adding entity graph

core/filters.py

@@ -4,7 +4,7 @@
 from strawberry import auto
 from typing import Optional
 from strawberry_django.filters import FilterLookup
-
+import strawberry_django
 print("Test")
 
 
@@ -114,6 +114,33 @@ class ViewFilter:
     is_global: auto
     provenance: ProvenanceFilter | None
 
+@strawberry.django.filter(models.PixelLabel)
+class PixelLabelFilter:
+    value: float | None = None
+    view: strawberry.ID | None = None
+    entity_kind: strawberry.ID | None = None
+    entity: strawberry.ID | None = None
+
+    def filter_value(self, queryset, info):
+        if self.value is None:
+            return queryset
+        return queryset.filter(value=self.value)
+
+    def filter_view(self, queryset, info):
+        if self.view is None:
+            return queryset
+        return queryset.filter(view_id=self.view)
+
+    def filter_entity_kind(self, queryset, info):
+        if self.entity_kind is None:
+            return queryset
+        return queryset.filter(entity_entity_kind_id=self.entity_kind)
+
+    def filter_entity(self, queryset, info):
+        if self.entity is None:
+            return queryset
+        return queryset.filter(entity_id=self.entity)
+
 
 @strawberry.django.filter(models.AffineTransformationView)
 class AffineTransformationViewFilter(ViewFilter):
@@ -132,6 +159,9 @@ class TimepointViewFilter(ViewFilter):
     ms_since_start: auto
     index_since_start: auto
 
+@strawberry.django.filter(models.PixelView)
+class PixelViewFilter(ViewFilter):
+    pass
 
 @strawberry.django.filter(models.OpticsView)
 class OpticsViewFilter(ViewFilter):
@@ -179,21 +209,28 @@ def filter_ids(self, queryset, info):
         return queryset.filter(id__in=self.ids)
 
 
-@strawberry.django.filter(models.Image)
+@strawberry_django.filter(models.Image)
 class ImageFilter:
     name: Optional[FilterLookup[str]]
     ids: list[strawberry.ID] | None
     store: ZarrStoreFilter | None
     dataset: DatasetFilter | None
     transformation_views: AffineTransformationViewFilter | None
     timepoint_views: TimepointViewFilter | None
+    not_derived: bool | None = None
 
     provenance: ProvenanceFilter | None
 
     def filter_ids(self, queryset, info):
         if self.ids is None:
             return queryset
         return queryset.filter(id__in=self.ids)
+
+    def filter_not_derived(self, queryset, info):
+        print("Filtering not derived")
+        if self.not_derived is None:
+            return queryset
+        return queryset.filter(origins=None)
 
 
 @strawberry.django.filter(models.ROI)
@@ -377,6 +414,11 @@ class SpecimenFilter(IDFilterMixin, SearchFilterMixin):
 class ProtocolFilter(IDFilterMixin, SearchFilterMixin):
     id: auto
 
+@strawberry.django.filter(models.ProtocolStep)
+class ProtocolStepFilter(IDFilterMixin, SearchFilterMixin):
+    id: auto
+
+
 @strawberry.django.filter(models.ProtocolStepMapping)
 class ProtocolStepMappingFilter(IDFilterMixin, SearchFilterMixin):
     id: auto

core/migrations/0003_historicalprotocolstep_plate_children_and_more.py

@@ -0,0 +1,32 @@
+# Generated by Django 4.2.8 on 2024-08-16 13:16
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("core", "0002_alter_protocolstepmapping_t"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="historicalprotocolstep",
+            name="plate_children",
+            field=models.JSONField(
+                blank=True,
+                default=list,
+                help_text="The children of the slate",
+                null=True,
+            ),
+        ),
+        migrations.AddField(
+            model_name="protocolstep",
+            name="plate_children",
+            field=models.JSONField(
+                blank=True,
+                default=list,
+                help_text="The children of the slate",
+                null=True,
+            ),
+        ),
+    ]

