fix conflict

.github/workflows/black.yml

@@ -6,7 +6,7 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: psf/black@stable
         with:
           src: "./applications/visualizer/backend"

.github/workflows/build.yml

@@ -0,0 +1,18 @@
+name: Build Frontend
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 21.7
+      - name: Install dependencies
+        working-directory: applications/visualizer/frontend
+        run: yarn install --frozen-lockfile
+      - name: Build App
+        working-directory: applications/visualizer/frontend
+        run: npm run build

applications/visualizer/Dockerfile

@@ -5,21 +5,21 @@ ENV APP_DIR=/app
 WORKDIR ${APP_DIR}
 COPY frontend/package.json ${APP_DIR}
 COPY frontend/yarn.lock ${APP_DIR}
-RUN yarn install --production --frozen-lockfile
+RUN yarn install --frozen-lockfile
 
 COPY frontend ${APP_DIR}
 RUN npm run build
 
 #####
 
-# FROM $CLOUDHARNESS_DJANGO
+ARG NO_SOURCEMAP
 FROM python:3.11
 
 ENV MODULE_NAME=backend
 ENV PORT=8080
 ENV WORKERS=2
 ENV APP_DIR=/usr/src/app
-
+ENV NO_SOURCEMAP=${NO_SOURCEMAP}
 ENV PRODUCTION=true
 
 WORKDIR ${APP_DIR}

applications/visualizer/api/openapi.yaml

@@ -0,0 +1,251 @@
+components:
+  schemas:
+    Dataset:
+      properties:
+        axes:
+          anyOf:
+          - type: object
+          - type: 'null'
+          title: Axes
+        collection:
+          maxLength: 20
+          title: Collection
+          type: string
+        description:
+          title: Description
+          type: string
+        id:
+          title: Id
+          type: string
+        name:
+          maxLength: 50
+          title: Name
+          type: string
+        time:
+          title: Time
+          type: number
+        type:
+          maxLength: 50
+          title: Type
+          type: string
+        visualTime:
+          title: Visual Time
+          type: number
+      required:
+      - id
+      - collection
+      - name
+      - description
+      - time
+      - visualTime
+      - type
+      title: Dataset
+      type: object
+    ErrorMessage:
+      properties:
+        detail:
+          title: Detail
+          type: string
+      required:
+      - detail
+      title: ErrorMessage
+      type: object
+    Input:
+      properties:
+        page:
+          default: 1
+          minimum: 1
+          title: Page
+          type: integer
+      title: Input
+      type: object
+    Neuron:
+      properties:
+        embryonic:
+          default: false
+          title: Embryonic
+          type: boolean
+        inhead:
+          default: false
+          title: Inhead
+          type: boolean
+        intail:
+          default: false
+          title: Intail
+          type: boolean
+        name:
+          title: Name
+          type: string
+        nclass:
+          maxLength: 30
+          title: Nclass
+          type: string
+        neurotransmitter:
+          maxLength: 10
+          title: Neurotransmitter
+          type: string
+        type:
+          maxLength: 10
+          title: Type
+          type: string
+      required:
+      - name
+      - nclass
+      - neurotransmitter
+      - type
+      title: Neuron
+      type: object
+    PagedNeuron:
+      properties:
+        count:
+          title: Count
+          type: integer
+        items:
+          items:
+            $ref: '#/components/schemas/Neuron'
+          title: Items
+          type: array
+      required:
+      - items
+      - count
+      title: PagedNeuron
+      type: object
+info:
+  description: ''
+  title: C. Elegans Visualizer
+  version: 1.0.0
+openapi: 3.1.0
+paths:
+  /api/cells:
+    get:
+      description: Returns all the cells (neurons) from the DB
+      operationId: get_all_cells
+      parameters:
+      - in: query
+        name: page
+        required: false
+        schema:
+          default: 1
+          minimum: 1
+          title: Page
+          type: integer
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/PagedNeuron'
+          description: OK
+      summary: Get All Cells
+      tags:
+      - neurons
+  /api/datasets:
+    get:
+      description: Returns all the datasets from the DB
+      operationId: get_all_datasets
+      parameters: []
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                items:
+                  $ref: '#/components/schemas/Dataset'
+                title: Response
+                type: array
+          description: OK
+      summary: Get All Datasets
+      tags:
+      - datasets
+  /api/datasets/{dataset}:
+    get:
+      description: Returns a specific dataset
+      operationId: get_dataset
+      parameters:
+      - in: path
+        name: dataset
+        required: true
+        schema:
+          title: Dataset
+          type: string
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/Dataset'
+          description: OK
+        '404':
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorMessage'
+          description: Not Found
+      summary: Get Dataset
+      tags:
+      - datasets
+  /api/datasets/{dataset}/neurons:
+    get:
+      description: Returns all the neurons of a dedicated dataset
+      operationId: get_dataset_neurons
+      parameters:
+      - in: path
+        name: dataset
+        required: true
+        schema:
+          title: Dataset
+          type: string
+      responses:
+        '200':
+          content:
+            application/json:
+              schema:
+                items:
+                  $ref: '#/components/schemas/Neuron'
+                title: Response
+                type: array
+          description: OK
+        '404':
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/ErrorMessage'
+          description: Not Found
+      summary: Get Dataset Neurons
+      tags:
+      - datasets
+  /api/live:
+    get:
+      description: Test if application is healthy
+      operationId: live
+      parameters: []
+      responses:
+        '200':
+          description: OK
+      summary: Live
+      tags:
+      - healthcheck
+  /api/ping:
+    get:
+      description: test the application is up
+      operationId: ping
+      parameters: []
+      responses:
+        '200':
+          description: OK
+      summary: Ping
+      tags:
+      - healthcheck
+  /api/ready:
+    get:
+      description: Test if application is ready to take requests
+      operationId: ready
+      parameters: []
+      responses:
+        '200':
+          description: OK
+      summary: Ready
+      tags:
+      - healthcheck
+servers: []
+

