def add_access_identifier(self,access_ident):
"""
Add an accessIdentifier to the domain.
1. Check if it exists already
2. Add it
Return value: 0 = Succes, <0 = failure
"""
res = self.l.search(conf.get('LDAPSERVER','basedn'),\
ldap.SCOPE_BASE,'(objectClass=skoleSysDomain)',['accessIdentifier'])
sres = self.l.result(res,0)
if sres[1]==[]:
# The domain entry does not exist probably missing the skoleSysDomain objectClass
return -13501
attribs = sres[1][0][1]
path = sres[1][0][0]
access = [access_ident]
if attribs.has_key('accessIdentifier'):
if attribs['accessIdentifier'].count(access_ident):
# Access identifier already exists on this domain
return -13502
access += attribs['accessIdentifier']
# Add it
try:
self.bind(conf.get('LDAPSERVER','admin'),conf.get('LDAPSERVER','passwd'))
self.touch_by_dict({path:{'accessIdentifier':access}})
except Exception, e:
print e
return -13503
def onCommandAlias(e):
if e.args and 'r' in e.switches:
name = e.args[0].lower()
command = aliases[name]
del aliases[name]
conf['aliases'] = aliases
e.window.write("* Deleted alias %s%s (was %s)" % (conf.get('command-prefix','/'),name,command))
events.load(__name__,reloading=True)
elif 'l' in e.switches:
e.window.write("* Current aliases:")
for i in aliases:
e.window.write("* %s%s: %s" % (conf.get('command-prefix','/'),i,aliases[i]))
elif len(e.args) >= 2:
name = e.args[0].lower()
command = ' '.join(e.args[1:])
aliases[name] = command
conf['aliases'] = aliases
e.window.write("* Created an alias %s%s to %s" % (conf.get('command-prefix','/'),name,command))
events.reload(__name__)
elif len(e.args) == 1:
name = e.args[0].lower()
if name in aliases:
e.window.write("* %s%s is an alias to %s" % (conf.get('command-prefix','/'),name,aliases[name]))
else:
e.window.write("* There is no alias %s%s" % (conf.get('command-prefix','/'),name))
else:
e.window.write(
"""Usage:
/alias \x02name\x02 \x02expression\x02 to create or replace an alias
/alias \x02name\x02 to look at an alias
/alias -r \x02name\x02 to remove an alias
/alias -l to see a list of aliases""")
def remove_host(self,hwaddr=None, hostname=None):
"""
Remove a registered SkoleSYS host from LDAP
"""
hostspath = "%s,%s" % (conf.get('LDAPSERVER','hosts_ou'),conf.get('LDAPSERVER','basedn'))
if hwaddr:
hwaddr = hostdef.check_hwaddr(hwaddr)
if not hwaddr:
return -1
res = self.l.search(hostspath,\
ldap.SCOPE_ONELEVEL,'(& (macAddress=%s)(objectclass=skoleSysHost))'%hwaddr,['dn'])
sres = self.l.result(res,0)
if sres[1]==[]:
return -2
dn = sres[1][0][0]
if hostname:
res = self.l.search(hostspath,\
ldap.SCOPE_ONELEVEL,'(& (hostName=%s)(objectclass=skoleSysHost))'%hostname,['dn'])
sres = self.l.result(res,0)
if sres[1]==[]:
return -3
dn = sres[1][0][0]
self.bind(conf.get('LDAPSERVER','admin'),conf.get('LDAPSERVER','passwd'))
self.delete(dn)
return 0
def groupdel(self,uid,groupname):
# Do not check if the user exists, just remove the uid
#res = self.l.search(conf.get('LDAPSERVER','basedn'),ldap.SCOPE_SUBTREE,'(& (uid=%s) (objectclass=posixaccount))'%uid,['dn'])
#sres = self.l.result(res,0)
#if sres[1]==[]:
# return -10401
res = self.l.search(conf.get('LDAPSERVER','basedn'),ldap.SCOPE_SUBTREE,'(& (cn=%s) (objectclass=posixgroup))'%groupname,['memberuid'])
sres = self.l.result(res,0)
if sres[1]==[]:
return -10402
attribs = sres[1][0][1]
path = sres[1][0][0]
if attribs.has_key('memberUid'):
if attribs['memberUid'].count(uid):
memberuid = attribs['memberUid']
memberuid.remove(uid)
else: return -10403
else: return -10403
try:
self.bind(conf.get('LDAPSERVER','admin'),conf.get('LDAPSERVER','passwd'))
self.touch_by_dict({path:{'memberuid':memberuid}})
except Exception, e:
print e
return -10404
def default_nicks():
try:
nicks = [conf.get('nick')] + conf.get('altnicks', [])
if not nicks[0]:
