def run_kmgdgis3D():
time.sleep(3)
exe = os.path.join(module_path().replace('\\script', '\\bin'), 'kmgdgis3D.exe')
if hasattr(sys, "frozen"):
exe = os.path.join(module_path(), 'kmgdgis3D.exe')
log('launching [%s]...' % exe)
p = Popen(exe)
def modify_config_js():
path = os.path.join(module_path(), '..', 'data', 'www', 'js', 'config.js')
l = []
with open(path) as f:
for i in f.readlines():
if len(i.strip())>14 and i.strip()[:14] == 'var g_app_root':
root = os.path.join(module_path(), '..','data', 'www')
root = root.replace('\\','/')
g_app_root = 'var g_app_root = "file:///' + root + '";\r\n'
l.append(g_app_root)
elif len(i.strip())>20 and i.strip()[:20] == 'var g_local_tile_url':
g_local_tile_path = 'var g_local_tile_url = "%s";\r\n' % gConfig['map_local_tiles_url']
l.append(g_local_tile_path)
elif "var g_default_basemap" in i:
if len(gConfig['map_local_tiles_url'])>0:
l.append("var g_default_basemap = 'basemap_esrilocal';\r\n")
else:
l.append("var g_default_basemap = 'basemap_googlesat';\r\n")
elif "'basemap_esrilocal':'本地地图'," in i:
if len(gConfig['map_local_tiles_url'])>0:
l.append("\t'basemap_esrilocal':'本地地图',\r\n")
else:
l.append("\t//'basemap_esrilocal':'本地地图',\r\n")
else:
l.append(i)
s = ''
for i in l:
s += dec(i)
#print(s)
with open(path, 'w') as f:
f.write(enc(s))
def Activated(self):
# So we can open the "Open File" dialog
mw = FreeCADGui.getMainWindow()
# Try to keep track of the previous path used to open as a convenience to the user
if self.previousPath is None:
# Start off defaulting to the Examples directory
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, 'Examples')
self.previousPath = exs_dir_path
filename = QtGui.QFileDialog.getOpenFileName(
mw, mw.tr("Open CadQuery Script"), self.previousPath,
mw.tr("CadQuery Files (*.py)"))
# Make sure the user didn't click cancel
if filename[0]:
self.previousPath = filename[0]
# Append this script's directory to sys.path
sys.path.append(os.path.dirname(filename[0]))
# We've created a library that FreeCAD can use as well to open CQ files
ImportCQ.open(filename[0])
def Activated(self):
import os
try:
from . import module_locator
except:
import module_locator
try:
from CadQuery.CQGui import ImportCQ
except:
from CQGui import ImportCQ
module_base_path = module_locator.module_path()
import cadquery
from PySide import QtGui, QtCore
msg = QtGui.QApplication.translate(
"cqCodeWidget",
"CadQuery " + cadquery.__version__ + "\r\n"
"CadQuery is a parametric scripting API "
"for creating and traversing CAD models\r\n"
"Author: David Cowden\r\n"
"License: Apache-2.0\r\n"
"Website: https://github.com/dcowden/cadquery\r\n",
None)
FreeCAD.Console.PrintMessage(msg)
#Getting the main window will allow us to start setting things up the way we want
mw = FreeCADGui.getMainWindow()
dockWidgets = mw.findChildren(QtGui.QDockWidget)
for widget in dockWidgets:
if widget.objectName() == "Report view":
widget.setVisible(True)
def __init__(self, gall_url, id):
self.gall_list = {}
self.kGALLERY_URL = gall_url
self.kLOCATION = id
self.start_urls = [
"http://gall.dcinside.com/board/view/?id=game_classic&no=6329821&page=1"
]
self.app_urls = {}
# find out current module(exeuctable) path and set to temporary download dir
# where we'll watch
collector_current_path = module_locator.module_path()
temp_download_dir = os.path.join(collector_current_path, 'dn_' + id)
if not os.path.exists(temp_download_dir):
logging.info("make a download dir : %s", temp_download_dir)
os.makedirs(temp_download_dir)
self.browser_options = {}
self.browser_options['download_folder'] = os.path.abspath(temp_download_dir)
# option --browser firefox
# option -c -f -???
# on linux, firefox causes an error when clicking links with delays.
self.web_driver = self.init_selenium_driver("chrome", self.browser_options)
def Activated(self):
FreeCAD.Console.PrintMessage(self.exFile + "\r\n")
#So we can open the "Open File" dialog
mw = FreeCADGui.getMainWindow()
#Start off defaulting to the Examples directory
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, 'Examples')
#We need to close any file that's already open in the editor window
CadQueryCloseScript().Activated()
#Append this script's directory to sys.path
sys.path.append(os.path.dirname(exs_dir_path))
#We've created a library that FreeCAD can use as well to open CQ files
ImportCQ.open(os.path.join(exs_dir_path, self.exFile))
docname = os.path.splitext(os.path.basename(self.exFile))[0]
FreeCAD.newDocument(docname)
#Execute the script
CadQueryExecuteScript().Activated()
#Get a nice view of our model
FreeCADGui.activeDocument().activeView().viewAxometric()
FreeCADGui.SendMsgToActiveView("ViewFit")
def show_help(self):
""" Purpose: This is called when the user selects the 'Help Text' menubar option. It opens the README.html file
in their default browser. If the file doesn't exist it opens the github readme page instead.
"""
# Grab the directory where the script is running.
readme = module_path()
# Determine our OS, attach the README.html file to the path, and open that file.
if sys.platform.startswith('darwin'):
readme += "/README.html"
if os.path.isfile(readme):
subprocess.call(('open', readme))
else:
try:
webbrowser.open('https://github.com/nprintz/jaide')
except webbrowser.Error:
pass
elif os.name == 'nt':
readme += "\\README.html"
if os.path.isfile(readme):
os.startfile(readme) # this works on windows, not sure why pylint shows an error.
else:
try:
webbrowser.open('https://github.com/nprintz/jaide')
except webbrowser.Error:
pass
elif os.name == 'posix':
readme += "/README.html"
if os.path.isfile(readme):
subprocess.call(('xdg-open', readme))
else:
try:
webbrowser.open('https://github.com/nprintz/jaide')
except webbrowser.Error:
pass
def __init__(self, gall_url, id):
self.gall_list = {}
self.kGALLERY_URL = gall_url
self.gallery_id = id
self.list_url = gall_url + id
self.view_url = self.list_url
self.app_urls = {}
# find out current module(exeuctable) path and set to temporary download dir
# where we'll watch
collector_current_path = module_locator.module_path()
temp_download_dir = os.path.join(collector_current_path, 'dn_' + id)
if not os.path.exists(temp_download_dir):
logging.info("make a download dir : %s", temp_download_dir)
os.makedirs(temp_download_dir)
self.browser_options = {}
self.browser_options['download_folder'] = os.path.abspath(
temp_download_dir)
# option --browser firefox
# option -c -f -???
# on linux, firefox causes an error when clicking links with delays.
self.web_driver = self.init_selenium_driver("chrome",
self.browser_options)
def show_examples(self):
""" Purpose: This method opens the example folder for the user, or open the github page for the example folder.
"""
# Grab the directory that the script is running from.
examples = module_path()
# Determin our OS, attach the README.html file to the path, and open that file.
if sys.platform.startswith('darwin'):
examples += "/examples/"
if os.path.isdir(examples):
subprocess.call(('open', examples))
else:
try:
webbrowser.open('https://github.com/nprintz/jaide/examples')
except webbrowser.Error:
pass
elif os.name == 'nt':
examples += "\\examples\\"
if os.path.isdir(examples):
os.startfile(examples) # this works on windows, not sure why pylint shows an error.
