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views.py
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views.py
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import csv
from datetime import timedelta
import json
import logging
import urllib
import uuid
from xml.parsers.expat import ExpatError
from django.conf import settings
from django.contrib.admin.views.decorators import staff_member_required
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User
from django.contrib.sites.models import RequestSite, Site
from django.contrib.sites.shortcuts import get_current_site
from django.core.mail import EmailMessage
from django.core.urlresolvers import reverse
from django.db import transaction
from django.http import (Http404, HttpResponse, HttpResponseBadRequest,
HttpResponseForbidden, HttpResponseNotFound,
HttpResponseRedirect, HttpResponseServerError,
JsonResponse)
from django.shortcuts import get_object_or_404, render, render_to_response
from django.template import RequestContext, loader
from django.utils import timezone
import boto3
import botocore
from guardian.shortcuts import (get_groups_with_perms, get_objects_for_user,
get_perms)
from guardian.core import ObjectPermissionChecker
from registration import signals
from registration.views import RegistrationView
import requests
from requests.exceptions import HTTPError
from rest_framework import authentication, status, viewsets
from rest_framework.authentication import SessionAuthentication
from rest_framework.authtoken.models import Token
from rest_framework.authtoken.views import ObtainAuthToken
from rest_framework.decorators import detail_route
from rest_framework.exceptions import APIException
from rest_framework.pagination import LimitOffsetPagination
from rest_framework.permissions import IsAuthenticated
from rest_framework.renderers import JSONRenderer
from rest_framework.response import Response
from rest_framework.views import APIView
import xmltodict
from data_set_manager.models import Attribute
from .forms import UserForm, UserProfileForm
from .models import (Analysis, CustomRegistrationProfile, DataSet, Event,
ExtendedGroup, Invitation, SiteProfile, SiteStatistics,
SiteVideo, UserProfile, Workflow)
from .serializers import (AnalysisSerializer, DataSetSerializer,
EventSerializer, ExtendedGroupSerializer,
InvitationSerializer, SiteProfileSerializer,
SiteVideoSerializer, UserProfileSerializer,
WorkflowSerializer)
from .utils import (api_error_response, get_data_set_for_view_set,
get_group_for_view_set, get_non_manager_groups_for_user)
logger = logging.getLogger(__name__)
def home(request):
return render(request, 'core/home.html')
def about(request):
return render_to_response('core/about.html',
{'site_name': get_current_site(request).name},
context_instance=RequestContext(request))
def dashboard(request):
return render_to_response('core/dashboard.html', {},
context_instance=RequestContext(request))
@login_required
def group_invite(request, token):
inv_list = Invitation.objects.filter(token_uuid=token)
if len(inv_list) == 0:
return render_to_response(
'core/group_invite.html',
{
'site': '{}://{}'.format(settings.REFINERY_URL_SCHEME,
get_current_site(request)),
'message': 'Invalid token. Not found or expired.'
