format black

ippisite/ippidb/models/targetcentric.py

@@ -166,6 +166,7 @@ class Chain(models.Model):
             partner_message = "with partner "
         return "{}{}".format(partner_message, self.protein.recommended_name_long)
 
+
 class InteractFile(models.Model):
     chain = models.ForeignKey(Chain, on_delete=models.CASCADE)
     label = models.CharField(max_length=250, blank=False, null=False)
@@ -175,7 +176,7 @@ class InteractFile(models.Model):
     )
 
     class Meta:
-        unique_together = [['chain', 'label']]
+        unique_together = [["chain", "label"]]
 
     def __unicode__(self):
         return "{}".format(self.interact_file)
@@ -245,9 +246,9 @@ class Partner(models.Model):
     type_binding = models.CharField(
         "Type of Binding", max_length=50, default="orthosteric", blank=False, null=False
     )
-    class Meta:
-        unique_together = [['ligand', 'chain']]
 
+    class Meta:
+        unique_together = [["ligand", "chain"]]
 
     def save(self, *args, **kwargs):
         if self.ligand and self.chain:
@@ -527,6 +528,7 @@ def interactdelete(sender, instance, **kwargs):
             ):
                 interactfile.interact_file.delete()
 
+
 @receiver(pre_save, sender=Chain)
 def updatemrcfile(sender, instance, **kwargs):
     try:

ippisite/ippidb/urls.py

@@ -24,7 +24,10 @@ ROUTER.register(r"ligand", views.LigandViewSet, basename="ligand")
 ROUTER.register(r"partner", views.PartnerViewSet, basename="partner")
 ROUTER.register(r"interactfile", views.InteractFileViewSet, basename="interactfile")
 ROUTER.register(r"cavity", views.CavityViewSet, basename="cavity")
-ROUTER.register(r"builddistances", views.BuildDistancesViewSet, basename="builddistances")
+ROUTER.register(
+    r"builddistances", views.BuildDistancesViewSet, basename="builddistances"
+)
+
 
 class IppiDbStaticSitemap(Sitemap):
     changefreq = "never"
@@ -80,11 +83,18 @@ urlpatterns = [
         name="contributor_card",
     ),
     re_path(r"^targetcentric/$", views.PDBView.as_view(), name="cavities"),
-    re_path(r"^targetcentric/tmaps$", views.pocketome_html, name='pocketome_html'),
-    re_path(r"^targetcentric/networks$", TemplateView.as_view(template_name="targetcentric_networks.html"), name="networks"),
-    #re_path(r"^targetcentric/networks$", views.NetworkView.as_view(), name="networks"),
-    
-    re_path(r"^cavity/(?P<pk>\d+)/near-cavities$", views.NearCavitiesHTMLFragmentView.as_view(), name="near_cavities"),
+    re_path(r"^targetcentric/tmaps$", views.pocketome_html, name="pocketome_html"),
+    re_path(
+        r"^targetcentric/networks$",
+        TemplateView.as_view(template_name="targetcentric_networks.html"),
+        name="networks",
+    ),
+    # re_path(r"^targetcentric/networks$", views.NetworkView.as_view(), name="networks"),
+    re_path(
+        r"^cavity/(?P<pk>\d+)/near-cavities$",
+        views.NearCavitiesHTMLFragmentView.as_view(),
+        name="near_cavities",
+    ),
     re_path(r"^api/", include(ROUTER.urls)),
     re_path(r"^compounds/$", views.CompoundListView.as_view(), name="compound_list"),
     re_path(

ippisite/ippidb/views/targetcentric.py

@@ -7,7 +7,7 @@ from operator import add
 from django.views.generic import ListView, DetailView
 from django.contrib import messages
 from django.db.models import Case, When, Value, IntegerField, F, Q
-from rest_framework import viewsets, status, views
+from rest_framework import viewsets
 from rest_framework.decorators import action
 from ippidb.models import (
     PDB,
@@ -21,7 +21,8 @@ from ippidb.models import (
     Cavity,
     MetaInformation,
     Network,
-    Job)
+    Job,
+)
 from ippidb.serializer import (
     PdbSerializer,
     DistanceSerializer,
@@ -31,25 +32,26 @@ from ippidb.serializer import (
     PartnerSerializer,
     InteractFileSerializer,
     CavitySerializer,
-    JobSerializer)
+    JobSerializer,
+)
 from rest_framework.permissions import IsAdminUser, SAFE_METHODS
-from rest_framework.authtoken.models import Token
 from ippidb.tasks import launch_build_matrix_distance
 from rest_framework.response import Response
 from django.views.decorators.clickjacking import xframe_options_exempt
 
 from django.shortcuts import render
 
+
 @xframe_options_exempt
 def pocketome_html(request):
-    return render(request, 'PocketBook_MST_Euclidean_log_trim_scratch_sec61.html')
+    return render(request, "PocketBook_MST_Euclidean_log_trim_scratch_sec61.html")
 
