def precomputeRepeatMap(request):
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "SkittleTree.settings")
from SkittleCore import GraphRequestHandler
from DNAStorage import StorageRequestHandler
specimen = request[0]
dbSpecimen = StorageRequestHandler.GetSpecimen(specimen)
chromosomes = StorageRequestHandler.GetRelatedChromosomes(dbSpecimen)
for chromosome in chromosomes:
length = StorageRequestHandler.GetChromosomeLength(specimen, chromosome)
chunks = range(1, length + 1, 2 ** 16)
for targetIndex in range(request[2], len(chunks), request[1]):
start = chunks[targetIndex]
state = makeRequestPacket(specimen, chromosome, start)
print "Computing: ", state.specimen, state.chromosome, state.start
GraphRequestHandler.handleRequest(state)
print "Done computing ", state.specimen, state.chromosome, state.start
def precomputeRepeatMap(request):
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "SkittleTree.settings")
from SkittleCore import GraphRequestHandler
from DNAStorage import StorageRequestHandler
specimen = request[0]
dbSpecimen = StorageRequestHandler.GetSpecimen(specimen)
chromosomes = StorageRequestHandler.GetRelatedChromosomes(dbSpecimen)
for chromosome in chromosomes:
length = StorageRequestHandler.GetChromosomeLength(specimen, chromosome)
chunks = range(1, length + 1, 2 ** 16)
for targetIndex in range(request[2], len(chunks), request[1]):
start = chunks[targetIndex]
state = makeRequestPacket(specimen, chromosome, start)
print "Computing: ", state.specimen, state.chromosome, state.start
GraphRequestHandler.handleRequest(state)
print "Done computing ", state.specimen, state.chromosome, state.start
def precomputeAnyGraph(request):
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "SkittleTree.settings")
from SkittleCore import GraphRequestHandler
from DNAStorage import StorageRequestHandler
specimen = request[2]
chromosomes = StorageRequestHandler.GetRelatedChromosomes(specimen)
for chromosome in chromosomes:
length = StorageRequestHandler.GetChromosomeLength(specimen, chromosome)
chunks = range(1, length+1, 2**16)[-7:]
for targetIndex in range(request[1], len(chunks),
request[0]): # this loop divies up the jobs by PID according to modulo nProcessors
start = chunks[targetIndex]
state = makeRequestPacket(specimen, chromosome, start, request[3], request[4])
print "Computing: ", state.specimen, state.chromosome, state.start
GraphRequestHandler.handleRequest(state)
print "Done computing ", state.specimen, state.chromosome, state.start
def precomputeAnyGraph(request):
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "SkittleTree.settings")
from SkittleCore import GraphRequestHandler
from DNAStorage import StorageRequestHandler
specimen = request[2]
# chromosomes = StorageRequestHandler.GetRelatedChromosomes(specimen)
for chromosome in ['chrY']: #chromosomes:
length = StorageRequestHandler.GetChromosomeLength(specimen, chromosome)
chunks = [1] #range(1, length+1, 2**16)[-7:]
for targetIndex in range(request[1], len(chunks),
request[0]):#this loop divies up the jobs by PID according to modulo nProcessors
start = chunks[targetIndex]
state = makeRequestPacket(specimen, chromosome, start, request[3], request[4])
print "Computing: ", state.specimen, state.chromosome, state.start
GraphRequestHandler.handleRequest(state)
print "Done computing ", state.specimen, state.chromosome, state.start
def graph(request, genus="h**o", species="sapiens", specimen="hg18", chromosome="chrY-sample"):
if IsUserForbidden(specimen, chromosome, request.user): #also checks existance
return HttpResponse(status=403)
state = createRequestPacket(request, specimen, chromosome)
graphSettings = None
if state.requestedGraph == 'h':
graphSettings = createHighlighterState(request, genus, species, specimen, chromosome)
state.searchStart = int(request.GET.get('searchStart', 1))
state.searchStop = int(request.GET.get('searchStop', 1))
image_data = GraphRequestHandler.handleRequest(state, graphSettings)
return HttpResponse(image_data, content_type="image/png")
def graph(request, genus="h**o", species="sapiens", specimen="hg18", chromosome="chrY-sample"):
if IsUserForbidden(specimen, chromosome, request.user): #also checks existance
return HttpResponse(status=403)
state = createRequestPacket(request, specimen, chromosome)
graphSettings = None
if state.requestedGraph == 'h':
graphSettings = createHighlighterState(request, genus, species, specimen, chromosome)
state.searchStart = int(request.GET.get('searchStart', 1))
state.searchStop = int(request.GET.get('searchStop', 1))
try:
image_data = GraphRequestHandler.handleRequest(state, graphSettings)
return HttpResponse(image_data, content_type="image/png")
except IOError as e:
print e
return HttpResponse(open('SkittleTree/UI/assets/gfx/bad_image.png', 'rb').read(), content_type="image/png")
def graph(request,
genus="h**o",
species="sapiens",
specimen="hg18",
chromosome="chrY-sample"):
if IsUserForbidden(specimen, chromosome,
request.user): #also checks existance
return HttpResponse(status=403)
state = createRequestPacket(request, specimen, chromosome)
graphSettings = None
if state.requestedGraph == 'h':
graphSettings = createHighlighterState(request, genus, species,
specimen, chromosome)
state.searchStart = int(request.GET.get('searchStart', 1))
state.searchStop = int(request.GET.get('searchStop', 1))
image_data = GraphRequestHandler.handleRequest(state, graphSettings)
return HttpResponse(image_data, content_type="image/png")
def state(request):
j = "graphStatus = " + json.dumps(GraphRequestHandler.generateGraphListForServer())
# j += "annotationSources = " + simplejson.dumps(StorageRequestHandler.getAnnotations())
j += ";graphOrder = ['n','b','t','o','m','s'];"
return HttpResponse(j,content_type="application/json")
def handle(self, *args, **options):
self.stdout.write(str(grh.GetRegisteredGraphsSymbols()) + "\n")
def state(request):
j = "graphStatus = " + json.dumps(
GraphRequestHandler.generateGraphListForServer())
# j += "annotationSources = " + simplejson.dumps(StorageRequestHandler.getAnnotations())
j += ";graphOrder = ['n','b','t','o','m','s'];"
return HttpResponse(j, content_type="application/json")
