Change docker to deploy using kubernetes

.gitignore

@@ -121,3 +121,6 @@ dump.rdb
 # default location of search export results
 rnacentral/export/results
 .gitsecret/keys/random_seed
+
+# environment variables
+.env

Dockerfile-kubernetes

+#------------------------------------------------------------------------------
+#
+# This Dockerfile is meant for containerized deployment with Kubernetes.
+#
+#-------------------------------------------------------------------------------
+
+FROM debian:latest
+
+RUN apt-get update && apt-get install -y \
+    g++ \
+    build-essential \
+    curl \
+    wget \
+    tar \
+    git \
+    python2.7 \
+    libpython2.7-dev \
+    python-pip \
+    redis-server \
+    memcached
+
+ARG RNACENTRAL_HOME=/srv/rnacentral
+ENV RNACENTRAL_HOME=$RNACENTRAL_HOME
+ENV RNACENTRAL_LOCAL=$RNACENTRAL_HOME/local
+
+RUN mkdir -p $RNACENTRAL_HOME/local
+RUN mkdir $RNACENTRAL_HOME/static
+
+# Install Infernal
+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
+
+# Download RNAcentral
+RUN \
+    cd $RNACENTRAL_HOME && \
+    git clone https://github.com/RNAcentral/rnacentral-webcode.git
+
+# Install Django requirements
+RUN pip install -r $RNACENTRAL_HOME/rnacentral-webcode/rnacentral/requirements.txt
+
+# Install node.js
+RUN curl -sL https://deb.nodesource.com/setup_12.x | bash -
+RUN apt-get install -y nodejs
+
+# Install node.js dependencies
+RUN cd $RNACENTRAL_HOME/rnacentral-webcode/rnacentral/portal/static && npm install --only=production
+
+COPY ./entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+ENTRYPOINT [ "/entrypoint.sh" ]
+
+# Expose a container port where the website is served
+EXPOSE 8000
+
+# Start up the app
+CMD python $RNACENTRAL_HOME/rnacentral-webcode/rnacentral/manage.py runserver 0.0.0.0:8000

docker-compose.yml

@@ -5,8 +5,20 @@ services:
   web:
     build:
       context: .
-      dockerfile: Dockerfile-development
+      dockerfile: Dockerfile-kubernetes
     volumes:
-      - ${RNACENTRAL_HOME}:/rnacentral/rnacentral-webcode
+      - "rnacentral_data:/rnacentral"
+    environment:
+      - DB_HOST=${DB_HOST}
+      - DB_NAME=${DB_NAME}
+      - DB_USER=${DB_USER}
+      - DB_PASSWORD=${DB_PASSWORD}
+      - DB_PORT=${DB_PORT}
+      - SECRET_KEY=${SECRET_KEY}
+    stdin_open: true
+    tty: true
     ports:
       - "9000:8000"
+
+volumes:
+  rnacentral_data:
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entrypoint.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=${SECRET_KEY:-'your_secret_key'}
+
+# Entrypoint variable
+RNACENTRAL_PROJECT_PATH="${RNACENTRAL_HOME}/rnacentral-webcode/rnacentral"
+
+# Add local_settings file
+if [ -f "${RNACENTRAL_PROJECT_PATH}"/rnacentral/local_settings.py ]
+then
+	echo "INFO: RNAcentral local_settings.py file already provisioned"
+else
+	echo "INFO: Creating RNAcentral local_settings.py file"
+	cat <<-EOF > "${RNACENTRAL_PROJECT_PATH}"/rnacentral/local_settings.py
+		from utils import get_environment
+		SECRET_KEY = "$SECRET_KEY"
+		DEBUG = True
+		ENVIRONMENT = get_environment()
+		INTERNAL_IPS = ('127.0.0.1', '192.168.99.1')
+		COMPRESS_ENABLED = False
+		RQ_QUEUES = {
+        "default": {
+            "HOST": "localhost",
+            "PORT": 8051,
+            "DB": 0,
+            "DEFAULT_TIMEOUT": 360,
+            "REMOTE_SERVER": None,
+        }
+    }
+		DATABASES = {
+        "default": {
+            "ENGINE": "django.db.backends.postgresql_psycopg2",
+            "NAME": "$DB_NAME",
+            "USER": "$DB_USER",
+            "PASSWORD": "$DB_PASSWORD",
+            "HOST": "$DB_HOST",
+            "PORT": "$DB_PORT",
+        }
+    }
+	EOF
+	chown -R nobody "${RNACENTRAL_PROJECT_PATH}"/rnacentral/local_settings.py
+fi
+
+exec "$@"
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