use entitycore for meshes and point cloud (#404)

* add logic to send brain region with ancestors in list query

* use atom for entities counts instead of promise

* add new version of brain regions tree

* dynamically render explore listing view

* add cell-composition to explore interactive

* use mtype etype alt_label on tree item

* clean unneeded files for v2/brain-region-tree

* remove unnecessary pages

* use brain atlas to calculate density and count using volume

* fix notification to use the App context (#400)

* use entitycore for meshes and point cloud

Author: bilalesi

.deployment-envs/.env.staging-next

@@ -28,4 +28,6 @@ NEXT_PUBLIC_ENTITY_CORE_PUBLIC_PROJECT_ID="0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6"
 
 NEXT_PUBLIC_DEFAULT_BRAIN_REGION_HIERARCHY_ID="e3e70682-c209-4cac-a29f-6fbed82c07cd"
 NEXT_PUBLIC_DEFAULT_SELECTED_BRAIN_REGION_ID="4642cddb-4fbe-4aae-bbf7-0946d6ada066"
-NEXT_PUBLIC_DEFAULT_ROOT_BRAIN_REGION_ANNOTATION_VALUE=8
+BASIC_CELL_GROUPS_AND_REGIONS_BRAIN_REGION_ANNOTATION_VALUE=8
+NEXT_PUBLIC_ROOT_BRAIN_REGION_ANNOTATION_VALUE=997
+NEXT_PUBLIC_ROOT_BRAIN_REGION_ID="f728b4fa-4248-4e3a-8a5d-2f346baa9455"

.env.development

@@ -24,5 +24,8 @@ NEXT_PUBLIC_AI_AGENT_URL="https://staging.openbraininstitute.org/api/agent/"
 
 NEXT_PUBLIC_DEFAULT_BRAIN_REGION_HIERARCHY_ID="e3e70682-c209-4cac-a29f-6fbed82c07cd"
 NEXT_PUBLIC_DEFAULT_SELECTED_BRAIN_REGION_ID="4642cddb-4fbe-4aae-bbf7-0946d6ada066"
+NEXT_PUBLIC_BASIC_CELL_GROUPS_AND_REGIONS_BRAIN_REGION_ANNOTATION_VALUE=8
+NEXT_PUBLIC_DEFAULT_BRAIN_ATLAS_ID="a25231be-54c0-4a14-a89a-a1b1c7bd5837"
+NEXT_PUBLIC_ROOT_BRAIN_REGION_ID="f728b4fa-4248-4e3a-8a5d-2f346baa9455"
+NEXT_PUBLIC_ROOT_BRAIN_REGION_ANNOTATION_VALUE=997
 NEXT_PUBLIC_DEFAULT_ROOT_BRAIN_REGION_ANNOTATION_VALUE=8
-NEXT_PUBLIC_DEFAULT_BRAIN_ATLAS_ID="a25231be-54c0-4a14-a89a-a1b1c7bd5837"

.env.development-next

@@ -31,4 +31,6 @@ NEXT_PUBLIC_ENTITY_CORE_PUBLIC_PROJECT_ID="0dbced5f-cc3d-488a-8c7f-cfb8ea039dc6"
 
 NEXT_PUBLIC_DEFAULT_BRAIN_REGION_HIERARCHY_ID="e3e70682-c209-4cac-a29f-6fbed82c07cd"
 NEXT_PUBLIC_DEFAULT_SELECTED_BRAIN_REGION_ID="4642cddb-4fbe-4aae-bbf7-0946d6ada066"
-NEXT_PUBLIC_DEFAULT_ROOT_BRAIN_REGION_ANNOTATION_VALUE=8
+NEXT_PUBLIC_BASIC_CELL_GROUPS_AND_REGIONS_BRAIN_REGION_ANNOTATION_VALUE=8
+NEXT_PUBLIC_ROOT_BRAIN_REGION_ID="f728b4fa-4248-4e3a-8a5d-2f346baa9455"
+NEXT_PUBLIC_ROOT_BRAIN_REGION_ANNOTATION_VALUE=997

src/api/apiClient.ts

@@ -4,7 +4,6 @@ import isNil from 'lodash/isNil';
 import { compactRecord } from '@/utils/dictionary';
 import { getSession } from '@/authFetch';
 import { log } from '@/utils/logger';
-import { env } from '@/env';
 
 type BackoffStrategy = {
   type: 'exponential' | 'custom';
@@ -337,14 +336,12 @@ class ApiClient {
           });
           return runRequest();
         }
-        if (env.NEXT_PUBLIC_DEPLOYMENT_ENV !== 'production') {
-          log('error', 'Request failed', {
-            status: response.status,
-            message:
-              (responseData as any).message || `Request failed with status ${response.status}`,
-            data: responseData,
-          });
-        }
+        log('error', 'Request failed', {
+          url: url.toString(),
+          status: response.status,
+          message: (responseData as any).message || `Request failed with status ${response.status}`,
+          data: responseData,
+        });
         throw Error(`Request ${request.url} failed `, {
           cause: {
             status: response.status,

src/api/entitycore/queries/general/brain-atlas.ts

@@ -104,23 +104,20 @@ export async function getBrainAtlasRegions({
  * @returns A promise that resolves to the brain atlas region data wrapped in an EntityCoreResponse.
  */
 export async function getBrainAtlasRegion({
-  id,
+  atlasRegionId,
   atlasId,
   context,
 }: {
-  id: string;
+  atlasRegionId: string;
   atlasId: string;
   context?: WorkspaceContext | null;
 }) {
   const api = await entityCoreApi();
-  return await api.get<EntityCoreResponse<IBrainAtlasRegion>>(
-    `${baseUri}/${atlasId}/regions/${id}`,
-    {
-      headers: {
-        accept: 'application/json',
-        'content-type': 'application/json',
-        ...getEntityCoreContext(context).headers,
-      },
-    }
-  );
+  return await api.get<IBrainAtlasRegion>(`${baseUri}/${atlasId}/regions/${atlasRegionId}`, {
+    headers: {
+      accept: 'application/json',
+      'content-type': 'application/json',
+      ...getEntityCoreContext(context).headers,
+    },
+  });
 }

