def add(silent=False):
params = menuUtils.getCurrentParams()
meta = menuUtils.getCurrentMeta()
import utils
utils.outputDict(params, 'menu_addtofaves - params')
utils.outputDict(meta, 'menu_addtofaves - meta')
if params == None:
if not silent:
import utils
utils.DialogOK(utils.GETTEXT(30260))
return
menuUtils.addToFaves(params, meta)
def add(silent=False):
params = menuUtils.getCurrentParams()
meta = menuUtils.getCurrentMeta()
import utils
utils.outputDict(params, 'menu_addtofaves - params')
utils.outputDict(meta, 'menu_addtofaves - meta')
if params == None:
if not silent:
import utils
utils.DialogOK(utils.GETTEXT(30260))
return
menuUtils.addToFaves(params, meta)
def addToFaves(params, meta=None):
try:
label = params['label']
thumb = params['thumb']
fanart = params['fanart']
path = params['path']
desc = params['description']
window = params['window']
filename = params['filename']
isFolder = params['isfolder']
cmd = getCmd(path, fanart, desc, window, filename, isFolder, meta)
copyFave(label, thumb, cmd)
except Exception, e:
utils.log('\n\nError in menuUtils.addToFaves : %s' % str(e))
utils.outputDict(params)
def addToFaves(params, meta=None):
try:
label = params['label']
thumb = params['thumb']
fanart = params['fanart']
path = params['path']
desc = params['description']
window = params['window']
filename = params['filename']
isFolder = params['isfolder']
cmd = getCmd(path, fanart, desc, window, filename, isFolder, meta)
copyFave(label, thumb, cmd)
except Exception, e:
utils.log('\n\nError in menuUtils.addToFaves : %s' % str(e))
utils.outputDict(params)
def doMenu(mode):
import menuUtils
utils.log('**** Context Menu Information ****')
window = xbmcgui.getCurrentWindowId()
DEBUG = ADDON.getSetting('DEBUG') == 'true'
if DEBUG:
utils.DialogOK('Current Window ID %d' % window)
utils.log('Capture window\t: %d' % window)
if window > 12999:
doStandard(useScript=False)
return
# to prevent master profile setting being used in other profiles
if mode == 0 and ADDON.getSetting('CONTEXT') != 'true':
doStandard(useScript=False)
return
folder = xbmc.getInfoLabel('Container.FolderPath')
path = xbmc.getInfoLabel('ListItem.FolderPath')
#ignore if in Super Favourites
if (ADDONID in folder) or (ADDONID in path):
doStandard(useScript=False)
return
if mode == 0 and whitelisted():
doStandard(useScript=False)
return
try:
params = menuUtils.getCurrentParams()
except:
params = None
if params == None:
doStandard(useScript=False)
return
try:
meta = menuUtils.getCurrentMeta()
except:
meta = {}
utils.outputDict(params, 'Capture Parameters')
utils.outputDict(meta, 'Capture Metadata')
folder = params['folder']
path = params['path']
label = params['label']
filename = params['filename']
thumb = params['thumb']
icon = params['icon']
playable = params['isplayable']
fanart = params['fanart']
isFolder = params['isfolder']
hasVideo = params['hasVideo']
desc = params['description']
window = params['window']
file = params['file']
isStream = params['isstream']
choice = 0
menu = []
localAddon = None
if MENU_QUICKLAUNCH:
menu.append((GETTEXT(30219), _QUICKLAUNCH))
plugins = []
try:
plugins = getPlugins()
addPlugins(menu, plugins, params, _EXTRABASE)
except Exception as e:
utils.log('Error adding plugins : %s' % str(e))