},
context_instance=RequestContext(request))
inv = inv_list[0]
user = request.user
ext_group_list = ExtendedGroup.objects.filter(id=int(inv.group_id))
ext_group = None if len(ext_group_list) == 0 else ext_group_list[0]
if not ext_group:
return render_to_response(
'core/group_invite.html',
{
'site': '{}://{}'.format(settings.REFINERY_URL_SCHEME,
get_current_site(request)),
'message': 'Invalid token. Unable to find pairing group'
},
context_instance=RequestContext(request))
ext_group.user_set.add(user)
# If the group is a manager group
if ext_group.is_manager_group():
for i in ext_group.managed_group.all():
i.user_set.add(user)
# We are done using this token
inv.delete()
return render_to_response(
'core/group_invite.html',
{
'site': '{}://{}'.format(settings.REFINERY_URL_SCHEME,
get_current_site(request)),
'message': '%s has been added to the group %s.' %
(user.username, ext_group.name),
'user': user,
'ext_group': ext_group
},
context_instance=RequestContext(request))
def custom_error_page(request, template, context_dict):
temp_loader = loader.get_template(template)
return temp_loader.render(context_dict, request)
@login_required()
def user(request, query):
try:
user = User.objects.get(username=query)
except User.DoesNotExist:
try:
user = get_object_or_404(UserProfile, uuid=query).user
except ValueError:
raise Http404()
# return all non-manager groups in profile
groups = get_non_manager_groups_for_user(user)
return render(request, 'core/user.html',
{'profile_user': user, 'user_groups': groups})
@login_required()
def user_profile(request):
return user(request, request.user.profile.uuid)
@login_required()
def user_edit(request, uuid):
try:
profile_object = get_object_or_404(UserProfile, uuid=uuid)
except ValueError:
raise Http404()
user_object = profile_object.user
if request.method == "POST":
uform = UserForm(data=request.POST, instance=user_object)
pform = UserProfileForm(data=request.POST, instance=profile_object)
if uform.is_valid() and pform.is_valid():
user = uform.save()
profile = pform.save(commit=False)
profile.user = user
profile.save()
return HttpResponseRedirect(
reverse('core.views.user', args=(uuid,))
)
else:
uform = UserForm(instance=user_object)
pform = UserProfileForm(instance=profile_object)
return render_to_response('core/edit_user.html',
{'profile_user': user_object,
'uform': uform, 'pform': pform},
context_instance=RequestContext(request))
@login_required()
def user_profile_edit(request):
return user_edit(request, request.user.profile.uuid)
@login_required()
def group(request, query):
group = get_object_or_404(ExtendedGroup, uuid=query)
# only group members are allowed to see group pages
if not request.user.is_superuser:
if group.id not in request.user.groups.values_list('id', flat=True):
return HttpResponseForbidden(
custom_error_page(request, '403.html',
{'user': request.user,
'msg': "view group %s" % group.name}))
return render_to_response('core/group.html', {'group': group},
context_instance=RequestContext(request))
def data_set_slug(request, slug):
d = get_object_or_404(DataSet, slug=slug)
return data_set(request, d.uuid)
def data_set(request, data_set_uuid, analysis_uuid=None):
data_set = get_object_or_404(DataSet, uuid=data_set_uuid)
public_group = ExtendedGroup.objects.public_group()
if not request.user.has_perm('core.read_meta_dataset', data_set):
if 'read_meta_dataset' not in get_perms(public_group, data_set):
if request.user.is_authenticated():
return HttpResponseForbidden(
custom_error_page(request, '403.html',
{user: request.user,
'msg': "view this data set"}))
else:
return HttpResponse(
custom_error_page(request, '401.html',
{'msg': "view this data set"}),
status='401')
# get studies
investigation = data_set.get_investigation()
studies = investigation.study_set.all()
# If repository mode, only return workflows tagged for the repository
if (settings.REFINERY_REPOSITORY_MODE):
workflows = Workflow.objects.filter(show_in_repository_mode=True)
else:
workflows = Workflow.objects.all()
study_uuid = studies[0].uuid
# used for solr field postfixes: FIELDNAME_STUDYID_ASSAY_ID_FIELDTYPE
study_id = studies[0].id
assay_uuid = studies[0].assay_set.all()[0].uuid
# used for solr field postfixes: FIELDNAME_STUDYID_ASSAY_ID_FIELDTYPE
assay_id = studies[0].assay_set.all()[0].id
return render_to_response(
'core/data_set.html',
{
"data_set": data_set,
"analysis_uuid": analysis_uuid,
"studies": studies,
"study_uuid": study_uuid,
"study_id": study_id,
"assay_uuid": assay_uuid,
"assay_id": assay_id,
"has_change_dataset_permission": 'change_dataset' in get_perms(
request.user, data_set
),
"workflows": workflows,
"isatab_archive": investigation.get_file_store_item(),
"pre_isatab_archive": investigation.get_file_store_item(),
"attribute_edit_types": ','.join(Attribute.editable_types)
},
context_instance=RequestContext(request))
def workflow_slug(request, slug):
w = get_object_or_404(Workflow, slug=slug)
return workflow(request, w.uuid)
def workflow(request, uuid):
workflow = get_object_or_404(Workflow, uuid=uuid)
public_group = ExtendedGroup.objects.public_group()
if not request.user.has_perm('core.read_workflow', workflow):
if 'read_workflow' not in get_perms(public_group, workflow):
if request.user.is_authenticated():
return HttpResponseForbidden(
custom_error_page(request, '403.html',
{user: request.user,
'msg': "view this workflow"}))
else:
return HttpResponse(
custom_error_page(request, '401.html',
{'msg': "view this workflow"}),
status='401')
# load graph dictionary from Galaxy
workflow = Workflow.objects.filter(uuid=uuid).get()
return render_to_response('core/workflow.html', {'workflow': workflow},
context_instance=RequestContext(request))
def solr_core_search(request):
"""Query Solr's core index for search.
