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Render Web Services

The Render Web Services module provides level 2 REST APIs to persisted collections of tile and transform specifications (see data model). The Render Web Services API documentation identifies the specific supported APIs.

Deployment Architecture

The Render Web Services module is packaged as a Java web application archive (war file) deployed on a Jetty web server/container. It connects to a MongoDB database where tile and transform specifications are persisted (see data model).

The web server and database components can be run on the same machine for small scale processing or evaluation purposes. For large scale processing needs, each component should be deployed on separate machines that are tuned for their specific purpose.

Basic Installation

These installation instructions cover setup of an evaluation instance with a collocated web server and database running on Ubuntu 16.04.

Note: In lieu of running these steps manually, you may prefer to use a Docker deployment instead.

1. Install Git and Maven

sudo apt-get install -y git maven

2. Clone the Repository

git clone https://github.com/saalfeldlab/render.git

3. Install JDK and Jetty

# assumes cloned render repository is in ./render
cd ./render
./render-ws/src/main/scripts/install.sh

4. Build the Render Modules

# assumes current directory is still the cloned render repository root (./render)
export JAVA_HOME=`readlink -m ./deploy/jdk*`
mvn package

5. Deploy Web Service

# assumes current directory is still the cloned render repository root (./render)
cp render-ws/target/render-ws-*.war deploy/jetty_base/webapps/render-ws.war

6. Install MongoDB 3.2

These instructions were taken from https://docs.mongodb.com/v3.2/tutorial/install-mongodb-on-ubuntu/

# import MongoDB public GPG key
sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv EA312927

# create a list file for MongoDB
echo "deb http://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/3.2 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.2.list

# reload local package database
sudo apt-get update

# install default MongoDB (2.6) packages
# NOTE: This step is not documented on the MongoDB web site, but for some reason is required to avoid "mongod: unrecognized service" errors later
#       See https://github.com/Microsoft/WSL/issues/1822 for details
sudo apt-get install -y mongodb

# install MongoDB packages (this should also start the mongod process)
sudo apt-get install -y mongodb-org=3.2.18 mongodb-org-server=3.2.18 mongodb-org-shell=3.2.18 mongodb-org-mongos=3.2.18 mongodb-org-tools=3.2.18

# Pin specific version of MongoDB
echo "mongodb-org hold" | sudo dpkg --set-selections
echo "mongodb-org-server hold" | sudo dpkg --set-selections
echo "mongodb-org-shell hold" | sudo dpkg --set-selections
echo "mongodb-org-mongos hold" | sudo dpkg --set-selections
echo "mongodb-org-tools hold" | sudo dpkg --set-selections

# Create systemd service file
# NOTE: This file has to be named mongodb.service (instead of mongod.service) for some reason
sudo echo """
[Unit]
Description=High-performance, schema-free document-oriented database
After=network.target
Documentation=https://docs.mongodb.org/manual

[Service]
User=mongodb
Group=mongodb
ExecStart=/usr/bin/mongod --quiet --config /etc/mongod.conf

[Install]
WantedBy=multi-user.target
""" > /lib/systemd/system/mongodb.service

7. Start MongoDB

# NOTE: The service has to be mongodb (instead of mongod) for some reason.
sudo service mongodb start

8. Start Jetty

# assumes current directory is still the cloned render repository root (./render)
deploy/jetty_base/jetty_wrapper.sh start

Using the Installation

The Render Web Services Example workflow steps demonstrate how this installation can be used for a small example project.