Data Viewer deployment

.env.template

@@ -0,0 +1,4 @@
+SERVICENAME=
+CASLOGINURL=
+CASVALIDATEURL=
+COMPOSE_PROJECT_NAME=

.gitignore

@@ -119,10 +119,8 @@ venv.bak/
 
 # credential file
 dj_local_conf.json
-root/.one_params
 
 # docker related file
-docker-compose.yml
 docker-compose-local.yml
 ibl_docker_setup.sh
 

apache/pni-apache.Dockerfile

@@ -0,0 +1,11 @@
+FROM httpd:2.4
+
+RUN apt-get update -y \
+    && apt-get install -y libapache2-mod-auth-cas ca-certificates\
+            libssl-dev libapache2-mod-fcgid \
+    && rm -rf /var/cache/apk/* \
+    && mkdir /tmp/cas && chown www-data:www-data /tmp/cas
+
+COPY ./http2.4.conf /usr/local/apache2/conf/httpd.conf
+
+COPY pni-apache.Dockerfile /Dockerfile

apache/sites/cas.conf

@@ -0,0 +1,24 @@
+#
+# mod_auth_cas is an Apache 2.0/2.2 compliant module that supports the
+# CASv1 and CASv2 protocols
+#
+<IfModule !mod_ssl.c>
+    LoadModule ssl_module modules/mod_ssl.so
+</IfModule>
+LoadModule auth_cas_module /usr/lib/apache2/modules/mod_auth_cas.so
+<IfModule mod_auth_cas.c>
+    CASVersion 2
+    CASDebug On
+    # Validate the authenticity of the login.goshen.edu SSL certificate by
+    # checking its chain of authority from the root CA.
+    #CASCertificatePath /etc/pki/tls/certs/
+    #CASValidateServer Off
+    CASValidateDepth 9
+    #CASCookiePath /var/lib/cas/
+    CASCookiePath /tmp/cas/
+    CASLoginURL ${CASLOGINURL}
+    CASValidateURL ${CASVALIDATEURL}
+    #CASProxyValidateURL ${CASPROXYVALIDATEURL}
+    CASTimeout 864000
+    CASIdleTimeout 864000
+</IfModule>

apache/sites/proxypass.conf

@@ -0,0 +1,32 @@
+ServerName ${SERVICEHOSTNAME}
+
+<VirtualHost _default_:80>
+
+    <Location />
+
+    #SSLRequireSSL
+    #SSLProtocol all -SSLv2 -SSLv3
+    AuthType CAS
+    CASScope /
+
+    Require valid-user
+
+    </Location>
+
+    RequestHeader set X-Remote-User %{REMOTE_USER}s
+    #RequestHeader set Remote-User %{REMOTE_USER}s
+
+    ProxyPreserveHost On
+    ProxyPass /ws ws://flask-root:5000/ws
+    ProxyPassReverse /ws ws://flask-root:5000/ws
+
+    ProxyPass / http://flask-root:5000/
+    ProxyPassReverse / http://flask-root:5000/
+
+
+    #RewriteRule .* - [E=X-Proxy-REMOTE-USER:%{REMOTE_USER}]
+    #RequestHeader set X-Proxy-REMOTE-USER %{REMOTE_USER}
+
+
+
+</VirtualHost>

docker-compose.yml

@@ -0,0 +1,39 @@
+version: '3'
+services:
+  apache:
+    env_file:
+      - .env
+    build:
+      context: ./apache
+      dockerfile: 'pni-apache.Dockerfile'
+    networks:
+      - proxy
+      - default
+    volumes:
+      - './apache/sites:/usr/local/apache2/conf/sites/:ro'
+    labels:
+      - "traefik.enable=true"
+      - "traefik.http.routers.${COMPOSE_PROJECT_NAME}-http.entrypoints=http"
+      - "traefik.http.routers.${COMPOSE_PROJECT_NAME}-https.entrypoints=https"
+      - "traefik.http.routers.${COMPOSE_PROJECT_NAME}-https.tls=true"
+      - "traefik.http.routers.${COMPOSE_PROJECT_NAME}-https.tls.certresolver=letsencrypt-resolver"
+      - "traefik.http.routers.${COMPOSE_PROJECT_NAME}-http.middlewares=${COMPOSE_PROJECT_NAME}-redirectscheme@docker"
+      - "traefik.http.routers.${COMPOSE_PROJECT_NAME}-http.rule=Host(`${SERVICEHOSTNAME}`)"
+      - "traefik.http.routers.${COMPOSE_PROJECT_NAME}-https.rule=Host(`${SERVICEHOSTNAME}`)"
+      - "traefik.http.middlewares.${COMPOSE_PROJECT_NAME}-redirectscheme.redirectscheme.scheme=https"
+      - "traefik.http.middlewares.${COMPOSE_PROJECT_NAME}-redirectscheme.redirectscheme.permanent=true"
+      - "traefik.http.services.${COMPOSE_PROJECT_NAME}.loadbalancer.server.port=80"
+      - "traefik.docker.network=proxy"
+  flask-root:
+    env_file:
+      - .env
+    build:
+      context: .
+      dockerfile: ./viewer/viewer.Dockerfile
+    expose:
+      - 5000
+
+
+networks:
+  proxy:
+    external: true

setup.py

@@ -4,7 +4,7 @@
 import sys
 
 setup(
-    name='Princeton Data Viewer',
+    name='princeton-u19-data-viewer',
     version='0.0.0',
     description="Data Viewer for Princeton Data pipeline",
     author='Shan Shen',

viewer/server.py

@@ -8,6 +8,7 @@
 
 import datajoint as dj
 
+
 def datajoint_dot():
     from bokeh.models import Div
     from bokeh.layouts import layout
@@ -41,7 +42,7 @@ def main():
         description='Princeton U19 DataJoint Interface')
     parser.add_argument('-p','--port',
                         type=int,
-                        default=5900,
+                        default=5000,
                         help='port for the bokeh server',
                         action='store')
     parser.add_argument('-n','--num-proc',
@@ -67,7 +68,8 @@ def main():
     os.environ['BOKEH_ALLOW_WS_ORIGIN']=','.join(['localhost:{0}',
                                                   '0.0.0.0:{0}',
                                                   '{1}:{0},{2}:{0}',
-                                                  '{1}.princeton.edu:{0}']).format(
+                                                  '{1}.princeton.edu:{0}',
+                                                  'braincogs01.pni.princeton.edu']).format(
         port, hostname, ipaddress)
 
     server = Server({'/': bkapp},
@@ -83,3 +85,4 @@ def main():
 
 if __name__ == '__main__':
     main()
+

viewer/viewer.Dockerfile

@@ -0,0 +1,9 @@
+FROM python:3.7.6-slim-buster
+RUN apt-get update && apt-get install -y openssh-server graphviz
+COPY . /data_viewer
+WORKDIR /data_viewer
+RUN pip install --upgrade pip
+RUN pip install -e /data_viewer
+EXPOSE 5000
+ENTRYPOINT [ "python" ]
+CMD [ "/data_viewer/viewer/server.py" ]