def display_genesets(request):
if 'tribe_token' in request.session:
access_token = request.session['tribe_token']
get_user = utils.retrieve_user_object(access_token)
if (get_user == 'OAuth Token expired' or get_user == []):
request.session.clear()
return connect_to_tribe(request)
else: # The user must be logged in and has access to her/himself
genesets = utils.retrieve_user_genesets(
access_token, {'full_genes': 'true', 'limit': 100}
)
tribe_user = get_user
return render(
request,
'display_genesets.html',
{
'tribe_url': TRIBE_URL,
'genesets': genesets,
'tribe_user': tribe_user,
'base_template': BASE_TEMPLATE
}
)
else:
return connect_to_tribe(request)
def get_token(request):
access_code = request.GET.__getitem__('code')
access_token = utils.get_access_token(access_code)
request.session['tribe_token'] = access_token
request.session['tribe_user'] = utils.retrieve_user_object(access_token)
if TRIBE_LOGIN_REDIRECT:
return HttpResponseRedirect(TRIBE_LOGIN_REDIRECT)
else:
return redirect('display_genesets')
def display_versions(request, geneset):
if 'tribe_token' in request.session:
access_token = request.session['tribe_token']
get_user = utils.retrieve_user_object(access_token)
if (get_user == 'OAuth Token expired' or get_user == []):
request.session.clear()
return connect_to_tribe(request)
else:
versions = utils.retrieve_user_versions(access_token, geneset)
for version in versions:
version['gene_list'] = []
for annotation in version['annotations']:
version['gene_list'].append(
annotation['gene']['standard_name'])
return render(request, 'display_versions.html', {
'versions': versions,
'base_template': BASE_TEMPLATE
})
def create_geneset(request):
"""
View to handle the creation of genesets on Tribe when users make
POST request to the '/tribe_client/create_geneset' URL.
Arguments:
request -- Request object, which contains a dictionary-like object
of POST data, among other things.
* In the POST data, there should be a 'geneset' object that contains
the information for the geneset being created. This 'geneset' is
passed in the POST data as a string, which we load as json to get a
dictionary. The general format for the data in this geneset object is:
geneset = {
organism: 'Mus musculus', # Required
title: 'Sample title', # Required
abstract: 'Sample abstract', # Optional
# Genes to be included in the geneset are sent in the 'annotations'
# dictionary, and this whole dictionary is optional. The geneset
# can have as many or as few annotations as desired. The format for
# the annotations dictionary is:
# {gene_id1: [<list of pubmed ids associated with that gene>],
# gene_id2: [<list of pubmed ids associated with that gene>]...}
# The type of identifier for the gene_ids is whatever is set
# in the CROSSREF setting.
annotations: {55982: [20671152, 19583951],
18091: [8887666], 67087: [],
22410:[]}
}
Returns:
Either -
a) The Tribe URL of the geneset that has just been created, or
b) A 401 Unauthorized response if the user is not signed in
N.B. To gracefully save to Tribe, your interface should handle the
case when a 400 and 401 responses are returned. One way to do this
for the 401 Unauthorized response, for example, is to catch the error
and send the user to the Tribe-login page ('/tribe_client' url, which
is named 'connect_to_tribe' in urls.py). Another way to handle this
response is to only allow the users to make a request
to this view (via a button, etc.) when they are already signed in.
"""
if not ('tribe_token' in request.session):
return HttpResponse('Unauthorized', status=401)
tribe_token = request.session['tribe_token']
is_token_valid = utils.retrieve_user_object(tribe_token)
if (is_token_valid == 'OAuth Token expired'):
request.session.clear()
return HttpResponse('Unauthorized', status=401)
geneset_info = request.POST.get('geneset')
geneset_info = json.loads(geneset_info)
geneset_info['xrdb'] = CROSSREF
tribe_response = utils.create_remote_geneset(
tribe_token, geneset_info, TRIBE_URL
)
try:
slug = tribe_response['slug']
creator = tribe_response['creator']['username']
geneset_url = TRIBE_URL + "/#/use/detail/" + creator + "/" + slug
html_safe_content = html.escape(geneset_url)
response = {'geneset_url': html_safe_content}
# If there is an error and a json object could not be loaded from the
# response, the create_remote_geneset() util function will return a
# raw response from Tribe, which will trigger a TypeError when trying
# to access a key from it like a dictionary.
except TypeError:
html_safe_content = html.escape(tribe_response.content)
return HttpResponseBadRequest(
'The following error has been returned by Tribe while attempting ' +
'to create a geneset: "' + html_safe_content + '"'
)
json_response = json.dumps(response)
return HttpResponse(json_response, content_type='application/json')