else:
try:
webbrowser.open('https://github.com/nprintz/jaide/examples')
except webbrowser.Error:
pass
elif os.name == 'posix':
examples += "/examples/"
if os.path.isdir(examples):
subprocess.call(('xdg-open', examples))
else:
try:
webbrowser.open('https://github.com/nprintz/jaide/examples')
except webbrowser.Error:
pass
def Activated(self):
FreeCAD.Console.PrintMessage(self.exFile + "\r\n")
#So we can open the "Open File" dialog
mw = FreeCADGui.getMainWindow()
#Start off defaulting to the Examples directory
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, 'Examples')
#We need to close any file that's already open in the editor window
CadQueryCloseScript().Activated()
#Append this script's directory to sys.path
sys.path.append(os.path.dirname(exs_dir_path))
#We've created a library that FreeCAD can use as well to open CQ files
ImportCQ.open(os.path.join(exs_dir_path, self.exFile))
docname = os.path.splitext(os.path.basename(self.exFile))[0]
FreeCAD.newDocument(docname)
#Execute the script
CadQueryExecuteScript().Activated()
#Get a nice view of our model
FreeCADGui.activeDocument().activeView().viewAxometric()
FreeCADGui.SendMsgToActiveView("ViewFit")
def Activated(self):
import os
try:
from . import module_locator
except:
import module_locator
try:
from CadQuery.CQGui import ImportCQ
except:
from CQGui import ImportCQ
module_base_path = module_locator.module_path()
import cadquery
from PySide import QtGui, QtCore
msg = QtGui.QApplication.translate(
"cqCodeWidget",
"CadQuery " + cadquery.__version__ + "\r\n"
"CadQuery is a parametric scripting API "
"for creating and traversing CAD models\r\n"
"Author: David Cowden\r\n"
"License: Apache-2.0\r\n"
"Website: https://github.com/dcowden/cadquery\r\n",
None)
FreeCAD.Console.PrintMessage(msg)
#Getting the main window will allow us to start setting things up the way we want
mw = FreeCADGui.getMainWindow()
dockWidgets = mw.findChildren(QtGui.QDockWidget)
for widget in dockWidgets:
if widget.objectName() == "Report view":
widget.setVisible(True)
def Arc2GeoJsonTunnel(name):
path = os.path.join(module_path(), JSON_DIR, 'arcjson_tunnel_%s.json' % name)
arcjson = None
if os.path.exists(path):
with open(path) as f:
arcjson = json.loads(f.read())
if arcjson:
offsetx, offsety = CalcOffset(name)
obj = {}
obj['type'] = 'FeatureCollection'
obj['features'] = []
for feature in arcjson['features']:
for path in feature['geometry']['paths']:
o = {}
o['type'] = 'Feature'
o['properties'] = {}
o['geometry'] = {}
o['geometry']['type'] = 'LineString'
o['geometry']['coordinates'] = []
for point in path:
lng, lat = ToGeographic(point[0] + offsetx, point[1] + offsety)
o['geometry']['coordinates'].append([lng, lat])
obj['features'].append(o)
path = '%s/geojson_tunnel_%s.json' % (JSON_DIR, name)
with open(path, 'w') as f:
f.write(json.dumps(obj, ensure_ascii=True, indent=4) + '\n')
def Activated(self):
module_base_path = module_locator.module_path()
templ_dir_path = os.path.join(module_base_path, 'Templates')
# Use the library that FreeCAD can use as well to open CQ files
ImportCQ.open(os.path.join(templ_dir_path, 'script_template.py'))
FreeCAD.Console.PrintMessage("Please save this template file as another name before creating any others.\r\n")
def Activated(self):
module_base_path = module_locator.module_path()
templ_dir_path = os.path.join(module_base_path, 'Templates')
# Use the library that FreeCAD can use as well to open CQ files
ImportCQ.open(os.path.join(templ_dir_path, 'script_template.py'))
FreeCAD.Console.PrintMessage("Please save this template file as another name before creating any others.\r\n")
def get_backlinks(onion_url):
""" Call backlink tester and return the number of backlinks. """
my_path = module_locator.module_path()
backlink_tool = my_path + "/backlinkers.py"
args = ["python", backlink_tool, "-c", onion_url]
proc = subprocess.Popen(args, stdout=subprocess.PIPE)
count = int(proc.communicate()[0])
return count
def GetDeviceList():
ret = []
path = os.path.join(module_path(), JSON_DIR)
for i in os.listdir(path):
p = os.path.join(path, i)
if os.path.isfile(p) and 'arcjson_device_' in i:
ret.append(i.replace('arcjson_device_', '').replace('.json', ''))
return ret
def get_backlinks(onion_url):
""" Call backlink tester and return the number of backlinks. """
my_path = module_locator.module_path()
backlink_tool = my_path + "/backlinkers.py"
args = ["python", backlink_tool, "-c", onion_url] # TODO: use the new backlinker spider instead?
proc = subprocess.Popen(args, stdout=subprocess.PIPE)
count = int(proc.communicate()[0])
return count
def save_popularity_data(data, onion_id):
""" Save the popularity data to """
my_path = module_locator.module_path()
document_dir = my_path.replace("/tools", "/popularity_stats/")
document_dir = document_dir + datetime.datetime.now().strftime("%y-%m-%d")
if not os.path.exists(document_dir):
os.makedirs(document_dir)
pretty_data = valid_pretty_json(data)
text2file(pretty_data, document_dir + "/" + onion_id + ".json")
def main():
"""Main function."""
my_path = module_locator.module_path()
json_data_dir = my_path.replace("/tools", "/tor2web_stats/")
onions_data = {}
for filename in os.listdir(json_data_dir):
if filename.endswith(".json"):
json_file = json_data_dir + filename
json_data = open(json_file)
day_data = json.load(json_data)
json_data.close()
time_stamp = day_data["date"].encode("ascii", "ignore")
for onion_data in day_data["hidden_services"]:
onion = onion_data["id"].lower()
access_count = int(onion_data["access_count"])
try:
found = False
last_time_stamp = onions_data[onion]#[-1].keys()[0]
for o in onions_data[onion]:
if o.keys()[0] == time_stamp:
o[time_stamp] = o[time_stamp] + access_count
found = True
break
if not found:
onions_data[onion].append({time_stamp: access_count})
except:
onions_data[onion] = []
onions_data[onion].append({time_stamp: access_count})
static_log = my_path.replace("/tools", "/ahmia/static/log/onion_site_history/")
onions = []
# Filter banned domains, get the list first
r = requests.get('https://127.0.0.1/banneddomains.txt', verify=False)
text = r.text.encode('ascii')
text = text.replace("http://", "")
text = text.replace("https://", "")
text = text.replace(".onion/", "")
ban_list = text.split("\n")
# Print to files
for onion in onions_data.keys():
data = onions_data[onion]
# Only show those onions that have over 100 active days
# Filter out banned domains
if len(data) > 100 and not onion in ban_list:
onions.append(onion)
if not onion in ban_list:
data = sorted(data, key=getKey)
pretty = json.dumps(data, indent=4, ensure_ascii=False)
file = open(static_log + onion + ".json", "w")
file.write(pretty+"\n")
file.close()
onions.sort()
pretty = json.dumps(onions, indent=4, sort_keys=True, ensure_ascii=False)
file = open(static_log + "onions.json", "w")
file.write(pretty+"\n")
file.close()
def Activated(self):
#We need to close any file that's already open in the editor window
CadQueryCloseScript().Activated()
module_base_path = module_locator.module_path()
templ_dir_path = os.path.join(module_base_path, 'Templates')
#Use the library that FreeCAD can use as well to open CQ files
ImportCQ.open(os.path.join(templ_dir_path, 'script_template.py'))
def Activated(self):
#We need to close any file that's already open in the editor window
CadQueryCloseScript().Activated()
module_base_path = module_locator.module_path()
templ_dir_path = os.path.join(module_base_path, 'Templates')
#Use the library that FreeCAD can use as well to open CQ files
ImportCQ.open(os.path.join(templ_dir_path, 'script_template.py'))
def save_popularity_data(data, onion_id):
""" Save the popularity data to """
my_path = module_locator.module_path()
document_dir = my_path.replace("/tools", "/popularity_stats/")
document_dir = document_dir + datetime.datetime.now().strftime("%y-%m-%d")
if not os.path.exists(document_dir):
os.makedirs(document_dir)
pretty_data = valid_pretty_json(data)
text2file(pretty_data, document_dir + "/" + onion_id + ".json")
def loader(tor2web_nodes):
"""Load visited domains information from tor2web nodes."""
my_path = module_locator.module_path()
filename = my_path.replace("/tools", "/ahmia/static/log/")
for node in tor2web_nodes:
print "\n Trying download from the %s \n" % node
md5list = get_md5list("abcd." + node)
if md5list:
filename = filename + node + "_md5filterlist.txt"
text2file(md5list, filename)
def loader(tor2web_nodes):
"""Load visited domains information from tor2web nodes."""
