Merge pull request #825 from cortex-lab/dev

User rest endpoint changes to allow delegate information access from clients - Photometry datasets

alyx/alyx/__init__.py

@@ -1 +1 @@
-VERSION = __version__ = '1.16.2'
+VERSION = __version__ = '1.17.0'

alyx/data/fixtures/data.datasettype.json

@@ -2209,5 +2209,16 @@
  "description": "Unique identifier assigned to each ROI when ALF files created after ROI detection.",
  "filename_pattern": ""
  }
+ },
+ {
+ "model": "data.datasettype",
+ "pk": "e0a71fbc-f8ff-42a1-bfa7-d7764ab4104d",
+ "fields": {
+ "json": null,
+ "name": "photometryROI.locations",
+ "created_by": null,
+ "description": "Look up table from photometry ROI, to fiber name registered in the database and Allen brain location",
+ "filename_pattern": "*photometryROI.locations*"
+ }
  }
 ]

alyx/misc/serializers.py

@@ -50,6 +50,8 @@ class Meta:
 class UserSerializer(serializers.ModelSerializer):
  subjects_responsible = serializers.SlugRelatedField(
  many=True, queryset=Subject.objects.all(), slug_field='nickname')
+ allowed_users = serializers.SlugRelatedField(
+ many=True, queryset=LabMember.objects.all(), slug_field='username')
 
  @staticmethod
  def setup_eager_loading(queryset):
@@ -58,7 +60,7 @@ def setup_eager_loading(queryset):
 
  class Meta:
  model = get_user_model()
- fields = ('id', 'username', 'email', 'subjects_responsible', 'lab')
+ fields = ('id', 'username', 'email', 'subjects_responsible', 'lab', 'allowed_users')
 
 
 class LabSerializer(serializers.HyperlinkedModelSerializer):

alyx/misc/tests_rest.py

@@ -20,6 +20,7 @@ def setUp(self):
  self.lab = Lab.objects.create(name='basement')
  self.public_user = get_user_model().objects.create(
  username='troublemaker', password='azerty', is_public_user=True)
+ self.public_user.allowed_users.set([self.superuser])
 
  def test_create_lab_membership(self):
  # first test creation of lab through rest endpoint
@@ -55,6 +56,12 @@ def test_public_user(self):
  def test_user_rest(self):
  response = self.client.get(reverse('user-list') + '/test')
  self.ar(response, 200)
+ response = self.client.get(reverse('user-list') + '/troublemaker')
+ self.ar(response, 200)
+ self.assertEqual(
+ response.data.get('allowed_users'),
+ list(self.public_user.allowed_users.all().values_list('username', flat=True))
+ )
 
  def test_note_rest(self):
  user = self.ar(self.client.get(reverse('user-list')), 200)
@@ -71,7 +78,7 @@ def test_note_rest(self):
 
 class TestCacheView(BaseTests):
  def setUp(self):
- # This doesn't need super user privilages but I didn't know how to create a normal user
+ # This doesn't need super user privileges but I didn't know how to create a normal user
  self.superuser = get_user_model().objects.create_user('test', 'test', 'test')
  self.client.login(username='test', password='test')
  self.tag = Tag.objects.create(name='2022_Q1_paper')

alyx/misc/urls.py

@@ -4,17 +4,14 @@
 from django.conf.urls import include
 
 
-user_list = mv.UserViewSet.as_view({'get': 'list'})
-user_detail = mv.UserViewSet.as_view({'get': 'retrieve'})
-
 urlpatterns = [
  path('', RedirectView.as_view(url='/admin')), # redirect the page to admin interface
  path('labs', mv.LabList.as_view(), name="lab-list"),
  path('labs/<str:name>', mv.LabDetail.as_view(), name="lab-detail"),
  path('notes', mv.NoteList.as_view(), name="note-list"),
  path('notes/<uuid:pk>', mv.NoteDetail.as_view(), name="note-detail"),
- path('users/<str:username>', user_detail, name='user-detail'),
- path('users', user_list, name='user-list'),
+ path('users', mv.UserList.as_view(), name="user-list"),
+ path('users/<str:username>', mv.UserDetail.as_view(), name="user-detail"),
  re_path('^uploaded/(?P<img_url>.*)', mv.UploadedView.as_view(), name='uploaded'),
  path('cache.zip', mv.CacheDownloadView.as_view(), name='cache-download'),
  re_path(r'^cache/info(?:/(?P<tag>\w+))?/$', mv.CacheVersionView.as_view(), name='cache-info'),

alyx/misc/views.py

@@ -10,7 +10,7 @@
  HttpResponse, FileResponse, JsonResponse, HttpResponseRedirect, HttpResponseNotFound
 )
 
-from rest_framework import viewsets, views
+from rest_framework import views
 from rest_framework.response import Response
 from rest_framework.decorators import api_view
 from rest_framework.reverse import reverse
@@ -69,15 +69,35 @@ def api_root(request, format=None):
  })
 