Queries are augmented with user and group information so that no datasets
is returned for which the user has no access.
For visualizing the repository it's important to know all datasets right
from the beginning. Because Django and Solr most likely run on the same
server, it's better to prefetch all dataset uuid and send them back
altogether rather than having to query from the client side twice.
"""
url = settings.REFINERY_SOLR_BASE_URL + "core/select"
headers = {
'Accept': 'application/json'
}
params = request.GET.dict()
# Generate access list
if not request.user.is_superuser:
if request.user.id is None:
access = ['g_{}'.format(settings.REFINERY_PUBLIC_GROUP_ID)]
else:
access = ['u_{}'.format(request.user.id)]
for group in request.user.groups.all():
access.append('g_{}'.format(group.id))
params['fq'] = params['fq'] + ' AND access:({})'.format(
' OR '.join(access))
try:
response = requests.get(url, params=params, headers=headers)
response.raise_for_status()
except HTTPError as e:
logger.error(e)
return HttpResponse(response, content_type='application/json')
def doi(request, id):
"""Forwarding requests to DOI's API"""
# Decode URL and replace dollar signs by forward slashes
# This encoding is needed because forward slashes cause 404 errors even
# when they are URL encoded as they are still regarded as forward
# slashes.
id = urllib.unquote(id).decode('utf8')
id = id.replace('$', '/')
url = "https://doi.org/{id}".format(id=id)
headers = {'Accept': 'application/json'}
try:
response = requests.get(url, headers=headers)
response.raise_for_status()
except HTTPError as e:
logger.error(e)
except requests.exceptions.ConnectionError:
return HttpResponse('Service currently unavailable', status=503)
return HttpResponse(response, content_type='application/json')
def pubmed_abstract(request, id):
"""Forwarding requests to PubMed's API
Example:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=XML&rettype=abstract&id=25344497
"""
url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
params = {
'db': 'pubmed',
'retmode': 'xml',
'rettype': 'abstract',
'id': id
}
headers = {
'Accept': 'text/xml'
}
try:
response = requests.get(url, params=params, headers=headers)
response.raise_for_status()
except HTTPError as e:
logger.error(e)
except requests.exceptions.ConnectionError:
return HttpResponse('Service currently unavailable', status=503)
try:
response_dict = xmltodict.parse(response.text)
except ExpatError:
return HttpResponse('Service currently unavailable', status=503)
return JsonResponse(response_dict)
def pubmed_search(request, term):
"""Forwarding requests to PubMed's API
Example:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmode=json&retmax=1&term=10.1093%2Fbioinformatics%2Fbtu707
"""
term = urllib.unquote(term).decode('utf8')
term = term.replace('$', '/')
url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
params = {
'db': 'pubmed',
'retmode': 'json',
'retmax': 1,
'term': term
}
headers = {
'Accept': 'application/json'
}
try:
response = requests.get(url, params=params, headers=headers)
response.raise_for_status()
except HTTPError as e:
logger.debug(e)
except requests.exceptions.ConnectionError:
return HttpResponse('Service currently unavailable', status=503)
return HttpResponse(response, content_type='application/json')
def pubmed_summary(request, id):
"""Forwarding requests to PubMed's API
Example:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=25344497
"""
url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
params = {
'db': 'pubmed',
'retmode': 'json',
'id': id
}
headers = {
'Accept': 'application/json'
}
try:
response = requests.get(url, params=params, headers=headers)
response.raise_for_status()
except HTTPError as e:
logger.error(e)
except requests.exceptions.ConnectionError:
return HttpResponse('Service currently unavailable', status=503)
return HttpResponse(response, content_type='application/json')
class WorkflowViewSet(viewsets.ViewSet):
"""
API endpoint that allows a workflow graph to be viewed.
