def setUp(self):
self.tempdir = tempfile.mkdtemp()
self.fs = Filesystem(prefix=self.tempdir)
self.app = Application(self.fs)
self.tasks_suite = TasksSuite()
self.tasks = [Task(1, "1"), Task(2, "2"), Task(3, "3")]
self.tasks_suite.extend(self.tasks)
def __init__(self, name, run_func, humanized_template, setup_func=None):
Task.__init__(self, name)
self.driver = get_browser()
if self.driver is None:
raise NotImplementedError(E_BROWSERTASK_NO_BROWSERS % self.name)
self.run_func = run_func
self.humanized_template = humanized_template
self.setup_func = setup_func
self.result = None
def __init__(self, name, run_func, humanized_template, setup_func = None):
Task.__init__(self, name)
self.driver = get_browser()
if self.driver is None:
raise NotImplementedError(E_BROWSERTASK_NO_BROWSERS % self.name)
self.run_func = run_func
self.humanized_template = humanized_template
self.setup_func = setup_func
self.result = None
def main():
handler = logging.FileHandler(LOG_FILE_NAME)
logger.addHandler(handler)
logger.setLevel("DEBUG") # WARNING")
logger.warning('Starting rename with params: [{}]'.format(' '.join(sys.argv[1:])))
parser = argparse.ArgumentParser()
parser.add_argument('-E', '--extract-only',
dest='extract_only',
action='store_true',
help=('Extract-only mode. Returns content of PDF'),
required=False)
parser.add_argument('-H', '--hash-only',
dest='hash_only',
action='store_true',
help=('Hash-only mode. Returns MD5 hash of input files'),
required=False)
parser.add_argument('-S', '--simulate',
dest='simulate',
action='store_true',
help=('Simulation mode. Outputs actions that would be taken'),
required=False)
parser.add_argument('-v', '--verbose',
dest='verbose',
action='store_true',
help=('Verbose mode. Outputs detailed information'),
required=False)
parser.add_argument('-q', '--quiet',
dest='quiet',
action='store_true',
help=('Quiet mode. Produces no console output'),
required=False)
parser.add_argument('location',
# dest='target',
action='store',
help='File or folder to process',
# required=True,
type=str)
try:
# TODO: next step: decouple the CLI arguments from the Task class. Possibly with a TaskBuilder?
task = Task(parser, logger)
task.execute()
except Exception as e:
logger.exception(e)
raise e
def _find_task(self) -> Tuple[Optional[Task], Optional[int]]:
file = open(self.file_name, 'r')
str_tasks = file.readlines()
file.close()
for index, task_str in enumerate(str_tasks):
task_dict = json.loads(task_str, object_hook=json_util.object_hook)
task = Task(**task_dict)
task.type = TaskType(task.type)
if task.type != self.task_type:
continue
return task, index
return None, None
def test_add_to_not_active_tasks_suite(self):
task = Task(1, "task")
self.cli.add(task)
self.cli.status()
output = self.stream.getvalue()
self.assertIn(task.description, output)
self.assertTrue(self.app.is_tasks_suite_active())
def test_add(self):
self.app.start_tasks_suite(self.tasks_suite)
task = Task(1, "task")
self.cli.add(task)
self.cli.status()
output = self.stream.getvalue()
self.assertIn(task.description, output)
def runMcl(matrixPath, inflation, workingDir, outputPath):
tempPath = os.path.join(os.path.dirname(outputPath), "temp_{}".format(os.path.basename(outputPath)))
args = [Configs.mclPath, matrixPath, "--abc", "-o", tempPath]
if inflation is not None:
args.extend(["-I", str(inflation)])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {tempPath : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
def runClustalOmegaGuideTree(fastaPath, workingDir, outputPath, threads = 1):
tempPath = os.path.join(os.path.dirname(outputPath), "temp_{}".format(os.path.basename(outputPath)))
args = [Configs.clustalPath]
args.extend(["-i", fastaPath, "--max-hmm-iterations=-1", "--guidetree-out={}".format(tempPath)])
args.extend(["--threads={}".format(threads)])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {tempPath : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
def start_onmyoji(self):
