Update demo httpd and add deployment docs

GMOD · Jun 20, 2024 · f53fe33 · f53fe33
1 parent 3c493da
commit f53fe33
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Showing 5 changed files with 476 additions and 11 deletions.
diff --git a/.github/workflows/deploy/compose.yml b/.github/workflows/deploy/compose.yml
@@ -23,6 +23,7 @@ services:
       - 3999:3999
     volumes:
       - uploaded-files-volume:/data/uploads
+    restart: unless-stopped
 
   client:
     build:
@@ -37,6 +38,7 @@ services:
       - /home/ec2-user/deployment/config.json:/usr/local/apache2/htdocs/config.json
       - /home/ec2-user/deployment/data/:/usr/local/apache2/htdocs/data/
       - /home/ec2-user/deployment/demoData/:/usr/local/apache2/htdocs/demoData/
+    restart: unless-stopped
 
   mongo-node-1:
     image: mongo:7
@@ -73,6 +75,7 @@ services:
     volumes:
       - mongo-node-1_data:/data/db
       - mongo-node-1_config:/data/configdb
+    restart: unless-stopped
 
   mongo-node-2:
     image: mongo:7
@@ -87,6 +90,7 @@ services:
     volumes:
       - mongo-node-2_data:/data/db
       - mongo-node-2_config:/data/configdb
+    restart: unless-stopped
 
 volumes:
   mongo-node-1_config: null

diff --git a/.github/workflows/deploy/httpd.conf b/.github/workflows/deploy/httpd.conf
@@ -147,7 +147,7 @@ LoadModule proxy_http_module modules/mod_proxy_http.so
 #LoadModule proxy_scgi_module modules/mod_proxy_scgi.so
 #LoadModule proxy_uwsgi_module modules/mod_proxy_uwsgi.so
 #LoadModule proxy_fdpass_module modules/mod_proxy_fdpass.so
-#LoadModule proxy_wstunnel_module modules/mod_proxy_wstunnel.so
+LoadModule proxy_wstunnel_module modules/mod_proxy_wstunnel.so
 #LoadModule proxy_ajp_module modules/mod_proxy_ajp.so
 #LoadModule proxy_balancer_module modules/mod_proxy_balancer.so
 #LoadModule proxy_express_module modules/mod_proxy_express.so
@@ -196,7 +196,7 @@ LoadModule dir_module modules/mod_dir.so
 #LoadModule speling_module modules/mod_speling.so
 #LoadModule userdir_module modules/mod_userdir.so
 LoadModule alias_module modules/mod_alias.so
-LoadModule rewrite_module modules/mod_rewrite.so
+#LoadModule rewrite_module modules/mod_rewrite.so
 
 <IfModule unixd_module>
 #
@@ -238,7 +238,7 @@ ServerAdmin [email protected]
 #
 # If your host doesn't have a registered DNS name, enter its IP address here.
 #
-ServerName localhost:8080
+#ServerName www.example.com:80
 
 #
 # Deny access to the entirety of your server's filesystem. You must
@@ -549,11 +549,5 @@ SSLRandomSeed startup builtin
 SSLRandomSeed connect builtin
 </IfModule>
 
