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 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")