Python pep8 format

.pep8

@@ -0,0 +1,3 @@
+[pycodestyle]
+max_line_length = 120
+ignore = E501

VRE/apps/api/exceptions.py

@@ -25,13 +25,16 @@ def json_schema_error_message(exc, context):
     #     }
     # ]
 
-    system_errors = exc.get_full_details()
+    try:
+        system_errors = exc.get_full_details()
+    except Exception as ex:
+        system_errors = [{'exception' : {'code' : 'exception', 'message' : 'Something went wrong'}}]
 
     if isinstance(system_errors, list):
-        system_errors = {'header' : system_errors}
+        system_errors = {'_no_field' : system_errors}
     elif system_errors.get('message') is not None:
         # If there is a message keyword in the main system errors, then it is not a form error, but a more general error
-        system_errors = {'header' : [system_errors]}
+        system_errors = {'_no_field' : [system_errors]}
 
     json_errors = []
     for errorfield, errors in system_errors.items():

VRE/apps/api/urls.py

@@ -1,7 +1,5 @@
 from django.urls import path, re_path, include
-
 from rest_framework import permissions, routers
-
 from drf_yasg.views import get_schema_view
 from drf_yasg import openapi
 
@@ -12,25 +10,25 @@ from . import views
 # from apps.storage.views import StorageEngineViewSet, StorageLocationViewSet
 from apps.study.views import Studies
 from apps.virtual_machine.views import (VirtualMachineViewSet,
-                                            VirtualMachineOperatingSystemViewSet,
-                                            VirtualMachineProfileViewSet,
-                                            VirtualMachineMemoryViewSet,
-                                            VirtualMachineNetworkViewSet,
-                                            VirtualMachineStorageViewSet,
-                                            VirtualMachineGPUViewSet,
-                                            VirtualMachineAccessViewSet)
+                                        VirtualMachineOperatingSystemViewSet,
+                                        VirtualMachineProfileViewSet,
+                                        VirtualMachineMemoryViewSet,
+                                        VirtualMachineNetworkViewSet,
+                                        VirtualMachineStorageViewSet,
+                                        VirtualMachineGPUViewSet,
+                                        VirtualMachineAccessViewSet)
 
 schema_view = get_schema_view(
-   openapi.Info(
-      title="Virtual Research Environment API",
-      default_version='v1',
-      description="Here you can see a list of API endpoints and actions that are available to communicate with the VRE API",
-      terms_of_service="https://www.rug.nl",
-      contact=openapi.Contact(email="vre_team@rug.nl"),
-      license=openapi.License(name="MIT License"),
-   ),
-   public=True,
-   permission_classes=(permissions.AllowAny,),
+    openapi.Info(
+        title="Virtual Research Environment API",
+        default_version='v1',
+        description="Here you can see a list of API endpoints and actions that are available to communicate with the VRE API",
+        terms_of_service="https://www.rug.nl",
+        contact=openapi.Contact(email="vre_team@rug.nl"),
+        license=openapi.License(name="MIT License"),
+    ),
+    public=True,
+    permission_classes=(permissions.AllowAny,),
 )
 
 api_router_v1 = routers.DefaultRouter()
@@ -60,20 +58,20 @@ api_router_v1.urls.append(path('vrw/', include('apps.vrw.urls')))
 # Main namespace for the API urls
 app_name = 'api'
 urlpatterns = [
-   re_path(r'^swagger(?P<format>\.json|\.yaml)$', schema_view.without_ui(cache_timeout=0), name='schema-json'),
-   path('swagger/', schema_view.with_ui('swagger', cache_timeout=0), name='schema-swagger-ui'),
-   path('redoc/', schema_view.with_ui('redoc', cache_timeout=0), name='schema-redoc'),
+    re_path(r'^swagger(?P<format>\.json|\.yaml)$', schema_view.without_ui(cache_timeout=0), name='schema-json'),
+    path('swagger/', schema_view.with_ui('swagger', cache_timeout=0), name='schema-swagger-ui'),
+    path('redoc/', schema_view.with_ui('redoc', cache_timeout=0), name='schema-redoc'),
 
-   # Authentication urls
-   path('auth/', include('djoser.urls')),
-   path('auth/', include('djoser.urls.jwt')),
-   # Custom login for getting the HAWK keys
-   path('auth/hawk/create/', views.Login.as_view(), name='api-login'),
+    # Authentication urls
+    path('auth/', include('djoser.urls')),
+    path('auth/', include('djoser.urls.jwt')),
+    # Custom login for getting the HAWK keys
+    path('auth/hawk/create/', views.Login.as_view(), name='api-login'),
 