if len(path) > 0:
if MENU_ADDTOFAVES:
menu.append((GETTEXT(30047), _ADDTOFAVES))
if MENU_ADDON_SETTINGS:
localAddon = utils.findAddon(path)
if localAddon:
name = utils.getSettingsLabel(localAddon)
menu.append((name, _SETTINGS))
if MENU_DEF_ISEARCH:
default = getDefaultSearch()
if len(default) > 0:
menu.append((GETTEXT(30098) % default, _SEARCHDEF))
if MENU_ISEARCH: menu.append((GETTEXT(30054), _SEARCH))
if MENU_IRECOMMEND: menu.append((GETTEXT(30088), _RECOMMEND))
if MENU_COPY_PROPS: menu.append((GETTEXT(30209), _COPYITEM))
if MENU_VIEW_IMAGES:
if len(thumb) > 0 or len(fanart) > 0:
menu.append((GETTEXT(30216), _SHOWIMAGE))
if MENU_SF_SETTINGS:
menu.append((GETTEXT(30049), _SF_SETTINGS))
stdMenu = False
if MENU_STD_MENU:
if (len(path) > 0) or (window == 10034): #10034 is profile dialog
stdMenu = True
menu.append((GETTEXT(30048), _STD_MENU))
if hasVideo:
if MENU_DOWNLOADS and isStream:
menu.append((GETTEXT(30259), _DOWNLOAD))
if len(menu) == 0:
doStandard(useScript=False)
return
nowPlaying = GETTEXT(30220)
menu.append((nowPlaying, _PLAYLIST))
if len(menu) == 0 or (len(menu) == 1 and stdMenu):
doStandard(useScript=False)
return
xbmcgui.Window(10000).setProperty('SF_MENU_VISIBLE', 'true')
dialog = ADDON.getSetting('CONTEXT_STYLE') == '1'
import menus
if dialog:
choice = menus.selectMenu(utils.TITLE, menu)
else:
choice = menus.showMenu(
ADDONID, menu,
useBuiltin=False) #False to allow right-click to std context menu
utils.log('selection\t\t: %s' % choice)
if choice >= _EXTRABASE:
module = (choice - _EXTRABASE) / 1000
option = (choice - _EXTRABASE) % 1000
utils.log('plugin\t\t: %s' % module)
utils.log('option\t\t: %s' % option)
try:
plugins[module].process(option, params)
except Exception as e:
utils.log('Error processing plugin: %s' % str(e))
if choice == _QUICKLAUNCH:
try:
quickLaunch()
except:
pass
if choice == _STD_MENU:
doStandard(useScript=True)
if choice == _PLAYLIST:
activateWindow('videoplaylist')
if choice == _DOWNLOAD:
try:
menuUtils.doDownload(file)
except:
pass
if choice == _SF_SETTINGS:
utils.ADDON.openSettings()
if choice == _SETTINGS:
xbmcaddon.Addon(localAddon).openSettings()
if choice == _ADDTOFAVES:
menuUtils.addToFaves(params, meta)
if choice == _LAUNCH_SF:
utils.LaunchSF()
if choice in [_SEARCH, _SEARCHDEF, _RECOMMEND]:
if utils.ADDON.getSetting('STRIPNUMBERS') == 'true':
label = utils.Clean(label)
thumb = thumb if len(thumb) > 0 else 'null'
fanart = fanart if len(fanart) > 0 else 'null'
#declared in default.py
_SUPERSEARCH = 0
_SUPERSEARCHDEF = 10
_RECOMMEND_KEY = 2700
valid = [10001, 10002, 10025, 10502]
if window not in valid:
window = 10025 #video window
import urllib
if choice == _RECOMMEND:
mode = _RECOMMEND_KEY
else:
mode = _SUPERSEARCH if (choice == _SEARCH) else _SUPERSEARCHDEF
if mode == _SUPERSEARCHDEF:
return launchDefaultSearch(label)
try:
meta = urllib.quote_plus(utils.convertDictToURL(meta))
except:
meta = ''
cmd = 'ActivateWindow(%d,"plugin://%s/?mode=%d&keyword=%s&image=%s&fanart=%s&meta=%s")' % (
window, ADDONID, mode, urllib.quote_plus(label),
urllib.quote_plus(thumb), urllib.quote_plus(fanart), meta)
activateCommand(cmd)
if choice == _COPYITEM:
#if not fanart:
# fanart = thumb
cmd = menuUtils.getCmd(path, fanart, desc, window, filename, isFolder,