src/api/entitycore/types/entities/brain-atlas.ts

@@ -2,6 +2,7 @@ import type {
   EntityCoreIdentifiable,
   Timestamps,
   ISpecies,
+  IAsset,
 } from '@/api/entitycore/types/shared/global';
 import {
   PaginationFilter,
@@ -28,6 +29,7 @@ export interface BrainAtlasRegionBase {
 
 export interface IBrainAtlasRegion extends BrainAtlasRegionBase, Timestamps {
   id: string;
+  assets: Array<IAsset>;
 }
 
 export interface IBrainAtlasFilter

src/app/app/build/(main)/cell-composition/interactive/page.tsx

@@ -1,7 +1,7 @@
 'use client';
 
 import useLiteratureCleanNavigate from '@/components/explore-section/Literature/useLiteratureCleanNavigate';
-import ThreeDeeBrain from '@/components/ThreeDeeBrain';
+import ThreeDeeBrain from '@/features/brain-atlas-viewer';
 
 export default function InteractiveView() {
   useLiteratureCleanNavigate();

src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/(secondary)/build/me-model/new/page.tsx

@@ -8,7 +8,7 @@ import { unwrap } from 'jotai/utils';
 import { useAtomValue } from 'jotai';
 
 import {
-  brainRegionHierarchyAtom,
+  brainRegionBasicCellGroupsRegionsHierarchyAtom,
   DEFAULT_BRAIN_REGION_ANNOTATION_FIELD,
   DEFAULT_BRAIN_REGION_QUERY_ID,
   useBrainRegionHierarchy,
@@ -41,7 +41,9 @@ export default function NewMEModelPage(props: Params) {
     virtualLabId,
     projectId,
   });
-  const brainRegionHierarchy = useAtomValue(useMemo(() => unwrap(brainRegionHierarchyAtom), []));
+  const brainRegionHierarchy = useAtomValue(
+    useMemo(() => unwrap(brainRegionBasicCellGroupsRegionsHierarchyAtom), [])
+  );
   const contributors = useAtomValue(virtualLabProjectUsersAtomFamily({ projectId, virtualLabId }))
     ?.data?.users;
 

src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/layout.tsx

@@ -6,17 +6,22 @@ import { useSetAtom } from 'jotai';
 import dynamic from 'next/dynamic';
 
 import SimpleErrorComponent from '@/components/GenericErrorFallback';
-import SideMenu from '@/components/SideMenu';
 
 import { Label, Content, LinkItemKey } from '@/constants/virtual-labs/sidemenu';
 import { idAtom as brainModelConfigIdAtom } from '@/state/brain-model-config';
 import { useSetBrainRegionFromQuery } from '@/hooks/brain-region-panel';
+import { Container as SideMenuContainer } from '@/components/SideMenu';
 import { generateLabUrl } from '@/util/virtual-lab/urls';
 import { resolveDataKey } from '@/utils/key-builder';
 import { defaultModelRelease } from '@/config';
 
 import type { ServerSideComponentProp, WorkspaceContext } from '@/types/common';
 
+const SideMenu = dynamic(() => import('@/components/SideMenu'), {
+  ssr: false,
+  loading: () => <SideMenuContainer />,
+});
+
 type Props = ServerSideComponentProp<WorkspaceContext, null> & {
   children: React.ReactNode;
 };
@@ -71,7 +76,6 @@ export default function Layout(props: Props) {
           />
         </div>
       </ErrorBoundary>
-      {/* <BrainRegionsTree /> */}
       <ErrorBoundary FallbackComponent={SimpleErrorComponent}>
         <Suspense
           fallback={

src/components/SideMenu/index.tsx

@@ -11,6 +11,7 @@ import {
 } from '@ant-design/icons';
 import Link from 'next/link';
 
+import { ReactNode } from 'react';
 import HelpMenu from '@/components/HelpMenu';
 import UserMenu from '@/components/user-menu';
 import { LabItem, LinkItem, ProjectItem } from '@/components/VerticalLinks';
@@ -54,15 +55,23 @@ function ProjectLink({ project, lab }: { project: ProjectItem; lab: LabItem }) {
   );
 }
 
-export default function SideMenu({ lab, project, links }: SideMenuProps) {
-  const result = useAtomValue(unwrap(virtualLabDetailAtomFamily(lab.id)));
+export function Container({ children }: { children?: ReactNode }) {
   return (
     <div
       className={classNames(
         'border-primary-7 bg-primary-9 text-light sticky top-0 flex h-screen w-[45px]',
         'flex-col items-center justify-center gap-2 border-r-[1px] transition-transform ease-in-out will-change-auto'
       )}
     >
+      {children}
+    </div>
+  );
+}
+
+export default function SideMenu({ lab, project, links }: SideMenuProps) {
+  const result = useAtomValue(unwrap(virtualLabDetailAtomFamily(lab.id)));
+  return (
+    <Container>
       <div className="flex w-[45px] grow flex-col items-center justify-between overflow-hidden">
         <div className="mt-4 flex w-full flex-col items-center gap-2 overflow-hidden">
           {links
@@ -119,6 +128,6 @@ export default function SideMenu({ lab, project, links }: SideMenuProps) {
           </Link>
         </div>
       </div>
-    </div>
+    </Container>
   );
 }