Refactor update creation api

This merge request does the following:

• Raise DRF errors rather than returning response to take advantage of the DRF exception handling mechanism
• Create serialisers for PUT request to simplify the code
• Improve validation checks in several places
• Fixes several issues in DRF infrastructure uses
• Fixes JSON fields handling
• Remove routes that do no fully qualify objects
• Implement a custom DRF exception handler that will allow to log errors
• Improve testing
• Improve permission management

beat/web/dataformats/serializers.py

@@ -27,7 +27,13 @@
 
 from rest_framework import serializers
 
-from ..common.serializers import ContributionSerializer, VersionableSerializer, DynamicFieldsSerializer, ContributionCreationSerializer
+from ..common.serializers import (
+    ContributionSerializer,
+    VersionableSerializer,
+    DynamicFieldsSerializer,
+    ContributionCreationSerializer,
+    ContributionModSerializer,
+)
 from ..algorithms.models import Algorithm
 from ..databases.models import Database, DatabaseSet
 
@@ -36,16 +42,22 @@ from .models import DataFormat
 import beat.core.dataformat
 
 
-#----------------------------------------------------------
+# ----------------------------------------------------------
 
 
 class DataFormatCreationSerializer(ContributionCreationSerializer):
     class Meta(ContributionCreationSerializer.Meta):
         model = DataFormat
-        beat_core_class = beat.core.dataformat
+        beat_core_class = beat.core.dataformat.DataFormat
 
 
-#----------------------------------------------------------
+class DataFormatModSerializer(ContributionModSerializer):
+    class Meta(ContributionModSerializer.Meta):
+        model = DataFormat
+        beat_core_class = beat.core.dataformat.DataFormat
+
+
+# ----------------------------------------------------------
 
 
 class BaseSerializer(DynamicFieldsSerializer):
@@ -53,37 +65,37 @@ class BaseSerializer(DynamicFieldsSerializer):
     accessibility = serializers.SerializerMethodField()
 
     class Meta(DynamicFieldsSerializer.Meta):
-        fields = '__all__'
-        default_fields = ['name', 'short_description', 'accessibility']
+        fields = "__all__"
+        default_fields = ["name", "short_description", "accessibility"]
 
     def get_accessibility(self, obj):
         return obj.get_sharing_display().lower()
 
 
-#----------------------------------------------------------
+# ----------------------------------------------------------
 
 
 class ReferencedDataFormatSerializer(BaseSerializer):
     class Meta(BaseSerializer.Meta):
         model = DataFormat
-        default_fields = BaseSerializer.Meta.default_fields + ['creation_date']
+        default_fields = BaseSerializer.Meta.default_fields + ["creation_date"]
 
 
-#----------------------------------------------------------
+# ----------------------------------------------------------
 
 
 class ReferencingSerializer(BaseSerializer):
     is_owner = serializers.SerializerMethodField()
 
     class Meta(BaseSerializer.Meta):
-        default_fields = BaseSerializer.Meta.default_fields + ['is_owner', 'version',]
+        default_fields = BaseSerializer.Meta.default_fields + ["is_owner", "version"]
 
     def get_is_owner(self, obj):
-        if hasattr(obj, 'author'):
-            return obj.author == self.context.get('user')
+        if hasattr(obj, "author"):
+            return obj.author == self.context.get("user")
 
 
-#----------------------------------------------------------
+# ----------------------------------------------------------
 
 
 class ReferencingDataFormatSerializer(ReferencingSerializer):
@@ -91,7 +103,7 @@ class ReferencingDataFormatSerializer(ReferencingSerializer):
         model = DataFormat
 
 
-#----------------------------------------------------------
+# ----------------------------------------------------------
 
 
 class ReferencingAlgorithmSerializer(ReferencingSerializer):
@@ -99,59 +111,78 @@ class ReferencingAlgorithmSerializer(ReferencingSerializer):
         model = Algorithm
 
 
-#----------------------------------------------------------
+# ----------------------------------------------------------
 
 
 class ReferencingDatabaseSerializer(VersionableSerializer):
     class Meta:
         model = Database
-        default_fields = ['name', 'short_description']
+        default_fields = ["name", "short_description"]
 
 
-#----------------------------------------------------------
+# ----------------------------------------------------------
 
 
 class DataFormatSerializer(ContributionSerializer):
     extend = serializers.SerializerMethodField()
-    referenced_dataformats = ReferencedDataFormatSerializer(many=True, source="referenced_formats")
-    needed_dataformats = ReferencedDataFormatSerializer(many=True, source='all_needed_dataformats')
+    referenced_dataformats = ReferencedDataFormatSerializer(
+        many=True, source="referenced_formats"
+    )
+    needed_dataformats = ReferencedDataFormatSerializer(
+        many=True, source="all_needed_dataformats"
+    )
     referencing_dataformats = serializers.SerializerMethodField()
     referencing_algorithms = serializers.SerializerMethodField()
     referencing_databases = serializers.SerializerMethodField()
 
     class Meta(ContributionSerializer.Meta):
         model = DataFormat
-        default_fields = ContributionSerializer.Meta.default_fields + ['extend']
+        default_fields = ContributionSerializer.Meta.default_fields + ["extend"]
 
     def get_extend(self, obj):
         return obj.extend.fullname() if obj.extend else None
 
-
     def get_referencing_dataformats(self, obj):
-        user = self.context.get('user')
+        user = self.context.get("user")
         dataformats = obj.referencing.for_user(user, True)
-        serializer = ReferencingDataFormatSerializer(dataformats, many=True, context=self.context)
+        serializer = ReferencingDataFormatSerializer(
+            dataformats, many=True, context=self.context
+        )
         return serializer.data
 
-
     def get_referencing_algorithms(self, obj):
-        user = self.context.get('user')
-        algorithms = Algorithm.objects.for_user(user, True).filter(endpoints=obj.algorithm_endpoints.all()).distinct()
-        serializer = ReferencingAlgorithmSerializer(algorithms, many=True, context=self.context)
+        user = self.context.get("user")
+        algorithms = (
+            Algorithm.objects.for_user(user, True)
+            .filter(endpoints=obj.algorithm_endpoints.all())
+            .distinct()
+        )
+        serializer = ReferencingAlgorithmSerializer(
+            algorithms, many=True, context=self.context
+        )
         return serializer.data
 
-
     def get_referencing_databases(self, obj):
-        databaseset = DatabaseSet.objects.filter(template__outputs=obj.database_outputs.distinct())
-        databases = Database.objects.filter(protocols__sets=databaseset).distinct().order_by('name')
-        serializer = ReferencingDatabaseSerializer(databases, many=True, context=self.context)
+        databaseset = DatabaseSet.objects.filter(
+            template__outputs=obj.database_outputs.distinct()
+        )
+        databases = (
+            Database.objects.filter(protocols__sets=databaseset)
+            .distinct()
+            .order_by("name")
+        )
+        serializer = ReferencingDatabaseSerializer(
+            databases, many=True, context=self.context
+        )
         return serializer.data
 
 
-#----------------------------------------------------------
+# ----------------------------------------------------------
 
 
 class FullDataFormatSerializer(DataFormatSerializer):
-
     class Meta(DataFormatSerializer.Meta):
-        default_fields = DataFormatSerializer.Meta.default_fields + DataFormatSerializer.Meta.extra_fields
+        default_fields = (
+            DataFormatSerializer.Meta.default_fields
+            + DataFormatSerializer.Meta.extra_fields
+        )