my_path = module_locator.module_path()
filename = my_path.replace("/tools", "/ahmia/static/log/")
for node in tor2web_nodes:
print "\n Trying download from the %s \n" % node
md5list = get_md5list("abcd." + node)
if md5list:
filename = filename + node + "_md5filterlist.txt"
text2file(md5list, filename)
def init_tunnel_name_file():
ret = {}
d = os.path.join(module_path(), DATA_DOCS_DIR)
path = os.path.join(d, gConfig['xls_tunnel_main'])
book = xlrd.open_workbook(path)
sheet = book.sheet_by_name(u'隧道文件对应')
row, col = find_boundary(sheet)
for i in range(row+1):
ret[sheet.cell_value(i,0)] = sheet.cell_value(i,1)
return ret
def CalcOffset(name):
offsetx, offsety = 0, 0
path = os.path.join(module_path(), JSON_DIR, 'tunnel_boundry_%s.json' % name)
boundry = None
if os.path.exists(path):
with open(path) as f:
boundry = json.loads(f.read())
if boundry:
mercstartx, mercstarty = ToWebMercator(boundry['lnglat']['startx'], boundry['lnglat']['starty'])
offsetx, offsety = mercstartx - boundry['dwg_mercator']['startx'], mercstarty - boundry['dwg_mercator']['starty']
return offsetx, offsety
def Cad2Geodatabase(dwgfile, reference_scale=2000):
#import arcpy
#from arcpy import env
PRJWGS1984 = arcpy.SpatialReference("WGS 1984")
PRJWEBMERCATOR = arcpy.SpatialReference("WGS 1984 Web Mercator (Auxiliary Sphere)")
CreateTunnelGDB()
ws = os.path.join(module_path(), WORKSPACE)
if not os.path.exists(ws):
os.mkdir(ws)
env.workspace = ws
input_cad_dataset = os.path.join(module_path(), DWG_DIR, dwgfile)
out_tmp_gdb_path = os.path.join(ws, "tmp.gdb")
if not os.path.exists(out_tmp_gdb_path):
arcpy.CreateFileGDB_management(ws, u"tmp.gdb")
out_tmp_dataset_name = dwgfile.replace('.dwg', '')
rs = str(reference_scale)
#ws = '%s/tmp.gdb' % WORKSPACE
DeleteExist(out_tmp_gdb_path, out_tmp_dataset_name)
arcpy.CADToGeodatabase_conversion(input_cad_dataset, out_tmp_gdb_path, out_tmp_dataset_name, rs, PRJWEBMERCATOR)
def GetADBExecutablePath():
arr = []
if '/' in gConfig['android']['sdk_root']:
arr = gConfig['android']['sdk_root'].split('/')
elif '\\' in gConfig['android']['sdk_root']:
arr = gConfig['android']['sdk_root'].split('\\')
adb = module_path()
if len(arr)>0:
adb = os.path.join(adb, *arr)
adb = os.path.join(adb, 'platform-tools', 'adb.exe')
return adb
def main():
"""Main function."""
my_path = module_locator.module_path()
access_file_path = my_path.replace("/tools", "/error/access.log")
json_pretty = analyser(access_file_path)
filename = my_path.replace("/tools", "/ahmia/static/log/access.json")
text2file(json_pretty, filename)
access_file_path = my_path.replace("/tools", "/error/hs_access.log")
json_pretty = analyser(access_file_path)
filename = my_path.replace("/tools", "/ahmia/static/log/hs_access.json")
text2file(json_pretty, filename)
def main():
"""Main function."""
my_path = module_locator.module_path()
access_file_path = my_path.replace("/tools", "/error/access.log")
json_pretty = analyser(access_file_path)
filename = my_path.replace("/tools", "/ahmia/static/log/access.json")
text2file(json_pretty, filename)
access_file_path = my_path.replace("/tools", "/error/hs_access.log")
json_pretty = analyser(access_file_path)
filename = my_path.replace("/tools", "/ahmia/static/log/hs_access.json")
text2file(json_pretty, filename)
def main():
"""Main function."""
my_path = module_locator.module_path()
document_dir = my_path.replace("/tools", "/tor2web_stats/")
timestamp = datetime.datetime.now().strftime("%y-%m-%d")
timestamp = "_" + timestamp + "-"
# Use Tor2web stats
for filename in os.listdir(document_dir):
if not filename.endswith(".json"):
continue
if timestamp in filename:
analyser(document_dir + filename)
def main():
"""Main function."""
my_path = module_locator.module_path()
document_dir = my_path.replace("/tools", "/tor2web_stats/")
timestamp = datetime.datetime.now().strftime("%y-%m-%d")
timestamp = "_" + timestamp + "-"
# Use Tor2web stats
for filename in os.listdir(document_dir):
if not filename.endswith(".json"):
continue
if timestamp in filename:
analyser(document_dir+filename)
def open(filename):
#All of the CQGui.* calls in the Python console break after opening if we don't do this
FreeCADGui.doCommand("import FreeCADGui as CQGui")
# Make sure that we enforce a specific version (2.7) of the Python interpreter
ver = hex(sys.hexversion)
interpreter = "python%s.%s" % (ver[2], ver[4]) # => 'python2.7'
# The extra version numbers won't work on Windows
if sys.platform.startswith('win'):
interpreter = 'python'
# Set up so that we can import from our embedded packages
module_base_path = module_locator.module_path()
libs_dir_path = os.path.join(module_base_path, 'Libs')
# Make sure we get the right libs under the FreeCAD installation
fc_base_path = os.path.dirname(os.path.dirname(module_base_path))
fc_lib_path = os.path.join(fc_base_path, 'lib')
#Getting the main window will allow us to find the children we need to work with
mw = FreeCADGui.getMainWindow()
# Grab just the file name from the path/file that's being executed
docname = os.path.basename(filename)
# Pull the font size from the FreeCAD-stored settings
fontSize = FreeCAD.ParamGet("User parameter:BaseApp/Preferences/Mod/cadquery-freecad-module").GetInt("fontSize")
# Set up the code editor
codePane = CodeEditor()
codePane.setFont(QtGui.QFont('SansSerif', fontSize))
codePane.setObjectName("cqCodePane_" + os.path.splitext(os.path.basename(filename))[0])
mdi = mw.findChild(QtGui.QMdiArea)
# add a code editor widget to the mdi area
sub = mdi.addSubWindow(codePane)
sub.setWindowTitle(docname)
sub.setWindowIcon(QtGui.QIcon(':/icons/applications-python.svg'))
sub.show()
mw.update()
#Pull the text of the CQ script file into our code pane
codePane.open(filename)
msg = QtGui.QApplication.translate(
"cqCodeWidget",
"Opened ",
None)
FreeCAD.Console.PrintMessage(msg + filename + "\r\n")
return
def __init__(self, output_dir, tmp_dir, resources_dir, argv):
self.output_dir = output_dir
self.tmp_dir = tmp_dir
self.resources_dir = resources_dir
program_settings = Settings()
program_path = module_locator.module_path()
program_settings.load_settings(
"%s/%s/%s" % (program_path, "Resources", "settings.ini"))
self.application_name = program_settings.read_setting(
"application_name")
self.php_version = program_settings.read_setting("php_version")
def ListExamples():
import os
import module_locator
dirs = []
# List all of the example files in an order that makes sense
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, 'Examples')
dirs = os.listdir(exs_dir_path)
dirs.sort()
return dirs
def Arc2GeoJsonDevice(name):
path = os.path.join(module_path(), JSON_DIR, 'arcjson_device_%s.json' % name)
arcjson = None
if os.path.exists(path):
with open(path) as f:
arcjson = json.loads(f.read())
if arcjson:
offsetx, offsety = CalcOffset(name)
obj = {}
for feature in arcjson['features']:
typ = feature['attributes']['type']
if not obj.has_key(typ):
obj[typ] = {}
obj[typ]['type'] = 'FeatureCollection'
obj[typ]['features'] = []
o = {}
o['type'] = 'Feature'
NAME = feature['attributes']['type']
if NAME is None:
NAME = ''
id = feature['attributes']['id']
if id is None:
id = ''
o['properties'] = {'NAME': NAME + id}
o['geometry'] = {}
o['geometry']['type'] = 'Point'
lng, lat = ToGeographic(feature['geometry']['x'] + offsetx, feature['geometry']['y'] + offsety)
o['geometry']['coordinates'] = [lng, lat]
obj[typ]['features'].append(o)
