circle(path[a], cfg.cheerio_radius / 2), "green")])
movie.background([(circle.Circle(path[b], cfg.cheerio_radius / 2), "green")])
movie.just_draw()
exit(0)
def remote_sensing():
count = 0
count_good = 0
for file_name in misc.all_file_names():
cfg = configuration.Configuration(file_name=file_name)
count1, count_good1 = remote_sensing1(cfg)
count += count1
count_good += count_good1
print(count, count_good, count_good/count)
exit(0)
def __init__(self, fake=False):
self.fake = fake
if fake:
self.table_name = self.fake_table_name
self.ddb = ddb.DDB(self.table_name, [('slack_uid', 'S')])
self.table = self.ddb.get_table()
self.users = {}
self.configuration = configuration.Configuration(fake=fake)
self.modified = {}
self.uc = user_created.UserCreated()
def main():
"""
Usage: python main.py [ -c config_file -s config_section ]
"""
parser = argparse.ArgumentParser()
parser.add_argument('-c', '--config_file', default="default.ini")
parser.add_argument('-s', '--config_section', default="DEFAULT")
args = parser.parse_args()
config_file = args.config_file #"default.ini"
config_section = args.config_section #"DEFAULT" # "DISJOINT" "TEST"
CONFIG = configuration.Configuration(config_file, config_section)
n_seed = int(CONFIG.get("random_seed"))
if n_seed != -1:
random.seed(n_seed) # for reproducibility
else:
n_seed = None
n_run = int(CONFIG.get("n_run"))
knn = int(CONFIG.get("knn"))
model_type = CONFIG.get("model_type")
prediction_type = CONFIG.get("prediction_type")
features = set(CONFIG.get("features").split("|"))
recalculate_similarity = CONFIG.get_boolean("recalculate_similarity")
disjoint_cv = CONFIG.get_boolean("disjoint_cv")
try:
split_both = CONFIG.get_boolean("pairwise_disjoint")
except:
split_both = False
output_file = CONFIG.get("output_file")
n_fold = int(CONFIG.get("n_fold"))
n_proportion = int(CONFIG.get("n_proportion"))
n_subset = int(CONFIG.get("n_subset")) # for faster results - subsampling
drug_disease_file = CONFIG.get("drug_disease_file")
drug_side_effect_file = CONFIG.get("drug_side_effect_file")
drug_structure_file = CONFIG.get("drug_structure_file")
drug_target_file = CONFIG.get("drug_target_file")
# Get data
data = get_data(drug_disease_file, drug_side_effect_file,
drug_structure_file, drug_target_file)
# Check prediction accuracy of ML classifier on the data set using the parameters above
check_ml(data,
n_run,
knn,
n_fold,
n_proportion,
n_subset,
model_type,
prediction_type,
features,
recalculate_similarity,
disjoint_cv,
split_both,
output_file,
model_fun=None,
n_seed=n_seed)
return
def new(self):
self.testReceptionPage.destroy()
self.configurationPage.destroy()
self.calibrationPage.destroy()
self.autrePage.destroy()
self.testReceptionPage = tR.TestReception(fenetre_principale=self)
self.testReceptionPage.pack()
self.configurationPage = conf.Configuration(fenetre_principale=self)
self.calibrationPage = calib.Calibration(fenetre_principale=self)
self.autrePage = autr.Autres(fenetre_principale=self)
def __init__(self,
dbus_conn,
object_path='/org/sugarlabs/listens/recognizer'):
dbus.service.Object.__init__(self, dbus_conn, object_path)
self._config = configuration.Configuration()
self._language_model = self._config.language_models['en'][0]
self._acoustic_model = self._config.acoustic_models['en']
self._phonetic_dictionary = self._config.phonetic_dictionaries['en']
self._language_model_param = self._config.language_models['en'][1]
self._pipeline = None
self._muted = False