-<VirtualHost *:80>
-    RewriteEngine on
-
-    RewriteCond %{DOCUMENT_ROOT}/$1 !-f
-    RewriteCond %{DOCUMENT_ROOT}/$1 !-d
-    RewriteRule ^/(.*)$ http://apollo-collaboration-server:3999/$1 [P,QSA]
-    ProxyPassReverse / http://apollo-collaboration-server:3999/
-</VirtualHost>
+ProxyPassMatch "^/apollo/(.*)$" "http://apollo-collaboration-server:3999/$1" upgrade=websocket connectiontimeout=3600 timeout=3600
+ProxyPassReverse "/apollo/" "http://apollo-collaboration-server:3999/"
diff --git a/docs/deployment/Dockerfile b/docs/deployment/Dockerfile
@@ -0,0 +1,75 @@
+FROM httpd:alpine
+ARG JBROWSE_VERSION
+ARG APOLLO_VERSION
+ARG FORWARD_HOSTNAME
+ARG FORWARD_PORT
+ARG URL
+COPY <<EOF /usr/local/apache2/conf/httpd.conf.append
+LoadModule proxy_module modules/mod_proxy.so
+LoadModule proxy_http_module modules/mod_proxy_http.so
+LoadModule proxy_wstunnel_module modules/mod_proxy_wstunnel.so
+ServerName localhost
+
+ProxyPassMatch "^/apollo/(.*)$" "http://${FORWARD_HOSTNAME}:${FORWARD_PORT}/\$1" upgrade=websocket connectiontimeout=3600 timeout=3600
+ProxyPassReverse "/apollo/" "http://${FORWARD_HOSTNAME}:${FORWARD_PORT}/"
+EOF
+COPY <<EOF /usr/local/apache2/htdocs/config.json
+{
+  "configuration": {
+    "theme": {
+      "palette": {
+        "primary": {
+          "main": "#24264a"
+        },
+        "secondary": {
+          "main": "#6f8fa2"
+        },
+        "tertiary": {
+          "main": "#1e4b34"
+        },
+        "quaternary": {
+          "main": "#6b4e2b"
+        }
+      }
+    }
+  },
+  "plugins": [
+    {
+      "name": "Apollo",
+      "url": "/jbrowse-plugin-apollo.umd.production.min.js"
+    }
+  ],
+  "internetAccounts": [
+    {
+      "type": "ApolloInternetAccount",
+      "internetAccountId": "apolloInternetAccount",
+      "name": "My Apollo Server",
+      "description": "A server for my annotations",
+      "domains": [
+        "${URL}"
+      ],
+      "baseURL": "${URL}/apollo/"
+    }
+  ],
+  "defaultSession": {
+    "name": "Apollo Demo",
+    "views": [
+      {
+        "type": "LinearGenomeView"
+      }
+    ]
+  }
+}
+EOF
+WORKDIR /usr/local/apache2/htdocs/
+RUN <<EOF
+set -o errexit
+set -o nounset
+set -o pipefail
+cat /usr/local/apache2/conf/httpd.conf.append >> /usr/local/apache2/conf/httpd.conf
+wget https://github.com/GMOD/jbrowse-components/releases/download/v$JBROWSE_VERSION/jbrowse-web-v$JBROWSE_VERSION.zip
+unzip -o jbrowse-web-v$JBROWSE_VERSION.zip
+rm jbrowse-web-v$JBROWSE_VERSION.zip
+wget --output-document=- --quiet https://registry.npmjs.org/@apollo-annotation/jbrowse-plugin-apollo/-/jbrowse-plugin-apollo-$APOLLO_VERSION.tgz | \
+  tar --extract --gzip --file=- --strip=2 package/dist/jbrowse-plugin-apollo.umd.production.min.js
+EOF
diff --git a/docs/deployment/compose.yml b/docs/deployment/compose.yml
@@ -0,0 +1,92 @@
+name: apollo-demo-site
+
+services:
+  apollo-collaboration-server:
+    image: ghcr.io/gmod/apollo-collaboration-server
+    depends_on:
+      mongo-node-1:
+        condition: service_healthy
+    env_file: .env
+    environment:
+      MONGODB_URI: mongodb://mongo-node-1:27017,mongo-node-2:27018/apolloDb?replicaSet=rs0
+      FILE_UPLOAD_FOLDER: /data/uploads
+      ALLOW_GUEST_USER: true
+      GUEST_USER_ROLE: admin
+      URL: http://localhost
+      JWT_SECRET: change_this_value
+      SESSION_SECRET: change_this_value
+    ports:
+      - 3999:3999
+    volumes:
+      - uploaded-files-volume:/data/uploads
+
+  client:
+    build:
+      args:
+        APOLLO_VERSION: 0.1.16
+        JBROWSE_VERSION: 2.11.2
+        FORWARD_HOSTNAME: apollo-collaboration-server
+        FORWARD_PORT: 3999
+        URL: http://localhost
+      context: .
+    depends_on:
+      - apollo-collaboration-server
+    ports:
+      - '80:80'
+
+  mongo-node-1:
+    image: mongo:7
+    command:
+      - '--replSet'
+      - rs0
+      - '--bind_ip_all'
+      - '--port'
+      - '27017'
+    healthcheck:
+      interval: 30s
+      retries: 3
+      start_interval: 5s
+      start_period: 2m
+      test: |
+        mongosh --port 27017 --quiet --eval "
+        try {
+          rs.status()
+          console.log('replica set ok')
+        } catch {
+          rs.initiate({
+            _id: 'rs0',
+            members: [
+              { _id: 0, host: 'mongo-node-1:27017', priority: 1 },
+              { _id: 1, host: 'mongo-node-2:27018', priority: 0.5 },
+            ],
+          })
+          console.log('replica set initiated')
+        }
+        "
+      timeout: 10s
+    ports:
+      - '27017:27017'
+    volumes:
+      - mongo-node-1_data:/data/db
+      - mongo-node-1_config:/data/configdb
+
+  mongo-node-2:
+    image: mongo:7
+    command:
+      - '--replSet'
+      - rs0
+      - '--bind_ip_all'
+      - '--port'
+      - '27018'
+    ports:
+      - '27018:27018'
+    volumes:
+      - mongo-node-2_data:/data/db
+      - mongo-node-2_config:/data/configdb
+
+volumes:
+  mongo-node-1_config: null
+  mongo-node-1_data: null
+  mongo-node-2_config: null
+  mongo-node-2_data: null
+  uploaded-files-volume: null