def investing(request):
# Handle file upload
file_form = FileForm(request.POST)
form = DocumentForm(request.POST, request.FILES)
if request.method == 'POST' and "uploadFile" in request.POST:
# Upload
if form.is_valid():
newdoc = Document(docfile = request.FILES['docfile'])
newdoc.save()
# Redirect to the document list after POST
return HttpResponseRedirect(reverse('dataloader.views.investing'))
elif request.method == 'POST' and "invest" in request.POST:
# Make Investments
if file_form.is_valid():
file_name = file_form.cleaned_data['file_input']
print "### FILE FOR INVESTMENTS: " + file_name
file_path = settings.MEDIA_ROOT + "/" + file_name
print file_path
cr = csv.reader(open(file_path))
# Starting from second row
for row in cr:
if row[0] == 'fund' or row[0] == 'individual':
investment_manager.fund(row)
elif row[0] == 'buy':
investment_manager.buy(row)
elif row[0] == 'sell':
investment_manager.sell(row)
elif row[0] == 'sellbuy':
investment_manager.sellbuy(row)
return HttpResponseRedirect(reverse('dataloader.views.investing'))
elif request.method == 'POST' and "clear" in request.POST:
# Clear Investments
print "### This should clear everything"
Activity.objects.all().delete()
StakeHold.objects.all().delete()
Port_Indi.objects.all().delete()
print "### OK check porfolio page"
else:
form = DocumentForm() # A empty, unbound form
file_form = FileForm()
# Load documents for the list page
documents = Document.objects.all()
return render_to_response(
'nav/investing.html',
{'documents': documents, 'form': form, 'file_form':file_form},
context_instance=RequestContext(request)
)
def upload_attachment(request, projectID):
if 'file' not in request.FILES:
raise IOError("Missing file")
if request.FILES['file'].size > 10 * 1024 * 1024:
raise IOError("File too large")
form = FileForm(request.POST, request.FILES)
if (form.is_valid()):
#set up parameters for database insert
fileObj = request.FILES['file']
projID = project_api.get_project(projectID)
fname = fileObj.name
fileUUID = str(uuid.uuid4())
#rename file object to have UUID as name to avoid conflicts when retrieving files
fileObj.name = fileUUID
f = ProjectFile(file=fileObj,
project=projID,
name=fname,
uuid=fileUUID)
f.save()
return redirect(request.POST['referer'])
def upload_attachment(request, projectID):
if 'file' not in request.FILES:
raise IOError("Missing file")
if request.FILES['file'].size > 10*1024*1024:
raise IOError("File too large")
form = FileForm(request.POST, request.FILES)
if(form.is_valid()):
#set up parameters for database insert
fileObj = request.FILES['file']
projID = project_api.get_project(projectID)
fname = fileObj.name
fileUUID = str(uuid.uuid4())
#rename file object to have UUID as name to avoid conflicts when retrieving files
fileObj.name=fileUUID
f = ProjectFile(file=fileObj,
project=projID,
name=fname,
uuid=fileUUID)
f.save()
return redirect(request.POST['referer'])
def upload(req):
up_files = 'yes'
if req.method == "POST":
ff = FileForm(req.POST, req.FILES)
folder_name = req.session.get('folder_name')
if ff.is_valid():
#获取表单数据
b = ' Byte'
file_name = ff.cleaned_data['file_name']
file_loc = ff.cleaned_data['file_loc']
file_handel = req.FILES['file_loc']
file_size = str(file_handel.size) + b
file_type_split1 = str(file_handel.name)
file_type_split2 = file_type_split1.split('.')