meta)
import clipboard
clipboard.setPasteProperties(thumb, fanart, desc, label, cmd, meta)
if choice == _SHOWIMAGE:
#if not fanart:
# fanart = thumb
import viewer
viewer.show(fanart, thumb, ADDONID)
def doMenu(mode):
import menuUtils
utils.log('**** Context Menu Information ****')
window = xbmcgui.getCurrentWindowId()
DEBUG = ADDON.getSetting('DEBUG') == 'true'
if DEBUG:
utils.DialogOK('Current Window ID %d' % window)
utils.log('Capture window\t: %d' % window)
if window > 12999:
doStandard(useScript=False)
return
# to prevent master profile setting being used in other profiles
if mode == 0 and ADDON.getSetting('CONTEXT') != 'true':
doStandard(useScript=False)
return
folder = xbmc.getInfoLabel('Container.FolderPath')
path = xbmc.getInfoLabel('ListItem.FolderPath')
#ignore if in Super Favourites
if (ADDONID in folder) or (ADDONID in path):
doStandard(useScript=False)
return
if mode == 0 and whitelisted():
doStandard(useScript=False)
return
try:
params = menuUtils.getCurrentParams()
except:
params = None
if params == None:
doStandard(useScript=False)
return
try:
meta = menuUtils.getCurrentMeta()
except:
meta = {}
utils.outputDict(params, 'Capture Parameters')
utils.outputDict(meta, 'Capture Metadata')
folder = params['folder']
path = params['path']
label = params['label']
filename = params['filename']
thumb = params['thumb']
icon = params['icon']
playable = params['isplayable']
fanart = params['fanart']
isFolder = params['isfolder']
hasVideo = params['hasVideo']
desc = params['description']
window = params['window']
file = params['file']
isStream = params['isstream']
choice = 0
menu = []
localAddon = None
if MENU_QUICKLAUNCH:
menu.append((GETTEXT(30219), _QUICKLAUNCH))
plugins = []
try:
plugins = getPlugins()
addPlugins(menu, plugins, params, _EXTRABASE)
except Exception, e:
utils.log('Error adding plugins : %s' % str(e))
def completeAnalysis(geneNetwork,
genome2sequence,
n,
c,
a=None,
clustType=None,
UniqID=None,
sep=None,
keyList=None,
handle=sys.stderr,
config=None):
"""Perform complete bipartite and twin analysis at a given identity threshold n"""
directory = "graphs" + str(n)
try:
os.mkdir(directory)
except OSError:
pass
# Names and file definitions
if clustType == 'cc':
seqCompFile = "CC.nodes" # compFile for sequences
eFile = "CC.edges"
iFile = "CC.info"
elif clustType == 'families':
seqCompFile = "family.nodes" # compFile for sequences
eFile = "family.edges"
iFile = "family.info"
else:
sys.exit("Bad clustering type -- see -C option")
edgeFile = "graph.edges" # edgeFile
trailFile = "graph.trail" # trailFile
geneNetworkDico = geneNetwork + ".dico"
geneNetworkGenes = geneNetwork + ".genes"
## ==============================
# c) assemble sequence families by computing the connected components
cmd2 = """%s -i %s -d %s -n %s -m %s -p %d""" % (
familydetector, geneNetwork, directory, geneNetworkGenes, clustType, n)
printLog(
"--------------------------------------------------\nRunning %s" %
cmd2, handle)
proc2 = Popen(args=[cmd2], shell=True, stdout=PIPE, executable="/bin/bash")
out = proc2.communicate()[0]
printLog(out.decode('utf-8'), handle)
mySeqCompFile = os.path.join(directory, seqCompFile)
myiFile = os.path.join(directory, iFile)