---
graph:
description: Returns workflow json
parameters:
- name: uuid
description: workflow uuid
paramType: query
type: string
required: true
...
"""
queryset = Workflow.objects.all()
serializer_class = WorkflowSerializer
lookup_field = 'uuid'
http_method_names = ['get']
@detail_route(methods=['get'])
def graph(self, request, *args, **kwargs):
return HttpResponse(
get_object_or_404(Workflow, uuid=kwargs.get("uuid")).graph
)
class EventAPIView(APIView):
"""
API endpoint that allows Events to be viewed
---
get:
description: End point which returns events associated with data
sets the request user has access to
...
"""
def get(self, request):
"""Queryset based on DataSets that the requesting User has permission
to access"""
data_sets_for_user = get_objects_for_user(
request.user,
'core.read_meta_dataset',
accept_global_perms=False
)
user_events = Event.objects.filter(
data_set__in=data_sets_for_user
).order_by('-date_time')
if len(user_events) > 50:
user_events = user_events[0:50]
serializer = EventSerializer(user_events, many=True,
context={'request': request})
return Response(serializer.data)
class DataSetViewSet(viewsets.ViewSet):
"""
API endpoint for viewing, editing, and deleting datasets.
---
destroy:
description: Owners can delete the dataset and associated objects
parameters:
- name: uuid
description: data set uuid
paramType: path
type: string
required: true
list:
description: Returns data_sets for user and filter params
(defaults to read_meta perms)
parameters:
- name: is_owner
description: Returns the users' owned data set
paramType: query
type: boolean
required: false
- name: is_public
description: Returns public data sets
paramType: query
type: boolean
required: false
- name: group
description: Requires group id to return data sets visible
to a group with read_meta
paramType: query
type: string
required: false
partial_update:
parameters_strategy:
form: replace
query: merge
description: Update a data set's owner and or update meta fields
parameters:
- name: uuid
description: data set uuid
paramType: path
type: string
required: true
- name: transfer_data_set
description: Flag to transfer a data set, requires
new_owner_email field
paramType: form
type: boolean
required: false
- name: new_owner_email
description: Requires a valid user email to transfer data
set ownership
paramType: form
type: string
required: false
- name: description
description: Update data set's description
paramType: form
type: string
required: false
- name: slug
description: Update data set url
paramType: form
type: string
required: false
- name: summary
description: Update data set's summary
paramType: form
type: string
required: false
- name: title
description: Update data set's title
paramType: form
type: string
required: false
retrieve:
description: Returns data set
parameters:
- name: uuid
description: data set uuid
paramType: path
type: string
required: true
...