file_type = file_type_split2[1]
#写入数据库
upload_time = timezone.now()
f = Folder.objects.get(folder_name=folder_name)
f.modify_time = upload_time
f.save()
f.file_set.create(file_name=file_name, file_loc=file_loc, file_size=file_size, file_type=file_type, upload_time=upload_time)
return HttpResponseRedirect('/online/index/')
else:
ff = FileForm()
return render(req, 'create_folder_new.html', {'ff': ff, 'up_files': up_files})
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 import_bookmark(request, template_name='bookmark/import_bookmark.html'):
file_form = FileForm(request.POST or None, request.FILES or None)
if request.method == 'POST' and file_form.is_valid():
file = request.FILES['file']
tags_input = file_form.cleaned_data['tags']
public = file_form.cleaned_data['public']
try:
bookmarks = parse_firefox_bookmark(file)
for bk in bookmarks:
try:
bookmark = Bookmark.objects.create(url=bk['url'],
title=bk['title'],
owner=request.user,
public=public)
if tags_input:
tags = tags_input
else:
tags = parse_tags(bk['tags'])
for tag in tags:
bookmark.tags.add(tag)
# Update the screen shot
update_bk_screen_shot_async(bookmark)
except Exception:
pass
return HttpResponseRedirect(reverse("my_bookmark"))
except Exception, e:
file_form._errors[NON_FIELD_ERRORS] = ErrorList([e.message])
def upload(req):
up_files = 'yes'
if req.method == "POST":
ff = FileForm(req.POST, req.FILES)
folder_name = req.session.get('folder_name')
if ff.is_valid():
#获取表单数据
b = ' Byte'
file_name = ff.cleaned_data['file_name']
file_loc = ff.cleaned_data['file_loc']
file_handel = req.FILES['file_loc']
file_size = str(file_handel.size) + b
file_type_split1 = str(file_handel.name)
file_type_split2 = file_type_split1.split('.')
file_type = file_type_split2[1]
#写入数据库
upload_time = timezone.now()
f = Folder.objects.get(folder_name=folder_name)
f.modify_time = upload_time
f.save()
f.file_set.create(file_name=file_name,
file_loc=file_loc,
file_size=file_size,
file_type=file_type,
upload_time=upload_time)
return HttpResponseRedirect('/online/index/')
else:
ff = FileForm()
return render(req, 'create_folder_new.html', {
'ff': ff,
'up_files': up_files
})
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 upload(request):
# Handle file upload
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
if form.is_valid():
logger.debug('File with type ' +
request.FILES['docfile'].content_type + ' uploaded.')
if request.FILES[
'docfile'].content_type == u'application/vnd.oasis.opendocument.text':
file_name = saveFile(request.FILES['docfile'])
logger.info('Converting file ' + file_name)
content = subprocess.check_output([
'OdtConverter/odt2html', '-x', 'OdtConverter/odt2html.xsl',
'EditorApp/static/media/' + file_name
])
logger.info('Deleting file ' + file_name)
os.remove('EditorApp/static/media/' + file_name)
logger.info('Saving imported document ' + file_name)
create_document(None, file_name, content)
elif request.FILES['docfile'].content_type[:5] == u'image':
saveFile(request.FILES['docfile'])
else:
form = FileForm()
form.error = 'Invalid type of document.'
logger.error('Wrong type of document.')
return render(request, 'upload.html', {'form': form})
# Redirect to the document list after POST
return HttpResponseRedirect('/')
else:
form = FileForm() # A empty, unbound form
return render(request, 'upload.html', {'form': form})
def upload_file(request, upload_path=None, upload_link=None):
form = FileForm(request.POST, request.FILES)
if form.is_valid():
uploaded_file = form.cleaned_data['file']
path = os.path.join(upload_path or UPLOAD_PATH, uploaded_file.name)
image_path = default_storage.save(path, uploaded_file)
image_url = default_storage.url(image_path)
if upload_link:
return HttpResponse(image_url)
return HttpResponse(json.dumps({'filelink': image_url, 'filename': uploaded_file.name}))
return HttpResponseForbidden()
def update_log(request):
if request.method == "POST":
form = FileForm(request.POST, request.FILES)
if form.is_valid():
cd = form.cleaned_data
handle_uploaded_file(cd)
return HttpResponse("Ok: File %s update success." % cd['name'])
else:
return HttpResponseBadRequest("<h1>Need more arguments</h1>")
else:
return HttpResponseBadRequest("<h1>Wrong request type</h1>")
def upload_file(request, upload_path=None, upload_link=None):
form = FileForm(request.POST, request.FILES)
if form.is_valid():
uploaded_file = form.cleaned_data['file']
path = os.path.join(upload_path or UPLOAD_PATH, uploaded_file.name)
image_path = default_storage.save(path, uploaded_file)
image_url = default_storage.url(image_path)
if upload_link:
return HttpResponse(image_url)
return HttpResponse(json.dumps({'filelink': image_url, 'filename': uploaded_file.name}))
return HttpResponseForbidden()
def upload_attachment(request, projectID):
if 'file' not in request.FILES:
raise IOError("Missing file")
if request.FILES['file'].size > 1100000:
raise IOError("File too large")
form = FileForm(request.POST, request.FILES)
if(form.is_valid()):
file = request.FILES['file']
f = ProjectFile(project = project_api.get_project(projectID), file = file, name = file.name)
f.save()
return redirect(request.POST['referer'])
def upload_attachment(request, projectID):
if 'file' not in request.FILES:
raise IOError("Missing file")
if request.FILES['file'].size > 1100000:
raise IOError("File too large")
form = FileForm(request.POST, request.FILES)
if(form.is_valid()):
file = request.FILES['file']
f = ProjectFile(project = project_api.get_project(projectID), file = file, name = file.name)
f.save()
return redirect(request.POST['referer'])
def add_containt(request):
if request.user.is_authenticated():
args = {}
if request.POST:
try:
request.POST['file_field']
file_form = FileForm(request.POST, request.FILES)
if file_form.is_valid():
file_name = request.FILES['file']
media_containt = Media_containt(file=file_name)
media_containt.save()
pdf_file_name = str(file_name).replace(' ', '_')
image_file_name = str(file_name).replace(' ',
'_').split('.')