 
 class IsAdminUserOrReadOnly(IsAdminUser):
     def has_permission(self, request, view):
         is_admin = super(IsAdminUserOrReadOnly, self).has_permission(request, view)
         return request.method in SAFE_METHODS or is_admin
- 
+
 
 class PdbViewSet(viewsets.ModelViewSet):
     """
@@ -68,7 +70,7 @@ class PdbViewSet(viewsets.ModelViewSet):
         elif code:
             queryset = PDB.objects.filter(code=code)
         return queryset
- 
+
 
 class ProteinViewSet(viewsets.ModelViewSet):
     serializer_class = ProteinSerializer
@@ -112,9 +114,11 @@ class LigandViewSet(viewsets.ModelViewSet):
         supplementary_id = self.request.GET.get("supplementary_id")
         if pdb:
             if pdb_ligand_id and supplementary_id:
-                queryset = queryset.filter(pdb=pdb, 
-                                                 pdb_ligand_id=pdb_ligand_id, 
-                                                 supplementary_id=supplementary_id)
+                queryset = queryset.filter(
+                    pdb=pdb,
+                    pdb_ligand_id=pdb_ligand_id,
+                    supplementary_id=supplementary_id,
+                )
             else:
                 queryset = queryset.filter(pdb=pdb)
         return queryset
@@ -130,7 +134,7 @@ class PartnerViewSet(viewsets.ModelViewSet):
         chain = self.request.GET.get("chain")
         ligand = self.request.GET.get("ligand")
         if chain:
-            queryset = queryset.filter(chain=chain)    
+            queryset = queryset.filter(chain=chain)
         if ligand:
             queryset = queryset.filter(ligand=ligand)
         return queryset
@@ -204,16 +208,17 @@ class BuildDistancesViewSet(viewsets.ModelViewSet):
         params_command = {"nb_neighbors": request.POST.get("nb_neighbors")}
         launch_build_matrix_distance.delay(params_command)
         url = request.url #TODO construct with the correct url job table
-        return Response({'message': 'Distances Matrix is building! Check {} to get status'.format(url)}, status=status.HTTP_200_OK)
+        return Response({'message': 'Distances Matrix is building! 
+        Check {} to get status'.format(url)}, status=status.HTTP_200_OK)
     """
 
-    @action(detail=False, methods=['get', 'post'])
+    @action(detail=False, methods=["get", "post"])
     def get_queryset(self):
-        jobs= Job.objects.all()
+        jobs = Job.objects.all()
         return jobs
 
     def create(self, request, *args, **kwargs):
-        params_command = {"nb_neighbors": request.data.get('nb_neighbors')}
+        params_command = {"nb_neighbors": request.data.get("nb_neighbors")}
         launch_build_matrix_distance.delay(params_command)
         job = Job.objects.last()
         serializer = self.get_serializer(job)
@@ -478,7 +483,7 @@ class NearCavitiesHTMLFragmentView(DetailView):
     def get_context_data(self, *, object_list=None, **kwargs):
         return dict(
             **super().get_context_data(**kwargs),
-            chaincount=self.request.GET.get('chaincount', '0'),
-            cavcount=self.request.GET.get('cavcount', '0'),
+            chaincount=self.request.GET.get("chaincount", "0"),
+            cavcount=self.request.GET.get("cavcount", "0"),
             avg_std=MetaInformation.objects.first(),
         )

ippisite/ippisite/authentication.py

@@ -6,16 +6,17 @@ from django.utils import timezone
 from django.conf import settings
 
 
-
-#this return left time
+# this return left time
 def expires_in(token):
     time_elapsed = timezone.now() - token.created
-    left_time = timedelta(seconds = settings.TOKEN_EXPIRED_AFTER_SECONDS) - time_elapsed
+    left_time = timedelta(seconds=settings.TOKEN_EXPIRED_AFTER_SECONDS) - time_elapsed
     return left_time
 
+
 # token checker if token expired or not
 def is_token_expired(token):
-    return expires_in(token) < timedelta(seconds = 0)
+    return expires_in(token) < timedelta(seconds=0)
+
 
 def token_expire_handler(token):
     is_expired = is_token_expired(token)
@@ -24,22 +25,26 @@ def token_expire_handler(token):
         token = None
     return is_expired, token
 
+
 class ExpiringTokenAuthentication(TokenAuthentication):
     """
     If token is expired then it will be removed
     and new one with different key will be created
     """
+
     def authenticate_credentials(self, key):
         try:
-            token = Token.objects.get(key = key)
+            token = Token.objects.get(key=key)
         except Token.DoesNotExist:
             raise AuthenticationFailed("Invalid Token")
-        
+
         if not token.user.is_active:
             raise AuthenticationFailed("User is not active")
 
         is_expired, token = token_expire_handler(token)
         if is_expired:
-            raise AuthenticationFailed("The Token is expired, return on the admin interface to generate a new token")
-        
-        return (token.user, token)
\ No newline at end of file
+            raise AuthenticationFailed(
+                "The Token is expired, return on the admin interface to generate a new token"
+            )
+
+        return (token.user, token)