for k in obj.keys():
code = GetDeviceCode(k)
if code:
path = os.path.join(module_path(), JSON_DIR, 'geojson_%s_%s.json' % (code, name))
print(enc1(os.path.basename(path)))
with open(path, 'w') as f:
f.write(json.dumps(obj[k], ensure_ascii=True, indent=4) + '\n')
def HandleDevicesReinstall(devices, pipe):
s = ''
for i in devices:
VirtualDeviceWarning(i, pipe)
s += '[%s]' % i
if pipe:pipe.send({'type':'notify','title':u'检测到有设备连接到本机', 'message':u'检测到以下[%d]个设备:%s' % (len(devices), s), 'show':3, })
adb = GetADBExecutablePath()
adb = '"%s"' % adb
apkpath = os.path.join(module_path(), 'kmgdgis_mobile_android-release.apk')
for i in devices:
cmd = '%s -s "%s" shell pm uninstall com.kmgdgis.mobile' % (adb, i)
RunCmd(pipe, cmd)
cmd = '%s -s "%s" install -l "%s"' % (adb, i, apkpath)
RunCmd(pipe, cmd)
def Activated(self):
FreeCAD.Console.PrintMessage(self.exFile + "\r\n")
# So we can open the "Open File" dialog
mw = FreeCADGui.getMainWindow()
# Start off defaulting to the Examples directory
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, 'Libs/cadquery/examples/FreeCAD')
# Append this script's directory to sys.path
sys.path.append(os.path.dirname(exs_dir_path))
# We've created a library that FreeCAD can use as well to open CQ files
ImportCQ.open(os.path.join(exs_dir_path, self.exFile))
def Activated(self):
FreeCAD.Console.PrintMessage(self.exFile + "\r\n")
# So we can open the "Open File" dialog
mw = FreeCADGui.getMainWindow()
# Start off defaulting to the Examples directory
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, 'Libs/cadquery/examples/FreeCAD')
# Append this script's directory to sys.path
sys.path.append(os.path.dirname(exs_dir_path))
# We've created a library that FreeCAD can use as well to open CQ files
ImportCQ.open(os.path.join(exs_dir_path, self.exFile))
def get_epub_info(fname, _filename):
try:
ns = {
'n':'urn:oasis:names:tc:opendocument:xmlns:container',
'pkg':'http://www.idpf.org/2007/opf',
'dc':'http://purl.org/dc/elements/1.1/'
}
# prepare to read from the .epub file
zip = zipfile.ZipFile(fname)
# find the contents metafile
txt = zip.read('META-INF/container.xml')
tree = etree.fromstring(txt)
cfname = tree.xpath('n:rootfiles/n:rootfile/@full-path',namespaces=ns)[0]
# grab the metadata block from the contents metafile
cf = zip.read(cfname)
tree = etree.fromstring(cf)
p = tree.xpath('/pkg:package/pkg:metadata',namespaces=ns)[0]
# repackage the data
res = {}
for s in ['title','language','creator','date','identifier']:
res[s] = p.xpath('dc:%s/text()'%(s),namespaces=ns)[0]
# Save cover in tmp folder
for member in zip.namelist():
filename = os.path.basename(member)
# skip directories
if not filename:
continue
res['cover-path'] = cover_source_path = os.path.abspath(os.path.join(module_path(), os.pardir)) + os.sep + "tmp" + os.sep + _filename + "_cover"
if filename.lower() == "cover.png":
# copy file (taken from zipfile's extract)
source = zip.open(member)
target = file(cover_source_path, "wb")
with source, target:
shutil.copyfileobj(source, target)
except Exception as ex:
return None
return res
def ListExamples():
import os
try:
from . import module_locator
except:
import module_locator
dirs = []
# List all of the example files in an order that makes sense
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, 'Libs/cadquery/examples/FreeCAD')
dirs = os.listdir(exs_dir_path)
dirs.sort()
return dirs
def ListExamples():
import os
try:
from . import module_locator
except:
import module_locator
dirs = []
# List all of the example files in an order that makes sense
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, 'Libs/cadquery/examples/FreeCAD')
dirs = os.listdir(exs_dir_path)
dirs.sort()
return dirs
def clearSpace():
json_pattern = "word_data.json"
main_script_path = module_locator.module_path()
file_pattern = os.path.join(main_script_path, json_pattern)
audio_directory = os.path.join(os.path.dirname(file_pattern),
'audio\\').strip()
image_directory = os.path.join(os.path.dirname(file_pattern),
'images\\').strip()
print(image_directory)
print(os.path.exists(image_directory))
if os.path.exists(image_directory):
shutil.rmtree(image_directory, ignore_errors=True)
print('initialised')
if os.path.exists(audio_directory):
shutil.rmtree(audio_directory, ignore_errors=True)
print('initialised')
def main(argv):
profitfile = ''
offerfile = ''
directory = module_locator.module_path()
try:
opts, args = getopt.getopt(argv, "hp:o:", ["pfile=", "ofile="])
except getopt.GetoptError:
print 'offers_evolution.py -p <profitfile> -o <offerfile>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'offers_evolution.py -p <profitfile> -o <offerfile>'
sys.exit()
elif opt in ("-p", "--pfile"):
profitfile = arg
elif opt in ("-o", "--ofile"):
offerfile = arg
if ((isBlank(profitfile) == False) and (isBlank(offerfile) == False)):
generate_figure(directory, profitfile, offerfile)
print 'Profit file is "', profitfile
print 'Offer file is "', offerfile
def main(argv):
inputfile = ''
outputfile = ''
directory = module_locator.module_path()
try:
opts, args = getopt.getopt(argv, "hi:o:", ["ifile=", "ofile="])
except getopt.GetoptError:
print 'offers_evolution.py -i <inputfile> -o <outputfile>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'offers_evolution.py -i <inputfile> -o <outputfile>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
if ((isBlank(inputfile) == False) and (isBlank(outputfile) == False)):
generate_figure(directory, inputfile, outputfile)
print 'Input file is "', inputfile
print 'Output file is "', outputfile
def main(argv):
inputfile = ''
outputfile = ''
directory = module_locator.module_path()
try:
opts, args = getopt.getopt(argv,"hi:o:",["ifile=","ofile="])
except getopt.GetoptError:
print 'offers_evolution.py -i <inputfile> -o <outputfile>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'offers_evolution.py -i <inputfile> -o <outputfile>'
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
if ((isBlank(inputfile) == False)
and (isBlank(outputfile) == False)):
generate_figure(directory, inputfile, outputfile)
print 'Input file is "', inputfile
print 'Output file is "', outputfile
def main(argv):
profitfile = ''
offerfile = ''
directory = module_locator.module_path()
try:
opts, args = getopt.getopt(argv,"hp:o:",["pfile=","ofile="])
except getopt.GetoptError:
print 'offers_evolution.py -p <profitfile> -o <offerfile>'
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print 'offers_evolution.py -p <profitfile> -o <offerfile>'
sys.exit()
elif opt in ("-p", "--pfile"):
profitfile = arg
elif opt in ("-o", "--ofile"):
offerfile = arg
if ((isBlank(profitfile) == False)
and (isBlank(offerfile) == False)):
generate_figure(directory, profitfile, offerfile)
print 'Profit file is "', profitfile
print 'Offer file is "', offerfile
def Activated(self):
#So we can open the "Open File" dialog
mw = FreeCADGui.getMainWindow()
#Try to keep track of the previous path used to open as a convenience to the user
if self.previousPath is None:
#Start off defaulting to the Examples directory
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, 'Examples')
self.previousPath = exs_dir_path
filename = QtGui.QFileDialog.getOpenFileName(
mw, mw.tr("Open CadQuery Script"), self.previousPath,
mw.tr("CadQuery Files (*.py)"))
#Make sure the user didn't click cancel
if filename[0]:
#We need to close any file that's already open in the editor window
