Merge branch 'master' into highlighting

# Conflicts:
#	src/main/resources/static/js/workflow.js

Author: Mark Robinson

.gitignore

@@ -19,4 +19,4 @@ nbproject/private/
 build/
 nbbuild/
 nbdist/
-.nb-gradle/
+.nb-gradle/docker-compose.override.yml

Dockerfile

@@ -1,7 +1,22 @@
 FROM maven:3.3-jdk-8-alpine
 MAINTAINER Stian Soiland-Reyes <[email protected]>
 
-RUN apk add --update graphviz && rm -rf /var/cache/apk/*
+# Build-time metadata as defined at http://label-schema.org
+ARG BUILD_DATE
+ARG VCS_REF
+ARG VERSION
+LABEL org.label-schema.build-date=$BUILD_DATE \
+  org.label-schema.name="CWL Viewer" \
+  org.label-schema.description="Viewer of Common Workflow Language" \
+  org.label-schema.url="https://view.commonwl.org/" \
+  org.label-schema.vcs-ref=$VCS_REF \
+  org.label-schema.vcs-url="https://github.com/common-workflow-language/cwlviewer" \
+  org.label-schema.vendor="Common Workflow Language project" \
+  org.label-schema.version=$VERSION \
+  org.label-schema.schema-version="1.0"
+
+
+RUN apk add --update graphviz ttf-freefont && rm -rf /var/cache/apk/*
 
 RUN mkdir /usr/share/maven/ref/repository
 
@@ -24,4 +39,6 @@ WORKDIR /tmp
 EXPOSE 8080
 
 # Expects mongodb on port 27017
-CMD ["/usr/bin/java", "-Dspring.data.mongodb.host=mongo", "-jar", "/usr/lib/cwlvisualizer.jar"]
+ENV SPRING_DATA_MONGODB_HOST=mongo
+ENV SPRING_DATA_MONGODB_PORT=27017
+CMD ["/usr/bin/java", "-jar", "/usr/lib/cwlvisualizer.jar"]

LICENSE.md

@@ -212,3 +212,11 @@ been federally registered with the United States Copyright Office.
 All rights reserved.
 
 Use rules apply: https://github.com/logos
+
+---------------------------------------------------------
+
+./src/main/resources/static/img/Docker-logo.png
+
+Copyright 2013-2015 Docker, Inc. All rights reserved.
+
+Use rules apply: https://www.docker.com/brand-guidelines

README.md

@@ -2,7 +2,7 @@
 
 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.
 
-[![Build Status](https://travis-ci.org/common-workflow-language/cwlviewer.svg?branch=master)](https://travis-ci.org/common-workflow-language/cwlviewer) [![Gitter](https://img.shields.io/gitter/room/gitterHQ/gitter.svg)](https://gitter.im/common-workflow-language/common-workflow-language?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![](https://images.microbadger.com/badges/image/commonworkflowlanguage/cwlviewer.svg)](https://microbadger.com/images/commonworkflowlanguage/cwlviewer "Get your own image badge on microbadger.com") [![Docker image commonworkflowlanguage/cwlviewer](https://images.microbadger.com/badges/version/commonworkflowlanguage/cwlviewer.svg)](https://hub.docker.com/r/commonworkflowlanguage/cwlviewer/ "Get your own version badge on microbadger.com")
+[![Build Status](https://travis-ci.org/common-workflow-language/cwlviewer.svg?branch=master)](https://travis-ci.org/common-workflow-language/cwlviewer) [![Gitter](https://img.shields.io/gitter/room/gitterHQ/gitter.svg)](https://gitter.im/common-workflow-language/common-workflow-language?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![](https://images.microbadger.com/badges/image/commonworkflowlanguage/cwlviewer.svg)](https://microbadger.com/images/commonworkflowlanguage/cwlviewer "MicroBadger commonworkflowlanguage/cwlviewer") [![Docker image commonworkflowlanguage/cwlviewer](https://images.microbadger.com/badges/version/commonworkflowlanguage/cwlviewer.svg)](https://hub.docker.com/r/commonworkflowlanguage/cwlviewer/ "Docker Hub commonworkflowlanguage/cwlviewer")
 
 
 
@@ -32,7 +32,16 @@ To stop and remove:
 
     docker-compose down
 
-If you change the source code, re-build with `docker-compose build`.
+If you change the source code, then use this `docker-compose.override.yml` and 
+re-build with `docker-compose build`:
+
+```yaml
+version: '2'
+services:
+  spring:
+    build: .
+```
+
 
 See the [docker-compose.yml](docker-compose.yml) file for details.
 
@@ -53,16 +62,41 @@ If you have modified the source code, then you may want to build the docker imag
 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 are running from the command line, you can override this by supplying
+system properties like `-Dspring.data.mongodb.host=mongo.example.org` and
+`-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`.
+**WARNING**: The above expose mongodb to the world on port `27017`.
+
+## Configuration
+
+There are a variety of configuration options detailed in the [application configuration file](https://github.com/common-workflow-language/cwlviewer/blob/master/src/main/resources/application.properties) which can be adjusted.
+
+When deploying with docker, these can be overriden externally by creating/modifying `docker-compose.override.yml` as follows:
+
+```yaml
+version: '2'
+services:
+  spring:
+    environment:
+            githubAPI.authentication: oauth
+            githubAPI.oauthToken: abcdefghhijklmnopqrstuvwxyz
+```
+
+The properties can alternatively be provided as system properties on the
+command line, e.g. `-DgithubAPI.authentication=oauth`
+`-DgithubAPI.oauthToken=abcdefghhijklmnopqrstuvwxyz` or via a [variety of other methods supported by Spring Boot](https://docs.spring.io/spring-boot/docs/current/reference/html/boot-features-external-config.html)
+
+### Github API
+
+If you run cwlviewer in production, you are likely to hit the GitHub API's rate limit of 60 requests/hr. This can be increased to 5000 requests/hr by using authentication (either basic or OAuth) by setting the `githubAPI.authentication` and either `githubAPI.oauthToken` or both `githubAPI.username` and `githubAPI.password` in the [application configuration file](https://github.com/common-workflow-language/cwlviewer/blob/master/src/main/resources/application.properties) depending on the method.
 
+OAuth tokens can be obtained using the [Github authorizations API](https://developer.github.com/v3/oauth_authorizations/).
 
 ## Building and Running
 

pom.xml

@@ -29,6 +29,14 @@
             <id>jitpack.io</id>
             <url>https://jitpack.io</url>
         </repository>
+        <repository>
+            <id>apache.snapshots</id>
+            <name>Apache Snapshot Repository</name>
+            <url>http://repository.apache.org/snapshots</url>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+        </repository>
     </repositories>
 
 	<dependencies>
@@ -72,7 +80,7 @@
         <dependency>
             <groupId>org.apache.taverna.language</groupId>
             <artifactId>taverna-robundle</artifactId>
-            <version>0.15.1-incubating</version>
+            <version>0.16.0-incubating-SNAPSHOT</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -90,6 +98,5 @@
 			</plugin>
 		</plugins>
 	</build>
-
-
+    
 </project>