myeFile = os.path.join(directory, eFile)
# renumber back families through geneNetworkDico
dic1 = ut.loadMapping(geneNetworkDico)
dic2 = ut.node2communityFasta(mySeqCompFile, sep=sep)
compDict = ut.composeDict(dic1, dic2)
ut.outputDict(compDict, mySeqCompFile, sep=sep)
cleanCmd = """rm %s %s""" % (myiFile, myeFile)
procClean = Popen(args=[cleanCmd], shell=True, executable="/bin/bash")
procClean.communicate()
## B) from the sequence families to the bipartite graph
# a) Cluster sequence families and quotient the graph
cmd3 = """%s -c %s -k %s -d %s %s %s %s""" % (
FactorGraph, mySeqCompFile, UniqID, directory, genome2sequence,
edgeFile, trailFile)
printLog(
"--------------------------------------------------\nRunning %s" %
cmd3, handle)
FG.Main(edgeFile=genome2sequence,
outEdgeFile=edgeFile,
outTrailFile=trailFile,
direct=directory,
community=mySeqCompFile,
comm_id=UniqID,
sep=sep,
log=handle,
header=cmd3)
os.chdir(directory)
printLog(
"--------------------------------------------------\ncd %s" %
directory, handle)
##
rad = "graph0"
# b) Remove the degree one nodes from the sequence side
edges = rad + ".edges"
cmd4 = """%s -d 1 -u 2 %s %s""" % (shaveGraph, edgeFile, edges)
printLog(
"--------------------------------------------------\nRunning %s" %
cmd4, handle)
SG.Main(edgeFile=edgeFile,
outEdgeFile=edges,
degree=1,
nodeType=2,
sep=sep,
log=handle)
# d) Compute twins and twin supports of the bipartite graph
twins = rad + ".twins"
twinComp = rad + ".twin_comp"
cmd6 = """%s -o %s -u 2 -c %s %s """ % (DetectTwins, twins, twinComp,
edges)
printLog(
"--------------------------------------------------\nRunning %s" %
cmd6, handle)
try:
DT.Main(edgeFile=edges,
outFile=twins,
sep=sep,
unilat='2',
comp=twinComp,
log=handle)
except IOError as e:
printLog("Error in %s: %s\nExiting." % (cmd6, e), handle)
return ()
## C) from the bipartite graph to the twins and articulation points
# a) twin quotienting
twinDir = "TwinQuotient"
try:
os.mkdir(twinDir)
except OSError:
pass
rad = "graph1"
newEdges = rad + ".edges"
newTrail = rad + ".trail"
cmd7 = """%s -c %s -k %s -d %s -t %s %s %s %s""" % (
FactorGraph, twins, UniqID, twinDir, trailFile, edges, newEdges,
newTrail)
printLog(
"--------------------------------------------------\nRunning %s" %
cmd7, handle)
try:
FG.Main(edgeFile=edges,
outEdgeFile=newEdges,
outTrailFile=newTrail,
direct=twinDir,
community=twins,
comm_id=UniqID,
in_trail=trailFile,
sep=sep,
log=handle,
header=cmd7)
except IOError as e:
printLog("Error in %s: %s\nExiting." % (cmd7, e), handle)
return ()
os.chdir(twinDir)
printLog(
"--------------------------------------------------\ncd %s" % twinDir,
handle)
# b) Computing articulation points and biconnected components
ART, BIC = getArticulationPoints(newEdges)
artPoints = rad + ".art"
aP = open(artPoints, "w")
printLog(
"--------------------------------------------------\nPrinting %d articulation points in %s"
% (len(ART), artPoints), handle)
for node in ART:
outString = """%s\t%s\n""" % (node, ",".join(
[str(ID) for ID in BIC[node]]))
aP.write(outString)
aP.close()
bcNb = 0
bicFile = rad + ".bic_comp"
bC = open(bicFile, "w")
for node in BIC:
for ID in BIC[node]:
bcNb = max(bcNb, ID)
bC.write("""%s\t%d\n""" % (node, ID))