# We're going to generate a nick based on the user's nick name
# and their public key.
import sugar.profile
import hashlib
user_name = sugar.profile.get_nick_name()
pubkey = sugar.profile.get_pubkey()
m = hashlib.sha1()
m.update(pubkey)
hexhash = m.hexdigest()
# Okay. Get all of the alphabetic bits of the username:
user_name_letters = "".join([x for x in user_name if x.isalpha()])
# If that came up with nothing, make it 'XO'. Also, shorten it
# if it's more than 11 characters (as we need 5 for - and the
# hash).
if len(user_name_letters) == 0:
user_name_letters = "XO"
if len(user_name_letters) > 11:
user_name_letters = user_name_letters[0:11]
# Finally, generate a nick by using those letters plus the first
# four hash bits of the user's public key.
user_nick = user_name_letters + "-" + hexhash[0:4]
nicks = [user_nick]
except:
nicks = ["purk"]
return nicks
def remove_access_identifier(self,access_ident):
"""
Remove an accessIdentifier from the domain. This method will also remove
the accessIdentifier from any user who has it granted.
1. Check if it exists
2. Remove it from domain
3. Remove it from users
Return value: 0 = Succes, <0 = failure
"""
res = self.l.search(conf.get('LDAPSERVER','basedn'),\
ldap.SCOPE_SUBTREE,'(accessIdentifier=%s)' % access_ident,['dn','accessIdentifier'])
sres = self.l.result(res,1)
self.bind(conf.get('LDAPSERVER','admin'),conf.get('LDAPSERVER','passwd'))
if not len(sres[1]):
# Access identifer does not exist on the domain
return -13601
for entry in sres[1]:
path = entry[0]
attribs = entry[1]
access = attribs['accessIdentifier']
access.remove(access_ident)
if not len(access):
access = None
try:
self.touch_by_dict({path:{'accessIdentifier':access}})
except Exception, e:
print e
return -13602
def default_nicks():
try:
nicks = [conf.get('nick')] + conf.get('altnicks', [])
if not nicks[0]:
# We're going to generate a nick based on the user's nick name
# and their public key.
from sugar3 import profile
import hashlib
user_name = profile.get_nick_name()
pubkey = profile.get_pubkey()
m = hashlib.sha1()
m.update(pubkey)
hexhash = m.hexdigest()
# Okay. Get all of the alphabetic bits of the username:
user_name_letters = "".join([x for x in user_name if x.isalpha()])
# If that came up with nothing, make it 'XO'. Also, shorten it
# if it's more than 11 characters (as we need 5 for - and the
# hash).
if len(user_name_letters) == 0:
user_name_letters = "XO"
if len(user_name_letters) > 11:
user_name_letters = user_name_letters[0:11]
# Finally, generate a nick by using those letters plus the first
# four hash bits of the user's public key.
user_nick = user_name_letters + "-" + hexhash[0:4]
nicks = [user_nick]
except:
nicks = ["purk"]
return nicks
def __init__(self, host: str = None, port: int = None, cert_path: str = None, macaroon_path: str = None):
self._host = host or conf.get('LND_HOST')
self._port = port or conf.get('LND_PORT')
self._cert_path = cert_path or conf.get('LND_CERT_PATH')
self._macaroon_path = macaroon_path or conf.get('LND_MACAROON_PATH')
self._encoded_macaroon = codecs.encode(open(conf.get('LND_MACAROON_PATH'), 'rb').read(), 'hex')
self._base_url = f'https://{self._host}:{self._port}/v1'
def default_nicks():
try:
nicks = [conf.get('nick')] + conf.get('altnicks',[])
if not nicks[0]:
import getpass
nicks = [getpass.getuser()]
except:
nicks = ["mrurk"]
return nicks
def onCommandThemeinfo(e):
e.window.write('%s %s by %s(Contact information: %s). Description: %s' % (conf.get('theme','Default'), theme.get('Version',default.get('Version','vX')), theme.get('Author',default.get('Author','unknown')), theme.get('Contact',default.get('Contact','None')), theme.get('Description',default.get('Description','None'))))
info = 'Events Themed: '
if conf.get('theme'):
for event in theme:
info += event+', '
else:
for event in default:
info += event+', '
e.window.write('%s (Themed/Total: %s/%s)' % (info[:len(info)-2], repr(len(theme)), repr(len(default))))
def autoconnect_set_data(do_autoconnect, network):
if 'start_networks' not in conf:
conf['start_networks'] = []
# note (n in C) != w
if (network in conf.get('start_networks')) != do_autoconnect:
if do_autoconnect:
conf.get('start_networks').append(network)
else:
conf.get('start_networks').remove(network)
def removegroup(self,groupname,backup_home,remove_home):
"""
Remove a group
Setting backup_home to True will create a tarball backup of the group's homedir
Setting remove_home to True truncate the gruop's homedir
"""
# check if the group exists
res = self.l.search(conf.get('LDAPSERVER','basedn'),\
ldap.SCOPE_SUBTREE,'(& (cn=%s)(objectclass=posixgroup))'%groupname,['dn','memberuid'])
sres = self.l.result(res,0)
if sres[1]==[]:
return -1
services = self.list_services(groupname)
if type(services) == list:
# service group
for sname in services:
self.detach_service(groupname,sname)
if sres[1][0][1].has_key('memberUid'):
import usermanager as uman
um = uman.UserManager()
for uid in sres[1][0][1]['memberUid']:
um.groupdel(uid,groupname)
path = sres[1][0][0]
self.bind(conf.get('LDAPSERVER','admin'),conf.get('LDAPSERVER','passwd'))
self.delete(path)
group_path = "%s/%s/groups/%s" % (conf.get('DOMAIN','domain_root'),conf.get('DOMAIN','domain_name'),groupname)
if os.path.exists(os.path.normpath(group_path)):