image_file_name[-1] = 'png'
image_file_name = '.'.join(image_file_name)
cmd = 'gs -o ' + media_files_url + image_file_name + ' -sDEVICE=pngalpha -dLastPage=1 ' + media_files_url + pdf_file_name
print cmd
subprocess.call(cmd, shell=True)
print 'save and redirect'
return HttpResponseRedirect('/elab/add/containt/')
else:
containt_form = ContaintForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
print file_form.errors
return render_to_response(
'html_template/admin_template/admin_pannel.html', args)
except Exception, e:
print "Exception-->", e
containt_form = ContaintForm(request.POST)
if containt_form.is_valid():
containt_form.save()
return HttpResponseRedirect('/elab/add/containt/')
else:
file_form = FileForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
print containt_form.errors
return render_to_response(
'html_template/admin_template/admin_pannel.html', args)
else:
containt_form = ContaintForm()
file_form = FileForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
return render_to_response(
'html_template/admin_template/admin_pannel.html', args)
def upload_file(request, upload_path=None, upload_link=None):
form = FileForm(request.POST, request.FILES)
if form.is_valid():
uploaded_file = form.cleaned_data['file']
file_name, extension = os.path.splitext(uploaded_file.name)
timestr = time.strftime(u"%Y%m%d-%H%M%S")
full_name = u'{0}{1}'.format(file_name+timestr, extension)
path = os.path.join(upload_path or UPLOAD_PATH, full_name)
image_path = default_storage.save(path, uploaded_file)
image_url = default_storage.url(image_path)
if upload_link:
return HttpResponse(image_url)
return HttpResponse(json.dumps({'filelink': image_url, 'filename': uploaded_file.name}))
return HttpResponseForbidden()
def create(request):
# return render(request, 'files/create.html', {"foo": "bar"})
print 'entrou no create'
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
print 'request is post!'
print form.errors
if form.is_valid():
print 'form is valid!'
# print 'analysis name should be ', form.cleaned_data['name']
# file.name = form.cleaned_data['name']
file = File.objects.create(user=request.user)
file.file = request.FILES.get('file')
file.name = str(os.path.splitext(file.file.name)[0])
file.user = request.user
file.save()
f = file.file
#fix permissions
#os.chmod("%s/genomes/%s/" % (settings.BASE_DIR, fastafile.user), 0777)
# os.chmod("%s/uploads/%s/%s" % (settings.BASE_DIR, fastafile.user, fastafile.id), 0777)
#Align.delay(analysis.id)
data = {
'files': [{
'deleteType': 'DELETE',
'name': file.name,
'url': '',
'thumbnailUrl': '',
'type': 'image/png',
'deleteUrl': '',
'size': f.size
}]
}
response = JSONResponse(data, mimetype=response_mimetype(request))
response['Content-Disposition'] = 'inline; filename=files.json'
return response
else:
form = FileForm()
return render(request, 'files/create.html', {'form': form})
def add_containt(request):
if request.user.is_authenticated():
args = {}
if request.POST:
try:
request.POST['file_field']
file_form = FileForm(request.POST, request.FILES)
if file_form.is_valid():
file_name = request.FILES['file']
media_containt = Media_containt(file=file_name)
media_containt.save()
pdf_file_name = str(file_name).replace(' ', '_')
image_file_name = str(file_name).replace(' ', '_').split('.')