CadQueryCloseScript().Activated()
self.previousPath = filename[0]
#Append this script's directory to sys.path
sys.path.append(os.path.dirname(filename[0]))
#We've created a library that FreeCAD can use as well to open CQ files
ImportCQ.open(filename[0])
docname = os.path.splitext(os.path.basename(filename[0]))[0]
FreeCAD.newDocument(docname)
#Execute the script
CadQueryExecuteScript().Activated()
#Get a nice view of our model
FreeCADGui.activeDocument().activeView().viewAxometric()
FreeCADGui.SendMsgToActiveView("ViewFit")
def Activated(self):
# So we can open the "Open File" dialog
mw = FreeCADGui.getMainWindow()
# Try to keep track of the previous path used to open as a convenience to the user
if self.previousPath is None:
# Start off defaulting to the Examples directory
module_base_path = module_locator.module_path()
exs_dir_path = os.path.join(module_base_path, "Examples")
self.previousPath = exs_dir_path
filename = QtGui.QFileDialog.getOpenFileName(
mw, mw.tr("Open CadQuery Script"), self.previousPath, mw.tr("CadQuery Files (*.py)")
)
# Make sure the user didn't click cancel
if filename[0]:
# We need to close any file that's already open in the editor window
CadQueryCloseScript().Activated()
self.previousPath = filename[0]
# Append this script's directory to sys.path
sys.path.append(os.path.dirname(filename[0]))
# We've created a library that FreeCAD can use as well to open CQ files
ImportCQ.open(filename[0])
docname = os.path.splitext(os.path.basename(filename[0]))[0]
FreeCAD.newDocument(docname)
# Execute the script
CadQueryExecuteScript().Activated()
# Get a nice view of our model
FreeCADGui.activeDocument().activeView().viewAxometric()
FreeCADGui.SendMsgToActiveView("ViewFit")
"""FreeCAD init script of the CadQuery module"""
# (c) 2014-2016 Jeremy Wright Apache 2.0 License
#TODO: The FreeCAD devs like to put as much init code as possible in here so that the module can be used without the
#TODO: GUI if desired
import os
import sys
import module_locator
# Set up so that we can import from our embedded packages
module_base_path = module_locator.module_path()
libs_dir_path = os.path.join(module_base_path, 'Libs')
sys.path.insert(0, libs_dir_path)
# Tack on our CadQuery library git subtree
cq_lib_path = os.path.join(libs_dir_path, 'cadquery-lib')
sys.path.insert(1, cq_lib_path)
# Make sure we get the right libs under the FreeCAD installation
fc_base_path = os.path.dirname(os.path.dirname(module_base_path))
fc_lib_path = os.path.join(fc_base_path, 'lib')
fc_bin_path = os.path.join(fc_base_path, 'bin')
# Make sure that the directories exist before we add them to sys.path
# This could cause problems or solve them by overriding what CQ is setting for the paths
if os.path.exists(fc_lib_path):
sys.path.insert(1, fc_lib_path)
if os.path.exists(fc_bin_path):
sys.path.insert(1, fc_bin_path)
def Activated(self):
import os, sys
import module_locator
from Gui import Command, ImportCQ
import Settings
#Set up so that we can import from our embedded packages
module_base_path = module_locator.module_path()
libs_dir_path = os.path.join(module_base_path, 'Libs')
sys.path.insert(0, libs_dir_path)
#Make sure we get the right libs under the FreeCAD installation
fc_base_path = os.path.dirname(os.path.dirname(module_base_path))
fc_lib_path = os.path.join(fc_base_path, 'lib')
fc_bin_path = os.path.join(fc_base_path, 'bin')
#Make sure that the directories exist before we add them to sys.path
#This could cause problems or solve them by overriding what CQ is setting for the paths
if os.path.exists(fc_lib_path):
sys.path.insert(1, fc_lib_path)
if os.path.exists(fc_bin_path):
sys.path.insert(1, fc_bin_path)
import cadquery
from pyqode.core.modes import FileWatcherMode
from pyqode.python.widgets import PyCodeEdit
from PySide import QtGui, QtCore
msg = QtGui.QApplication.translate(
"cqCodeWidget",
"CadQuery " + cadquery.__version__ + "\r\n"
"CadQuery is a parametric scripting language "
"for creating and traversing CAD models\r\n"
"Author: David Cowden\r\n"
"License: LGPL\r\n"
"Website: https://github.com/dcowden/cadquery\r\n",
None,
QtGui.QApplication.UnicodeUTF8)
FreeCAD.Console.PrintMessage(msg)
#Make sure that we enforce a specific version (2.7) of the Python interpreter
ver = hex(sys.hexversion)
interpreter = "python%s.%s" % (ver[2], ver[4]) # => 'python2.7'
#If the user doesn't have Python 2.7, warn them
if interpreter != 'python2.7':
msg = QtGui.QApplication.translate(
"cqCodeWidget",
"Please install Python 2.7",
None,
QtGui.QApplication.UnicodeUTF8)
FreeCAD.Console.PrintError("\r\n" + msg)
#The extra version numbers won't work on Windows
if sys.platform.startswith('win'):
interpreter = 'python'
#Getting the main window will allow us to start setting things up the way we want
mw = FreeCADGui.getMainWindow()
# TODO: Fix the extra newline foolishness with the output in the report view
dockWidgets = mw.findChildren(QtGui.QDockWidget)
for widget in dockWidgets:
if widget.objectName() == "Report view":
widget.setVisible(True)
#Add a new widget here that's a simple text area to begin with. It will become the CQ coding area
cqCodeWidget = QtGui.QDockWidget("CadQuery Code View")
cqCodeWidget.setObjectName("cqCodeView")
mw.addDockWidget(QtCore.Qt.LeftDockWidgetArea, cqCodeWidget)
#Set up the text area for our CQ code
server_path = os.path.join(module_base_path, 'cq_server.py')
#Windows needs some extra help with paths
if sys.platform.startswith('win'):
codePane = PyCodeEdit(server_script=server_path, interpreter=interpreter
, args=['-s', fc_lib_path, libs_dir_path])
else:
codePane = PyCodeEdit(server_script=server_path, interpreter=interpreter
, args=['-s', libs_dir_path])
# Allow easy use of an external editor
if Settings.use_external_editor:
codePane.modes.append(FileWatcherMode())
codePane.modes.get(FileWatcherMode).file_reloaded.connect(self.AutoExecute)
codePane.modes.get(FileWatcherMode).auto_reload = True
codePane.setObjectName("cqCodePane")
#Add the text area to our dock widget
cqCodeWidget.setWidget(codePane)
#Set up the paths to allow us to open and execute our introduction example
example_path = os.path.join(module_base_path, 'Examples')
example_path = os.path.join(example_path, 'Ex000_Introduction.py')
# TODO: Enable this for FreeCAD 0.16 or greater
# Make sure we get the correct MdiArea object
# for child in mw.children():
# if child.__class__ == QtGui.QMdiArea:
# mdiArea = child
#
# # Set up the editor in a new subwindow
# #sub_window = QtGui.QMdiSubWindow(mw.centralWidget())
# sub_window = QtGui.QMdiSubWindow(mdiArea)
# #sub_window.setWidget(codePane)
# sub_window.setWidget(QtGui.QPlainTextEdit())
# sub_window.setWindowTitle('Ex000_Introduction.py')
# sub_window.setWindowIcon(QtGui.QIcon(':/icons/applications-python.svg'))
#
# #mw.centralWidget().addSubWindow(sub_window)
# mdiArea.addSubWindow(sub_window)
ImportCQ.open(example_path)
docname = os.path.splitext(os.path.basename(example_path))[0]
FreeCAD.newDocument(docname)
Command.CadQueryExecuteScript().Activated()
#Get a nice view of our example
FreeCADGui.activeDocument().activeView().viewAxometric()
FreeCADGui.SendMsgToActiveView("ViewFit")
def main(args, g_params):
parser = argparse.ArgumentParser(
description='TOPCONS2_OCTOPUS workflow master script',
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog='''\