core/migrations/0004_remove_entity_parent_remove_historicalentity_parent.py

@@ -0,0 +1,20 @@
+# Generated by Django 4.2.8 on 2024-08-18 15:16
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("core", "0003_historicalprotocolstep_plate_children_and_more"),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name="entity",
+            name="parent",
+        ),
+        migrations.RemoveField(
+            model_name="historicalentity",
+            name="parent",
+        ),
+    ]

core/migrations/0005_entityrelation_only_one_relation_per_kind.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.8 on 2024-08-18 19:44
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("core", "0004_remove_entity_parent_remove_historicalentity_parent"),
+    ]
+
+    operations = [
+        migrations.AddConstraint(
+            model_name="entityrelation",
+            constraint=models.UniqueConstraint(
+                fields=("left", "kind", "right"), name="only_one_relation_per_kind"
+            ),
+        ),
+    ]

core/models.py

@@ -1,3 +1,4 @@
+import uuid
 from django.db import models
 from django.contrib.auth import get_user_model
 from django.forms import FileField
@@ -342,6 +343,10 @@ class ProtocolStep(models.Model):
         related_name="entities",
         help_text="The reagents that were used in this step (you can specifiy properties of the reagents in the entity)",
     )
+    plate_children = models.JSONField(
+        help_text="The children of the slate", null=True, blank=True,
+        default=list
+    )
 
     history = HistoryField()
 
@@ -1127,6 +1132,15 @@ class Meta:
     def __str__(self) -> str:
         return f"{self.label} in {self.ontology}"
 
+    def create_entity(self, group, name: str = None,  instance_kind: str = None, metrics: dict = None) -> "Entity":
+        return Entity.objects.create(
+            name=name or str(uuid.uuid4()),
+            group=group,
+            kind=self,
+            instance_kind=instance_kind,
+            metrics=metrics or {}
+        )
+
 
 class EntityGroup(models.Model):
     """An EntityGroup is a collection of Entities.
@@ -1176,15 +1190,6 @@ class Entity(models.Model):
         related_name="entities",
         help_text="The group this entity belongs to",
     )
-
-    parent = models.ForeignKey(
-        "self",
-        on_delete=models.CASCADE,
-        related_name="parts",
-        null=True,
-        blank=True,
-        help_text="The entity this entity is part of",
-    )
     kind = models.ForeignKey(
         EntityKind,
         on_delete=models.CASCADE,
@@ -1245,6 +1250,15 @@ class EntityRelation(models.Model):
         help_text="Associated metrics this relation",
     )
 
+    class Meta:
+        constraints = [
+            models.UniqueConstraint(
+                fields=["left", "kind", "right"],
+                name="only_one_relation_per_kind",
+            )
+        ]
+
+
 
 class EntityMetric(models.Model):
     kind = models.OneToOneField(

core/mutations/entity.py

@@ -41,7 +41,6 @@ def create_entity(
         group=group,
         kind=input_kind,
         defaults=dict(
-            parent=models.Entity.objects.get(id=input.parent) if input.parent else None,
             name=input.name or uuid.uuid4().hex,
             instance_kind=input.instance_kind,
         )

core/mutations/image.py

@@ -13,7 +13,9 @@
     PartialSpecimenViewInput,
     PartialAcquisitionViewInput,
     PartialAffineTransformationViewInput,
+    PartialPixelViewInput,
     PartialScaleViewInput,
+    _create_pixel_view_from_partial,
     view_kwargs_from_input,
 )
 from django.conf import settings
@@ -204,7 +206,7 @@ class FromArrayLikeInput:
     channel_views: list[PartialChannelViewInput] | None = None
     transformation_views: list[PartialAffineTransformationViewInput] | None = None
     acquisition_views: list[PartialAcquisitionViewInput] | None = None
-    label_views: list[PartialLabelViewInput] | None = None
+    pixel_views: list[PartialPixelViewInput] | None = None
     specimen_views: list[PartialSpecimenViewInput] | None = None
     rgb_views: list[PartialRGBViewInput] | None = None
     timepoint_views: list[PartialTimepointViewInput] | None = None
@@ -280,16 +282,6 @@ def from_array_like(
                 **view_kwargs_from_input(specimenview),
             )
 
