def table_platform(request):
'''
Display the div table of the
first 10 line of the given platform
'''
if request.is_ajax():
if request.method == 'POST':
try:
list_annot = request.POST['list_annot']
except MultiValueDictKeyError:
list_annot = ''
platform_id = request.POST['platform_id']
if list_annot == '':
table = geo_annot_tab(platform_id,10)
return HttpResponse(table,mimetype="text/html")
else:
args = simplejson.dumps(platform_id)+','+list_annot
send_to_queue('ocelot.Platforms.utils','get_geo_annot_split',args)
return HttpResponse('The request was sent to the queue.',mimetype="text/html")
#return HttpResponseRedirect('/admin/chip/')
else:
return HttpResponse("Not Found",mimetype="text/plain")
else:
return HttpResponse("Not Found",mimetype="text/plain")
def DSparse(request,dataset_id):
'''
Parse the XML and display the various information
of the dataset...might be dismiss in order to do it
client side with JavaSrcipt
'''
dictionary = list(Dictionary.objects.filter(dataset_id = dataset_id))
metainfo = list(MetaInfo.objects.filter(dataset_id = dataset_id))
if not dictionary:
return HttpResponseRedirect('/admin/geo/')
else:
dictionary = dictionary[0]
if not metainfo:
metainfo = MetaInfo(dataset_id = dataset_id)
else:
metainfo = metainfo[0]
datasets = list(Datasets.objects.all())
platforms = GPL2title(dataset_id)
platform_list = []
for platform in platforms:
platform_list.append(platform['id'])
metainfo.platform = ",".join(platform_list)
# Collect the metainfo to pass to the
# Autocomplete
treatments = []
subtypes = []
diseases = []
for dataset in datasets:
treats = dataset.treatment.split(',')
for treatment in treats:
if treatment not in treatments:
treatments.append(treatment.strip())
dis = dataset.disease.split(',')
for disease in dis:
if disease not in diseases:
diseases.append(disease.strip())
subtps = dataset.subtype.split(',')
for subtype in subtps:
if subtype not in subtypes:
subtypes.append(subtype.strip())
treatments = simplejson.dumps(treatments)
subtypes = simplejson.dumps(subtypes)
diseases = simplejson.dumps(diseases)
req = getGEOurl(dataset_id,'meta')
with contextlib.closing(urlopen(req)) as geo:
DS = GEOdsParse(geo)
acc = DS['accessions'].split(' ')
for a in acc:
if not a.startswith('GSM'):
acc.remove(a)
released = DS['released'].split('-')
metainfo.released = datetime.date(int(released[0].strip()),int(released[1].strip()),int(released[2].strip()))
metainfo.saved = datetime.date.today()
del DS['released']
del DS['accessions']
acclen = len(acc)
doGSMtable.needs_autoescape = True
GSMtable = doGSMtable(dataset_id)
# Form part:
if request.method == 'GET':
dictform = geoforms.GEOForm(instance=dictionary)
metaform = geoforms.GEOMetaForm(instance=metainfo)
if request.method == 'POST':
dictform = geoforms.GEOForm(data=request.POST,instance=dictionary)
metaform = geoforms.GEOMetaForm(data=request.POST,instance=metainfo)
if dictform.is_valid() and metaform.is_valid():
dictform.save()
metaform.save()
dictionary = Dictionary.objects.get(dataset_id__exact = dataset_id)
metainfo = MetaInfo.objects.get(dataset_id__exact = dataset_id)
metainfo.treatment = metainfo.treatment.replace(', ',',').strip(',')
metainfo.subtype = metainfo.subtype.replace(', ',',').strip(',')
metainfo.disease = metainfo.disease.replace(', ',',').strip(',')
metainfo.samples_count = acclen
metainfo.save()
for platform in platforms:
plt = list(Platform.objects.filter(platform_id = platform['id']))
if not plt:
plt = Platform(platform_id = platform['id'], name = platform['title'] )
plt.save()
already_indexed = list(Datasets.objects.filter(dataset_id__exact = dataset_id))
if already_indexed:
RegisterGSE(dictionary,metainfo)
send_to_queue('ocelot.pyGEO.utils','get_express',simplejson.dumps(dataset_id))
return HttpResponseRedirect('/admin/geo/')
payload = dict(platforms=platforms, dictform=dictform, metaform=metaform, DS=DS, GSMtable=GSMtable, dataset_id=dataset_id, acclen=acclen, treatments=treatments, diseases=diseases, subtypes=subtypes)
return render_to_response('geo_parse.html',payload,RequestContext(request))