bC.close()
printLog(
"--------------------------------------------------\nPrinting %d biconnected components in %s"
% (bcNb + 1, bicFile), handle)
## D) annotations and twin component analysis
if a:
edges = rad + ".edges"
twins = rad + ".twins"
twinComp = rad + ".twin_comp"
cmd9 = """%s -o %s -u 2 -c %s %s """ % (DetectTwins, twins, twinComp,
edges)
printLog(
"--------------------------------------------------\nRunning %s" %
cmd9, handle)
try:
DT.Main(edgeFile=edges,
outFile=twins,
sep=sep,
unilat='2',
comp=twinComp,
log=handle)
except IOError as e:
printLog("Error in %s: %s\nExiting." % (cmd9, e), handle)
return ()
runDescription(a,
radical=rad,
ID=UniqID,
keyList=keyList,
handle=handle,
config=config)
def Main(edgeFile=None,outFile=None,sep=None,unilat=None,twin_supp=None,Twin_Supp=None,min_supp=None,min_size=None,nodeType=None,comp=None,debug=None,log=None):
""" Main program """
i0 = time.clock()
inext = i0
## File reading options ========================================
if not outFile:
outFile = edgeFile+".twins"
thr = min_supp
try:
k_part = int(nodeType)
except (TypeError,ValueError):
k_part = nodeType
## File reading ========================================
if not os.stat(edgeFile).st_size:
if myModule() == "__main__.py":
sys.exit("Error: Empty file %s" % edgeFile)
else:
raise IOError("Empty file %s" % edgeFile)
g = ut.myReadGraph(edgeFile)
print(g.summary())
id2name = {}
name2id = {}
for n in g.vs():
name = n['name']
ind = n.index
id2name[ind] = name
name2id[name] = ind
inext = myTimer(i0,"Loading graph",handle=log)
## Program body ===========================================
# Adjacency list computation ------------------------------
getName = lambda x:id2name[x]
nodes = None
if unilat:
typeSet = set(map(lambda x:int(x),unilat.strip().split(",")))
typeDict = defaultdict(int)
if k_part == 2 or not k_part:
typeDict.update(ut.rawNodeType(edgeFile))
elif k_part != 1:
typeDict.update(ut.loadNodeType(k_part))
nodes = (n.index for n in g.vs() if typeDict[n['name']] in typeSet)
ADJ = ut.getAdjlist(g,nodes=nodes)
inext = myTimer(inext,"Computation of adjacency list",handle=log)
# Twin computation ----------------------------------------
support,twins = ut.detectRepeated(ADJ,k_init=0,debug=debug) # support: groupID -> common_list_of_neighbours; twins: node -> groupID_of_its_twin_class
inext = myTimer(inext,"Computation of twins",handle=log)
new_support = dict([(gid,tuple(map(getName,support[gid]))) for gid in support])
new_twins = dict([(id2name[node],twins[node]) for node in twins])
support = new_support
twins = new_twins
inext = myTimer(inext,"Renumbering of twins",handle=log)
sniwt = ut.InvertMap(twins) # groupID -> list_of_twin_nodes
inext = myTimer(inext,"Computation of twin support",handle=log)
# Computation of components (twins + support)
if comp:
with open(comp,'w') as h:
for key,val in iter(twins.items()):
outString = str(key)+sep+str(val)+"\n"
h.write(outString)
inext = myTimer(inext,"Writing twins file",handle=log)
for val,nodes in iter(support.items()):
for node in nodes:
outString = str(node)+sep+str(val)+"\n"
h.write(outString)
inext = myTimer(inext,"Writing twins component file",handle=log)
# Computation of twinSupport (twinID twinNb twinSupport)
if twin_supp:
with open(twin_supp,'w') as g:
for i,nodeList in iter(sniwt.items()):
supp = support[i]
if len(supp) >= thr and len(nodeList) >= min_size: # Threshold for trivial twins (new option 15/12/15)
vals = [str(i),str(len(nodeList)),str(len(supp))]
vals.extend(list(map(lambda x:str(x),supp)))
g.write("\t".join(vals)+"\n")
inext = myTimer(inext,"Writing twins support file",handle=log)
# Computation of TwinSupport (twinID twinNodes twinSupport)
if Twin_Supp:
with open(Twin_Supp,'w') as g:
for i,nodeList in iter(sniwt.items()):
supp = support[i]
if len(supp) >= thr and len(nodeList) >= min_size: # Threshold for trivial twins (new option 15/12/15)
myTwins = ",".join(map(lambda x:str(x),nodeList))
mySupport = ",".join(map(lambda x:str(x),supp))
vals = [str(i)]
vals.extend(list(map(lambda x:str(x),supp)))
g.write("\t".join(vals)+"\n")
inext = myTimer(inext,"Writing Twins Support file",handle=log)
ut.outputDict(twins,outFile,sep=sep)
allTwins = len(sniwt.keys())
t = len([i for (i,v) in iter(sniwt.items()) if len(v) == 1])
try:
tp = 100*float(t)/float(allTwins)
except:
tp = 0
nt = allTwins - t
try:
ntp = 100*float(nt)/float(allTwins)
except:
ntp = 0
printLog("""Found %s twins, %s trivial twins (%.2f%%) and %s non-trivial twins (%.2f%%)""" % (allTwins,t,tp,nt,ntp),log)
## Ending ======================================================
prog = myModule()
if prog == "__main__.py":
prog = sys.argv[0].split("/")[-1]
inext = myTimer(i0,"Total computing time for %s" % prog,handle=log)
return
def doMenu(mode):
import menuUtils
utils.log('**** Context Menu Information ****')
window = xbmcgui.getCurrentWindowId()
DEBUG = ADDON.getSetting('DEBUG') == 'true'
if DEBUG:
utils.DialogOK('Current Window ID %d' % window)
utils.log('Capture window\t: %d' % window)
#active = [0, 1, 2, 3, 25, 40, 500, 501, 502, 601, 2005]
#if window-10000 not in active:
# doStandard(useScript=False)
# return
if window > 12999:
doStandard(useScript=False)
return
# to prevent master profile setting being used in other profiles
if mode == 0 and ADDON.getSetting('CONTEXT') != 'true':
doStandard(useScript=False)
return
folder = xbmc.getInfoLabel('Container.FolderPath')
path = xbmc.getInfoLabel('ListItem.FolderPath')
#ignore if in Super Favourites
if (ADDONID in folder) or (ADDONID in path):
doStandard(useScript=False)
return
if mode == 0 and whitelisted():
doStandard(useScript=False)
return
params = menuUtils.getCurrentParams()
meta = menuUtils.getCurrentMeta()
if params == None:
doStandard(useScript=False)
return
utils.outputDict(params, 'Capture Parameters')
utils.outputDict(meta, 'Capture Metadata')
folder = params['folder']
path = params['path']
label = params['label']
filename = params['filename']
thumb = params['thumb']
icon = params['icon']
playable = params['isplayable']
fanart = params['fanart']
isFolder = params['isfolder']
hasVideo = params['hasVideo']
desc = params['description']
window = params['window']
file = params['file']
isStream = params['isstream']
choice = 0
menu = []
localAddon = None
if MENU_QUICKLAUNCH:
menu.append((GETTEXT(30219), _QUICKLAUNCH))
plugins = []
try:
plugins = getPlugins()
addPlugins(menu, plugins, params, _EXTRABASE)
except Exception, e:
utils.log('Error adding plugins : %s' % str(e))