-   # Extra /api/info path for checking if the Hawk authentication is working.
-   # Also this will give the full url to the OpenAPI documentation
-   path('info/', views.Info.as_view(), name='api-info'),
+    # Extra /api/info path for checking if the Hawk authentication is working.
+    # Also this will give the full url to the OpenAPI documentation
+    path('info/', views.Info.as_view(), name='api-info'),
 
-   # Add extra namespace for versioning the API
-   path('v1/', include((api_router_v1.urls,'v1'))),
-]
+    # Add extra namespace for versioning the API
+    path('v1/', include((api_router_v1.urls, 'v1'))),
+]

VRE/apps/study/__init__.py

@@ -1 +1 @@
-default_app_config = 'apps.study.apps.StudyConfig'
+default_app_config = 'apps.study.apps.StudyConfig'

VRE/apps/study/admin.py

@@ -7,18 +7,20 @@ from .models import Study, StudyRole
 # Register your models here.
 admin.site.register(StudyRole)
 
+
 class role_inline(admin.TabularInline):
     model = StudyRole
     extra = 1
 
+
 @admin.register(Study)
 class StudyAdmin(admin.ModelAdmin):
     inlines = (role_inline,)
 
-    list_display    = ('name', 'total_files', 'total_file_size', 'total_invitations', 'created_at')
-    ordering        = ('-created_at','name', )
-    search_fields   = ('name', )
+    list_display = ('name', 'total_files', 'total_file_size', 'total_invitations', 'created_at')
+    ordering = ('-created_at', 'name', )
+    search_fields = ('name', )
     readonly_fields = ('upload_uuid', 'api_upload_url', 'total_files', 'total_file_size', 'total_invitations', 'created_at', 'updated_at')
 
-    def total_file_size(self,obj):
+    def total_file_size(self, obj):
         return filesizeformat(obj.total_file_size)

VRE/apps/study/apps.py

@@ -2,20 +2,21 @@ from django.apps import AppConfig
 from django.conf import settings
 from django.utils.translation import ugettext_lazy as _
 
+
 class StudyConfig(AppConfig):
     name = 'apps.study'
     label = 'study'
     verbose_name = _('Study')
     verbose_name_plural = _('Studies')
 
-    if not hasattr(settings,'DEFAULT_VM_PROFILE'):
+    if not hasattr(settings, 'DEFAULT_VM_PROFILE'):
         settings.DEFAULT_VM_PROFILE = 2
 
-    if not hasattr(settings,'DEFAULT_VM_OS'):
+    if not hasattr(settings, 'DEFAULT_VM_OS'):
         settings.DEFAULT_VM_OS = 2
 
     def ready(self):
         """
         Load custom signals for creating :term:`VRW` models
         """
-        import apps.study.signals
+        import apps.study.signals

VRE/apps/study/models.py

@@ -13,6 +13,8 @@ from apps.university.models import StudyField
 import uuid
 
 # Create your models here.
+
+
 class StudyManager(models.Manager):
     """
     This is a custom study manager for getting extra information from a study model like:
@@ -31,25 +33,26 @@ class StudyManager(models.Manager):
         This will overrule/alter the existing queryset.
         """
         return super().get_queryset().select_related('storagelocation').annotate(
-                                                                                _total_files=Count('files', distinct=True),
-                                                                                _total_file_size=Sum('files__filesize', distinct=True),
-                                                                                _total_invitations=Count('invitations', distinct=True),
-                                                                        )
+            _total_files=Count('files', distinct=True),
+            _total_file_size=Sum('files__filesize', distinct=True),
+            _total_invitations=Count('invitations', distinct=True),
+        )
+
 
 class StudyRoleNames(models.TextChoices):
     """Research study role options
 
     Valid status values:
      - Administrator
-     - Owner
      - Researcher
      - Member
     """
 
-    ADMIN      = ('ADMIN',      _('Administrator'))
-    OWNER      = ('OWNER',      _('Owner'))
+    ADMIN = ('ADMIN', _('Administrator'))
+#    OWNER      = ('OWNER',      _('Owner'))
     RESEARCHER = ('RESEARCHER', _('Researcher'))
-    MEMBER     = ('MEMBER',     _('Member'))
+    MEMBER = ('MEMBER', _('Member'))
+
 
 class Study(MetaDataModel):
     """
@@ -75,35 +78,34 @@ class Study(MetaDataModel):
         verbose_name_plural = _('studies')
         ordering = ['name']
 
+    owner = models.ForeignKey(Researcher, verbose_name=Researcher._meta.verbose_name, on_delete=models.CASCADE, help_text=_('The researcher that is the owner this study. By default the researcher that has created this study.'))
+    name = models.CharField(_('Name'), max_length=200, help_text=_('Name of the research study.'))
+    description = models.TextField(_('Description'), blank=True, null=True, help_text=_('Enter a short description for this study.'))
 
