def Upload(request):
status = None
message = ""
if request.is_ajax() or request.method == 'POST':
# form = uploadFileForm(request.POST, request.FILES)
if request.method == 'POST':
genomeInfo = {
'kingdom': request.POST.get('Kingdom', u''),
'class': request.POST.get('Class', None),
'genus': request.POST.get('Genus', None),
'species': request.POST.get('Species', None),
'specimen': request.POST.get('specimenName', "Unknown"),
'genomeName': request.POST.get('genomeName', None),
'source': request.POST.get('source', None),
'dateSequenced': request.POST.get('dateSequenced', None),
'description': request.POST.get('description', None),
'isPublic': request.POST.get('isPublic', False),
'chromosome': request.POST.get('chromosomeName', None)
}
filePath = StorageRequestHandler.HandleUploadedFile(
request.FILES['file'], genomeInfo, request.user)
uploads = StorageRequestHandler.GetUserImports(request.user).distinct()
return render(request,
'uploadStatus.json', {'uploads': uploads},
content_type="application/json")
context = {
'status': status,
'message': message,
'existingSpecimens': StorageRequestHandler.GetTreeList(request.user)
}
return render(request, 'upload.html', context)
def index(request):
if request.user.is_authenticated():
chromosomes = FastaFiles.objects.filter(
Q(Public=True) | Q(User=request.user))
else:
chromosomes = FastaFiles.objects.filter(Public=True)
specimenNames = chromosomes.values('Specimen__Name').distinct()
specimenNames = [
n.values()[0] for n in specimenNames if n.values()[0] != "businesscard"
]
specimens = Specimen.objects.filter(Name__in=specimenNames)
if request.GET.get('user'):
specimens = specimens.filter(fastafiles__User__email=request.GET.get(
'user')).distinct() #only return uploads from specified user
if request.GET.get('kingdom'):
specimens = specimens.filter(
Kingdom__iexact=request.GET.get('kingdom'))
if request.GET.get('class'):
specimens = specimens.filter(Class__iexact=request.GET.get('class'))
if request.GET.get('genus'):
specimens = specimens.filter(Genus__iexact=request.GET.get('genus'))
if request.GET.get('species'):
specimens = specimens.filter(
Species__iexact=request.GET.get('species'))
tree = StorageRequestHandler.GetTreeList(request.user)
context = {'specimens': specimens, 'tree': tree}
return render(request, 'index.html', context)
def readFile(state):
# assert isinstance(state, RequestPacket)
try:
filePath = StorageRequestHandler.GetFastaFilePath(state.specimen, state.chromosome, state.start)
if state.scale < 100000: # TODO: this is set really high right now for testing. Originally 10
print "opening file ", filePath, " for ", state.specimen, state.chromosome, str(state.start)
if not filePath:
return None
result = None
with open(filePath, 'r') as rawFile:
result = rawFile.read()
return result
# print 'Opened File'
#
# for line in rawFile: # 1MB chunks at a time
# collection.append( line )
#
# seq = ''.join(collection)
# return seq #FastaFile(seq)
except IOError:
print "Couldn't open file. Maybe it doesn't exist."
return None
def tryGetGraphPNG(state):
fileName = StorageRequestHandler.GetPngFilePath(state)
try:
data = open(fileName, 'rb').read()
print "Found cached file: ", fileName
return data
except:
return None
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 ['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 readAndAppendNextChunk(self, addPadding=False):
assert StorageRequestHandler.GetFastaFilePath(
self.specimen, self.chromosome,
1) is not None, "Specimen and Chromosome is not in the database"
startBackup = self.start
if not self.seq:
self.seq = '' #ensure that seq is at least a string object
self.start = self.start + len(
self.seq) # jump to the end of the current sequence (+ chunkSize)
#print "Requesting",self.specimen, self.chromosome, self.start
sequence = readFile(
self
) # see if there's a file that begins where you end, this will stop on a partial file
if sequence is not None:
self.seq = self.seq + sequence #append two sequences together
elif addPadding:
self.seq = self.seq + ('N' * chunkSize)
self.start = startBackup
self.length = len(self.seq)
return self
def testSampleFilePath(self):
path = StorageRequestHandler.GetFastaFilePath('hg18', 'chrY-sample', 1)
print path
self.assertNotEqual(None, path, "Didn't return a path")
def getFastaFilePath(self):
return StorageRequestHandler.GetFastaFilePath(self.specimen,
self.chromosome,
self.start)
def taxonomy(request):
json_response = "currentTaxonomy = " + json.dumps(
StorageRequestHandler.GetTreeList())
return HttpResponse(json_response, content_type="application/json")