MAINT: Upgrade to Django 1.11 (#45)

ccdb/api/urls.py

@@ -38,11 +38,12 @@ router.register(r'species', species_viewsets.SpeciesViewSet)
 router.register(r'collection-species',
                 species_viewsets.CollectionSpeciesViewSet)
 
+app_name = 'api'
 urlpatterns = [
     url(r'^auth/login/', api_v.Login.as_view()),
     url(r'^auth/password/reset/confirm/',
         api_v.PasswordResetConfirm.as_view()),
     url(r'^auth/password/reset/', api_v.PasswordReset.as_view()),
     url(r'^auth/', include('djoser.urls.authtoken')),
-    url(r'^v1/', include(router.urls, namespace='v1')),
+    url(r'^v1/', include((router.urls, 'api_v1'), namespace='v1')),
 ]

ccdb/collections_ccdb/filters.py

@@ -9,43 +9,43 @@ from ccdb.species.models import Species
 
 class CollectionFilter(filters.FilterSet):
     project = ModelMultipleChoiceFilter(
-        name='project__id',
+        field_name='project__id',
         to_field_name='id',
         queryset=Project.objects.all(),
     )
 
     region = ModelMultipleChoiceFilter(
-        name='study_location__site__region__id',
+        field_name='study_location__site__region__id',
         to_field_name='id',
         queryset=Region.objects.all(),
     )
 
     site = ModelMultipleChoiceFilter(
-        name='study_location__site__id',
+        field_name='study_location__site__id',
         to_field_name='id',
         queryset=Site.objects.all(),
     )
 
     study_location = ModelMultipleChoiceFilter(
-        name='study_location__id',
+        field_name='study_location__id',
         to_field_name='id',
         queryset=StudyLocation.objects.all(),
     )
 
     collection_method = ModelMultipleChoiceFilter(
-        name='collection_method__id',
+        field_name='collection_method__id',
         to_field_name='id',
         queryset=CollectionMethod.objects.all(),
     )
 
     adfg_permit = ModelMultipleChoiceFilter(
-        name='adfg_permit__id',
+        field_name='adfg_permit__id',
         to_field_name='id',
         queryset=ADFGPermit.objects.all(),
     )
 
     species = ModelMultipleChoiceFilter(
-        name='collection_species__species__id',
+        field_name='collection_species__species__id',
         to_field_name='id',
         queryset=Species.objects.all(),
     )

ccdb/collections_ccdb/models.py

@@ -56,13 +56,17 @@ class ADFGPermit(models.Model):
 
 
 class Collection(models.Model):
-    project = models.ForeignKey('projects.Project', related_name='collections')
+    project = models.ForeignKey('projects.Project', related_name='collections',
+                                on_delete=models.CASCADE)
     study_location = models.ForeignKey('locations.StudyLocation',
-                                       related_name='collections')
+                                       related_name='collections',
+                                       on_delete=models.CASCADE)
     collection_type = models.ForeignKey(CollectionType,
-                                        related_name='collections')
+                                        related_name='collections',
+                                        on_delete=models.CASCADE)
     collection_method = models.ForeignKey(CollectionMethod,
-                                          related_name='collections')
+                                          related_name='collections',
+                                          on_delete=models.CASCADE)
     number_of_traps = models.IntegerField(blank=True, null=True)
     collection_start_date = models.DateField(blank=True, null=True)
     collection_start_time = models.TimeField(blank=True, null=True)
@@ -71,16 +75,21 @@ class Collection(models.Model):
     notes = models.TextField(blank=True, null=False)
     storage_location = models.ForeignKey('locations.StorageLocation',
                                          blank=True, null=True,
-                                         related_name='collections')
+                                         related_name='collections',
+                                         on_delete=models.CASCADE)
     specimen_state = models.CharField(max_length=50, blank=True)
     process_type = models.ForeignKey('processing.ProcessType', blank=True,
-                                     null=True, related_name='collections')
+                                     null=True, related_name='collections',
+                                     on_delete=models.CASCADE)
     reagent = models.ForeignKey('processing.Reagent', blank=True, null=True,
-                                related_name='collections')
+                                related_name='collections',
+                                on_delete=models.CASCADE)
     adfg_permit = models.ForeignKey(ADFGPermit, blank=True, null=True,
-                                    related_name='collections')
+                                    related_name='collections',
+                                    on_delete=models.CASCADE)
     collection_flaw = models.ForeignKey(Flaw, blank=True, null=True,
-                                        related_name='collections')
+                                        related_name='collections',
+                                        on_delete=models.CASCADE)
     display_name = models.CharField(max_length=255, editable=False)
 
     def save(self, *args, **kwargs):
@@ -101,13 +110,15 @@ class Collection(models.Model):
 
