README.md

@@ -17,9 +17,9 @@ Requirements:
 
 *Windows not fully supported in development mode due to lack of support for symbolic links.
 
-Setup
+Inizialize
 
-	$ rosetta/setup
+	$ cp docker-compose-dev.yml docker-compose.yml
 
 Build
 
@@ -46,6 +46,12 @@ Clean
 Webapp service configuraion parameters and their defaults:
 
       - SAFEMODE=false
+      - DJANGO_DB_ENGINE="django.db.backends.postgresql_psycopg2"
+      - DJANGO_DB_NAME="rosetta"
+      - DJANGO_DB_USER="rosetta_master"
+      - DJANGO_DB_PASSWORD="949fa84a"
+      - DJANGO_DB_HOST="postgres"
+      - DJANGO_DB_PORT=5432
       - DJANGO_DEV_SERVER=true
       - DJANGO_DEBUG=true
       - DJANGO_LOG_LEVEL=ERROR

docker-compose-dev.yml

@@ -10,7 +10,6 @@ services:
     privileged: true
     volumes:
       - ./data/shared:/shared
-      # - ./data/singularity_cache:/rosetta/.singularity/cache # Not working, check permissions...
 
   slurmclusterworker:
     image: "rosetta/slurmclusterworker"
@@ -54,6 +53,12 @@ services:
     hostname: webapp
     environment:
       - SAFEMODE=False
+      - DJANGO_DB_ENGINE="django.db.backends.postgresql_psycopg2"
+      - DJANGO_DB_NAME="rosetta"
+      - DJANGO_DB_USER="rosetta_master"
+      - DJANGO_DB_PASSWORD="949fa84a"
+      - DJANGO_DB_HOST="postgres"
+      - DJANGO_DB_PORT=5432
       - DJANGO_DEV_SERVER=True
       - DJANGO_DEBUG=True
       - DJANGO_LOG_LEVEL=CRITICAL
@@ -68,6 +73,7 @@ services:
       #- ROSETTA_TASKS_PROXY_HOST=
       #- ROSETTA_TASKS_TUNNEL_HOST=
       - ROSETTA_HOST=localhost
+      
     ports:
       - "8080:8080"
       - "7000-7020:7000-7020"

rosetta/setup

-#!/bin/bash
-
-# Use dev (local) database for backend if not alredy set up
-if [ ! -f services/webapp/db_conf.sh ]; then
-    echo "Using dev webapp database settings."
-    cp services/webapp/db_conf-dev.sh  services/webapp/db_conf.sh
-else
-    echo "Not using dev webapp database settings as settings are already present."
-fi
-
-
-# Use dev docker-compose.yml if not already set up
-if [ ! -f docker-compose.yml ]; then
-    echo "Using dev docker-compose.yml"
-    cp docker-compose-dev.yml docker-compose.yml
-else
-    echo "Not using dev docker-compose.yml as already present."
-fi

services/webapp/Dockerfile

@@ -60,9 +60,6 @@ COPY code /opt/code
 # Fix permissions
 RUN chown -R rosetta:rosetta /opt/code
 
-# Copy db conf
-COPY db_conf.sh /db_conf.sh
-
 # Prepare for logs
 RUN mkdir /var/log/webapp/ && chown rosetta:rosetta /var/log/webapp/
 

services/webapp/code/rosetta/core_app/utils.py

@@ -637,9 +637,9 @@ Listen '''+str(task.tcp_tunnel_port)+'''
 <VirtualHost *:'''+str(task.tcp_tunnel_port)+'''>
     ServerAdmin admin@rosetta.platform
     SSLEngine on
-    SSLCertificateFile /root/certificates/rosetta_platform/rosetta_platform.crt
-    SSLCertificateKeyFile /root/certificates/rosetta_platform/rosetta_platform.key
-    SSLCACertificateFile /root/certificates/rosetta_platform/rosetta_platform.ca-bundle
+    SSLCertificateFile /etc/letsencrypt/live/'''+rosetta_tasks_proxy_host+'''/cert.pem
+    SSLCertificateKeyFile /etc/letsencrypt/live/'''+rosetta_tasks_proxy_host+'''/privkey.pem
+    SSLCACertificateFile /etc/letsencrypt/live/'''+rosetta_tasks_proxy_host+'''/fullchain.pem
     DocumentRoot /var/www/html
 </VirtualHost>
 
@@ -649,10 +649,10 @@ Listen '''+str(task.tcp_tunnel_port)+'''
     ServerAdmin admin@rosetta.platform
     
     SSLEngine on
-    SSLCertificateFile /root/certificates/rosetta_platform/rosetta_tasks.crt
-    SSLCertificateKeyFile /root/certificates/rosetta_platform/rosetta_tasks.key
-    SSLCACertificateFile /root/certificates/rosetta_platform/rosetta_tasks.ca-bundle
-    
+    SSLCertificateFile /etc/letsencrypt/live/'''+rosetta_tasks_proxy_host+'''/cert.pem
+    SSLCertificateKeyFile /etc/letsencrypt/live/'''+rosetta_tasks_proxy_host+'''/privkey.pem
+    SSLCACertificateFile /etc/letsencrypt/live/'''+rosetta_tasks_proxy_host+'''/fullchain.pem
+        
     SSLProxyEngine On
     SSLProxyVerify none 
     SSLProxyCheckPeerCN off
@@ -700,13 +700,13 @@ Listen '''+str(task.tcp_tunnel_port)+'''
             out = os_shell('ssh -o StrictHostKeyChecking=no proxy "sudo ln -s /shared/etc_apache2_sites_enabled/{0}.conf /etc/apache2/sites-enabled/{0}.conf"'.format(task.uuid), capture=True)
             if out.exit_code != 0:
                 logger.error(out.stderr)
-                raise ErrorMessage('Somthing went wrong when activating the task proxy conf')        
+                raise ErrorMessage('Something went wrong when activating the task proxy conf')        
             
             # Reload apache conf on Proxy
             out = os_shell('ssh -o StrictHostKeyChecking=no proxy "sudo apache2ctl graceful"', capture=True)
             if out.exit_code != 0:
                 logger.error(out.stderr) 
-                raise ErrorMessage('Somthing went wrong when loading the task proxy conf')        
+                raise ErrorMessage('Something went wrong when loading the task proxy conf')        
             
 
 

services/webapp/db_conf-dev.sh

-#!/bin/bash
-
-# SQlite Django DB conf
-#export DJANGO_DB_ENGINE="django.db.backends.sqlite3"
-#export DJANGO_DB_NAME="/data/resources/database.sqlite3"
-
-# Postgres Django DB conf
-export DJANGO_DB_ENGINE="django.db.backends.postgresql_psycopg2"
-export DJANGO_DB_NAME="rosetta"
-export DJANGO_DB_USER="rosetta_master"
-export DJANGO_DB_PASSWORD="949fa84a"
-export DJANGO_DB_HOST="postgres"
-export DJANGO_DB_PORT=5432

services/webapp/run_webapp.sh

@@ -14,9 +14,6 @@ echo ""
 # Load env
 source /env.sh
 
-# Database conf
-source /db_conf.sh
-
 # Stay quiet on Python warnings
 export PYTHONWARNINGS=ignore