def file_edit(request, file_id, response_format='html'):
"File edit page"
file = get_object_or_404(File, pk=file_id)
if not request.user.profile.has_permission(file, mode='w'):
return user_denied(request, message="You don't have access to this File")
if request.POST:
if 'cancel' not in request.POST:
form = FileForm(
request.user.profile, None, request.POST, request.FILES, instance=file)
if form.is_valid():
file = form.save()
return HttpResponseRedirect(reverse('documents_file_view', args=[file.id]))
else:
return HttpResponseRedirect(reverse('documents_file_view', args=[file.id]))
else:
form = FileForm(request.user.profile, None, instance=file)
context = _get_default_context(request)
context.update({'form': form,
'file': file})
return render_to_response('documents/file_edit', context,
context_instance=RequestContext(request),
response_format=response_format)
def file_upload_typed(request, folder_id=None, response_format='html'):
"File upload to preselected folder"
folder = None
if folder_id:
folder = get_object_or_404(Folder, pk=folder_id)
if not request.user.profile.has_permission(folder, mode='x'):
folder = None
if request.POST:
if 'cancel' not in request.POST:
form = FileForm(
request.user.profile, folder_id, request.POST, request.FILES)
if form.is_valid():
file = form.save()
file.set_user_from_request(request)
return HttpResponseRedirect(reverse('documents_file_view', args=[file.id]))
else:
return HttpResponseRedirect(reverse('document_index'))
else:
form = FileForm(request.user.profile, folder_id)
context = _get_default_context(request)
context.update({'form': form,
'folder': folder})
return render_to_response('documents/file_upload_typed', context,
context_instance=RequestContext(request),
response_format=response_format)
def attach_file(request,content_type_id,pk):
ct = ContentType.objects.get(id=content_type_id)
klass = ct.model_class()
obj = klass.objects.get(pk=pk)
if request.method == 'GET':
form = FileForm()
elif request.method == 'POST':
form = FileForm(request.POST,request.FILES)
if form.is_valid():
obj = form.save(commit=False)
obj.uploaded_by=request.user
obj.object_id = pk
obj.content_type = ct
obj.name = obj.file.name
obj.save()
return Response(FileSerializer(obj).data)
else:
return Response({'errors':form.errors},status=404)
def file_upload(request, response_format='html'):
"New file form"
if request.POST:
if 'cancel' not in request.POST:
file = File()
form = FileForm(
request.user.profile, None, request.POST, request.FILES, instance=file)
if form.is_valid():
file = form.save()
file.set_user_from_request(request)
return HttpResponseRedirect(reverse('documents_file_view', args=[file.id]))
else:
return HttpResponseRedirect(reverse('document_index'))
else:
form = FileForm(request.user.profile, None)
context = _get_default_context(request)
context.update({'form': form})
return render_to_response('documents/file_upload', context,
context_instance=RequestContext(request),
response_format=response_format)
def file_form(request):
# if not request.user.is_staff or not request.user.is_superuser:
# raise Http404;
if request.POST:
form = FileForm(request.POST, request.FILES)
if form.is_valid():
instance = form.save(commit=False)
instance.user = request.user
instance.save()
# read CSV file and define parameters
input_file_name = re.search(r'/(media/.*)', instance.file.url)
fileID = instance.id
input_file = vcf.Reader(open(input_file_name.group(1), "r"))
# output_somatic_file = open('media/somatic_mutation-'+str(fileID)+'.tsv', 'wb')
# output_germline_file = open('media/germline_mutation-'+str(fileID)+'.tsv', 'wb')
logs = open('media/logs-' + str(fileID) + '.txt', 'w')
somatic_mutation_array = []
germline_mutation_array = []
# Read vcf file and create seperate arrays for somatic and germline mutation
for record in input_file:
chr = re.search(r'chr(.*)', str(record.CHROM))
start_pos = str(record.POS)
if record.REF == '-':
end_pos = record.POS + 1
else:
end_pos = start_pos
ref = str(record.REF)
alt = re.search(r'\[(.*)\]', str(record.ALT))
oncoTator = 'http://www.broadinstitute.org/oncotator/mutation/' + chr.group(
1
) + '_' + start_pos + '_' + end_pos + '_' + ref + '_' + alt.group(
1)
try:
oncoTator_response = requests.get(oncoTator)
except ConnectionError as e:
print e
logs.write(str(e))
oncoTator_response = "No response"
if oncoTator_response != "No response" and oncoTator_response.status_code != 500:
mutation = json.loads(oncoTator_response.text)
if "ERROR" in mutation:
logs.write("OncoTator is giving error for url:" +
oncoTator + " Error message: " +
str(oncoTator_response.text))
else:
if mutation["CGC_Cancer Germline Mut"] == "yes":
germline_mutation_array.append(mutation)
if mutation["CGC_Cancer Somatic Mut"] == "yes":
somatic_mutation_array.append(mutation)
logs.close()
# write values from arrays to tsv files
# fieldnames = []
# for key in somatic_mutation_array[0]:
# fieldnames.append(str(key))
# tsv_somatic_file = csv.DictWriter(output_somatic_file, fieldnames=fieldnames, delimiter='\t')
# tsv_somatic_file.writeheader()
for mutation in somatic_mutation_array:
# tsv_somatic_file.writerow(mutation)
ssnp = somatic_snp.objects.create(
study_name=instance,
