documentation on docker

Author: stain

NOTICE.md

@@ -1,13 +1,14 @@
-Copyright 2016 Mark Robinson
+Copyright (c) 2016 Mark Robinson
+Copyright (c) 2016 University of Manchester
 
-Licensed under the Apache License, Version 2.0 (the "License"); 
-you may not use this file except in compliance with the License. 
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
 You may obtain a copy of the License at:
 
 http://www.apache.org/licenses/LICENSE-2.0
 
-Unless required by applicable law or agreed to in writing, software 
-distributed under the License is distributed on an "AS IS" BASIS, 
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or 
-implied. See the License for the specific language governing 
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+implied. See the License for the specific language governing
 permissions and limitations under the License.

README.md

@@ -1,16 +1,90 @@
-## About
+# CWL Viewer
 
-This is a work-in-progress [Spring Boot](http://projects.spring.io/spring-boot/) MVC application which fetches [Common Workflow Language](http://www.commonwl.org/) files from a Github repository and creates a page for it detailing the main workflow and its inputs, outputs and steps
+This is a work-in-progress [Spring Boot](http://projects.spring.io/spring-boot/) MVC application which fetches [Common Workflow Language](http://www.commonwl.org/) files from a Github repository and creates a page for it detailing the main workflow and its inputs, outputs and steps.
+
+## License
+
+Distributed under the [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0).
+See the file [LICENSE.md](LICENSE.md) for details, and
+[NOTICE.md](NOTICE.md) for required attribution notices.
+
+## Contribute
+
+Feel free to contribute! You may [raise an issue](https://github.com/common-workflow-language/cwlviewer/issues),
+provide a [pull request](https://github.com/common-workflow-language/cwlviewer/pulls)
+or join the [gitter chat for common-workflow-language](https://gitter.im/common-workflow-language/common-workflow-language)!
+
+
+## Running with Docker
+
+This application can be started with [Docker](https://www.docker.com/).
+
+If you have [Docker Compose](https://docs.docker.com/compose/install/), then to start
+MongoDB and CWLViewer exposed on port `8080`, run:
+
+    docker-compose up
+
+To stop and remove:
+
+    docker-compose down
+
+If you change the source code, re-build with `docker-compose build`.
+
+See the [docker-compose.yml](docker-compose.yml) file for details.
+
+If you don't want to use Docker Compose, you can do the equivalent manually with `docker`:
+
+    docker build -t cwlviewer .
+    docker run --name cwlviewer-mongo -p 27017:27017 -d mongo
+    docker run --name cwlviewer -p 8080:8080 --link cwlviewer-mongo:mongo -d cwlviewer
+    docker logs -f cwlviewer
+
+## Requirement: MongoDB
+
+You will need to have [MongoDB](https://www.mongodb.com/) running,
+by default on `localhost:27017`.
+
+(You can override this by supplying system properties like
+`-Dspring.data.mongodb.host=mongo` or `-Dspring.data.mongodb.port=1337`)
+
+If you have Docker, but are not using the Docker Compose method above,
+you may start MongoDB with [Docker](https://www.docker.com/) using:
+
+    docker run --name cwlviewer-mongo -p 27017:27017 -d mongo
+
+Note that this exposes mongodb to the world on port `27017`.
 
 
 ## Building and Running
 
+To compile you will need [Java 8](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or OpenJDK 8 (`apt install openjdk-8-jdk`),
+as well as [Apache Maven 3](https://maven.apache.org/download.cgi) (`apt install maven`).
+
 Spring Boot uses an embedded HTTP server. The Spring Boot Maven plugin includes a run goal which can be used to quickly compile and run it:
 
 ```
 $ mvn spring-boot:run
 ```
 
-Alternatively, you can run the application from your IDE as a simple Java application by importing the Maven project
 
-It is also possible to build a war file which is executable and deployable into an external container by [following the instructions here](that is both executable and deployable into an external container)
+Alternatively, you can run the application from your IDE as a simple Java application by importing the Maven project.
+
+You can create an executable JAR file by using:
+
+    mvn clean install
+
+Afterwards, run:
+
+    java -jar target/cwlvisualizer*.jar
+
+(The exact filename will vary per version)
+
+Once CWL Visualizer is running, you should see log output somewhat like:
+
+```
+()..)
+s.b.c.e.t.TomcatEmbeddedServletContainer : Tomcat started on port(s): 8080 (http)
+org.researchobject.CwlViewerApplication  : Started CwlViewerApplication in 28.604 seconds
+```
+
+Now check out http://localhost:8080/ to access CWL Viewer.

src/main/resources/application.properties

@@ -19,4 +19,12 @@ totalFileSizeLimit = 10000000
 # Authentication increases rate limit from 50 requests/hr to 5000 requests/hr
 githubAPI.authentication = false
 githubAPI.username = username
-githubAPI.password = password
+githubAPI.password = password
+
+#=======================
+# MongoDB settings
+#=======================
+spring.data.mongodb.host = localhost
+spring.data.mongodb.port = 27017
+# For complete list of MongoDB properties, see
+# https://github.com/spring-projects/spring-boot/blob/v1.4.2.RELEASE/spring-boot-autoconfigure/src/main/java/org/springframework/boot/autoconfigure/mongo/MongoProperties.java