Created 2015-05-05, updated 2018-02-16, Peters Christoph and Nanjiang Shu
Examples:
''')
parser.add_argument(
'inFile',
metavar='inFile',
help='Specify the input amino acid sequence file in FASTA format')
parser.add_argument('out_path',
metavar='out_path',
help='Specify the outpath for result')
parser.add_argument(
'blastDir',
metavar='blastDir',
help='Specify the path for psiblast, which contains bin/blastpgp')
parser.add_argument(
'blastDB',
metavar='blastDB',
help='Specify the name of the blastdb, including the path')
parser.add_argument(
'-tmpdir',
'--tmpdir',
metavar='DIR',
dest='TMPPATH',
help=
'Specify the directory where the temporary files will be written to')
parser.add_argument('-debug',
'--debug',
action='store_true',
default=False,
dest='isDEBUG',
help='Output debug info')
parser.add_argument('-RM',
'--remove-individual-files',
action='store_true',
default=False,
dest='isRemoveFile',
help='Delete result for individual sequences')
args = parser.parse_args()
g_params['DEBUG'] = args.isDEBUG
g_params['REMOVE_IND_FILES'] = args.isRemoveFile
inFile = os.path.abspath(args.inFile)
out_path = os.path.abspath(args.out_path)
blastDir = os.path.abspath(args.blastDir)
blastDB = os.path.abspath(args.blastDB)
if args.TMPPATH != None:
g_params['TMPPATH'] = os.path.abspath(args.TMPPATH)
if not os.access(g_params['TMPPATH'], os.W_OK):
print >> sys.stderr, "Error. TMPPATH '%s' not writable. Exit." % (
g_params['TMPPATH'])
return 1
if not os.access(out_path, os.W_OK):
print >> sys.stderr, "Error. out_path '%s' not writable. Exit." % (
out_path)
return 1
os.environ['TMPPATH'] = g_params['TMPPATH']
DEBUG = g_params['DEBUG']
TMPPATH = g_params['TMPPATH']
if not os.path.exists(inFile):
print >> sys.stderr, "inFile %s does not exist. Exit." % (inFile)
sys.exit(1)
if not os.path.exists(out_path):
try:
os.makedirs(out_path)
except OSError:
print >> sys.stderr, "Failed to create out_path %s. Exit." % (
out_path)
sys.exit(1)
if not "BLASTDB" in os.environ: # this fixed the warning message of unset 'BLASTDB'
try:
blastdbpath = os.path.realpath(os.path.dirname(blastDB))
os.environ['BLASTDB'] = blastdbpath
except:
pass
# Set the working dir to the script location
my_path = module_locator.module_path()
os.chdir(my_path)
inFile_rootname = os.path.basename(os.path.splitext(inFile)[0])
# Timing remove from final version
#print "Timing remove from final version"
timingfile = "%s/%s" % (out_path, "time.txt")
topfile_OCTOPUS = "%s/%s.OCTOPUS.topfa" % (out_path, inFile_rootname)
topfile_SPOCTOPUS = "%s/%s.SPOCTOPUS.topfa" % (out_path, inFile_rootname)
fpout_OCTOPUS = open(topfile_OCTOPUS, "w")
fpout_SPOCTOPUS = open(topfile_SPOCTOPUS, "w")
with open(timingfile, "w") as timingFileOut:
with open(inFile, "rU") as seqFile:
for index, entry in enumerate(list(SeqIO.parse(seqFile, "fasta"))):
# Timing remove from final version
# print "Timing remove from final version"
start = time.time()
#Create folders for tmp data and output
used_pfam = "pfam"
tmpDir = tempfile.mkdtemp(prefix="%s/seq_" %
(TMPPATH) + str(index) + "_") + "/"
os.chmod(tmpDir, 0755)
tmpDir_pfam = tmpDir
tmpDir_cdd = ""
tmpDir_uniref = ""
protnamefile = "%s/query.fa.txt" % (tmpDir)
try:
fpout = open(protnamefile, "w")
print >> fpout, "query"
fpout.close()
except IOError:
print >> sys.stderr, "Failed to write to protnamefile %s. "\
"Exit."%(protnamefile)
sys.exit(1)
outDir = "%s%s%s/" % (out_path, os.sep, "seq_%d" % (index))
if os.path.exists(tmpDir) is False:
os.mkdir(tmpDir)
if os.path.exists(outDir) is False:
os.mkdir(outDir)
# if os.path.exists(outDir + "Topcons/") is False:
# os.mkdir(outDir + "Topcons/")
# outfile = "%s/%s"%(tmpDir, "query.fa")
with open(tmpDir + "query.fa", "w") as outFile:
outFile.write(">query" + "\n" + str(entry.seq))
with open(outDir + "seq.fa", "w") as outFile:
outFile.write(">query" + "\n" + str(entry.seq))
startDir = os.getcwd()
# At the same time the profiles can be created
cmd = ["./fa2prfs_pfamscan_v2.sh", tmpDir_pfam, blastDir]
cmdline = " ".join(cmd)
rmsg = ""
try:
print "cmdline: ", cmdline
rmsg = subprocess.check_call(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
print "errmsg:", e
print "rmsg:", rmsg
pass
query_seqdbfile = "%s/%s" % (tmpDir_pfam, "query.hits.db")
filesize = 0
try:
filesize = os.path.getsize(query_seqdbfile)
except OSError:
filesize = -1
pass
if DEBUG:
print "After fa2prfs_pfamscan_v2.sh filesize(%s)=%d" % (
query_seqdbfile, filesize)
# In case we do not find a hit, we have to run hmmscan on the cdd database
if filesize <= 0:
tmpDir_cdd = tempfile.mkdtemp(prefix="%s/seq_cdd_" %
(TMPPATH) + str(index) +
"_") + "/"
os.chmod(tmpDir_cdd, 0755)
with open(tmpDir_cdd + "query.fa", "w") as outFile:
outFile.write(">query" + "\n" + str(entry.seq))
used_pfam = "cdd"
cmd = ["./fa2prfs_hmmscan.sh", tmpDir_cdd, blastDir]
cmdline = " ".join(cmd)
try:
print "\ncmdline:", cmdline
rmsg = subprocess.check_call(cmd,
stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
print "errmsg:", e
print "rmsg:", rmsg
pass
tmpDir = tmpDir_cdd
query_seqdbfile = "%s/%s" % (tmpDir_cdd, "query.hits.db")
try:
filesize = os.path.getsize(query_seqdbfile)
except OSError:
filesize = -1
pass
if DEBUG:
print "After fa2prfs_hmmscan.sh filesize(%s)=%d" % (
query_seqdbfile, filesize)
# In case we do not find a hit, we have to run the old script
if filesize <= 0:
tmpDir_uniref = tempfile.mkdtemp(prefix="%s/seq_uniref_" %
(TMPPATH) + str(index) +
"_") + "/"
os.chmod(tmpDir_uniref, 0755)
with open(tmpDir_uniref + "query.fa", "w") as outFile:
outFile.write(">query" + "\n" + str(entry.seq))
used_pfam = "uniref"
cmd = [
"./fa2prfs_fallback_v2.sh", tmpDir_uniref, blastDir,
blastDB
]
cmdline = " ".join(cmd)
try:
print "\ncmdline:", cmdline
rmsg = subprocess.check_call(cmd,
stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
print e
print rmsg
pass
tmpDir = tmpDir_uniref
query_seqdbfile = "%s/%s" % (tmpDir_uniref,
"query.hits.db")
try:
filesize = os.path.getsize(query_seqdbfile)
except OSError:
filesize = -1
pass
if DEBUG:
print "After fa2prfs_fallback_v2.sh filesize(%s)=%d" % (
query_seqdbfile, filesize)
# Once the profile is created start all other predictors
os.chdir(os.path.abspath("../predictors/spoctopus/"))
outDir_SPOCTOPUS = outDir + os.sep + "SPOCTOPUS"
if not os.path.exists(outDir_SPOCTOPUS):
os.makedirs(outDir_SPOCTOPUS)
cmd = [
"./SPOCTOPUS.sh", protnamefile, tmpDir + "PSSM_PRF_FILES/",
tmpDir + "RAW_PRF_FILES/", outDir_SPOCTOPUS, "-N"
] #output also the ANN result for SPOCTOPUS, changed 2016-01-26
cmdline = " ".join(cmd)
if DEBUG:
print "cmdline:", cmdline
p_spoctopus = subprocess.Popen(cmd)
os.chdir(startDir)
os.chdir(os.path.abspath("../predictors/spoctopus/"))
outDir_OCTOPUS = outDir + os.sep + "OCTOPUS"
if not os.path.exists(outDir_OCTOPUS):
os.makedirs(outDir_OCTOPUS)
cmd = [
"./OCTOPUS.sh", protnamefile, tmpDir + "PSSM_PRF_FILES/",
tmpDir + "RAW_PRF_FILES/", outDir_OCTOPUS, "-N"
] #output also the ANN result for OCTOPUS, changed 2016-01-26
cmdline = " ".join(cmd)
if DEBUG:
print "cmdline:", cmdline
p_octopus = subprocess.Popen(cmd)
os.chdir(startDir)
p_spoctopus.communicate() #now wait for OCTOPUS
p_octopus.communicate() #now wait for SPOCTOPUS
count_pred = 2
end = time.time()
lines = 0
with open(tmpDir + "query.hits.db") as inFile:
for line in inFile:
if line.find(">") == -1:
lines += 1
timingFileOut.write(
str(entry.id) + ";" + str(end - start) + ";" + used_pfam +