 
 class DatasheetAttachment(models.Model):
-    collection = models.ForeignKey(Collection, related_name='datasheets')
+    collection = models.ForeignKey(Collection, related_name='datasheets',
+                                   on_delete=models.CASCADE)
     datasheet = models.FileField("Datasheet",
                                  upload_to='collections/datasheets/%Y/%m/%d')
 
 
 class CollectionTrap(models.Model):
-    collection = models.ForeignKey(Collection, related_name='traps')
+    collection = models.ForeignKey(Collection, related_name='traps',
+                                   on_delete=models.CASCADE)
     number_of_traps = models.IntegerField()
     date_opened = models.DateField()
     time_opened = models.TimeField()
@@ -126,7 +137,8 @@ class CollectionTrap(models.Model):
 
 
 class CollectionMeasurement(models.Model):
-    collection = models.ForeignKey(Collection, related_name='env_measurements')
+    collection = models.ForeignKey(Collection, related_name='env_measurements',
+                                   on_delete=models.CASCADE)
     date_measured = models.DateField()
     time_measured = models.TimeField()
     water_temp_c = models.FloatField(null=True)

ccdb/experiments/models.py

@@ -18,7 +18,8 @@ class Experiment(models.Model):
     code = models.CharField(max_length=10, blank=True)
     description = models.CharField(max_length=255, blank=True)
     flaw = models.ForeignKey(Flaw, blank=True, null=True,
-                             related_name='experiments')
+                             related_name='experiments',
+                             on_delete=models.CASCADE)
     sort_order = models.IntegerField(blank=True, null=True)
     collections = models.ManyToManyField('collections_ccdb.Collection')
 
@@ -31,7 +32,8 @@ class Experiment(models.Model):
 
 
 class ProtocolAttachment(models.Model):
-    experiment = models.ForeignKey(Experiment, related_name='protocols')
+    experiment = models.ForeignKey(Experiment, related_name='protocols',
+                                   on_delete=models.CASCADE)
     protocol = models.FileField(upload_to='experiments/protocols/%Y/%m/%d')
 
     def __str__(self):
@@ -40,7 +42,8 @@ class ProtocolAttachment(models.Model):
 
 class TreatmentType(models.Model):
     experiment = models.ForeignKey(Experiment, blank=True, null=True,
-                                   related_name='treatment_types')
+                                   related_name='treatment_types',
+                                   on_delete=models.CASCADE)
     name = models.CharField(max_length=200)
     code = models.CharField(max_length=25, blank=True)
     treatment_type = models.CharField(max_length=50, blank=True)
@@ -65,15 +68,20 @@ class TreatmentType(models.Model):
 
 class Treatment(models.Model):
     treatment_type = models.ForeignKey(TreatmentType,
-                                       related_name='treatments')
+                                       related_name='treatments',
+                                       on_delete=models.CASCADE)
     container = models.ForeignKey('misc.Container', blank=True, null=True,
-                                  related_name='treatments')
+                                  related_name='treatments',
+                                  on_delete=models.CASCADE)
     study_location = models.ForeignKey('locations.StudyLocation',
-                                       related_name='treatments')
+                                       related_name='treatments',
-    species = models.ForeignKey('species.Species', related_name='treatments')
+                                       on_delete=models.CASCADE)
+    species = models.ForeignKey('species.Species', related_name='treatments',
+                                on_delete=models.CASCADE)
     sex = models.CharField(max_length=25)
     flaw = models.ForeignKey(Flaw, blank=True, null=True,
-                             related_name='treatments')
+                             related_name='treatments',
+                             on_delete=models.CASCADE)
     display_name = models.CharField(max_length=255, editable=False)
 
     def save(self, *args, **kwargs):
@@ -93,14 +101,16 @@ class Treatment(models.Model):
 
 class TreatmentReplicate(models.Model):
     treatment = models.ForeignKey(Treatment,
-                                  related_name='treatment_replicates')
+                                  related_name='treatment_replicates',
+                                  on_delete=models.CASCADE)
     name = models.CharField(max_length=50)
     setup_date = models.DateField(blank=True, null=True)
     setup_time = models.TimeField(blank=True, null=True)
     setup_sample_size = models.IntegerField(blank=True, null=True)
     mass_g = models.FloatField(blank=True, null=True)
     flaw = models.ForeignKey(Flaw, blank=True, null=True,
-                             related_name='treatment_replicates')
+                             related_name='treatment_replicates',
+                             on_delete=models.CASCADE)
     display_name = models.CharField(max_length=255, editable=False)
 
     def save(self, *args, **kwargs):
@@ -118,13 +128,15 @@ class TreatmentReplicate(models.Model):
 