"""
http_method_names = ['get', 'delete', 'patch']
lookup_field = 'uuid'
def get_object(self, uuid):
return get_data_set_for_view_set(uuid)
def list(self, request):
params = request.query_params
paginator = LimitOffsetPagination()
paginator.default_limit = 100
filters = {
'is_owner': params.get('is_owner'),
'is_public': params.get('public')
}
try:
filters['group'] = ExtendedGroup.objects.get(
id=params.get('group')
)
except Exception:
filters['group'] = None
user_data_sets = get_objects_for_user(
request.user,
"core.read_meta_dataset",
accept_global_perms=False
).order_by('-modification_date')
filtered_data_sets = []
check_own = filters.get('is_owner')
all_owner_perms = ObjectPermissionChecker(request.user)
all_owner_perms.prefetch_perms(user_data_sets)
check_public = filters.get('is_public')
all_public_perms = ObjectPermissionChecker(
ExtendedGroup.objects.public_group()
)
all_public_perms.prefetch_perms(user_data_sets)
group = filters.get('group')
if group:
all_group_perms = ObjectPermissionChecker(filters.get('group'))
all_group_perms.prefetch_perms(user_data_sets)
for data_set in user_data_sets:
is_public = all_public_perms.has_perm('read_meta_dataset',
data_set)
if request.user.is_superuser:
is_owner = data_set.get_owner() == request.user
else:
is_owner = all_owner_perms.has_perm('share_dataset', data_set)
setattr(data_set, 'public', is_public)
setattr(data_set, 'is_owner', is_owner)
if not data_set.is_valid:
logger.warning(
"DataSet with UUID: {} is invalid, and most likely is "
"still being created".format(data_set.uuid)
)
continue
elif check_own or check_public or group:
if group:
group_perms = all_group_perms.has_perm('read_meta_dataset',
data_set)
# need to check for filter and then check data set perms
if check_own and check_public and group:
if is_owner and is_public and group_perms:
filtered_data_sets.append(data_set)
elif check_own and group:
if is_owner and group_perms:
filtered_data_sets.append(data_set)
elif check_own and check_public:
if is_owner and is_public:
filtered_data_sets.append(data_set)
elif check_public and group:
if is_public and group_perms:
filtered_data_sets.append(data_set)
elif check_own and is_owner or check_public and is_public\
or group and group_perms:
filtered_data_sets.append(data_set)
else:
filtered_data_sets.append(data_set)
total_data_sets = len(filtered_data_sets)
paged_data_sets = paginator.paginate_queryset(filtered_data_sets,
request)
serializer = DataSetSerializer(paged_data_sets, many=True,
context={'request': request})
return Response({'data_sets': serializer.data,
'total_data_sets': total_data_sets})
def retrieve(self, request, uuid):
data_set = self.get_object(uuid)
public_group = ExtendedGroup.objects.public_group()
if not ('read_meta_dataset' in get_perms(public_group, data_set) or
request.user.has_perm('core.read_meta_dataset', data_set)):
return Response(
uuid, status=status.HTTP_401_UNAUTHORIZED
)
serializer = DataSetSerializer(data_set, context={'request': request})
serialized_data = serializer.data
# isa_archive_uuid only needed for data set details
investigation_link = data_set.get_latest_investigation_link()
investigation = investigation_link.investigation
file_store_item = investigation.get_file_store_item()
if investigation.is_isa_tab_based():
serialized_data['isa_archive_uuid'] = file_store_item.uuid
serialized_data['isa_archive_url'] = \
file_store_item.get_datafile_url()
else:
serialized_data['pre_isa_archive_uuid'] = file_store_item.uuid
return Response(serialized_data)
def is_user_authorized(self, user, data_set):
if (not user.is_authenticated() or
not user.has_perm('core.change_dataset', data_set)):
return False
else:
return True
def destroy(self, request, uuid):
if not request.user.is_authenticated():
return HttpResponseForbidden(
content="User {} is not authenticated".format(request.user))
try:
data_set = DataSet.objects.get(uuid=uuid)
except NameError as e:
logger.error(e)
return HttpResponseBadRequest(content="Bad Request")
except DataSet.DoesNotExist as e:
logger.error(e)
return HttpResponseNotFound(content="DataSet with UUID: {} "
