Docker for local development

ca4a2924 · carlosribas · ff6ff70e · ca4a2924 · ca4a2924 · ca4a2924
Commit ca4a2924 authored May 13, 2021 by carlosribas
Hide whitespace changes
Inline Side-by-side

Showing with 241 additions and 0 deletions

Dockerfile-local Dockerfile-local +65 -0

docker-compose.local.yml docker-compose.local.yml +58 -0

entrypoint-local.sh entrypoint-local.sh +118 -0

No files found.
--- a/Dockerfile-local
+++ b/Dockerfile-local
+#------------------------------------------------------------------------------
+#
+# This Dockerfile is meant for containerized deployment with Kubernetes.
+#
+#-------------------------------------------------------------------------------
+
+FROM python:3.8-slim
+
+RUN apt-get update && apt-get install -y \
+    g++ \
+    build-essential \
+    curl \
+    tar \
+    git \
+    vim \
+    supervisor && \
+    rm -rf /var/lib/apt/lists/*
+
+ENV RNACENTRAL_LOCAL=/srv/rnacentral/local
+ENV SUPERVISOR_CONF_DIR=/srv/rnacentral/supervisor
+
+# Create folders
+RUN \
+    mkdir -p $RNACENTRAL_LOCAL && \
+    mkdir -p $SUPERVISOR_CONF_DIR && \
+    mkdir /srv/rnacentral/log && \
+    mkdir /srv/rnacentral/static
+
+# Install Infernal and node.js
+RUN \
+    cd $RNACENTRAL_LOCAL && \
+    curl -OL http://eddylab.org/infernal/infernal-1.1.1.tar.gz && \
+    tar -xvzf infernal-1.1.1.tar.gz && \
+    cd infernal-1.1.1 && \
+    ./configure --prefix=$RNACENTRAL_LOCAL/infernal-1.1.1 && \
+    make && \
+    make install && \
+    cd easel && \
+    make install && \
+    cd $RNACENTRAL_LOCAL && \
+    rm infernal-1.1.1.tar.gz && \
+    curl -sL https://deb.nodesource.com/setup_lts.x | bash - && \
+    apt-get install -y nodejs
+
+# Set work directory
+ENV RNACENTRAL_HOME=/srv/rnacentral/rnacentral-webcode
+RUN mkdir -p $RNACENTRAL_HOME
+WORKDIR $RNACENTRAL_HOME
+
+# Copy requirements
+COPY rnacentral/requirements* .
+
+# Install requirements
+RUN pip3 install -r requirements.txt && pip3 install -r requirements_dev.txt
+
+# Install NPM dependencies
+ADD rnacentral/portal/static/package.json rnacentral/portal/static/
+RUN cd rnacentral/portal/static && npm install --only=production
+
+# Run entrypoint
+COPY ./entrypoint-local.sh /
+ENTRYPOINT ["/entrypoint-local.sh"]
+
+# Supervisor
+CMD [ "/bin/sh", "-c", "/usr/bin/supervisord -c ${SUPERVISOR_CONF_DIR}/supervisord.conf" ]
--- a/docker-compose.local.yml
+++ b/docker-compose.local.yml
+version: '3'
+
+services:
+  # RNAcentral website
+  rnacentral:
+    build:
+      context: .
+      dockerfile: Dockerfile-local
+    environment:
+      - DB_HOST=${DB_HOST}
+      - DB_NAME=${DB_NAME}
+      - DB_USER=${DB_USER}
+      - DB_PASSWORD=${DB_PASSWORD}
+      - DB_PORT=${DB_PORT}
+      - SECRET_KEY=${SECRET_KEY}
+      - DJANGO_DEBUG=${DJANGO_DEBUG}
+      - S3_HOST=${S3_HOST}
+      - S3_KEY=${S3_KEY}
+      - S3_SECRET=${S3_SECRET}
+      - EBI_SEARCH_ENDPOINT=${EBI_SEARCH_ENDPOINT}
+    command: python manage.py runserver 0.0.0.0:8000
+    ports:
+      - 8000:8000
+    volumes:
+      - ./openssl/openssl.cnf:/etc/ssl/openssl.cnf
+      - ./rnacentral:/srv/rnacentral/rnacentral-webcode
+    depends_on:
+      - redis
+    networks:
+      - redis-network
+      - memcached-network
+
+  # Redis server
+  redis:
+    image: redis:6.0.8-alpine
+    ports:
+      - 8051:8051
+    command: redis-server --port 8051
+    restart: always
+    networks:
+      - redis-network
+
+  # Memcached server
+  memcached:
+    image: memcached:1.6.7-alpine
+    ports:
+      - 8052:8052
+    command: memcached -m 512m -p 8052
+    depends_on:
+      - rnacentral
+    networks:
+      - memcached-network
+
+networks:
+  redis-network:
+    driver: bridge
+  memcached-network:
+    driver: bridge
\ No newline at end of file
--- a/entrypoint-local.sh
+++ b/entrypoint-local.sh
+#!/bin/sh
+set -e
+
