allow interventions to be none closes #701

backend/pkdb_app/info_nodes/models.py

@@ -368,7 +368,7 @@ def validate_numeric(self, data):
                                     f"for all measurement types except "
                                     f"<{self.CAN_NEGATIVE}>.", "detail": data})
 
-    def validate_complete(self, data):
+    def validate_complete(self, data, time_allowed: bool = True):
         """Complete validation."""
 
         # check unit
@@ -378,24 +378,25 @@ def validate_complete(self, data):
         choice = data.get("choice", None)
         d_choice = self.validate_choice(choice)
 
-        time_unit = data.get("time_unit", None)
-        time = data.get("time", None)
+        if time_allowed:
+            time_unit = data.get("time_unit", None)
+            time = data.get("time", None)
 
-        if time_unit and time_unit != "NR":
-            self.validate_time_unit(time_unit)
+            if time_unit and time_unit != "NR":
+                self.validate_time_unit(time_unit)
 
-        if self.time_required:
-            details = f"for measurement type `{self.info_node.name}`"
+            if self.time_required:
+                details = f"for measurement type `{self.info_node.name}`"
 
-            if time != "NR":
-                _validate_required_key_and_value(data, "time", details=details)
-                if time_unit != "NR":
-                    _validate_required_key_and_value(data, "time_unit", details=details)
+                if time != "NR":
+                    _validate_required_key_and_value(data, "time", details=details)
+                    if time_unit != "NR":
+                        _validate_required_key_and_value(data, "time_unit", details=details)
 
-        if time == "NR":
-            data["time"] = None
-        if time_unit == "NR":
-            data["time_unit"] = None
+            if time == "NR":
+                data["time"] = None
+            if time_unit == "NR":
+                data["time_unit"] = None
 
         return {"choice": d_choice}
 

backend/pkdb_app/info_nodes/serializers.py

@@ -31,11 +31,6 @@ class MeasurementTypeableSerializer(EXMeasurementTypeableSerializer):
     time = FloatNRField(allow_null=True)
 
 
-    def to_representation(self, instance):
-        rep = super().to_representation(instance)
-        return rep
-
-
 class SynonymSerializer(WrongKeyValidationSerializer):
     pk = serializers.IntegerField(read_only=True)
     class Meta:

backend/pkdb_app/outputs/models.py

@@ -109,7 +109,7 @@ class OutputTypes(models.TextChoices):
 
     group = models.ForeignKey(Group, null=True, blank=True, on_delete=models.CASCADE)
     individual = models.ForeignKey(Individual, null=True, blank=True, on_delete=models.CASCADE)
-    interventions = models.ManyToManyField(Intervention, through="OutputIntervention", related_name="outputs")
+    interventions = models.ManyToManyField(Intervention, through="OutputIntervention", related_name="outputs", null=True, blank=True)
     subset = models.ForeignKey('data.Subset', on_delete=models.CASCADE, null=True, blank=True, related_name="pks")
 
     tissue = models.ForeignKey(Tissue, related_name="outputs", null=True, blank=True, on_delete=models.CASCADE)
@@ -130,7 +130,7 @@ def null_attr(self, attr):
 
     def is_timecourse(self):
         if self.timecourse:
-            if self.timecourse.data.data_type=="timecourse":
+            if self.timecourse.data.data_type == "timecourse":
                 return True
         return False
 

backend/pkdb_app/outputs/serializers.py

@@ -19,7 +19,7 @@
     CommentElasticSerializer
 from ..interventions.models import Intervention
 from ..serializers import (
-    ExSerializer, StudySmallElasticSerializer, SidNameLabelSerializer)
+    ExSerializer, StudySmallElasticSerializer, SidNameLabelSerializer, PKField)
 from ..subjects.models import Group, DataFile, Individual
 from ..subjects.serializers import (
     EXTERN_FILE_FIELDS, GroupSmallElasticSerializer, IndividualSmallElasticSerializer)
@@ -51,6 +51,7 @@
 # Outputs
 # ----------------------------------
 