# The group has a homedir, maybe do stuff...
if backup_home:
try:
print "Backing up the group home folder of \"%s\"..." % groupname
cnt = 0
cnt_str = ''
backup_path = "%s.bz2" % (os.path.normpath(group_path))
while os.path.exists(backup_path):
cnt+=1
cnt_str = str(cnt)
backup_path = "%s_%s.bz2" % (os.path.normpath(group_path),cnt_str)
os.system('tar cjpf %s %s' % (backup_path,os.path.normpath(group_path)))
except Exception, e:
print e
return -2
if remove_home:
try:
print "Deleting the group home folder of \"%s\"..." % groupname
os.system('rm %s -R -f' % (os.path.normpath(group_path)))
except Exception, e:
print e
return -3
def autoconnect_set_data(do_autoconnect, network):
if 'start_networks' not in conf:
conf['start_networks'] = []
# note (n in C) != w
if (network in conf.get('start_networks')) != do_autoconnect:
if do_autoconnect:
conf.get('start_networks').append(network)
else:
conf.get('start_networks').remove(network)
save_config()
def ipaddr_exists(self,ipaddr):
"""
check if a ip address is already statically reserved to a certain host
"""
hostspath = "%s,%s" % (conf.get('LDAPSERVER','hosts_ou'),conf.get('LDAPSERVER','basedn'))
res = self.l.search(hostspath,\
ldap.SCOPE_ONELEVEL,'(& (ipHostNumber=%s)(objectclass=skoleSysHost))'%ipaddr,['cn'])
sres = self.l.result(res,0)
if sres[1]==[]:
return False
return True
def deluser(self,uid,backup_home,remove_home):
res = self.l.search(conf.get('LDAPSERVER','basedn'),ldap.SCOPE_SUBTREE,'uid=%s'%uid,['dn'])
sres = self.l.result(res,0)
if sres[1]==[]:
return -10201
try:
self.bind(conf.get('LDAPSERVER','admin'),conf.get('LDAPSERVER','passwd'))
self.delete(sres[1][0][0])
except Exception, e:
print e
return -10202
def __init__(self, win):
if conf.get('colind-title'):
height = 67
else:
height = 46
self.win = win
self.window = gtk.Window(gtk.WINDOW_POPUP)
winx = windows.manager.get_position()[0] + win.input.get_allocation().x + 5
winy = windows.manager.get_position()[1] + win.input.get_allocation().y - height + 22
self.window.move(winx,winy)
self.window.set_title('Color Index')
self.window.set_size_request(174,height)
self.window.set_border_width(3)
all = gtk.VBox(True, 2)
self.window.add(all)
if conf.get('colind-title'):
toolbar = gtk.HBox(False)
all.pack_start(toolbar)
tool_lab = gtk.Label('Color Index')
tool_lab.set_size_request(149,19)
tool_event = gtk.EventBox()
toolbar.pack_start(tool_lab)
toolbar.pack_start(tool_event)
tool_but = gtk.Label('X')
tool_event.add(tool_but)
tool_event.set_events(gtk.gdk.BUTTON_PRESS_MASK)
tool_event.connect('button_press_event', self.select)
top_row = gtk.HBox(True, 2)
bot_row = gtk.HBox(True, 2)
all.pack_start(top_row)
all.pack_start(bot_row)
event_box = []
color_lab = []
for col in range(16):
event_box.append(gtk.EventBox())
if col < 8:
top_row.pack_start(event_box[col])
else:
bot_row.pack_start(event_box[col])
color_lab.append(gtk.Label(str(col).zfill(2)))
event_box[col].add(color_lab[col])
event_box[col].set_events(gtk.gdk.BUTTON_PRESS_MASK)
event_box[col].connect('button_press_event', self.select, str(col).zfill(2))
event_box[col].modify_bg(gtk.STATE_NORMAL,event_box[col].get_colormap().alloc_color(parse_mirc.colors[col]))
self.window.show_all()
self.window.window.set_keep_above(True)
def add_machine(self,netbiosname,ntdomain):
hostspath = conf.get('LDAPSERVER','basedn')
res = self.l.search(hostspath,\
ldap.SCOPE_ONELEVEL,'(&(objectclass=sambaDomain)(sambaDomainName=%s))'% ntdomain ,['sambaSID'])
sres = self.l.result(res,0)
if sres[1]==[]:
return -1 # Domain does not exist
machine_info = {
'sambaSID': '%s-' % sres[1][0][1]['sambaSID'][0],
'uid': netbiosname,
'cn': netbiosname,
'gidNumber': '2005',
'homeDirectory': '/dev/null',
'sambaAcctFlags': '[W]',
'objectClass': ['sambaSamAccount','posixAccount','account','top'],
'uidNumber':str(self.max(conf.get('LDAPSERVER','basedn'),
