Merge branch 'develop' into feature/CELE-70

applications/visualizer/api/openapi.json

@@ -411,6 +411,13 @@
             "title": "Id",
             "type": "string"
           },
+          "neuron3DUrl": {
+            "title": "Neuron3Durl",
+            "type": "string"
+          },
+          "emData": {
+            "$ref": "#/components/schemas/EMData"
+          },
           "collection": {
             "maxLength": 20,
             "title": "Collection",
@@ -452,6 +459,8 @@
         },
         "required": [
           "id",
+          "neuron3DUrl",
+          "emData",
           "collection",
           "name",
           "description",
@@ -462,6 +471,39 @@
         "title": "Dataset",
         "type": "object"
       },
+      "EMData": {
+        "properties": {
+          "min_zoom": {
+            "title": "Min Zoom",
+            "type": "integer"
+          },
+          "max_zoom": {
+            "title": "Max Zoom",
+            "type": "integer"
+          },
+          "nb_slices": {
+            "title": "Nb Slices",
+            "type": "integer"
+          },
+          "resource_url": {
+            "title": "Resource Url",
+            "type": "string"
+          },
+          "segmentation_url": {
+            "title": "Segmentation Url",
+            "type": "string"
+          }
+        },
+        "required": [
+          "min_zoom",
+          "max_zoom",
+          "nb_slices",
+          "resource_url",
+          "segmentation_url"
+        ],
+        "title": "EMData",
+        "type": "object"
+      },
       "ErrorMessage": {
         "properties": {
           "detail": {
@@ -488,6 +530,10 @@
             "title": "Datasetids",
             "type": "array"
           },
+          "model3DUrl": {
+            "title": "Model3Durl",
+            "type": "string"
+          },
           "nclass": {
             "maxLength": 30,
             "title": "Nclass",
@@ -522,6 +568,7 @@
         "required": [
           "name",
           "datasetIds",
+          "model3DUrl",
           "nclass",
           "neurotransmitter",
           "type"

applications/visualizer/api/openapi.yaml

@@ -46,13 +46,18 @@ components:
         description:
           title: Description
           type: string
+        emData:
+          $ref: '#/components/schemas/EMData'
         id:
           title: Id
           type: string
         name:
           maxLength: 50
           title: Name
           type: string
+        neuron3DUrl:
+          title: Neuron3Durl
+          type: string
         time:
           title: Time
           type: number
@@ -65,6 +70,8 @@ components:
           type: number
       required:
       - id
+      - neuron3DUrl
+      - emData
       - collection
       - name
       - description
@@ -73,6 +80,31 @@ components:
       - type
       title: Dataset
       type: object
+    EMData:
+      properties:
+        max_zoom:
+          title: Max Zoom
+          type: integer
+        min_zoom:
+          title: Min Zoom
+          type: integer
+        nb_slices:
+          title: Nb Slices
+          type: integer
+        resource_url:
+          title: Resource Url
+          type: string
+        segmentation_url:
+          title: Segmentation Url
+          type: string
+      required:
+      - min_zoom
+      - max_zoom
+      - nb_slices
+      - resource_url
+      - segmentation_url
+      title: EMData
+      type: object
     ErrorMessage:
       properties:
         detail:
@@ -110,6 +142,9 @@ components:
           default: false
           title: Intail
           type: boolean
+        model3DUrl:
+          title: Model3Durl
+          type: string
         name:
           title: Name
           type: string
@@ -128,6 +163,7 @@ components:
       required:
       - name
       - datasetIds
+      - model3DUrl
       - nclass
       - neurotransmitter
       - type

applications/visualizer/backend/api/api.py

@@ -1,15 +1,14 @@
 from collections import defaultdict
-from typing import Optional
+from typing import Iterable, Optional
 
-from django.http import HttpResponse
 from ninja import NinjaAPI, Router, Schema, Query
 from ninja.pagination import paginate, PageNumberPagination
 from django.shortcuts import aget_object_or_404
-from django.db.models import Q, F, Value, CharField, Func, OuterRef
+from django.db.models import Q
 from django.db.models.manager import BaseManager
-from django.db.models.functions import Coalesce, Concat
+from django.conf import settings
 
-from .schemas import Dataset, Neuron, Connection
+from .schemas import Dataset, EMData, Neuron, Connection
 from .models import (
     Dataset as DatasetModel,
     Neuron as NeuronModel,
@@ -50,13 +49,36 @@ def api_operation(self, *args, **kwargs):
 #     )
 
 
+def annotate_dataset(datasets: Iterable[DatasetModel]):
+    for dataset in datasets:
+        dataset_id = dataset.id
+        dataset.neuron3D_url = (  # type: ignore
+            settings.DATASET_NEURON_REPRESENTATION_3D_URL_FORMAT.format(
+                dataset=dataset_id
+            )
+        )
+        dataset.em_data = EMData(  # type: ignore
+            min_zoom=0,
+            max_zoom=0,
+            nb_slices=0,
+            # resource_url=settings.DATASET_EMDATA_URL_FORMAT.format(dataset=dataset_id),
+            # segmentation_url=settings.DATASET_EMDATA_SEGMENTATION_URL_FORMAT.format(
+            # dataset=dataset_id
+            # ),
+            resource_url=settings.DATASET_EMDATA_URL_FORMAT,
+            segmentation_url=settings.DATASET_EMDATA_SEGMENTATION_URL_FORMAT,
+        )
+
+
 @api.get("/datasets", response=list[Dataset], tags=["datasets"])
 async def get_datasets(request, ids: Optional[list[str]] = Query(None)):
     """Returns all datasets or a filtered list based on provided IDs"""
     if ids:
         datasets = await to_list(DatasetModel.objects.filter(id__in=ids))
     else:
         datasets = await to_list(DatasetModel.objects.all())
+
+    annotate_dataset(datasets)
     return datasets
 