+
 class OutputSerializer(MeasurementTypeableSerializer):
 
     group = serializers.PrimaryKeyRelatedField(
@@ -62,13 +63,10 @@ class OutputSerializer(MeasurementTypeableSerializer):
         required=False,
         allow_null=True,
     )
-    interventions = serializers.PrimaryKeyRelatedField(
+    interventions = PKField(
         queryset=Intervention.objects.all(),
-        many=True,
-        read_only=False,
-        required=False,
-        allow_null=True,
-    )
+        many=True, required=True, allow_null=True)
+
     tissue = utils.SlugRelatedField(
         slug_field="name",
         queryset=InfoNode.objects.filter(ntype=InfoNode.NTypes.Tissue),
@@ -91,10 +89,12 @@ class Meta:
     def to_internal_value(self, data):
         data.pop("comments", None)
         data.pop("descriptions", None)
+        data.pop("image", None)
+        data.pop("source", None)
 
         data = self.retransform_map_fields(data)
         data = self.to_internal_related_fields(data)
-        self.validate_wrong_keys(data, additional_fields=OutputExSerializer.Meta.fields)
+        self.validate_wrong_keys(data)
         return super(serializers.ModelSerializer, self).to_internal_value(data)
 
     def validate(self, attrs):
@@ -103,7 +103,6 @@ def validate(self, attrs):
         self.validate_group_individual_output(attrs)
 
         _validate_required_key(attrs, "measurement_type")
-
         _validate_required_key(attrs, "substance")
         _validate_required_key(attrs, "tissue")
         _validate_required_key(attrs, "interventions")
@@ -173,7 +172,6 @@ def to_internal_value(self, data):
         for output in temp_outputs:
             outputs_from_file = self.entries_from_file(output)
             outputs.extend(outputs_from_file)
-
         # ----------------------------------
         # finished
         # ----------------------------------
@@ -191,7 +189,7 @@ def to_internal_value(self, data):
         [data.pop(field, None) for field in drop_fields]
         data["outputs"] = outputs
         data = self.transform_map_fields(data)
-        self.validate_wrong_keys(data, OutputSerializer.Meta.fields)
+        self.validate_wrong_keys(data)
         return super(serializers.ModelSerializer, self).to_internal_value(data)
 
     def validate_label_map(self, value) -> None:

backend/pkdb_app/serializers.py

@@ -8,6 +8,7 @@
 from django.core.exceptions import ObjectDoesNotExist, MultipleObjectsReturned
 from django.db.models import Q
 from rest_framework import serializers
+from rest_framework.fields import empty
 from rest_framework.settings import api_settings
 
 from pkdb_app.behaviours import map_field
@@ -354,8 +355,6 @@ def make_entry(self, entry, template, data, source):
                     try:
                         entry_value = getattr(entry, values[1])
 
-
-
                     except AttributeError:
 
                         raise serializers.ValidationError(
@@ -464,7 +463,7 @@ def to_representation(self, instance):
         request = self.context.get('request')
 
         # url representation of file
-        for file in ["source","image"]:
+        for file in ["source", "image"]:
             if file in rep:
                 if "||" not in str(rep[file]):
                     rep[file] = request.build_absolute_uri(getattr(instance, file).file.url)
@@ -530,6 +529,8 @@ def to_internal_related_fields(self, data):
                             f"intervention <{intervention}> does not exist, check interventions."
                         )
                 data["interventions"] = interventions
+            else:
+                data["interventions"] = []
         return data
 
 
@@ -784,4 +785,4 @@ def to_internal_value(self, data):
         try:
             return float(data)
         except (TypeError, ValueError):
-            self.fail('invalid')
+            self.fail('invalid')

backend/pkdb_app/subjects/serializers.py

@@ -102,7 +102,7 @@ def validate(self, attrs):
                     if attrs[info_node] is not None:
                         attrs[info_node] = getattr(attrs[info_node], info_node)
 
-            attrs["choice"] = attrs["measurement_type"].validate_complete(data=attrs)["choice"]
+            attrs["choice"] = attrs["measurement_type"].validate_complete(data=attrs, time_allowed=False)["choice"]
 
         except ValueError as err:
             raise serializers.ValidationError(err)

backend/pkdb_app/utils.py

@@ -149,20 +149,20 @@ def _create(validated_data, model_manager=None, model_serializer=None,
     return instance, popped_data
 
 
-def initialize_normed(notnorm_instance):
-    norm = copy.copy(notnorm_instance)
+def initialize_normed(not_norm_instance):
+    norm = copy.copy(not_norm_instance)
     norm.pk = None
     norm.normed = True
     norm.normalize()
-    norm.raw_id = notnorm_instance.pk
+    norm.raw_id = not_norm_instance.pk
 
     try:
-        norm.individual_id = notnorm_instance.individual.pk
+        norm.individual_id = not_norm_instance.individual.pk
     except AttributeError:
         pass
 
     try:
-        norm.group_id = notnorm_instance.group.pk
+        norm.group_id = not_norm_instance.group.pk
     except AttributeError:
         pass