ECHO-564 add verify, 2fa and database migrations

echo/.devcontainer/devcontainer.json

@@ -1,7 +1,7 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/universal
 {
-  "name": "dembrane/pilot",
+  "name": "dembrane/echo",
   // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
   // "image": "mcr.microsoft.com/devcontainers/base:ubuntu",
   "dockerComposeFile": "docker-compose.yml",
@@ -11,23 +11,25 @@
   "features": {},
   // Use 'forwardPorts' to make a list of ports inside the container available locally.
   // Use 'postCreateCommand' to run commands after the container is created.
-  "postCreateCommand": "chmod +x ./setup.sh && ./setup.sh",
+  "postCreateCommand": "chmod +x ./.devcontainer/setup.sh && ./.devcontainer/setup.sh",
   "customizations": {
     "vscode": {
       "extensions": [
+        // ts
         "YoavBls.pretty-ts-errors",
         "bradlc.vscode-tailwindcss",
+        "biomejs.biome",
+        // python
         "ms-python.python",
         "charliermarsh.ruff",
         "matangover.mypy",
+        "anysphere.cursorpyright", // for cursor
+        // general
+        "github.vscode-pull-request-github",
         "ms-azuretools.vscode-docker",
         "mhutchie.git-graph",
         "cweijan.vscode-postgresql-client2",
-        "github.vscode-pull-request-github",
-        "nguyenngoclong.terminal-keeper",
-        "biomejs.biome",
-        // for cursor specifically lol
-        "anysphere.cursorpyright"
+        "nguyenngoclong.terminal-keeper"
       ]
     }
   },

echo/.devcontainer/docker-compose-s3.yml

@@ -0,0 +1,15 @@
+services:
+  minio:
+    image: minio/minio:latest
+    ports:
+      - 9000:9000
+      - 9001:9001
+    entrypoint: >
+      /bin/sh -c " /usr/bin/mc config host add myminio http://minio:9000 $$MINIO_ROOT_USER $$MINIO_ROOT_PASSWORD; /usr/bin/mc mb --ignore-existing myminio/dembrane; /usr/bin/mc policy set download myminio/dembrane; minio server /mnt/data --console-address ":9001" "
+    environment:
+      - MINIO_ROOT_USER=dembrane
+      - MINIO_ROOT_PASSWORD=dembrane
+      - MINIO_VOLUMES=/mnt/data
+    volumes:
+      - ./minio_data:/mnt/data
+    restart: unless-stopped

echo/.devcontainer/docker-compose.yml

@@ -1,59 +1,41 @@
-version: '3.8'
-
 services:
-  minio:
-    image: minio/minio:latest
-    ports:
-      - 9000:9000
-      - 9001:9001
-    entrypoint: >
-      /bin/sh -c "
-      /usr/bin/mc config host add myminio http://minio:9000 $$MINIO_ROOT_USER $$MINIO_ROOT_PASSWORD;
-      /usr/bin/mc mb --ignore-existing myminio/dembrane;
-      /usr/bin/mc policy set download myminio/dembrane;
-      minio server /mnt/data --console-address ":9001"
-      "
-    environment:
-      - MINIO_ROOT_USER=dembrane
-      - MINIO_ROOT_PASSWORD=dembrane
-      - MINIO_VOLUMES=/mnt/data
-    volumes:
-      - ./minio_data:/mnt/data
-    restart: unless-stopped
-
   redis:
-    image: valkey/valkey:8.0
+    image: valkey/valkey:8.0.6-alpine
     volumes:
       - ./redis_data:/data
+    networks:
+      - dembrane-network
 
   postgres:
-    image: pgvector/pgvector:0.6.2-pg16
+    image: pgvector/pgvector:0.8.1-pg16
     restart: unless-stopped
     ports:
-      - 5432:5432      
-      - 7474:7474  # Neo4j Browser
-      - 7687:7687  # Neo4j Bolt protocol
-      - 5173:5173
-      - 5174:5174
+      - 5432:5432
     environment:
       POSTGRES_DB: dembrane
       POSTGRES_USER: dembrane
       POSTGRES_PASSWORD: dembrane
     volumes:
       - ./postgres_data:/var/lib/postgresql/data
       - ./init.sql:/docker-entrypoint-initdb.d/init.sql
+    networks:
+      - dembrane-network
 