section = self.ui.tabWidget.currentIndex()
# 读取配置
self.get_conf(section)
if section == 0:
# 御魂
if self.ui.mitama_single.isChecked():
# 单刷
self.fight = SingleFight()
elif self.ui.mitama_driver.isChecked():
# 司机
self.fight = DriverFighter()
elif self.ui.mitama_passenger.isChecked():
# 乘客
self.fight = FighterPassenger()
elif self.ui.mitama_dual.isChecked():
# 双开
self.fight = DualFighter()
elif section == 1:
# 探索
self.fight = ExploreFight()
elif section == 2:
# 百鬼夜行
self.fight = Ghost()
elif section == 3:
# 结界突破
if self.ui.individual.isChecked():
# 个人突破
self.fight = Breakthrough()
elif self.ui.shack.isChecked():
# 个人突破
self.fight = ShackBreakthrough()
elif section == 4:
self.fight = Task()
task = threading.Thread(target=self.fight.start)
task.start()
def setUp(self):
self.tempdir = tempfile.mkdtemp()
self.fs = Filesystem(prefix=self.tempdir)
self.app = Application(self.fs)
self.stream = StringIO()
self.cli = CLI(self.app, self.stream)
self.task = Task(30, "desc")
self.tasks_suite = TasksSuite()
self.tasks_suite.append(self.task)
def runMafftGuideTree(fastaPath, workingDir, outputPath, threads = 1):
tempPath = os.path.join(os.path.dirname(outputPath), "temp_{}".format(os.path.basename(outputPath)))
treeFile = os.path.join(os.path.dirname(fastaPath), "{}.tree".format(os.path.basename(fastaPath)))
args = [Configs.mafftPath, "--retree", "0", "--treeout", "--parttree",
"--quiet", "--thread", str(threads), "--anysymbol"]
args.extend(["--partsize", "1000"])
args.extend([fastaPath, ">", tempPath])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {treeFile : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
def runMafft(fastaPath, subtablePath, workingDir, outputPath, threads = 1):
tempPath = os.path.join(os.path.dirname(outputPath), "temp_{}".format(os.path.basename(outputPath)))
args = [Configs.mafftPath, "--localpair", "--maxiterate", "1000", "--ep", "0.123",
"--quiet", "--thread", str(threads), "--anysymbol"]
if subtablePath is not None:
args.extend(["--merge", subtablePath])
args.extend([fastaPath, ">", tempPath])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {tempPath : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
def test_execute_add(self):
minutes = 1
description = "task"
task = Task(minutes, description)
args = ["", "add", str(minutes), description]
self.cli.execute(args)
self.cli.status()
output = self.stream.getvalue()
self.assertIn(task.description, output)
def create_task(self, task_type: TaskType, content: Any):
content_str = self.dump_content(content)
task = asdict(Task(type=task_type,
content=content_str,
source_ip=self._get_ip_address(),
creation_time=datetime.utcnow()))
file = open(self.file_name, 'a')
self._log_task(task)
file.write(f'{json.dumps(task, default=json_util.default)}\n')
file.close()
def runRaxmlNg(fastaFilePath, workingDir, outputPath, threads = 8):
# raxml-ng --msa prim.phy --model GTR+G --prefix T4 --threads 2 --seed 2 --tree pars{25},rand{25}
baseName = os.path.basename(outputPath).replace(".","")
raxmlFile = os.path.join(workingDir, "{}.raxml.bestTree".format(baseName))
seed = random.randint(1, 1000000)
args = [Configs.raxmlPath,
"--msa", fastaFilePath,
"--prefix", baseName,
"--threads", str(threads),
"--seed", str(seed)]
if Configs.inferDataType(fastaFilePath) == "protein":
args.extend(["--model", "LG+G"])
else:
args.extend(["--model", "GTR+G"])
args.extend(["--tree", "pars{{{}}}".format(1)])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {raxmlFile : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
def runFastTree(fastaFilePath, workingDir, outputPath, mode = "normal", intree = None):
tempPath = os.path.join(os.path.dirname(outputPath), "temp_{}".format(os.path.basename(outputPath)))
args = [Configs.fasttreePath]
if Configs.inferDataType(fastaFilePath) == "protein":
args.extend(["-lg"])
else:
args.extend(["-nt", "-gtr"])
if intree is not None:
args.extend(["-intree", intree])
if mode == "fast":
args.extend(["-fastest", "-nosupport"])