'objectclass=posixaccount','uidNumber',
int(conf.get('DOMAIN','uid_start')))+1)}
path = "%s,%s,%s,%s" % \
('uid=%s'%netbiosname,\
conf.get('LDAPSERVER','smb_machines_ou'),\
conf.get('LDAPSERVER','samba_ou'),\
conf.get('LDAPSERVER','basedn'))
self.bind(conf.get('LDAPSERVER','admin'),conf.get('LDAPSERVER','passwd'))
self.touch_by_dict({path:machine_info})
def onConnect(e):
if conf.get('debug'):
debug = get_debug(e.network)
if debug:
windows.mutate(DebugWindow, e.network, debug.id)
else:
events.run('debug', e.window, e.network)
def insert_depth_data(item):
"""保存深度统计"""
# 跳过start_coords为0的数据
start = item.get('start_coords')
if start == 0:
return
end = item.get('end_coords')
barcode = item.get('barcode')
ont_conf = conf.get('ont')
depth_position_step = ont_conf.get('depth_position_step')
read_length_step = ont_conf.get('depth_read_length_step')
# 计算位置
if start % depth_position_step == 0 and start != 0:
r_start = int(start / depth_position_step) - 1
else:
r_start = math.floor(start / depth_position_step)
r_end = math.ceil(end / depth_position_step)
# 计算读长
read_len = math.ceil(item.get('read_len') / read_length_step)
# 保存数据
for i in range(r_start, r_end):
for ii in range(0, read_len):
key = '%s_%s_%s' % (i, barcode, ii)
redis_cli.hincrby('CELL:DEPTH:%s' % cell(item.get('path')), key)
for i in range(1, r_end):
for ii in range(0, read_len):
key = '%s_%s_%s' % (i, barcode, ii)
redis_cli.hsetnx('CELL:DEPTH:%s' % cell(item.get('path')), key, 0)
def open_file(filename):
flags = gobject.SPAWN_LEAVE_DESCRIPTORS_OPEN | gobject.SPAWN_SEARCH_PATH
filename = str(filename) #gobject won't accept unicode strings
if conf.get('open-file-command'):
command = conf['open-file-command'].split(' ') + [filename]
try:
gobject.spawn_async(command,flags=flags)
except OSError:
print "Unable to start %s" % command
elif open_file_cmd:
try:
command = open_file_cmd + (filename,)
gobject.spawn_async(command,flags=flags)
except OSError:
print "Unable to start %s" % command
else:
paths = os.getenv("PATH") or os.defpath
for cmdfile, cmd in os_commands:
for path in paths.split(os.pathsep):
if os.access(os.path.join(path,cmdfile),os.X_OK):
globals()['open_file_cmd'] = cmd
try:
command = cmd + (filename,)
gobject.spawn_async(command,flags=flags)
except OSError:
print "Unable to start %s" % command
return
print "Unable to find a method to open %s." % filename
def onDisconnect(e):
if hasattr(e.network, '_reconnect_source'):
e.network._reconnect_source.unregister()
del e.network._reconnect_source
if hasattr(e.network, 'connect_timestamp'):
if e.error and conf.get('autoreconnect', True):
delay = time.time() - \
e.network.connect_timestamp > 30 and 30 or 120
def do_reconnect():
if not e.network.status:
server(network=e.network)
def do_announce_reconnect():
if not e.network.status:
windows.get_default(
e.network).write(
"* Will reconnect in %s seconds.." %
delay)
e.network._reconnect_source = ui.register_timer(
delay *
1000,
do_reconnect)
e.network._reconnect_source = ui.register_idle(
do_announce_reconnect)
def get_autojoin_list(network):
perform = conf.get('networks', {}).get(network.name, {}).get('perform', ())
channels = set()
for line in perform:
if line.startswith('join ') and ' ' not in line[5:]:
channels.update(line[5:].split(','))
return channels
def get_autojoin_list(network):
perform = conf.get('networks',{}).get(network.name,{}).get('perform',())
channels = set()
for line in perform:
if line.startswith('join ') and ' ' not in line[5:]:
channels.update(line[5:].split(','))
return channels
def onSocketConnect(e):
timeout = conf.get("server_traffic_timeout", 120)*1000
e.network._message_timeout = False
if timeout:
e.network._message_timeout_source = ui.register_timer(timeout, check_timeout, e.network)
else:
e.network._message_timeout_source = None
def __init__(self, server="irc.default.org", port=6667, nicks=[],
