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 taxonomy(request):
json_response = "currentTaxonomy = " + json.dumps(
StorageRequestHandler.GetTreeList())
return HttpResponse(json_response, content_type="application/json")