"not found.".format(uuid))
except DataSet.MultipleObjectsReturned as e:
logger.error(e)
return HttpResponseServerError(
content="Multiple DataSets returned for this request")
if data_set.get_owner() == request.user:
data_set_deleted = data_set.delete()
if data_set_deleted[0]:
return Response({"data": data_set_deleted[1]})
else:
return HttpResponseBadRequest(content=data_set_deleted[1])
return Response('Unauthorized to delete data set with uuid: {'
'}'.format(uuid), status=status.HTTP_401_UNAUTHORIZED)
def partial_update(self, request, uuid, format=None):
self.data_set = self.get_object(uuid)
self.current_site = get_current_site(request)
# check edit permission for user
if self.is_user_authorized(request.user, self.data_set):
# update data set's owner
current_owner = self.data_set.get_owner()
if request.data.get('transfer_data_set') and current_owner == \
request.user:
new_owner_email = request.data.get('new_owner_email')
try:
new_owner = User.objects.get(email=new_owner_email)
except Exception:
return Response(uuid, status=status.HTTP_404_NOT_FOUND)
try:
with transaction.atomic():
self.data_set.transfer_ownership(current_owner,
new_owner)
perm_groups = self.update_group_perms(new_owner)
except Exception as e:
return Response(
e, status=status.HTTP_412_PRECONDITION_FAILED
)
self.send_transfer_notification_email(current_owner,
new_owner, perm_groups)
serializer = DataSetSerializer(self.data_set,
context={'request': request})
return Response(serializer.data,
status=status.HTTP_202_ACCEPTED)
# update data set's fields
serializer = DataSetSerializer(
self.data_set,
data=request.data,
partial=True,
context={'request': request}
)
if serializer.is_valid():
serializer.save()
return Response(
serializer.data, status=status.HTTP_202_ACCEPTED
)
return Response(
serializer.errors, status=status.HTTP_400_BAD_REQUEST
)
else:
return Response(
uuid, status=status.HTTP_401_UNAUTHORIZED
)
def send_transfer_notification_email(self, old_owner, new_owner,
perm_groups):
"""
Helper method which emails the old and new owner of the data set
transfer and which groups have access
:param old_owner: data set's previous owner obj
:param new_owner: data set's new owner obj
:param perm_groups: obj with two obj of permission groups
"""
subject = "{}: Data Set ownership transfer".format(
settings.EMAIL_SUBJECT_PREFIX
)
old_owner_name = old_owner.get_full_name() or \
old_owner.username
new_owner_name = new_owner.get_full_name() or \
new_owner.username
temp_loader = loader.get_template(
'core/owner_transfer_notification.txt'
)
context_dict = {
'site': self.current_site,
'old_owner_name': old_owner_name,
'old_owner_uuid': str(old_owner.profile.uuid),
'new_owner_name': new_owner_name,
'new_owner_uuid': str(new_owner.profile.uuid),
'data_set_name': self.data_set.name,
'data_set_uuid': self.data_set.uuid,
'groups_with_access': perm_groups.get('groups_with_access'),
'groups_without_access': perm_groups.get('groups_without_access')
}
email = EmailMessage(subject, temp_loader.render(context_dict),
to=[new_owner.email, old_owner.email])
email.send()
return email
def update_group_perms(self, new_owner):
"""
Helper method which updates the groups access to the data set based
on the new_owner's memberships
transfer and which groups have access
:param new_owner: data set's new owner obj
"""
new_owner_group_ids = new_owner.groups.all().\
values_list('id', flat=True)
all_groups_with_ds_access = get_groups_with_perms(
self.data_set, attach_perms=True
)
groups_with_access = []
groups_without_access = []
for group in all_groups_with_ds_access:
group_details = {
'name': group.extendedgroup.name,
'profile': 'http://{}/groups/{}'.format(
self.current_site,
group.extendedgroup.uuid
)
}
if group.id in new_owner_group_ids:
groups_with_access.append(group_details)
else:
self.data_set.unshare(group)
groups_without_access.append(group_details)
return {"groups_with_access": groups_with_access,
"groups_without_access": groups_without_access}
class AnalysisAPIView(APIView):
"""
API endpoint that allows for Analyses to be retrieved or deleted.