username="", fullname="", name=None, **kwargs):
self.server = server
self.port = port
self.name = name or server
self.nicks = nicks or default_nicks()
self.me = self.nicks[0]
self.username = username or "urk"
self.fullname = fullname or conf.get("fullname", self.username)
self.password = ''
self.isupport = {
'NETWORK': server,
'PREFIX': '(ohv)@%+',
'CHANMODES': 'b,k,l,imnpstr',
}
self.prefixes = {'o':'@', 'h':'%', 'v':'+', '@':'o', '%':'h', '+':'v'}
self.status = DISCONNECTED
self.failedhosts = [] #hosts we've tried and failed to connect to
self.channel_prefixes = '&#+$' # from rfc2812
self.on_channels = set()
self.requested_joins = set()
self.requested_parts = set()
self.buffer = ''
def onClose(e):
nwindows = list(windows.get_with(network=e.window.network))
if isinstance(e.window, windows.ChannelWindow):
cwindows = list(windows.get_with(
network=e.window.network,
wclass=windows.ChannelWindow
))
#if we only have one window for the network, don't bother to part as
# we'll soon be quitting anyway
if len(nwindows) != 1 and irc_script.ischan(e.window.network, e.window.id):
e.window.network.part(e.window.id)
if len(nwindows) == 1:
events.trigger("CloseNetwork", window=e.window, network=e.window.network)
elif isinstance(e.window, windows.StatusWindow) and conf.get('status'):
events.trigger("CloseNetwork", window=e.window, network=e.window.network)
for window in nwindows:
if window != e.window:
window.close()
if len(windows.manager) == 1:
windows.new(windows.StatusWindow, irc.Network(), "status")
def transform_bcolor(start, end):
if (start.get('background',99) != end.get('background',99)):
confcolors = conf.get('colors', colors)
result = start.copy()
if 'foreground' in end:
try:
fg_index = list(confcolors).index(end['foreground'].upper())
except ValueError:
return '','',start
result['foreground'] = end['foreground']
else:
fg_index = 99
result.pop('foreground',None)
if 'background' in end:
try:
bg_index = list(confcolors).index(end['background'].upper())
except ValueError:
return '','',start
result['background'] = end['background']
else:
bg_index = 99
del result['background']
return '\x03%02i,%02i' % (fg_index, bg_index), ',', result
else:
return '','',start
def restart_service(self,groupname,servicename):
"""
Restart service taking new rescent changes in use.
"""
res = self.l.search(conf.get('LDAPSERVER','basedn'),\
ldap.SCOPE_SUBTREE,'(& (cn=%s)(objectclass=skoleSysServiceGroup))'%groupname,['dn','memberuid','servicelist'])
sres = self.l.result(res,0)
if sres[1]==[]:
return -1 # Group does not exist
dn = sres[1][0][0]
servicelist = []
if sres[1][0][1].has_key('serviceList'):
servicelist = sres[1][0][1]['serviceList']
if not servicelist.count(servicename):
return -4 # Group is not attached to the service
import skolesys.services as s
if not s.groupservices().count(servicename):
return -2 # the service does not exist
service_inst = s.create_groupserviceinterface(servicename,groupname)
if not service_inst:
return -3 # the service failed to load
return service_inst.restart()
def edit_network(self, cell, path_string, new_text):
network_list = self.networks.get_model()
old_text = network_list[path_string][0]
networks = conf.get('networks')
networks[new_text] = networks.pop(old_text, {})
start_networks = conf.get('start_networks', [])
if old_text in start_networks:
start_networks[start_networks.index(old_text)] = new_text
iter = network_list.get_iter_from_string(path_string)
network_list.set_value(iter, 0, new_text)
self.infobox.network = new_text
save_config()
def transform_bcolor(start, end):
if (start.get('background', 99) != end.get('background', 99)):
confcolors = conf.get('colors', colors)
result = start.copy()
if 'foreground' in end:
try:
fg_index = list(confcolors).index(end['foreground'].upper())
except ValueError:
return '', '', start