-    owner          = models.ForeignKey(Researcher, verbose_name=Researcher._meta.verbose_name, on_delete=models.CASCADE, help_text=_('The researcher that is the owner this study. By default the researcher that has created this study.'))
-    name           = models.CharField(_('Name'), max_length=200, help_text=_('Name of the research study.'))
-    description    = models.TextField(_('Description'), blank=True, null=True, help_text=_('Enter a short description for this study.'))
-
-    code           = models.CharField(_('Code'), max_length=50, help_text=_('The research study code.'))
-    human_subject  = models.BooleanField(_('Human subject'), help_text=_('Is this research study using real humans.'))
-    field          = models.ForeignKey(StudyField, verbose_name=StudyField._meta.verbose_name, on_delete=models.CASCADE, help_text=_('The study field for this reaserch study.'))
+    code = models.CharField(_('Code'), max_length=50, help_text=_('The research study code.'))
+    human_subject = models.BooleanField(_('Human subject'), help_text=_('Is this research study using real humans.'))
+    field = models.ForeignKey(StudyField, verbose_name=StudyField._meta.verbose_name, on_delete=models.CASCADE, help_text=_('The study field for this reaserch study.'))
 
-    contributors   = models.ManyToManyField(Researcher,  related_name='contributors', through='StudyRole', through_fields=('study','researcher'))
+    contributors = models.ManyToManyField(Researcher, related_name='contributors', through='StudyRole', through_fields=('study', 'researcher'))
 
     # These are used for accepting files (datadrops)
-    upload_code = models.CharField(_('Upload code'), max_length=20,  default=get_random_int_value, editable=False, help_text=_('A unique upload code. Will be generated when a new study is saved.'))
-    upload_uuid = models.UUIDField(_('Upload url key'), unique=True,    default=uuid.uuid4,           editable=False, help_text=_('A unique upload url. Will be generated when a new study is saved.'))
+    upload_code = models.CharField(_('Upload code'), max_length=20, default=get_random_int_value, editable=False, help_text=_('A unique upload code. Will be generated when a new study is saved.'))
+    upload_uuid = models.UUIDField(_('Upload url key'), unique=True, default=uuid.uuid4, editable=False, help_text=_('A unique upload url. Will be generated when a new study is saved.'))
 
     # Here we load our custom StudyManager so we always have the amount of files, total file size and amount of invitations directly accessable
-    objects     = StudyManager()
+    objects = StudyManager()
 
     @property
     def has_storage(self):
         """boolean: Returns true when there is at least one storage location connected to this study"""
-        #print(dir(self.storagelocation))
+        # print(dir(self.storagelocation))
         return self.storagelocation is not None
 
     @property
     def get_absolute_url(self):
         """str: Returns the full url to the study detail page."""
         return 'aaa'
-        #return reverse('study:detail', kwargs={'study_id': self.pk})
+        # return reverse('study:detail', kwargs={'study_id': self.pk})
 
     @property
     def web_upload_url(self):
@@ -134,12 +136,13 @@ class Study(MetaDataModel):
         """str: Returns a readable string for the study."""
         return f'{self.name}'
 
+
 class StudyRole(MetaDataModel):
-    study      = models.ForeignKey(Study, verbose_name=Study._meta.verbose_name, on_delete=models.CASCADE, help_text=_('Study'))
+    study = models.ForeignKey(Study, verbose_name=Study._meta.verbose_name, on_delete=models.CASCADE, help_text=_('Study'))
     researcher = models.ForeignKey(Researcher, verbose_name=Researcher._meta.verbose_name, on_delete=models.CASCADE, help_text=_('Researcher'))
-    role       = models.CharField(_('Role'), max_length=10, choices=StudyRoleNames.choices, default=StudyRoleNames.MEMBER, help_text=_('The role withing this research study.'))
-    active     = models.BooleanField(_('Active'), default=True, help_text=_(''))
+    role = models.CharField(_('Role'), max_length=10, choices=StudyRoleNames.choices, default=StudyRoleNames.MEMBER, help_text=_('The role withing this research study.'))
+    active = models.BooleanField(_('Active'), default=True, help_text=_(''))
 
     def __str__(self):
         """str: Returns a readable string for the study role."""
-        return f'{self.researcher} is {self.role} of {self.study.name}'
+        return f'{self.researcher} is {self.role} of {self.study.name}'