gene=mutation["gene"],
chromosome=mutation["ESP_Chromosome"],
start=mutation["start"],
end=mutation["end"],
ref_allele=mutation["ref_allele"],
alt_allele=mutation["alt_allele"],
variant_class=mutation["variant_classification"],
variant_type=mutation["variant_type"],
ensemblID=mutation["HGNC_Ensembl Gene ID"])
# output_somatic_file.close()
# tsv_germline_file = csv.DictWriter(output_germline_file, fieldnames=fieldnames, delimiter='\t')
# tsv_germline_file.writeheader()
for mutation in germline_mutation_array:
# tsv_germline_file.writerow(mutation)
gsnp = germline_snp.objects.create(
study_name=instance,
gene=mutation["gene"],
chromosome=mutation["ESP_Chromosome"],
start=mutation["start"],
end=mutation["end"],
ref_allele=mutation["ref_allele"],
alt_allele=mutation["alt_allele"],
variant_class=mutation["variant_classification"],
variant_type=mutation["variant_type"],
ensemblID=mutation["HGNC_Ensembl Gene ID"])
# output_germline_file.close()
# fileread = open('media/germline_mutation-'+str(fileID)+'.tsv', 'r')
# TSVfile = File(fileread)
# instance.germline_result.save('media/germline_mutation-'+str(fileID)+'.tsv', TSVfile, save=True)
#
# fileread = open('media/somatic_mutation-' + str(fileID) + '.tsv', 'r')
# TSVfile = File(fileread)
# instance.somatic_result.save('media/somtic_mutation-' + str(fileID) + '.tsv', TSVfile, save=True)
return HttpResponseRedirect('/result/')
else:
form = FileForm()
return render(request, 'oncotator/snp_tools.html', {'form': form})
def file_form(request):
# if not request.user.is_staff or not request.user.is_superuser:
# raise Http404;
if request.POST:
form = FileForm(request.POST, request.FILES)
if form.is_valid():
instance = form.save(commit=False)
instance.user = request.user
instance.save()
# read CSV file and define parameters
input_file_name = re.search(r'/(media/.*)', instance.file.url)
fileID = instance.id
input_file = vcf.Reader(open(input_file_name.group(1), "r"))
# output_somatic_file = open('media/somatic_mutation-'+str(fileID)+'.tsv', 'wb')
# output_germline_file = open('media/germline_mutation-'+str(fileID)+'.tsv', 'wb')
logs = open('media/logs-'+str(fileID)+'.txt', 'w')
somatic_mutation_array = []
germline_mutation_array = []
# Read vcf file and create seperate arrays for somatic and germline mutation
for record in input_file:
chr = re.search(r'chr(.*)', str(record.CHROM))
start_pos = str(record.POS)
if record.REF == '-':
end_pos = record.POS + 1
else:
end_pos = start_pos
ref = str(record.REF)
alt = re.search(r'\[(.*)\]', str(record.ALT))
oncoTator = 'http://www.broadinstitute.org/oncotator/mutation/' + chr.group(
1) + '_' + start_pos + '_' + end_pos + '_' + ref + '_' + alt.group(1)
try:
oncoTator_response = requests.get(oncoTator)
except ConnectionError as e:
print e
logs.write(str(e))
oncoTator_response = "No response"
if oncoTator_response != "No response" and oncoTator_response.status_code != 500:
mutation = json.loads(oncoTator_response.text)
if "ERROR" in mutation:
logs.write("OncoTator is giving error for url:" + oncoTator + " Error message: " + str(oncoTator_response.text))
else:
if mutation["CGC_Cancer Germline Mut"] == "yes":
germline_mutation_array.append(mutation)
if mutation["CGC_Cancer Somatic Mut"] == "yes":
somatic_mutation_array.append(mutation)
logs.close()
# write values from arrays to tsv files
# fieldnames = []
# for key in somatic_mutation_array[0]:
# fieldnames.append(str(key))
# tsv_somatic_file = csv.DictWriter(output_somatic_file, fieldnames=fieldnames, delimiter='\t')
# tsv_somatic_file.writeheader()
for mutation in somatic_mutation_array:
# tsv_somatic_file.writerow(mutation)
ssnp = somatic_snp.objects.create(study_name=instance, gene=mutation["gene"], chromosome=mutation["ESP_Chromosome"], start=mutation["start"], end=mutation["end"], ref_allele=mutation["ref_allele"], alt_allele=mutation["alt_allele"], variant_class=mutation["variant_classification"],variant_type=mutation["variant_type"], ensemblID=mutation["HGNC_Ensembl Gene ID"])
# output_somatic_file.close()
# tsv_germline_file = csv.DictWriter(output_germline_file, fieldnames=fieldnames, delimiter='\t')
# tsv_germline_file.writeheader()
for mutation in germline_mutation_array:
# tsv_germline_file.writerow(mutation)
gsnp = germline_snp.objects.create(study_name=instance, gene=mutation["gene"], chromosome=mutation["ESP_Chromosome"], start=mutation["start"], end=mutation["end"], ref_allele=mutation["ref_allele"], alt_allele=mutation["alt_allele"], variant_class=mutation["variant_classification"],variant_type=mutation["variant_type"], ensemblID=mutation["HGNC_Ensembl Gene ID"])
# output_germline_file.close()
# fileread = open('media/germline_mutation-'+str(fileID)+'.tsv', 'r')
# TSVfile = File(fileread)
# instance.germline_result.save('media/germline_mutation-'+str(fileID)+'.tsv', TSVfile, save=True)
#
# fileread = open('media/somatic_mutation-' + str(fileID) + '.tsv', 'r')
# TSVfile = File(fileread)
# instance.somatic_result.save('media/somtic_mutation-' + str(fileID) + '.tsv', TSVfile, save=True)
return HttpResponseRedirect('/result/')
else:
form = FileForm()
return render(request, 'oncotator/snp_tools.html', {'form': form})