result['foreground'] = end['foreground']
else:
fg_index = 99
result.pop('foreground', None)
if 'background' in end:
try:
bg_index = list(confcolors).index(end['background'].upper())
except ValueError:
return '', '', start
result['background'] = end['background']
else:
bg_index = 99
del result['background']
return '\x03%02i,%02i' % (fg_index, bg_index), ',', result
else:
return '', '', start
def drop_nicklist(paned, event):
width = paned.get_allocated_width()
pos = paned.get_position()
double_click, nicklist_pos = paned._moving
if double_click:
# if we're "hidden", then we want to unhide
if width - pos <= 10:
# get the normal nicklist width
conf_nicklist = conf.get("ui-gtk/nicklist-width", 200)
# if the normal nicklist width is "hidden", then ignore it
if conf_nicklist <= 10:
paned.set_position(width - 200)
else:
paned.set_position(width - conf_nicklist)
# else we hide
else:
paned.set_position(width)
else:
if pos != nicklist_pos:
conf["ui-gtk/nicklist-width"] = width - pos - 6
def onClose(e):
nwindows = list(windows.get_with(core.manager, network=e.window.network))
if isinstance(e.window, windows.ChannelWindow):
cwindows = list(
windows.get_with(core.manager,
network=e.window.network,
wclass=windows.ChannelWindow))
#if we only have one window for the network, don't bother to part as
# we'll soon be quitting anyway
if len(nwindows) != 1 and irc_script.ischan(e.window.network,
e.window.id):
e.window.network.part(e.window.id)
if len(nwindows) == 1:
core.events.trigger("CloseNetwork",
window=e.window,
network=e.window.network)
elif isinstance(e.window, windows.StatusWindow) and conf.get('status'):
core.events.trigger("CloseNetwork",
window=e.window,
network=e.window.network)
for window in nwindows:
if window != e.window:
window.close()
if len(core.manager) == 1:
windows.new(windows.StatusWindow, irc.Network(), "status", core)
def group_exists(self,groupname):
# check if the group exists already
res = self.l.search(conf.get('LDAPSERVER','basedn'),\
ldap.SCOPE_SUBTREE,'(& (cn=%s)(objectclass=posixgroup))'%groupname,['cn'])
sres = self.l.result(res,0)
if sres[1]==[]:
return False
return True
def onSocketConnect(e):
timeout = conf.get("server_traffic_timeout", 120) * 1000
e.network._message_timeout = False
if timeout:
e.network._message_timeout_source = ui.register_timer(
timeout, check_timeout, e.network)
else:
e.network._message_timeout_source = None
def onHighlight(e):
lowertext = e.text.lower()
for word in conf.get('highlight_words', []) + [e.network.me] + e.network.nicks:
lowerword = word.lower()
pos = lowertext.find(lowerword, 0)
while pos != -1:
e.Highlight.append((pos, pos+len(word)))
pos = lowertext.find(lowerword, pos+1)
def generate_invoice_request(amount: float, memo: str = None):
invoice = lnd.generate_invoice(amount, memo, conf.get('INVOICE_TIMEOUT'))
if invoice is not None:
return json.dumps(invoice)
else:
abort(500, 'Unable to generate a new invoice')
def check_timeout(network):
if network._message_timeout:
network.raw("PING %s" % network.me)
timeout = conf.get("server_death_timeout", 240)*1000
network._message_timeout_source = ui.register_timer(timeout, check_death_timeout, network)
return False
else:
network._message_timeout = True
return True # call this function again
def onHighlight(e):
lowertext = e.text.lower()
for word in conf.get('highlight_words', []) + \
[e.network.me] + e.network.nicks:
lowerword = word.lower()
pos = lowertext.find(lowerword, 0)
while pos != -1:
e.Highlight.append((pos, pos + len(word)))
pos = lowertext.find(lowerword, pos + 1)
def user_exists(self,uid):
res = self.l.search(conf.get('LDAPSERVER','basedn'),\
ldap.SCOPE_SUBTREE,'(& (uid=%s)(objectclass=posixaccount)(objectclass=person))'%uid,['dn'])
sres = self.l.result(res,0)
if sres[1]==[]:
return False
return True
def parser_config():
"""Rewrite tornado default parser_config_file.