 
-class UserViewSet(viewsets.ReadOnlyModelViewSet):
+class UserFilter(BaseFilterSet):
+ class Meta:
+ model = get_user_model()
+ exclude = ['json']
+
+
+class UserList(generics.ListCreateAPIView):
  """
- Lists all users with the subjects which they are responsible for.
+ get: **FILTERS**
+ - 'id'
+ - 'username'
+ - 'email'
+ - 'subjects_responsible'
+ - 'lab'
+ - 'allowed_users'
+ [===> user model reference](/admin/doc/models/misc.labmember)
  """
- queryset = get_user_model().objects.all()
- queryset = UserSerializer.setup_eager_loading(queryset)
+ queryset = UserSerializer.setup_eager_loading(get_user_model().objects.all())
  serializer_class = UserSerializer
+ permission_classes = rest_permission_classes()
+ filter_class = UserFilter
  lookup_field = 'username'
+
+
+class UserDetail(generics.RetrieveUpdateDestroyAPIView):
+ queryset = UserSerializer.setup_eager_loading(get_user_model().objects.all())
+ serializer_class = UserSerializer
  permission_classes = rest_permission_classes()
+ lookup_field = 'username'
 
 
 class LabFilter(BaseFilterSet):

requirements_frozen.txt

@@ -1,8 +1,8 @@
 asgiref==3.7.2
 backports.zoneinfo==0.2.1
-boto3==1.28.78
-botocore==1.31.78
-certifi==2023.7.22
+boto3==1.33.4
+botocore==1.33.4
+certifi==2023.11.17
 cffi==1.16.0
 charset-normalizer==3.3.2
 click==8.1.7
@@ -12,7 +12,7 @@ coreapi==2.3.3
 coreschema==0.0.4
 coverage==6.5.0
 coveralls==3.3.1
-cryptography==41.0.5
+cryptography==41.0.7
 cycler==0.12.1
 Django==4.2.7
 django-admin-list-filter-dropdown==1.0.3
@@ -24,22 +24,22 @@ django-ipware==5.0.2
 django-js-asset==2.1.0
 django-mptt==0.14.0
 django-polymorphic==3.1.0
-django-reversion==5.0.6
+django-reversion==5.0.8
 django-storages==1.14.2
-django-structlog==6.0.0
+django-structlog==6.0.1
 django-test-without-migrations==0.6
 djangorestframework==3.14.0
 docopt==0.6.2
 docutils==0.20.1
 drfdocs==0.0.11
 flake8==6.1.0
-fonttools==4.44.0
-globus-cli==3.18.0
-globus-sdk==3.28.0
+fonttools==4.45.1
+globus-cli==3.19.0
+globus-sdk==3.30.0
 iblutil==1.7.1
-idna==3.4
+idna==3.6
 importlib-metadata==6.8.0
-importlib-resources==6.1.0
+importlib-resources==6.1.1
 itypes==1.2.0
 Jinja2==3.1.2
 jmespath==1.0.1
@@ -48,7 +48,7 @@ llvmlite==0.41.1
 lxml==4.9.3
 Markdown==3.5.1
 MarkupSafe==2.1.3
-matplotlib==3.7.3
+matplotlib==3.7.4
 mccabe==0.7.0
 numba==0.58.1
 numpy==1.24.4
@@ -57,7 +57,7 @@ packaging==23.2
 pandas==2.0.3
 Pillow==10.1.0
 psycopg2-binary==2.9.9
-pyarrow==14.0.0
+pyarrow==14.0.1
 pycodestyle==2.11.1
 pycparser==2.21
 pyflakes==3.1.0
@@ -68,7 +68,7 @@ python-magic==0.4.27
 pytz==2023.3.post1
 PyYAML==6.0.1
 requests==2.31.0
-s3transfer==0.7.0
+s3transfer==0.8.2
 six==1.16.0
 sqlparse==0.4.4
 structlog==23.2.0

scripts/sync_ucl/prune_cortexlab.py

@@ -83,7 +83,8 @@
 
 # only imports users that are relevant to IBL
 users_to_import = ['cyrille', 'Gaelle', 'kenneth', 'lauren', 'matteo', 'miles', 'nick', 'olivier',
- 'Karolina_Socha', 'Hamish', 'laura', 'niccolo', 'SamuelP', 'miriam.jansen', 'carolina.quadrado']
+ 'Karolina_Socha', 'Hamish', 'laura', 'niccolo', 'SamuelP', 'miriam.jansen',
+ 'carolina.quadrado']
 users_to_leave = LabMember.objects.using('cortexlab').exclude(username__in=users_to_import)
 users_to_keep = Dataset.objects.using('cortexlab').values_list('created_by', flat=True).distinct()
 users_to_leave = users_to_leave.exclude(pk__in=users_to_keep)