---
delete:
description: Owners can delete an analyses
parameters:
- name: uuid
description: used to indentify analysis
paramType: param
type: string
required: true
get:
description: Returns analyses filtered by either data set or user
parameters:
- name: data_set_uuid
description: param to have analyses filtered by a data set
paramType: param
type: string
required: false
...
"""
http_method_names = ['get', 'delete']
def get(self, request):
data_set_uuid = request.query_params.get('data_set_uuid')
paginator = LimitOffsetPagination()
paginator.default_limit = 100
# return cross-dataset analyses per user
if data_set_uuid is None:
data_sets = get_objects_for_user(request.user,
'core.read_meta_dataset')
filtered_analyses = Analysis.objects.filter(
data_set__in=data_sets.values_list("id", flat=True)
).order_by('-time_start')
paged_analyses = paginator.paginate_queryset(filtered_analyses,
request)
serializer = AnalysisSerializer(paged_analyses, many=True)
return Response(serializer.data)
data_set = get_data_set_for_view_set(data_set_uuid)
public_group = ExtendedGroup.objects.public_group()
if not ('read_meta_dataset' in get_perms(public_group, data_set) or
request.user.has_perm('core.read_meta_dataset', data_set)):
return Response(data_set_uuid, status=status.HTTP_401_UNAUTHORIZED)
analyses = Analysis.objects.filter(
data_set=data_set
).order_by('-time_start')
paged_analyses = paginator.paginate_queryset(analyses, request)
serializer = AnalysisSerializer(paged_analyses, many=True)
return Response(serializer.data)
def delete(self, request, uuid):
if not request.user.is_authenticated():
return HttpResponseForbidden(
content="User {} is not authenticated".format(request.user))
else:
try:
analysis_deleted = Analysis.objects.get(uuid=uuid).delete()
except NameError as e:
logger.error(e)
return HttpResponseBadRequest(content="Bad Request")
except Analysis.DoesNotExist as e:
logger.error(e)
return HttpResponseNotFound(content="Analysis with UUID: {} "
"not found.".format(uuid))
except Analysis.MultipleObjectsReturned as e:
logger.error(e)
return HttpResponseServerError(
content="Multiple Analyses returned for this request")
else:
if analysis_deleted[0]:
return Response({"data": analysis_deleted[1]})
else:
return HttpResponseBadRequest(content=analysis_deleted[1])
class GroupViewSet(viewsets.ViewSet):
"""
API endpoint for creating, deleting, and getting groups. Also, data set
owners can update a group's data set permissions.
---
create:
description: Users can create groups
parameters:
- name: name
description: Group name needs to be unique
paramType: form
type: string
required: true
destroy:
description: Managers can delete groups
parameters:
- name: uuid
description: group uuid
paramType: path
type: string
required: true
list:
description: Returns groups filtered on data set or user
(defaults to read_meta perms)
parameters:
- name: data_set_uuid
description: Returns groups based on data set
paramType: query
type: string
required: false
- name: all_perms
description: Limits query set to groups the user is member of
paramType: query
type: boolean
required: false
partial_update:
description: Data set owners can update group's perms for data sets
parameters:
- name: data_set_uuid
description: data set uuid
paramType: path
type: string
required: true
- name: perm_list
description: object containing change, read, and read_meta
field perms.
paramType: form
type: string
required: false
...
"""
http_method_names = ['get', 'delete', 'patch', 'post']
lookup_field = 'uuid'
def get_object(self, uuid):
return get_group_for_view_set(uuid)
def get_user(self, id):
try:
return User.objects.get(id=id)
except User.DoesNotExist as e:
logger.error(e)
raise Http404
except User.MultipleObjectsReturned as e:
logger.error(e)
raise APIException("Multiple users returned for this request.")
def create(self, request):
group_name = request.data.get('name')
if request.user.is_anonymous():
return Response(
self.request.user, status=status.HTTP_401_UNAUTHORIZED
)
serializer = ExtendedGroupSerializer(data={'name': group_name})
if serializer.is_valid():