"""
for name in conf :
value = conf.get(name)
if name in options :
options[name].set( value )
else :
define( name , default=value )
def quit(self, msg=None):
if self.status:
try:
if msg == None:
msg = conf.get('quitmsg', "%s - %s" % (urk.long_version, urk.website))
self.raw("QUIT :%s" % msg)
except:
pass
self.disconnect()
def redis_init():
redis_conf = conf.get('redis', {})
client = redis.Redis(
host=redis_conf.get('host', 'redis-server'),
port=redis_conf.get('port', 6379),
db=redis_conf.get('database', 1),
decode_responses=True
)
return client
def after_request(response):
if response.status == '200 OK':
if response.headers.get('Content-Type', {}) == 'text/html; charset=utf-8':
response.headers['Content-Type'] = 'application/json'
response.headers['X-Server-Version'] = conf.get('VERSION')
response.headers['X-Request-Id'] = request.headers.get('X-Request-ID', '')
return response
def check_timeout(network):
if network._message_timeout:
network.raw("PING %s" % network.me)
timeout = conf.get("server_death_timeout", 240) * 1000
network._message_timeout_source = ui.register_timer(
timeout, check_death_timeout, network)
return False
else:
network._message_timeout = True
return True # call this function again
def quit(self, msg=None):
if self.status:
try:
if msg == None:
msg = conf.get(
'quitmsg',
"%s - %s" % (info.long_version, info.website))
self.raw("QUIT :%s" % msg)
except:
pass
self.disconnect()
def influxdb_init():
influxdb_conf = conf.get('influxdb', {})
client = InfluxDBClient(
host=influxdb_conf.get('host', 'influxdb-server'),
port=influxdb_conf.get('port', 8086),
username=influxdb_conf.get('username', ''),
password=influxdb_conf.get('password', ''),
database=influxdb_conf.get('database', 'telegraf'),
gzip=True
)
return client
def get_mirc_color(number):
if number == '99':
return None
number = int(number) & 15
confcolors = conf.get('colors', colors)
try:
return confcolors[number]
except:
# someone edited their colors wrongly
return colors[number]
def check_death_timeout(network):
if network._message_timeout:
network.raw("QUIT :Server missing, presumed dead")
network.disconnect(
error="The server seems to have stopped talking to us")
else:
network._message_timeout = False
timeout = conf.get("server_traffic_timeout", 120) * 1000
if timeout:
network._message_timeout_source = ui.register_timer(
timeout, check_timeout, network)
else:
network._message_timeout_source = None
def __init__(self, core):
gtk.VBox.__init__(self)
# threading stuff
gtk.gdk.threads_init()
self.core = core
self.events = core.events
self.tabs = Notebook()
self.tabs.set_property("tab-pos",
conf.get("ui-gtk/tab-pos", gtk.POS_BOTTOM))
self.tabs.set_scrollable(True)
self.tabs.set_property("can-focus", False)
self.pack_end(self.tabs)
def __init__(self, core):
Gtk.VBox.__init__(self)
# threading stuff
Gdk.threads_init()
self.core = core
self.events = core.events
self.tabs = Notebook()
self.tabs.set_property(
"tab-pos", conf.get("ui-Gtk/tab-pos", Gtk.PositionType.BOTTOM))
self.tabs.set_scrollable(True)
self.tabs.set_property("can-focus", False)
self.pack_end(self.tabs, False, True, 0)
def onCommandAlias(e):
if e.args and 'r' in e.switches:
name = e.args[0].lower()
command = aliases[name]
del aliases[name]
conf['aliases'] = aliases
e.window.write("* Deleted alias %s%s (was %s)" %
(conf.get('command-prefix', '/'), name, command))
core.events.load(__name__, reloading=True)
elif 'l' in e.switches:
e.window.write("* Current aliases:")
for i in aliases:
e.window.write("* %s%s: %s" %
(conf.get('command-prefix', '/'), i, aliases[i]))
elif len(e.args) >= 2:
name = e.args[0].lower()
command = ' '.join(e.args[1:])
aliases[name] = command
conf['aliases'] = aliases
e.window.write("* Created an alias %s%s to %s" %
(conf.get('command-prefix', '/'), name, command))
core.events.reload(__name__)
elif len(e.args) == 1:
name = e.args[0].lower()
if name in aliases:
e.window.write(
"* %s%s is an alias to %s" %
(conf.get('command-prefix', '/'), name, aliases[name]))
else:
e.window.write("* There is no alias %s%s" %
(conf.get('command-prefix', '/'), name))
else:
e.window.write("""Usage:
/alias \x02name\x02 \x02expression\x02 to create or replace an alias
/alias \x02name\x02 to look at an alias
/alias -r \x02name\x02 to remove an alias
/alias -l to see a list of aliases""")
def __init__(self,
core,
activity,
server="irc.freenode.net",
port=8001,
nicks=[],
username="",
fullname="",
name=None,
**kwargs):
self.core = core
self.manager = core.manager