image_file_name[-1] = 'png'
image_file_name = '.'.join(image_file_name)
cmd = 'gs -o '+media_files_url+image_file_name+' -sDEVICE=pngalpha -dLastPage=1 '+media_files_url+pdf_file_name
print cmd
subprocess.call(cmd, shell=True)
print 'save and redirect'
return HttpResponseRedirect('/elab/add/containt/')
else:
containt_form = ContaintForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
print file_form.errors
return render_to_response('html_template/admin_template/admin_pannel.html', args)
except Exception, e:
print "Exception-->", e
containt_form = ContaintForm(request.POST)
if containt_form.is_valid():
containt_form.save()
return HttpResponseRedirect('/elab/add/containt/')
else:
file_form = FileForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
print containt_form.errors
return render_to_response('html_template/admin_template/admin_pannel.html', args)
else:
containt_form = ContaintForm()
file_form = FileForm()
args['containt_form'] = containt_form
args['file_form'] = file_form
return render_to_response('html_template/admin_template/admin_pannel.html', args)
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 batch_import_bulletin_by_excel(request):
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
if form.is_valid():
if request.FILES['filefield'].name.split('.')[-1] == 'xlsx':
try:
utils.handle_uploaded_file(request, f=request.FILES['filefield'])
except ObjectDoesNotExist, e:
error_message = '科室和医生组合不存在，请检查所上传表格内容后重新上传'
return render(request, 'publisher/file.html',
{'form': form, 'error_message': error_message,
'loginname': request.session['loginname']})
return render(request, 'publisher/file.html',
{'form': form, 'error_message': '上传成功！',
'loginname': request.session['loginname']})
else:
error_message = '文件格式错误，请上传Excel文件（.xlsl)'
form = FileForm()
return render(request, 'publisher/file.html', {'form': form, 'error_message': error_message, 'loginname': request.session['loginname']})
def upload_gl(request):
if request.method != "POST":
forecast_obj = Forecast.objects.get(id=request.GET.get('forecast'))
context = {'file_category': 'GL Projections'}
context['file_type'] = '.json'
context['obj_label'] = forecast_obj.label
form = FileForm()
context['form'] = form
return render_to_response('forecasts/upload_gl.html', RequestContext(request, context))
else:
form = FileForm(request.POST, request.FILES)
if form.is_valid():
upload = request.FILES.values()[0]
file_name = upload._name
data = json.loads(upload.file.read())
forecast_obj = Forecast.objects.get(id=request.GET.get('forecast'))
forecast_obj.projections = data
forecast_obj.save()
return HttpResponseRedirect('/forecasts/forecast/%s' % forecast_obj.id)
def batch_import_bulletin_by_excel(request):
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
if form.is_valid():
if request.FILES['filefield'].name.split('.')[-1] == 'xlsx':
utils.handle_uploaded_file(request,
f=request.FILES['filefield'])
return render(request, 'publisher/file.html', {
'form': form,
'error_message': '上传成功！'
})
else:
error_message = '文件格式错误，请上传Excel文件（.xlsl)'
form = FileForm()
return render(request, 'publisher/file.html', {
'form': form,
'error_message': error_message
})
else:
form = FileForm()
return render(request, 'publisher/file.html', {'form': form})
def upload_file(request, **config):
file_type = config['file_type']
context = {'file_type': file_type,}
form = FileForm(request.POST, request.FILES)
if form.is_valid():
upload = request.FILES.values()[0]
file_name = upload._name
file_name_with_timestamp = save_file(upload)
company = utils.get_company(request)
model = config.pop('model')
unique = config.pop('unique')
name_cleaner_path = config.pop('name_cleaner')
value_cleaner_path = config.pop('value_cleaner')
exclude_path = config.pop('exclude')
post_process_path = config.pop('post_process')
#result is zero if it was able to start the background task successfully.
result, out, err = process_incoming_file(model, unique, name_cleaner, value_cleaner, exclude, post_process,
file_type=config['file_type'],
file_name=file_name_with_timestamp,
company=company,
task_title="%s data for %s" % (file_type, company),
task_success_url=reverse('upload_complete'),
)
if result != 0:
context.update({'file_name': file_name, 'success': False, 'out': out, 'err': err})
messages.error(request, 'Could not process the file provided, please see below')
return render(request, 'uploaded.html', context)
else:
return HttpResponseRedirect(reverse('task_result', kwargs={'pid':out,}))
else:
context.update({'file_name': file_name, 'success': False, 'out': out, 'err': err})
messages.error(request, 'Could not process the file provided, please see below')
return render(request, 'uploaded.html', context)
def create(request):
# return render(request, 'files/create.html', {"foo": "bar"})
print 'entrou no create'
if request.method == 'POST':
form = FileForm(request.POST, request.FILES)
print 'request is post!'
print form.errors
if form.is_valid():
print 'form is valid!'