 class AliveDeadCount(models.Model):
     treatment_replicate = models.ForeignKey(TreatmentReplicate,
-                                            related_name='alive_dead_counts')
+                                            related_name='alive_dead_counts',
+                                            on_delete=models.CASCADE)
     status_date = models.DateField()
     status_time = models.TimeField(blank=True, null=True)
     count_alive = models.IntegerField(blank=True, null=True)
     count_dead = models.IntegerField(blank=True, null=True)
     flaw = models.ForeignKey(Flaw, blank=True, null=True,
-                             related_name='alive_dead_counts')
+                             related_name='alive_dead_counts',
+                             on_delete=models.CASCADE)
 
     def __str__(self):
         return "{}".format(self.status_date)

ccdb/locations/models.py

@@ -16,7 +16,7 @@ class Region(models.Model):
 
 class Site(models.Model):
     region = models.ForeignKey(Region, blank=True, null=True,
-                               related_name='sites')
+                               related_name='sites', on_delete=models.CASCADE)
     name = models.CharField(max_length=100)
     code = models.CharField(max_length=10, blank=True)
     description = models.CharField(max_length=255, blank=True)
@@ -46,14 +46,16 @@ class MunicipalLocation(models.Model):
 
 
 class StudyLocation(models.Model):
-    site = models.ForeignKey(Site, related_name='study_locations')
+    site = models.ForeignKey(Site, related_name='study_locations',
+                             on_delete=models.CASCADE)
     name = models.CharField(max_length=100)
     code = models.CharField(max_length=10)
     study_location_type = models.CharField(max_length=50, blank=True)
     treatment_type = models.CharField(max_length=100, blank=True)
     municipal_location = models.ForeignKey(MunicipalLocation,
                                            blank=True, null=True,
-                                           related_name='study_locations')
+                                           related_name='study_locations',
+                                           on_delete=models.CASCADE)
     collecting_location = models.BooleanField(default=False)
     description = models.CharField(max_length=255, blank=True)
     sort_order = models.IntegerField(blank=True, null=True)

ccdb/misc/models.py

@@ -25,7 +25,8 @@ class MeasurementType(models.Model):
         'MeasurementUnit',
         blank=True,
         null=True,
-        related_name='measurement_types'
+        related_name='measurement_types',
+        on_delete=models.CASCADE,
     )
     sort_order = models.IntegerField(blank=True, null=True)
 
@@ -71,12 +72,15 @@ class Container(models.Model):
     code = models.CharField(max_length=10, blank=True)
     application = models.CharField(max_length=50, blank=True)
     color = models.ForeignKey(Color, blank=True, null=True,
-                              related_name='containers')
+                              related_name='containers',
+                              on_delete=models.CASCADE)
     material = models.ForeignKey(Material, blank=True, null=True,
-                                 related_name='containers')
+                                 related_name='containers',
+                                 on_delete=models.CASCADE)
     volume = models.FloatField(blank=True, null=True)
     measurement_unit = models.ForeignKey(MeasurementUnit, blank=True,
-                                         null=True, related_name='containers')
+                                         null=True, related_name='containers',
+                                         on_delete=models.CASCADE)
     sort_order = models.IntegerField(blank=True, null=True)
 
     def __str__(self):

ccdb/processing/models.py

@@ -42,19 +42,24 @@ class Flaw(models.Model):
 
 
 class Processing(models.Model):
-    process_type = models.ForeignKey(ProcessType, related_name='processings')
+    process_type = models.ForeignKey(ProcessType, related_name='processings',
-    container = models.ForeignKey('misc.Container', related_name='processings')
+                                     on_delete=models.CASCADE)
+    container = models.ForeignKey('misc.Container', related_name='processings',
+                                  on_delete=models.CASCADE)
     container_label = models.CharField(max_length=50)
     process_date = models.DateField(blank=True, null=True)
     process_time = models.TimeField(blank=True, null=True)
     reagent = models.ForeignKey(Reagent, blank=True, null=True,
-                                related_name='processings')
+                                related_name='processings',
+                                on_delete=models.CASCADE)
     reagent_volume = models.FloatField(blank=True, null=True)
     measurement_unit = models.ForeignKey('misc.MeasurementUnit', blank=True,
-                                         null=True, related_name='processings')
+                                         null=True, related_name='processings',
+                                         on_delete=models.CASCADE)
     minutes_in_reagent = models.IntegerField(blank=True, null=True)
     flaw = models.ForeignKey(Flaw, blank=True, null=True,
-                             related_name='processings')
+                             related_name='processings',
+                             on_delete=models.CASCADE)
 
     def __str__(self):
         return "{} {} {}".format(self.process_date, self.process_type,

ccdb/projects/models.py

@@ -32,7 +32,8 @@ class Grant(models.Model):
 
 
 class GrantReport(models.Model):
-    grant = models.ForeignKey(Grant, related_name='reports')
+    grant = models.ForeignKey(Grant, related_name='reports',
+                              on_delete=models.CASCADE)
     title = models.CharField(max_length=200)
     report_type = models.CharField(max_length=50, blank=True)
     description = models.CharField(max_length=255, blank=True)