self.server = server
self.port = port
self.events = core.events
self.activity = activity
self.name = name or server
self.nicks = nicks or default_nicks()
self.me = self.nicks[0]
self.username = username or "urk"
self.fullname = fullname or conf.get("fullname", self.username)
self.password = ''
self.isupport = {
'NETWORK': server,
'PREFIX': '(ohv)@%+',
'CHANMODES': 'b,k,l,imnpstr',
}
self.prefixes = {
'o': '@',
'h': '%',
'v': '+',
'@': 'o',
'%': 'h',
'+': 'v'
}
self.status = DISCONNECTED
self.failedhosts = [] # hosts we've tried and failed to connect to
self.channel_prefixes = '&#+$' # from rfc2812
self.on_channels = set()
self.requested_joins = set()
self.requested_parts = set()
self.buffer = ''
def demux_map(dataset):
print(dataset)
csv_reference_file = conf.get('celery').get('csv_reference_file')
csv_output_path = conf.get('celery').get('csv_output_path')
csv_guppy_barcoding_threads = conf.get('celery').get('csv_guppy_barcoding_threads')
reference_file = 'reference_file=%s' % csv_reference_file
for data in dataset:
for value in data.get('values'):
fields = dict(zip(data.get('columns'), value))
filename = os.path.basename(fields.get('path'))
os.chdir('/tmp')
command = [
'snakemake',
'--snakefile /opt/scripts/demux_map/Snakefile',
'--configfile /opt/scripts/demux_map/config.yaml',
'--cores 2',
'--config',
'input_fastq=%s/%s' % (data.get('tags').get('dir'), filename),
'output_path=%s' % os.path.join(csv_output_path, data.get('tags').get('cell')),
reference_file,
'guppy_barcoding_threads=%s' % csv_guppy_barcoding_threads
]
if not os.system(' '.join(command)) == 0:
sys.exit(1)
def onConnect(e):
network_info = conf.get('networks', {}).get(e.network.name, {})
for command in network_info.get('perform', []):
while command.startswith(COMMAND_PREFIX):
command = command[len(COMMAND_PREFIX):]
core.events.run(command, e.window, e.network)
tojoin = ','.join(network_info.get('join', []))
if tojoin:
core.events.run('join -n %s' % tojoin, e.window, e.network)
if hasattr(e.network, 'temp_perform'):
for command in e.network.temp_perform:
core.events.run(command, e.window, e.network)
del e.network.temp_perform
def transform_color(start, end):
if (start.get('foreground', 99) != end.get('foreground', 99)):
confcolors = conf.get('colors', colors)
result = start.copy()
if 'foreground' in end:
try:
index = list(confcolors).index(end['foreground'].upper())
except ValueError:
return '', '', start
result['foreground'] = end['foreground']
else:
index = 99
del result['foreground']
return '\x03%02i' % index, ',', result
else:
return '', '', start
def test_fastq_watch(self):
test_fastq_file = 'test.fastq'
data_dir = conf.get('ont').get('fastq_watch_path')
cell = 'TEST-CELL'
chip = 'TEST-CHIP'
fastq_dir = os.path.join(data_dir, cell, chip, 'fastq_pass')
if not os.path.exists(fastq_dir):
os.makedirs(fastq_dir)
tmp_fastq_file = os.path.join(fastq_dir, '%s.tmp' % test_fastq_file)
fastq_file = tmp_fastq_file[:-4]
shutil.copyfile(test_fastq_file, tmp_fastq_file)
shutil.move(tmp_fastq_file, fastq_file)
time.sleep(1)
sql = "select * from fastq_watch where cell = '%s' and dir = '%s' and path = '%s'" % (
cell, fastq_dir, fastq_file)
res = influxdb_cli.query(sql)
self.assertGreater(len(list(res.get_points())), 0)
def add_autojoin(network, channel):
if 'networks' not in conf:
conf['networks'] = {}
if network.name not in conf['networks']:
conf['networks'][network.name] = {'server': network.server}
conf['start_networks'] = conf.get('start_networks',
[]) + [network.name]
if 'perform' in conf['networks'][network.name]:
perform = conf['networks'][network.name]['perform']
else:
perform = conf['networks'][network.name]['perform'] = []
for n, line in enumerate(perform):
if line.startswith('join ') and ' ' not in line[5:]:
perform[n] = "%s,%s" % (line, channel)
break
else:
perform.append('join %s' % channel)
def handle():
ont_conf = conf.get('ont')
read_length_step = ont_conf.get('read_length_step')
scan_iter = redis_cli.scan_iter(match='CELL:READ_LEN:*')
measurement = 'reads_length_stats'
influxdb_data = []
for key in scan_iter:
for k, v in redis_cli.hgetall(key).items():
barcode, read_len = k.split('_')
display_read_len = int(read_len) * read_length_step
data = '%s,%s %s' % (
measurement, 'cell=%s,barcode=%s,read_len=%s' % (
key[14:],
barcode,
'%s-%s' % ((read_length_step *
(int(read_len) - 1)) + 1, display_read_len),
), 'value=%s' % v)
influxdb_data.append(data)
influxdb_cli.write_points(points=influxdb_data, protocol='line')