   neo4j:
-    image: neo4j:5.26.4
+    image: neo4j:5.26.16-community
+    restart: unless-stopped
     volumes:
       - ./neo4j_data/logs:/logs
       - ./neo4j_data/config:/config
       - ./neo4j_data/data:/data
       - ./neo4j_data/plugins:/plugins
+    ports:
+      - 7474:7474 # Neo4j Browser
+      - 7687:7687 # Neo4j Bolt protocol
     environment:
       - NEO4J_AUTH=neo4j/admin@dembrane
-    network_mode: service:postgres
-    restart: unless-stopped
+    networks:
+      - dembrane-network
 
   directus:
     build:
@@ -64,6 +46,8 @@ services:
     volumes:
       - ../directus/uploads:/directus/uploads
       - ../directus/templates:/directus/templates
+    env_file:
+      - ../directus/.env
     environment:
       - PUBLIC_URL=http://localhost:8055
       - PORT=8055
@@ -88,19 +72,9 @@ services:
       - USER_INVITE_URL_ALLOW_LIST=http://localhost:5173/invite
       - USER_REGISTER_URL_ALLOW_LIST=http://localhost:5173/verify-email
       - PASSWORD_RESET_URL_ALLOW_LIST=http://localhost:5173/password-reset
-      - STORAGE_LOCATIONS=local,s3
-      - STORAGE_S3_KEY=dembrane
-      - STORAGE_S3_SECRET=dembrane
-      - STORAGE_S3_BUCKET=dembrane
-      - STORAGE_S3_ENDPOINT=http://minio:9000
-      - EMAIL_TRANSPORT="smtp"
-      - EMAIL_FROM=""
-      - EMAIL_SMTP_HOST=""
-      - EMAIL_SMTP_PORT=587
-      - EMAIL_SMTP_USER=""
-      - EMAIL_SMTP_PASSWORD=""
-      - EMAIL_SMTP_SECURE=false
-      - EMAIL_SMTP_IGNORE_TLS=false
+      - STORAGE_LOCATIONS=local
+    networks:
+      - dembrane-network
 
     depends_on:
       - postgres
@@ -111,6 +85,10 @@ services:
       context: ../server
       dockerfile: Dockerfile
       target: base
+    ports:
+      - 8000:8000
+      - 5173:5173
+      - 5174:5174
     environment:
       - DIRECTUS_SECRET=secret
       - DIRECTUS_TOKEN=admin
@@ -120,22 +98,29 @@ services:
       - ADMIN_BASE_URL=http://localhost:5173
       - PARTICIPANT_BASE_URL=http://localhost:5174
       - DIRECTUS_BASE_URL=http://directus:8055
-      - DEBUG_MODE=1
       - DISABLE_SENTRY=1
       - SERVE_API_DOCS=1
       - DISABLE_REDACTION=1
       - STORAGE_S3_KEY=dembrane
       - STORAGE_S3_SECRET=dembrane
       - STORAGE_S3_BUCKET=dembrane
       - STORAGE_S3_ENDPOINT=http://minio:9000
-      - NEO4J_URL=bolt://neo4j:7687
-
+      - NEO4J_URI=bolt://neo4j:7687
+      - NEO4J_USERNAME=neo4j
+      - NEO4J_PASSWORD=admin@dembrane
+
     volumes:
       - ../..:/workspaces:cached
+      # for docker passthrough
       - /var/run/docker.sock:/var/run/docker.sock
-    network_mode: service:postgres
+    networks:
+      - dembrane-network
     command: sleep infinity
     depends_on:
       - postgres
       - redis
       - neo4j
+
+networks:
+  dembrane-network:
+    driver: bridge