applications/visualizer/frontend/additional.d.ts

@@ -0,0 +1,6 @@
+declare module '*.svg' {
+    import React = require('react');
+    export const ReactComponent: React.FC<React.SVGProps<SVGSVGElement>>;
+    const src: string;
+    export default src;
+}

applications/visualizer/frontend/package.json

@@ -1,7 +1,7 @@
 {
   "name": "c-elegans-app",
   "private": true,
-  "version": "0.0.0",
+  "version": "0.0.1",
   "type": "module",
   "scripts": {
     "dev": "vite",
@@ -25,7 +25,7 @@
     "@react-three/drei": "^9.105.4",
     "@react-three/fiber": "^8.16.2",
     "@reduxjs/toolkit": "^2.2.3",
-    "@types/three": "^0.163.0",
+    "@types/three": "^0.164.0",
     "file-saver": "^2.0.5",
     "react": "^18.2.0",
     "react-color": "^2.19.3",
@@ -47,4 +47,4 @@
     "typescript": "^5.2.2",
     "vite": "^5.2.0"
   }
-}
+}

applications/visualizer/frontend/settings/threeDSettings.ts

@@ -1,11 +1,14 @@
+import { Vector3 } from "three";
+
+
 export const CAMERA_FOV = 50
-export const CAMERA_POSITION = [0, 0, 50]
+export const CAMERA_POSITION = new Vector3(0, 0, 50)
 export const CAMERA_NEAR = 0.1
 export const CAMERA_FAR = 2000
 
 export const LIGHT_1_COLOR = 0x404040
 export const LIGHT_2_COLOR = 0xccccff
-export const LIGHT_2_POSITION = [-1, 0.75, -0.5]
+export const LIGHT_2_POSITION = new Vector3(-1, 0.75, -0.5)
 
 export const SCENE_BACKGROUND = '0xd9d8d4'