-    if input.label_views is not None:
-        for labelview in input.label_views:
-            models.LabelView.objects.create(
-                image=image,
-                fluorophore_id=labelview.fluorophore,
-                primary_antibody_id=labelview.primary_antibody,
-                secondary_antibody_id=labelview.secondary_antibody,
-                **view_kwargs_from_input(labelview),
-            )
-
     if input.scale_views is not None:
         for scaleview in input.scale_views:
             models.ScaleView.objects.create(
@@ -370,6 +362,10 @@ def from_array_like(
                 **view_kwargs_from_input(transformationview),
             )
 
+    if input.pixel_views:
+        for pixelview in input.pixel_views:
+            _create_pixel_view_from_partial(image, pixelview)
+
     return image
 
 

core/mutations/protocol_step.py

@@ -1,10 +1,25 @@
 from kante.types import Info
 import strawberry
-from core import types, models
+from core import types, models, scalars
 import uuid
 
 
 
+@strawberry.input
+class PlateChildInput:
+    id: strawberry.ID | None = None
+    type: str | None = None
+    text: str | None = None
+    children: list["PlateChildInput"] | None = None
+    value: str | None = None
+    color: str | None = None
+    fontSize: str | None = None
+    backgroundColor: str | None = None
+    bold: bool | None = None
+    italic: bool | None = None
+    underline: bool | None = None
+
+
 
 
 @strawberry.input
@@ -13,6 +28,19 @@ class ProtocolStepInput:
     reagents: list[strawberry.ID] | None = None
     kind: strawberry.ID
     description: str | None = None
+    plate_children: list[PlateChildInput] | None = None
+
+
+@strawberry.input
+class UpdateProtocolStepInput:
+    name: str | None = None
+    id: strawberry.ID 
+    reagents: list[strawberry.ID] | None = None
+    kind: strawberry.ID | None = None
+    description: str | None = None
+    plate_children: list[PlateChildInput] | None = None
+
+
 
 @strawberry.input
 class MapProtocolStepInput:
@@ -38,11 +66,12 @@ def create_protocol_step(
 
 
 
-    step, _ = models.ProtocolStep.objects.update_or_create(
+    step, _ = models.ProtocolStep.objects.get_or_create(
         name=input.name,
         defaults=dict(
             kind=input_kind,
             description=input.description or "",
+            plate_children=input.plate_children or [],
         ),
     )
 
@@ -64,6 +93,37 @@ def map_protocol_step(info: Info, input: MapProtocolStepInput) -> types.Protocol
     return mapping
 
 
+def child_to_str(child):
+    if child.get("children", []) is None:
+        return " ".join([child_to_str(c) for c in child["children"]]),
+    else:
+        return child.get("value", child.get("text", "")) or ""
+
+
+def plate_children_to_str(children):
+    return " ".join([child_to_str(c) for c in children])
+
+
+def update_protocol_step(
+    info: Info,
+    input: UpdateProtocolStepInput,
+) -> types.ProtocolStep:
+    step = models.ProtocolStep.objects.get(id=input.id)
+    step.name = input.name if input.name else step.name
+    step.description = input.description if input.description else plate_children_to_str([strawberry.asdict(i) for i in input.plate_children])
+    step.plate_children = [strawberry.asdict(i) for i in input.plate_children] if input.plate_children else step.plate_children
+    step.kind = models.EntityKind.objects.get(id=input.kind) if input.kind else step.kind
+
+
+    if input.reagents:
+
+        step.reagents.clear()
+        for reagent in input.reagents:
+            step.reagents.add(models.Entity.objects.get(id=reagent))
+
+    step.save()
+    return step
+
 
 def delete_protocol_step(
     info: Info,