elif mode == "faster":
args.extend(["-fastest", "-nosupport", "-mlnni", "4" ])
elif mode == "noml":
args.extend(["-fastest", "-nosupport", "-noml"])
args.extend([fastaFilePath, ">", tempPath])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {tempPath : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
def getRemoteTask():
from tasks.task import Task
config = getConfig()
r = requests.get(config["centerBaseURL"] + "/nodes/" + config["id"] +
"/tasks")
data = json.loads(r.content)
tasks = data["tasks"]
nexttask = None
for task in tasks:
if task["status"] < 2:
nexttask = task
task = nexttask
if not task:
return None
id = task["id"]
range = long2ip(task["startIP"]) + "-" + long2ip(task["endIP"])
if task["startIP"] == task["endIP"]:
range = long2ip(task["startIP"])
startPort = task["startPort"]
endPort = task["endPort"]
plugins = task["plugins"]
for plugin in plugins:
r = requests.get(config["centerBaseURL"] + "/plugins/" + plugin)
plugindata = r.content
f = open(path.join(pluginsdir, plugin + ".py"), "w", encoding="utf-8")
f.write(plugindata.decode())
f.close()
task = Task(id, range, startPort, endPort, plugins)
return task
def __init__(self, init_pose=None, init_velocities=None, init_angle_velocities=None, runtime=5., target_pos=None):
Task.__init__(self, init_pose=init_pose, init_velocities=init_velocities,
init_angle_velocities=init_angle_velocities, runtime=runtime, target_pos=target_pos)
position = self.sim.pose[0:3]
self.init_distance = self._get_distance(position)
def __init__(self, fs, inputs):
Task.__init__(self, fs)
self.inputs = inputs
self._parents = self.create_parents()
self.path = os.path.join(self.fs, self.name())
def __init__(self, name, run_func, humanized_template, setup_func=None):
Task.__init__(self, name)
self.run_func = run_func
self.humanized_template = humanized_template
self.setup_func = setup_func
self.result = None
def runHmmSearch(hmmModelPath, fragPath, workingDir, outputPath):
tempPath = os.path.join(os.path.dirname(outputPath), "temp_{}".format(os.path.basename(outputPath)))
args = [Configs.hmmsearchPath,"--noali", "--cpu", "1", "-o", tempPath, "-E", "99999999", "--max"]
args.extend([hmmModelPath, fragPath])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {tempPath : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
class MyMainWindow(QMainWindow):
def __init__(self, parent=None):
super(MyMainWindow, self).__init__(parent)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.ui.textEdit.ensureCursorVisible()
h = GuiLogger()
h.edit = self.ui.textEdit
logger = logging.getLogger()
logger.setLevel(logging.INFO)
logger.addHandler(h)
def set_conf(self, conf, section):
'''
设置参数至配置文件
'''
# 一般参数
conf.set('watchdog', 'watchdog_enable',
str(self.ui.checkBox.isChecked()))
conf.set('watchdog', 'max_win_time', str(self.ui.lineEdit.text()))
conf.set('watchdog', 'max_op_time', str(self.ui.lineEdit_2.text()))
# 御魂参数
if section == 0 or section == 4:
# 御魂
conf.set('mitama', 'mitama_click_partner_left',
str(self.ui.mitama_click_partner_left.isChecked()))
conf.set('mitama', 'mitama_click_partner_right',
str(self.ui.mitama_click_partner_right.isChecked()))
# 探索参数
if section == 1 or section == 4:
# 探索
conf.set('explore', 'fight_boss_enable',
str(self.ui.checkBox_2.isChecked()))
conf.set('explore', 'tupo_enable',
str(self.ui.checkBox_4.isChecked()))
conf.set('explore', 'slide_shikigami',
str(self.ui.checkBox_3.isChecked()))
conf.set('explore', 'slide_shikigami_progress',
str(self.ui.horizontalSlider.value()))
conf.set('explore', 'zhunbei_delay',
str(self.ui.lineEdit_3.text()))
# 百鬼夜行参数
if section == 2 or section == 4:
pass
# 结界突破参数
if section == 3 or section == 4:
pass
# 专项任务参数
if section == 4:
conf.set('task', 'tansuo', str(self.ui.lineEdit_4.text()))
conf.set('task', 'yuhun', str(self.ui.lineEdit_5.text()))
conf.set('task', 'juexing', str(self.ui.lineEdit_6.text()))
conf.set('task', 'tupo', str(self.ui.lineEdit_7.text()))
# 御魂
conf.set('mitama', 'mitama_click_partner_left', 'True')