 
@@ -82,10 +104,12 @@ async def get_datasets(request, ids: Optional[list[str]] = Query(None)):
 )
 async def get_dataset(request, dataset: str):
     """Returns a specific dataset"""
-    return await aget_object_or_404(DatasetModel, id=dataset)
+    obj = await aget_object_or_404(DatasetModel, id=dataset)
+    annotate_dataset((obj,))
+    return obj
 
 
-def annotate_neurons_w_dataset_ids(neurons: BaseManager[NeuronModel]) -> None:
+def annotate_neurons(neurons: BaseManager[NeuronModel]) -> None:
     """Queries the datasets ids for each neuron."""
     neuron_names = neurons.values_list("name", flat=True).distinct()
     pre = (
@@ -104,15 +128,18 @@ def annotate_neurons_w_dataset_ids(neurons: BaseManager[NeuronModel]) -> None:
     for neuron, dataset in pre.union(post):
         neurons_dataset_ids[neuron].add(dataset)
 
+    # Add dataset ids and 3D representation path
     for neuron in neurons:
-        neuron.dataset_ids = neurons_dataset_ids[neuron.name]  # type: ignore
+        name = neuron.name
+        neuron.dataset_ids = neurons_dataset_ids[name]  # type: ignore
+        neuron.model3D_url = settings.NEURON_REPRESENTATION_3D_URL_FORMAT.format(name=name)  # type: ignore
 
 
 def neurons_from_datasets(
     neurons: BaseManager[NeuronModel], dataset_ids: list[str]
 ) -> BaseManager[NeuronModel]:
     """Filters neurons belonging to specific datasets."""
-    return neurons.filter(
+    neurons = neurons.filter(
         Q(
             name__in=ConnectionModel.objects.filter(
                 dataset__id__in=dataset_ids
@@ -124,6 +151,7 @@ def neurons_from_datasets(
             ).values_list("post", flat=True)
         )
     )
+    return neurons
 
 
 @api.get(
@@ -134,7 +162,8 @@ def neurons_from_datasets(
 def get_dataset_neurons(request, dataset: str):
     """Returns all the neurons of a dedicated dataset"""
     neurons = neurons_from_datasets(NeuronModel.objects, [dataset])
-    annotate_neurons_w_dataset_ids(neurons)
+    annotate_neurons(neurons)
+
     return neurons
 
 
@@ -144,17 +173,14 @@ def search_cells(
     name: Optional[str] = Query(None),
     dataset_ids: Optional[list[str]] = Query(None),
 ):
-    neurons = NeuronModel.objects
+    neurons = NeuronModel.objects.all()
 
     if name:
         neurons = neurons.filter(name__istartswith=name)
 
     if dataset_ids:
         neurons = neurons_from_datasets(neurons, dataset_ids)
-    else:
-        neurons = neurons.all()
-
-    annotate_neurons_w_dataset_ids(neurons)
+    annotate_neurons(neurons)
 
     return neurons
 
@@ -163,15 +189,12 @@ def search_cells(
 @paginate(PageNumberPagination, page_size=50)  # BUG: this is not being applied
 def get_all_cells(request, dataset_ids: Optional[list[str]] = Query(None)):
     """Returns all the cells (neurons) from the DB"""
-    neurons = NeuronModel.objects
+    neurons = NeuronModel.objects.all()
 
     if dataset_ids:
         neurons = neurons_from_datasets(neurons, dataset_ids)
-    else:
-        neurons = neurons.all()
-
-    annotate_neurons_w_dataset_ids(neurons)
 
+    annotate_neurons(neurons)
     return neurons
 
 

applications/visualizer/backend/api/schemas.py

@@ -1,3 +1,5 @@
+from django.conf import settings
+
 from ninja import ModelSchema, Schema
 from .models import (
     Dataset as DatasetModel,
@@ -19,8 +21,24 @@ class Config(Schema.Config):
         populate_by_name = True
 
 
+class Artifact(Schema): ...
+
+
+class Model3D(Artifact): ...
+
+
+class EMData(Artifact):
+    min_zoom: int
+    max_zoom: int
+    nb_slices: int
+    resource_url: str
+    segmentation_url: str
+
+
 class Dataset(ModelSchema, BilingualSchema):
     id: str
+    neuron3D_url: str
+    em_data: EMData
 
     class Meta:
         model = DatasetModel
@@ -38,6 +56,7 @@ class Meta:
 class Neuron(ModelSchema, BilingualSchema):
     name: str
     dataset_ids: list[str]
+    model3D_url: str
 
     class Meta:
         model = NeuronModel