VRE/apps/study/permissions.py

@@ -1,5 +1,6 @@
 from rest_framework.permissions import BasePermission
 
+
 class IsStudyContributor(BasePermission):
     def has_object_permission(self, request, view, obj):
-        return obj.contributors.filter(researcher=request.user.researcher).exists()
+        return obj.contributors.filter(researcher=request.user.researcher).exists()

VRE/apps/study/tests.py

@@ -14,24 +14,26 @@ from django.urls import reverse
 import random
 
 # Create your tests here.
+
+
 class StudyCreateTest(TestCase):
 
-    fixtures = ('university_initial_data','virtual_machine_initial_data')
+    fixtures = ('university_initial_data', 'virtual_machine_initial_data')
 
     @classmethod
     def setUpTestData(cls):
         cls.firstname = 'Jan'
-        cls.lastname  = 'Doedel'
-        cls.email     = 'dummy@rug.nl'
-        cls.username  = 'dummy@rug.nl'
-        cls.password  = ';t2QG*LLtzdnC*'
+        cls.lastname = 'Doedel'
+        cls.email = 'dummy@rug.nl'
+        cls.username = 'dummy@rug.nl'
+        cls.password = ';t2QG*LLtzdnC*'
 
-        cls.faculty   = Faculty.objects.get(pk=9)
+        cls.faculty = Faculty.objects.get(pk=9)
 
         # Create a new user
-        cls.user = User.objects.create_user(username = cls.username, password = cls.password, email = cls.email)
+        cls.user = User.objects.create_user(username=cls.username, password=cls.password, email=cls.email)
         cls.user.first_name = cls.firstname
-        cls.user.last_name  = cls.lastname
+        cls.user.last_name = cls.lastname
         cls.user.save()
 
         # Make a researcher member of a faculty
@@ -42,7 +44,7 @@ class StudyCreateTest(TestCase):
 
         # Create some extra researchers.....
         for x in range(5):
-            user = User.objects.create_user(username = f'Username_{x}', password = f'{cls.password}_{x}', email = f'researcher_{x}@rug.nl')
+            user = User.objects.create_user(username=f'Username_{x}', password=f'{cls.password}_{x}', email=f'researcher_{x}@rug.nl')
             user.first_name = f'Rs_{x}'
             user.last_name = f'LN_{x}'
             user.save()
@@ -52,7 +54,7 @@ class StudyCreateTest(TestCase):
 
                 cls.valid_contributor = user
             else:
-                user.researcher.faculty = Faculty.objects.get(pk=random.randint(2,8))
+                user.researcher.faculty = Faculty.objects.get(pk=random.randint(2, 8))
                 cls.invalid_contributor = user
 
             user.researcher.save()
@@ -62,7 +64,7 @@ class StudyCreateTest(TestCase):
         self.client = RequestsClient()
 
         # Get a JWT token
-        login_data = {'username' : self.username, 'password' : self.password }
+        login_data = {'username': self.username, 'password': self.password}
         endpoint = 'http://testserver/api/auth/jwt/create/'
         response = self.client.post(endpoint, json=login_data)
 
@@ -95,7 +97,7 @@ class StudyCreateTest(TestCase):
         # Check if we are the only reseacher....
         self.assertEqual(len(study['contributors']), 1)
         # And make sure we are 'ADMIN'
-        self.assertEqual(study['contributors'][0]['role'],'ADMIN')
+        self.assertEqual(study['contributors'][0]['role'], 'ADMIN')
         self.assertEqual(study['contributors'][0]['researcher']['id'], self.user.researcher.id)
 
         # And now we should have 1 study
@@ -121,7 +123,7 @@ class StudyCreateTest(TestCase):
         }
         response = self.client.post(endpoint, json=data)
         self.assertEqual(response.status_code, 400)
-        self.assertEqual(response.json()[0]['message'],f'Study field {study_field} is not valid for faculty {self.faculty}')
+        self.assertEqual(response.json()[0]['message'], f'Study field {study_field} is not valid for faculty {self.faculty}')
 
     def test_update_study(self):
         # We need a new study to test with.....:(
@@ -130,7 +132,7 @@ class StudyCreateTest(TestCase):
         # Get the first study through Django Models, which should be the new created study
         study = Study.objects.get(contributors__in=[self.user.researcher])
 
-        endpoint = 'http://testserver' + reverse('api:v1:study-detail',kwargs={ 'pk' : study.id})
+        endpoint = 'http://testserver' + reverse('api:v1:study-detail', kwargs={'pk': study.id})
         data = {
             "name": "Test Onderzoek - UPDATE",
             "description": "Doe maar een lange onderzoek - UPDATE",
@@ -140,7 +142,7 @@ class StudyCreateTest(TestCase):
         }
         response = self.client.put(endpoint, json=data)
 