+# SYSTEM OPTIONS (set on Docker build)
+RNACENTRAL_HOME=$RNACENTRAL_HOME
+
+# External database settings
+DB_HOST=${DB_HOST:-'hh-pgsql-public.ebi.ac.uk'}
+DB_NAME=${DB_NAME:-'pfmegrnargs'}
+DB_USER=${DB_USER:-'reader'}
+DB_PORT=${DB_PORT:-'5432'}
+DB_PASSWORD=${DB_PASSWORD:-'NWDMCE5xdipIjRrp'}
+
+# RNAcentral specific settings
+SECRET_KEY=${SECRET_KEY:-$(python -c 'from django.core.management.utils import get_random_secret_key; print(get_random_secret_key())')}
+DJANGO_DEBUG=${DJANGO_DEBUG:-'False'}
+EBI_SEARCH_ENDPOINT=${EBI_SEARCH_ENDPOINT:-'http://www.ebi.ac.uk/ebisearch/ws/rest/rnacentral'}
+S3_HOST=${S3_HOST}
+S3_KEY=${S3_KEY}
+S3_SECRET=${S3_SECRET}
+
+# Supervisor
+SUPERVISOR_CONF_DIR=${SUPERVISOR_CONF_DIR:-"/srv/rnacentral/supervisor"}
+
+# Entrypoint variable
+LOGS=/srv/rnacentral/log
+
+# Add debug_toolbar info
+if ! grep -q debug_toolbar "${RNACENTRAL_HOME}"/rnacentral/urls.py; then
+  sed -i "13 a import debug_toolbar" "${RNACENTRAL_HOME}"/rnacentral/urls.py ; \
+  sed -i "31 a \ \ \ \ url(r'^__debug__/', include(debug_toolbar.urls))," "${RNACENTRAL_HOME}"/rnacentral/urls.py ; \
+  sed -i "129 a \ \ \ \ 'debug_toolbar.middleware.DebugToolbarMiddleware'," "${RNACENTRAL_HOME}"/rnacentral/settings.py ; \
+  sed -i "188 a \ \ \ \ 'debug_toolbar'," "${RNACENTRAL_HOME}"/rnacentral/settings.py ; \
+fi
+
+# Add local_settings file
+if [ -f "${RNACENTRAL_HOME}"/rnacentral/local_settings.py ]
+then
+	echo "INFO: RNAcentral local_settings.py file already provisioned"
+else
+	echo "INFO: Creating RNAcentral local_settings.py file"
+	cat <<-EOF > "${RNACENTRAL_HOME}"/rnacentral/local_settings.py
+		import os
+		from .utils import get_environment
+		SECRET_KEY = "$SECRET_KEY"
+		DEBUG = True
+		EBI_SEARCH_ENDPOINT = "$EBI_SEARCH_ENDPOINT"
+		ENVIRONMENT = get_environment()
+		INTERNAL_IPS = ('127.0.0.1', '192.168.99.1')
+		DEBUG_TOOLBAR_CONFIG = {'SHOW_TOOLBAR_CALLBACK': lambda request: DEBUG}
+		COMPRESS_ENABLED = False
+		S3_SERVER = {
+        "HOST": "$S3_HOST",
+        "KEY": "$S3_KEY",
+        "SECRET": "$S3_SECRET",
+        "BUCKET": "ebi-rnacentral",
+    }
+		CACHES = {
+        "default": {
+            "BACKEND": "django.core.cache.backends.memcached.MemcachedCache",
+            "LOCATION": "memcached",
+        },
+        "sitemaps": {
+            "BACKEND": "rnacentral.utils.cache.SitemapsCache",
+            "LOCATION": os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__)))), 'rnacentral', 'sitemaps')
+        }
+    }
+		RQ_QUEUES = {
+        "default": {
+            "HOST": "redis",
+            "PORT": 8051,
+            "DB": 0,
+            "DEFAULT_TIMEOUT": 360,
+            "REMOTE_SERVER": None,
+        }
+    }
+		DATABASES = {
+        "default": {
+            "ENGINE": "django.db.backends.postgresql_psycopg2",
+            "NAME": "$DB_NAME",
+            "USER": "$DB_USER",
+            "PASSWORD": "$DB_PASSWORD",
+            "HOST": "$DB_HOST",
+            "PORT": "$DB_PORT",
+        }
+    }
+	EOF
+fi
+
+# Supervisor setup
+if [ -f "${SUPERVISOR_CONF_DIR}"/supervisord.conf ]
+then
+	echo "INFO: Supervisord configuration file already provisioned"
+else
+	echo "INFO: Creating Supervisord configuration file"
+	cat <<-EOF > "${SUPERVISOR_CONF_DIR}"/supervisord.conf
+		[supervisord]
+		pidfile=${SUPERVISOR_CONF_DIR}/supervisord.pid
+		logfile=${LOGS}/supervisord.log
+		user=rnacentral
+		logfile_maxbytes=50MB
+		logfile_backups=2
+		loglevel=info
+		nodaemon=true
+
+		[program:rqworkers]
+		command=python $RNACENTRAL_HOME/manage.py rqworker
+		directory=$RNACENTRAL_HOME/rnacentral
+		numprocs=1
+		process_name=%(program_name)s_%(process_num)s
+		autorestart=true
+		autostart=true
+		stderr_logfile=${LOGS}/rqworkers.err.log
+		stdout_logfile=${LOGS}/rqworkers.out.log
+	EOF
+fi
+
+exec "$@"
\ No newline at end of file