ccdb/species/models.py

@@ -19,8 +19,10 @@ class Species(models.Model):
 
 class TrapSpecies(models.Model):
     collection_trap = models.ForeignKey('collections_ccdb.CollectionTrap',
-                                        related_name='trap_species')
+                                        related_name='trap_species',
-    species = models.ForeignKey(Species, related_name='trap_species')
+                                        on_delete=models.CASCADE)
+    species = models.ForeignKey(Species, related_name='trap_species',
+                                on_delete=models.CASCADE)
     sex = models.CharField(max_length=25, blank=True)
     count = models.IntegerField(blank=True, null=True)
     count_estimated = models.BooleanField(default=False)
@@ -34,8 +36,10 @@ class TrapSpecies(models.Model):
 
 class CollectionSpecies(models.Model):
     collection = models.ForeignKey('collections_ccdb.Collection',
-                                   related_name='collection_species')
+                                   related_name='collection_species',
-    species = models.ForeignKey(Species, related_name='collection_species')
+                                   on_delete=models.CASCADE)
+    species = models.ForeignKey(Species, related_name='collection_species',
+                                on_delete=models.CASCADE)
     sex = models.CharField(max_length=25, blank=True)
     count = models.IntegerField(blank=True, null=True)
     count_estimated = models.BooleanField(default=False)

ccdb/utils/models.py

@@ -14,7 +14,7 @@ class AdminSection(models.Model):
 class AdminEntry(models.Model):
     package = models.CharField(max_length=255)
     model = models.CharField(max_length=255)
-    section = models.ForeignKey(AdminSection)
+    section = models.ForeignKey(AdminSection, on_delete=models.CASCADE)
     sort = models.IntegerField()
 
     def admin_url(self, request=None):

ccdb/utils/tests/test_viewsets.py

@@ -1,4 +1,4 @@
-from django.core.urlresolvers import reverse
+from django.urls import reverse
 
 from rest_framework import status
 from rest_framework.test import APITestCase

config/settings/local.py

@@ -27,14 +27,6 @@ INTERNAL_IPS = ('127.0.0.1', )
 
 TEST_RUNNER = 'django.test.runner.DiscoverRunner'
 
-# http://stackoverflow.com/a/28560805/313548
-class DisableMigrations(object):
-    def __contains__(self, item):
-        return True
-
-    def __getitem__(self, item):
-        return "notmigrations"
-
 TESTS_IN_PROGRESS = False
 if 'test' in sys.argv[1:] or 'jenkins' in sys.argv[1:]:
     logging.disable(logging.CRITICAL)
@@ -44,7 +36,8 @@ if 'test' in sys.argv[1:] or 'jenkins' in sys.argv[1:]:
     DEBUG = False
     TEMPLATE_DEBUG = False
     TESTS_IN_PROGRESS = True
-    MIGRATION_MODULES = DisableMigrations()
+    MIGRATION_MODULES = {app[app.rfind('.') + 1:]: None
+                         for app in INSTALLED_APPS}
 
 MANIFEST_URL = env('MANIFEST_URL', default=None)
 CORS_ORIGIN_ALLOW_ALL = False

config/urls.py

@@ -4,13 +4,13 @@ from django.conf.urls.static import static
 from django.contrib import admin
 from django.views.generic import RedirectView
 from django.views import defaults as default_views
-from django.core.urlresolvers import reverse_lazy
+from django.urls import reverse_lazy
 
 urlpatterns = [
-    url(settings.ADMIN_URL, include(admin.site.urls)),
+    url(settings.ADMIN_URL, admin.site.urls),
     url(r'^api-auth/', include('rest_framework.urls',
                                namespace='rest_framework')),
-    url(r'^api/', include('ccdb.api.urls', namespace='api')),
+    url(r'^api/', include('ccdb.api.urls')),
     url(r'^$', RedirectView.as_view(url=reverse_lazy('admin:index'),
                                     permanent=True)),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)

requirements/base.txt

@@ -1,4 +1,4 @@
-django==1.10.8
+django==1.11.9
 
 # Configuration
 django-environ==0.4.1
@@ -17,8 +17,8 @@ python-dateutil==2.5.3
 requests==2.11.0
 
 # REST
-djangorestframework==3.6.4
+djangorestframework==3.7.7
 django-cors-headers==1.3.1
 django-filter==1.1
 djoser==0.7.0
-djangorestframework-jsonapi==2.1.1
+djangorestframework-jsonapi==2.2.0

requirements/local.txt

@@ -1,7 +1,7 @@
 -r base.txt
 
 Werkzeug==0.11.10
-django-extensions==1.7.1
+django-extensions==1.9.9
 flake8==3.0.4
 pygraphviz==1.3.1
 ipython==5.1.0