# print 'analysis name should be ', form.cleaned_data['name']
# file.name = form.cleaned_data['name']
file = File.objects.create(user=request.user)
file.file= request.FILES.get('file')
file.name= str(os.path.splitext(file.file.name)[0])
file.user = request.user
file.save()
f = file.file
#fix permissions
#os.chmod("%s/genomes/%s/" % (settings.BASE_DIR, fastafile.user), 0777)
# os.chmod("%s/uploads/%s/%s" % (settings.BASE_DIR, fastafile.user, fastafile.id), 0777)
#Align.delay(analysis.id)
data = {'files': [{'deleteType': 'DELETE', 'name': file.name, 'url': '', 'thumbnailUrl': '', 'type': 'image/png', 'deleteUrl': '', 'size': f.size}]}
response = JSONResponse(data, mimetype=response_mimetype(request))
response['Content-Disposition'] = 'inline; filename=files.json'
return response
else:
form = FileForm()
return render(request, 'files/create.html', {'form':form})
def upload_gl(request):
if request.method != "POST":
forecast_obj = Forecast.objects.get(id=request.GET.get('forecast'))
context = {'file_category': 'GL Projections'}
context['file_type'] = '.json'
context['obj_label'] = forecast_obj.label
form = FileForm()
context['form'] = form
return render_to_response('forecasts/upload_gl.html',
RequestContext(request, context))
else:
form = FileForm(request.POST, request.FILES)
if form.is_valid():
upload = request.FILES.values()[0]
file_name = upload._name
data = json.loads(upload.file.read())
forecast_obj = Forecast.objects.get(id=request.GET.get('forecast'))
forecast_obj.projections = data
forecast_obj.save()
return HttpResponseRedirect('/forecasts/forecast/%s' %
forecast_obj.id)
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 import_bookmark(request, template_name='bookmark/import_bookmark.html'):
file_form = FileForm(request.POST or None, request.FILES or None)
if request.method == 'POST' and file_form.is_valid():
file = request.FILES['file']
tags_input = file_form.cleaned_data['tags']
public =file_form.cleaned_data['public']
try:
bookmarks = parse_firefox_bookmark(file)
for bk in bookmarks:
try:
bookmark = Bookmark.objects.create(url=bk['url'], title=bk['title'], owner=request.user, public=public)
if tags_input:
tags = tags_input
else:
tags=parse_tags(bk['tags'])
for tag in tags:
bookmark.tags.add(tag)
# Update the screen shot
update_bk_screen_shot_async(bookmark)
except Exception:
pass
return HttpResponseRedirect(reverse("my_bookmark"))
except Exception, e:
file_form._errors[NON_FIELD_ERRORS] = ErrorList([e.message])
def upload_file(request, **config):
file_type = config['file_type']
context = {
'file_type': file_type,
}
form = FileForm(request.POST, request.FILES)
if form.is_valid():
upload = request.FILES.values()[0]
file_name = upload._name
file_name_with_timestamp = save_file(upload)
company = utils.get_company(request)
model = config.pop('model')
unique = config.pop('unique')
name_cleaner = config.pop('name_cleaner')
value_cleaner = config.pop('value_cleaner')
exclude = config.pop('exclude')
post_process = config.pop('post_process')
#result is zero if it was able to start the background task successfully.
result, out, err = process_incoming_file(
model,
unique,
name_cleaner,
value_cleaner,
exclude,
post_process,
file_type=config['file_type'],
file_name=file_name_with_timestamp,
company=company,
task_title="%s data for %s" % (file_type, company),
task_success_url=reverse('upload_complete'),
)
if result != 0:
context.update({
'file_name': file_name,
'success': False,
'out': out,
'err': err
})
messages.error(
request,
'Could not process the file provided, please see below')
return render_to_response('uploaded.html',
context,
context_instance=RequestContext(request))
else:
return HttpResponseRedirect(
reverse('task_result', kwargs={
'pid': out,
}))
else:
context.update({
'file_name': file_name,
'success': False,
'out': out,
'err': err
})
messages.error(
request, 'Could not process the file provided, please see below')
return render_to_response('uploaded.html',
context,
context_instance=RequestContext(request))
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})