";" + str(lines) + ";" + str(count_pred) + "\n")
#Remove the tmpFolder
if not DEBUG: #debugging
if os.path.exists(tmpDir) is True:
p = subprocess.call(["rm", "-rf", tmpDir])
if os.path.exists(tmpDir_cdd) is True:
p = subprocess.call(["rm", "-rf", tmpDir_cdd])
if os.path.exists(tmpDir_uniref) is True:
p = subprocess.call(["rm", "-rf", tmpDir_uniref])
if os.path.exists(tmpDir_pfam) is True:
p = subprocess.call(["rm", "-rf", tmpDir_pfam])
else:
print "tmpDir=%s" % (tmpDir)
p = subprocess.call(["python", "correct_Topo.py", outDir])
topfile = "%s/%s/%s" % (outDir, "OCTOPUS", "query.top")
if os.path.exists(topfile):
top = myfunc.ReadFile(topfile).strip()
if top:
fpout_OCTOPUS.write(">%s\n" % (entry.description))
fpout_OCTOPUS.write("%s\n" % (top))
topfile = "%s/%s/%s" % (outDir, "SPOCTOPUS", "query.top")
if os.path.exists(topfile):
top = myfunc.ReadFile(topfile).strip()
if top:
fpout_SPOCTOPUS.write(">%s\n" % (entry.description))
fpout_SPOCTOPUS.write("%s\n" % (top))
if g_params['REMOVE_IND_FILES']:
shutil.rmtree(outDir)
def Activated(self):
module_base_path = module_locator.module_path()
templ_dir_path = os.path.join(module_base_path, 'Templates')
# Use the library that FreeCAD can use as well to open CQ files
ImportCQ.open(os.path.join(templ_dir_path, 'script_template.py'))
def main(args, g_params):
parser = argparse.ArgumentParser(
description='TOPCONS2 workflow master script',
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog='''\
Created 2015-05-05, updated 2017-12-11, Peters Christoph and Nanjiang Shu
Examples:
''')
parser.add_argument('inFile', metavar='inFile',
help='Specify the input amino acid sequence file in FASTA format')
parser.add_argument('out_path', metavar='out_path',
help='Specify the outpath for result')
parser.add_argument('blastDir', metavar='blastDir',
help='Specify the path for psiblast, which contains bin/blastpgp')
parser.add_argument('blastDB', metavar='blastDB',
help='Specify the name of the blastdb, including the path')
parser.add_argument('-tmpdir', '--tmpdir', metavar='DIR', dest='TMPPATH',
help='Specify the directory where the temporary files will be written to')
parser.add_argument('-debug', '--debug', action='store_true', default=False, dest='isDEBUG',
help='Output debug info')
parser.add_argument('-plot','--plot', action='store', dest='isPlot', default='yes',
choices=['yes', 'no'], help='Whether output figure (default = yes)' )
args = parser.parse_args()
g_params['DEBUG'] = args.isDEBUG
inFile = os.path.abspath(args.inFile)
out_path = os.path.abspath(args.out_path)
blastDir = os.path.abspath(args.blastDir)
blastDB = os.path.abspath(args.blastDB)
g_params['isPlot'] = args.isPlot
if args.TMPPATH != None:
g_params['TMPPATH'] = os.path.abspath(args.TMPPATH)
if not os.access(g_params['TMPPATH'], os.W_OK):
print >> sys.stderr, "Error. TMPPATH '%s' not writable. Exit."%(g_params['TMPPATH'])
return 1
if not os.access(out_path, os.W_OK):
print >> sys.stderr, "Error. out_path '%s' not writable. Exit."%(out_path)
return 1
os.environ['TMPPATH'] = g_params['TMPPATH']
DEBUG = g_params['DEBUG']
if not os.path.exists(inFile):
print >> sys.stderr, "inFile %s does not exist. Exit."%(inFile)
sys.exit(1)
if not os.path.exists(out_path):
try:
os.makedirs(out_path)
except OSError:
print >> sys.stderr, "Failed to create out_path %s. Exit."%(out_path)
sys.exit(1)
if not "BLASTDB" in os.environ: # this fixed the warning message of unset 'BLASTDB'
try:
blastdbpath = os.path.realpath(os.path.dirname(blastDB))
os.environ['BLASTDB'] = blastdbpath
except:
pass
# Set the working dir to the script location
my_path = module_locator.module_path()
os.chdir(my_path)
# Timing remove from final version
#print "Timing remove from final version"
timingfile = "%s/%s"%(out_path, "time.txt")
with open(timingfile, "w") as timingFileOut:
with open(inFile, "rU") as seqFile:
for index, entry in enumerate(list(SeqIO.parse(seqFile, "fasta"))):
# Timing remove from final version
# print "Timing remove from final version"
start = time.time()
#Create folders for tmp data and output
used_pfam = "pfam"
tmpDir = tempfile.mkdtemp(prefix="%s/seq_"%(g_params['TMPPATH']) + str(index) + "_") + "/"
os.chmod(tmpDir, 0755)
tmpDir_pfam = tmpDir
tmpDir_cdd = ""
tmpDir_uniref = ""
# Changed by Nanjiang at 2015-02-05 23:07:44, no random suffix in the folder,
# since the specified out_path should be exclusively for this query
protnamefile = "%s/query.fa.txt"%(tmpDir)
try:
fpout = open(protnamefile, "w")
print >> fpout, "query"
fpout.close()
except IOError:
print >> sys.stderr, "Failed to write to protnamefile %s. "\
"Exit."%(protnamefile)
sys.exit(1)
outDir = "%s%s%s/"%(out_path, os.sep, "seq_%d"%(index))
if os.path.exists(tmpDir) is False:
os.mkdir(tmpDir)
if os.path.exists(outDir) is False:
os.mkdir(outDir)
if os.path.exists(outDir + "Topcons/") is False:
os.mkdir(outDir + "Topcons/")
# outfile = "%s/%s"%(tmpDir, "query.fa")
with open(tmpDir + "query.fa", "w") as outFile:
outFile.write(">query" + "\n" + str(entry.seq))
with open(outDir + "seq.fa", "w") as outFile:
outFile.write(">query" + "\n" + str(entry.seq))
startDir = os.getcwd()
# Run Philius because it does not need the profile
os.chdir(os.path.abspath("../predictors/Philius/"))
cmd = ["./runPhilius.sh", tmpDir + "query.fa", outDir]
cmdline = " ".join(cmd)
if DEBUG:
print "cmdline:", cmdline
p_philius = subprocess.Popen(cmd)
os.chdir(startDir)
# At the same time the profiles can be created
cmd = ["./fa2prfs_pfamscan_v2.sh", tmpDir_pfam, blastDir]
cmdline = " ".join(cmd)
rmsg = ""
try:
print "cmdline: ", cmdline
rmsg = subprocess.check_call(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
print "errmsg:", e
print "rmsg:", rmsg
pass
query_seqdbfile = "%s/%s"%(tmpDir_pfam, "query.hits.db")
filesize = 0
try:
filesize = os.path.getsize(query_seqdbfile)
except OSError:
filesize = -1
pass
if DEBUG:
print "After fa2prfs_pfamscan_v2.sh filesize(%s)=%d"%(query_seqdbfile, filesize)
# In case we do not find a hit, we have to run hmmscan on the cdd database
if filesize <= 0:
tmpDir_cdd = tempfile.mkdtemp(prefix="%s/seq_cdd_"%(g_params['TMPPATH']) + str(index) + "_") + "/"
os.chmod(tmpDir_cdd, 0755)
with open(tmpDir_cdd + "query.fa", "w") as outFile:
outFile.write(">query" + "\n" + str(entry.seq))
used_pfam = "cdd"
cmd = ["./fa2prfs_hmmscan.sh", tmpDir_cdd, blastDir]
cmdline = " ".join(cmd)
try:
print "\ncmdline:",cmdline
rmsg = subprocess.check_call(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
print "errmsg:", e
print "rmsg:", rmsg
pass
tmpDir = tmpDir_cdd
query_seqdbfile = "%s/%s"%(tmpDir_cdd, "query.hits.db")
try:
filesize = os.path.getsize(query_seqdbfile)
except OSError:
filesize = -1
pass
if DEBUG:
print "After fa2prfs_hmmscan.sh filesize(%s)=%d"%(query_seqdbfile, filesize)
# In case we do not find a hit, we have to run the old script
if filesize <= 0:
tmpDir_uniref = tempfile.mkdtemp(prefix="%s/seq_uniref_"%(g_params['TMPPATH']) + str(index) + "_") + "/"
os.chmod(tmpDir_uniref, 0755)
with open(tmpDir_uniref + "query.fa", "w") as outFile:
outFile.write(">query" + "\n" + str(entry.seq))
used_pfam = "uniref"
cmd = ["./fa2prfs_fallback_v2.sh", tmpDir_uniref, blastDir, blastDB]
cmdline = " ".join(cmd)
try:
print "\ncmdline:", cmdline
rmsg = subprocess.check_call(cmd, stderr=subprocess.STDOUT)
except subprocess.CalledProcessError, e:
print e
print rmsg
pass
tmpDir = tmpDir_uniref