conf.set('mitama', 'mitama_click_partner_right', 'False')
# 探索
conf.set('explore', 'fight_boss_enable', 'True')
conf.set('explore', 'tupo_enable', 'False')
def get_conf(self, section):
conf = configparser.ConfigParser()
# 读取配置文件
conf.read('conf.ini', encoding="utf-8")
# 修改配置
try:
self.set_conf(conf, section)
except:
conf.add_section('watchdog')
conf.add_section('explore')
conf.add_section('mitama')
conf.add_section('task')
self.set_conf(conf, section)
# 保存配置文件
with open('conf.ini', 'w') as configfile:
conf.write(configfile)
def start_onmyoji(self):
section = self.ui.tabWidget.currentIndex()
# 读取配置
self.get_conf(section)
if section == 0:
# 御魂
if self.ui.mitama_single.isChecked():
# 单刷
self.fight = SingleFight()
elif self.ui.mitama_driver.isChecked():
# 司机
self.fight = DriverFighter()
elif self.ui.mitama_passenger.isChecked():
# 乘客
self.fight = FighterPassenger()
elif self.ui.mitama_dual.isChecked():
# 双开
self.fight = DualFighter()
elif section == 1:
# 探索
self.fight = ExploreFight()
elif section == 2:
# 百鬼夜行
self.fight = Ghost()
elif section == 3:
# 结界突破
if self.ui.individual.isChecked():
# 个人突破
self.fight = Breakthrough()
elif self.ui.shack.isChecked():
# 个人突破
self.fight = ShackBreakthrough()
elif section == 4:
self.fight = Task()
task = threading.Thread(target=self.fight.start)
task.start()
def stop_onmyoji(self):
try:
self.fight.deactivate()
except:
pass
def runHmmBuild(alignmentPath, workingDir, outputPath):
tempPath = os.path.join(os.path.dirname(outputPath), "temp_{}".format(os.path.basename(outputPath)))
args = [Configs.hmmbuildPath,'--ere', '0.59', "--cpu", "1"]
args.extend(["--symfrac", "0.0", "--informat", "afa", tempPath, alignmentPath])
taskArgs = {"command" : subprocess.list2cmdline(args), "fileCopyMap" : {tempPath : outputPath}, "workingDir" : workingDir}
return Task(taskType = "runCommand", outputFile = outputPath, taskArgs = taskArgs)
def __init__(self, fs, inputs, density=512):
Task.__init__(self, fs)
self.inputs = inputs
self.inputs = (*inputs, density)
self._parents = self.create_parents()
self.path = os.path.join(self.fs, self.name() + ".npy")
def main():
in_args = get_input_args()
exportPath = './data/'
if not os.path.exists(exportPath):
os.makedirs(exportPath)
# z axis is up
init_pose = np.array([0.0, 0.0, 1.0, 0.0, 0.0, 0.0])
target_pos = np.array([0.0, 0.0, 10.0])
task = Task(init_pose=init_pose, target_pos=target_pos, runtime=15.0)
#agent = PolicySearch_Agent(task)
#agent = Basic_Agent(task)
agent = DDPG_Agent(task)
# before training
resultsAll = []
high_score = -1000000.0
low_score = 1000000.0
# do this in each episode
for i_episode in range(1, in_args.num_episodes + 1):
# start a new episode
state = agent.reset_episode()
score = 0
episode_results = {
'time': [],
'x': [],
'y': [],
'z': [],
'phi': [],
'theta': [],
'psi': [],
'vx': [],
'vy': [],
'vz': [],
'reward': [],
}
while True:
action = agent.act(state)
next_state, reward, done = task.step(action)
agent.step(action, reward, next_state, done)
state = next_state
score += reward
high_score = max(high_score, score)
low_score = min(low_score, score)
# track the results for offline analysis
episode_results['time'].append(task.sim.time)
episode_results['x'].append(state[0])
episode_results['y'].append(state[1])
episode_results['z'].append(state[2])
episode_results['phi'].append(state[3])
episode_results['theta'].append(state[4])
episode_results['psi'].append(state[5])
episode_results['vx'].append(state[6])
episode_results['vy'].append(state[7])
episode_results['vz'].append(state[8])
episode_results['reward'].append(reward)
if done:
print(
"\rEpisode = {:4d}, score = {:7.3f}, low score = {:7.3f}, high score = {:7.3f}"
.format(i_episode, score, low_score, high_score),
end="")
break
resultsAll.append(episode_results)
sys.stdout.flush()
# save results for later analysis
with open("{}results0.bin".format(exportPath), 'wb') as pickleFile:
pickle.dump(resultsAll, pickleFile)
print("\n")
