Added Docker configuration files and updated readme

Author: Rinke Hoekstra

.dockerignore

@@ -0,0 +1 @@
+.git

Dockerfile.guidelines

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+FROM python:2.7.13-wheezy
+
+MAINTAINER rinke.hoekstra@vu.nl
+
+ENV GUIDELINES_APP="/usr/local/guidelines"
+
+COPY ./requirements.txt /requirements.txt
+RUN pip install -r requirements.txt
+
+COPY ./src ${GUIDELINES_APP}
+
+COPY entrypoint.sh /sbin/entrypoint.sh
+RUN chmod 755 /sbin/entrypoint.sh
+
+WORKDIR ${GUIDELINES_APP}
+ENTRYPOINT ["/sbin/entrypoint.sh"]
+CMD ["app:start"]
+EXPOSE 5000

Dockerfile.stardog

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+FROM java:8-jre-alpine
+
+ENV STARDOG_VERSION 4.1.2
+
+ENV STARDOG_HOME /data
+ENV STARDOG_INSTALL_DIR /opt/stardog
+
+ENV STARDOG_START_PARAMS ""
+ENV STARDOG_DB_NAME guidelines
+ENV STARDOG_CREATE_PARAMS "-n ${STARDOG_DB_NAME} -v -o versioning.enabled=true preserve.bnode.ids=false strict.parsing=false --"
+ENV STARDOG_JAVA_ARGS "-Xms2g -Xmx2g -XX:MaxDirectMemorySize=2g"
+ENV PATH ${STARDOG_INSTALL_DIR}/bin:${PATH}
+
+RUN mkdir -p ${STARDOG_HOME}
+RUN mkdir -p ${STARDOG_INSTALL_DIR}
+
+WORKDIR ${STARDOG_INSTALL_DIR}
+
+RUN apk update
+RUN apk add unzip bash
+
+ADD stardog-*.zip /tmp
+RUN unzip -d /tmp /tmp/stardog-*.zip
+RUN rm -f /tmp/stardog-*.zip
+RUN cp -r /tmp/stardog-*/* ${STARDOG_INSTALL_DIR}/
+RUN rm -rf /tmp/stardog-*
+
+ADD stardog-license-key.bin ${STARDOG_INSTALL_DIR}
+ADD stardog.properties ${STARDOG_INSTALL_DIR}
+ADD start-stardog-service.sh ${STARDOG_INSTALL_DIR}
+RUN chmod +x ${STARDOG_INSTALL_DIR}/start-stardog-service.sh
+
+WORKDIR ${STARDOG_HOME}
+
+CMD ${STARDOG_INSTALL_DIR}/start-stardog-service.sh
+
+EXPOSE 5820

docker-compose.yml

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+version: '3'
+services:
+  guidelines:
+    build:
+      context: .
+      dockerfile: Dockerfile.guidelines
+    ports:
+      - "127.0.0.1:5000:5000"
+    environment:
+      - ENDPOINT_URL=http://stardog:5820/guidelines/query
+      - UPDATE_URL=http://stardog:5820/guidelines/update
+  stardog:
+    build:
+      context: .
+      dockerfile: Dockerfile.stardog
+    environment:
+      - STARDOG_START_PARAMS=--disable-security
+    volumes:
+      - ./src/data/:/var/data
+    ports:
+      - "127.0.0.1:5820:5820"

entrypoint.sh

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+#!/bin/bash
+set -e #exit on errors
+
+#print statements as they are executed
+[[ -n $DEBUG_ENTRYPOINT ]] && set -x
+
+case ${1} in
+  app:start)
+    python run.py
+    ;;
+  app:help)
+    echo "Available options:"
+    echo " app:start        - Starts TMR4i Guidelines Explorer (default)"
+    echo " [command]        - Execute the specified command, eg. /bin/bash."
+    ;;
+  *)
+    exec "$@"
+    ;;
+esac
+
+exit 0

readme.md

@@ -1,14 +1,38 @@
 # Guidelines Demo
 
-This web application can show off the coolness of the TMR and TMR4I ontologies developed by Veruska Zamborlini in detecting interactions between the recommendations of medical guidelines
+This web application can show off the coolness of the TMR and TMR4I ontologies developed by Veruska Zamborlini in detecting interactions between the recommendations of medical guidelines.
 
-## Setup
+This repository also contains the `metis` application that runs with Swish. You can find a separate readme file in that directory. 
+
+## Setup (using Docker)
+
+* Make sure you have docker installed on your system (<http://docker.com>)
+* Open up a terminal window and clone or download this repository to a location of your choice:
+
+```
+git clone https://github.com/Data2Semantics/guidelines.git
+```
+* Change into the `guidelines` directory
+* Download the latest version of Stardog from <https://stardog.com>
+* Copy the zipfile for the latest version of Stardog into this directory (e.g. `stardog-5.0-beta.zip`).
+* Also copy the `stardog-license-key.bin` file into this directory
+* From the command line run `docker-compose build` to create the Docker images
+
+### Starting (using Docker)
+
+* Change into the `guidelines` directory and run `docker-compose up`
+* Go to `http://localhost:5000` and have fun!
+
+## Setup (from source)
 
 * Make sure you have `pip` and `virtualenv` installed (`easy_install pip`, `pip install virtualenv`)
 * Go to the directory in which you cloned this Git repository, and install a virtual environment: `virtualenv .`
 * Activate the virtual environment: `source bin/activate`
 * Install the required packages: `pip install -r requirements.txt`
 * Make sure you have a properly installed Stardog server running, with **security disabled** (`stardog-admin server start --disable-security`)
 * Go to the `src` directory, and run `create-stardog.sh` and then `reset-stardog.sh`
+
+### Starting (from source)
+
 * Inside the `src` directory, run `python run.py`
-* Go to `http://localhost:5000` and have fun!
+* Go to `http://localhost:5000` and have fun!