query_seqdbfile = "%s/%s"%(tmpDir_uniref,"query.hits.db")
try:
filesize = os.path.getsize(query_seqdbfile)
except OSError:
filesize = -1
pass
if DEBUG:
print "After fa2prfs_fallback_v2.sh filesize(%s)=%d"%(query_seqdbfile, filesize)
print "Final working dir: tmpdir=", tmpDir
# Once the profile is created start all other predictors
os.chdir(os.path.abspath("../predictors/scampi-msa/"))
cmd = ["perl", "run_SCAMPI_MSA.pl", tmpDir , outDir]
cmdline = " ".join(cmd)
if DEBUG:
print "cmdline:", cmdline
p_scampi = subprocess.Popen(cmd)
os.chdir(startDir)
os.chdir(os.path.abspath("../predictors/spoctopus/"))
outDir_SPOCTOPUS = outDir + os.sep + "SPOCTOPUS"
if not os.path.exists(outDir_SPOCTOPUS):
os.makedirs(outDir_SPOCTOPUS)
cmd = ["./SPOCTOPUS.sh", protnamefile ,tmpDir + "PSSM_PRF_FILES/", tmpDir + "RAW_PRF_FILES/", outDir_SPOCTOPUS, "-N"] #output also the ANN result for SPOCTOPUS, changed 2016-01-26
cmdline = " ".join(cmd)
if DEBUG:
print "cmdline:", cmdline
p_spoctopus = subprocess.Popen(cmd)
os.chdir(startDir)
os.chdir(os.path.abspath("../predictors/spoctopus/"))
outDir_OCTOPUS = outDir + os.sep + "OCTOPUS"
if not os.path.exists(outDir_OCTOPUS):
os.makedirs(outDir_OCTOPUS)
cmd = ["./OCTOPUS.sh", protnamefile,tmpDir + "PSSM_PRF_FILES/", tmpDir + "RAW_PRF_FILES/", outDir_OCTOPUS, "-N"] #output also the ANN result for OCTOPUS, changed 2016-01-26
cmdline = " ".join(cmd)
if DEBUG:
print "cmdline:", cmdline
p_octopus = subprocess.Popen(cmd)
os.chdir(startDir)
os.chdir(os.path.abspath("../predictors/PolyPhobius/"))
cmd = ["perl", "run_polyphobius.pl", tmpDir, outDir]
cmdline = " ".join(cmd)
if DEBUG:
print "cmdline:", cmdline
p_polyphobius = subprocess.Popen(cmd)
os.chdir(startDir)
p_philius.communicate() #now wait for philius
p_scampi.communicate() #now wait for SCAMPI MSA
p_spoctopus.communicate() #now wait for OCTOPUS
p_octopus.communicate() #now wait for SPOCTOPUS
p_polyphobius.communicate() #now wait for PolyPhobius
# Kostas wants (SP)Octopus to be "o"*len when Scampi does not predict a membrane
subprocess.call(["python","./check_if_ntm.py", outDir + "SCAMPI_MSA/query.top", outDir + "OCTOPUS/query.top", outDir + "SPOCTOPUS/query.top"])
# When the predictors are done we can run topcons
os.chdir(os.path.abspath("../predictors/topcons/"))
results = []
count_pred = 0
try:
if os.stat(outDir + "OCTOPUS/query.top").st_size != 0:
results.append("%s/%s"%(outDir, "OCTOPUS/"))
count_pred += 1
except OSError:
# In case of a random crash we predict without spoctopus
pass
try:
if os.stat(outDir + "SPOCTOPUS/query.top").st_size != 0:
results.append("%s/%s"%(outDir , "SPOCTOPUS/"))
count_pred += 1
except OSError:
# In case of a random crash we predict without octopus
pass
try:
if os.stat(outDir + "philius/query.top").st_size != 0:
results.append("%s/%s"%( outDir, "philius/"))
count_pred += 1
except OSError:
pass
try:
if os.stat(outDir + "PolyPhobius/query.top").st_size != 0:
results.append("%s/%s"%(outDir, "PolyPhobius/"))
count_pred += 1
except OSError:
pass
if os.stat(outDir + "SCAMPI_MSA/query.top").st_size != 0:
results.append("%s/%s"%( outDir, "SCAMPI_MSA/"))
count_pred += 1
outdir_topcons = "%s/Topcons/"%(outDir)
#cmd = ["./TOPCONS.sh", protnamefile, outdir_topcons] + results
# 2015-02-23, the syntax of TOPCONS.sh has been changed
cmd = ["./TOPCONS.sh", protnamefile, outdir_topcons, outDir]
cmdline = " ".join(cmd)
#os.system("./TOPCONS.sh " + tmpDir + "query.fa.txt " + outDir + "Topcons/ " + results)
#print "./TOPCONS.sh " + tmpDir + "query.fa.txt " + outDir + "Topcons/ " + results
#subprocess.call(["./TOPCONS.sh", tmpDir + "query.fa.txt", outDir + "Topcons/", outDir + "OCTOPUS/", outDir + "philius/", outDir + "PolyPhobius/", outDir + "SPOCTOPUS/", outDir + "SCAMPI_MSA/"])
if DEBUG:
print "cmdline: cmdline"
try:
rmsg = subprocess.check_call(cmd)
except subprocess.CalledProcessError, e:
print >> sys.stderr, str(e)
pass
parser.add_argument(
'-clinicalInfoFile',
'--clinicalInfoFile',
help=
'File with clinical hotspot and indel filenames per cancer type. If not wanted set to false! Default: clinicalCancerTypeFiles.txt',
type=str,
default="clinicalCancerTypeFiles.txt")
args = parser.parse_args()
info = {}
clinicalInfo = {}
# Go through file with info about different clinical files
if not args.clinicalInfoFile.lower() == "false":
# Using module module_locator to determine the path of the pythonscript directory
my_path = module_locator.module_path()
my_pathParts = my_path.split("/") # Split path on /
# Get the path of the SERA_script folder
ciFilePath = ""
for i in range(1, (len(my_pathParts) - 2)):
ciFilePath += "/" + my_pathParts[i]
# Add the path to the file with info about files corresponding to different cancer types
ciFilePath += "/res/" + args.clinicalInfoFile
# Go through the cancer type file and add info about the corresponding files to a directory
with open(ciFilePath, 'r') as cifile:
for line in cifile:
if not re.match('$', line): # If line is not empty start working
line = line.strip()
infoParts = line.split("=")
cancer = infoParts[1].lower()
import os
import subprocess
import sys
import shutil
import logging
import datetime
import dropbox
import zipfile
import errno
#Setting up logging and other housekeeping
myDate = datetime.datetime.now().strftime("%y-%m-%d")
myTime = datetime.datetime.now().strftime("%H:%M")
myDateTime = datetime.datetime.now().strftime("%y-%m-%d %H:%M")
scriptdir = module_locator.module_path()
logdir = scriptdir + '\\logs\\'
tempdir = 'C:\\temp\\Plex Backup-%s\\' % myDate
regbackupfile = tempdir + "PlexRegistry-" + myDate + ".reg"
PlexDBDir = os.environ['LOCALAPPDATA'] + "\\Plex Media Server\\"
PZtemp = tempdir + "PlexBackup-" + myDate + ".zip"
BackupFile = tempdir + "PB-" + myDate + ".zip"
BackupDir = tempdir
allowZip64 = True
DB_appkey = '2tenjnd5fxlxxzj'
DB_appsecret = '7jfpfvnx7seew3i'
ACCESS_TYPE = 'app_folder'
auth_token = 'bB7LjlOoHncAAAAAAAAkCLBdTWfmixI2IMiSy6lSLqAPD6YEgUHYCcFjFleqte6j'
db = dropbox.client.DropboxClient(auth_token)
logger = logging.getLogger('Plex Backup')
__author__ = 'naetech'
import os
import module_locator
from Classes.Settings import Settings
from Classes.PHP import PHP
from Classes.GUI import GUI
program_path = module_locator.module_path()
print("Program path is: %s" % program_path)
program_settings = Settings()
settings_file_path = "%s/%s" % (program_path, "settings.ini")
program_settings.load_settings(settings_file_path)
php_path = str(program_settings.read_setting("php_path"))
if not os.path.exists(php_path):
# perhaps we should try something relative
php_path = "%s/%s" % (program_path, php_path)
port = str(program_settings.read_setting("port"))
webroot = str(program_settings.read_setting("webroot"))
if not os.path.exists(webroot):
# perhaps we should try something relative
#!/usr/bin/python
import sys
import pygame
from pygame.locals import *
from constants import BLACK, WHITE
from Player import Player
from Ball import Ball
import random
import os
import module_locator
base_dir = module_locator.module_path()
STATUS_FADE = USEREVENT + 1
class Game():
def __init__(self, args):
random.seed()
pygame.init()
self.use_ai = 'ai' in args
self.no_sound = 'nosound' in args
self.screenshot_counter = 0
self.setup_sounds()
self.status_msg = ''
self.status_level = 0
icon = pygame.image.load(os.path.join(base_dir, 'screenshot.png'))
pygame.display.set_icon(icon)
self.reset()
def reset(self):