-         # And now we should have 1 study
+        # And now we should have 1 study
         endpoint = 'http://testserver' + reverse('api:v1:study-list')
         response = self.client.get(endpoint)
 
@@ -149,7 +151,6 @@ class StudyCreateTest(TestCase):
         self.assertEqual(len(response.json()['results']), 1)
         self.assertEqual(response.json()['results'][0]['id'], study.id)
 
-
     def test_add_new_contributor(self):
         # We need a new study to test with.....:(
         self.test_create_study()
@@ -157,10 +158,10 @@ class StudyCreateTest(TestCase):
         # Get the first study through Django Models, which should be the new created study
         study = Study.objects.get(contributors__in=[self.user.researcher])
 
-        endpoint = 'http://testserver' + reverse('api:v1:study-contributors', kwargs={ 'pk' : study.id})
+        endpoint = 'http://testserver' + reverse('api:v1:study-contributors', kwargs={'pk': study.id})
         data = [{
-            "researcher_id" : self.valid_contributor.researcher.id,
-            "role"          : "RESEARCHER"
+            "researcher_id": self.valid_contributor.researcher.id,
+            "role": "RESEARCHER"
         }]
         response = self.client.post(endpoint, json=data)
 
@@ -176,12 +177,12 @@ class StudyCreateTest(TestCase):
         # Get the first study through Django Models, which should be the new created study
         study = Study.objects.get(contributors__in=[self.user.researcher])
 
-        endpoint = 'http://testserver' + reverse('api:v1:study-contributors', kwargs={ 'pk' : study.id})
+        endpoint = 'http://testserver' + reverse('api:v1:study-contributors', kwargs={'pk': study.id})
         data = [{
-            "researcher_id" : self.invalid_contributor.researcher.id,
-            "role"          : "RESEARCHER"
+            "researcher_id": self.invalid_contributor.researcher.id,
+            "role": "RESEARCHER"
         }]
         response = self.client.post(endpoint, json=data)
 
         # We expect ONLY 1 contributors now. The invalid researcher should not be added
-        self.assertEqual(len(response.json()), 1)
+        self.assertEqual(len(response.json()), 1)

VRE/apps/university/models.py

@@ -5,6 +5,8 @@ from django.utils.translation import gettext_lazy as _
 from lib.models.base import MetaDataModel
 
 # Create your models here.
+
+
 class University(MetaDataModel):
     """
     A model to represent a University. This model is used to combine faculties and their study fields. Also researchers are member of a university.
@@ -25,8 +27,8 @@ class University(MetaDataModel):
         verbose_name_plural = _('universities')
         ordering = ['name']
 
-    name    = models.CharField(_('Name'), max_length=200, help_text=_('The name of the university.'))
-    email   = models.EmailField(_('Email address'),max_length=200, help_text=_('The general email address for this university.'))
+    name = models.CharField(_('Name'), max_length=200, help_text=_('The name of the university.'))
+    email = models.EmailField(_('Email address'), max_length=200, help_text=_('The general email address for this university.'))
     website = models.CharField(_('Website'), max_length=200, help_text=_('The full url to this university website.'))
 
     def __str__(self):
@@ -52,8 +54,8 @@ class Faculty(MetaDataModel):
         verbose_name_plural = _('faculties')
         ordering = ['name']
 
-    name         = models.CharField(_('Name'), max_length=200, help_text=_('The name of the faculty.'))
-    university   = models.ForeignKey(University, verbose_name=University._meta.verbose_name, on_delete=models.CASCADE, help_text=_('To wich university belongs this faculty'))
+    name = models.CharField(_('Name'), max_length=200, help_text=_('The name of the faculty.'))
+    university = models.ForeignKey(University, verbose_name=University._meta.verbose_name, on_delete=models.CASCADE, help_text=_('To wich university belongs this faculty'))
 
     def __str__(self):
         """str: Returns a readable string for the facutlty."""
@@ -78,10 +80,9 @@ class StudyField(MetaDataModel):
         verbose_name_plural = _('study fields')
         ordering = ['name']
 
-    name    = models.CharField(_('Name'), max_length=200, help_text=_('The name of the study field.'))
+    name = models.CharField(_('Name'), max_length=200, help_text=_('The name of the study field.'))
     faculty = models.ForeignKey(Faculty, verbose_name=Faculty._meta.verbose_name, on_delete=models.CASCADE, help_text=_('To wich faculty belongs this study'))
 
     def __str__(self):
         """str: Returns a readable string for the studyfield."""
         return f'{self.name}'
-