Merge branch 'master' into hotfix-git-checkout

Author: stain

README.md

@@ -1,6 +1,6 @@
 # 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 [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/cwlviewer?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")
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.823534.svg)](https://doi.org/10.5281/zenodo.823534)
@@ -17,14 +17,14 @@ See the file [LICENSE.md](LICENSE.md) for details, and
 
 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)!
+or join the [gitter chat for cwlviewer](https://gitter.im/common-workflow-language/cwlviewer)!
 
 
 ## Recommended - Running with Docker
 
-This application can be started with [Docker](https://www.docker.com/).
+This application can be started with [Docker](https://www.docker.com/) and [Docker Compose](https://docs.docker.com/compose/install/).
 
-If you have [Docker Compose](https://docs.docker.com/compose/install/), then to start CWLViewer exposed on port `8080`, run:
+To start CWLViewer exposed on port `8080`, run:
 
     docker-compose up
 
@@ -36,24 +36,14 @@ If you change the source code, then use this `docker-compose.override.yml` and
 re-build with `docker-compose build`:
 
 ```yaml
-version: '2'
+version: '3.2'
 services:
   spring:
     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`
-and the [commonworkflowlanguage/cwlviewer](https://hub.docker.com/r/commonworkflowlanguage/cwlviewer/builds/) docker image.
-
-    docker run --name cwlviewer-mongo -p 27017:27017 -d mongo
-    docker run --name cwlviewer -p 8080:8080 --link cwlviewer-mongo:mongo -d commonworkflowlanguage/cwlviewer
-    docker logs -f cwlviewer
-    
-    
-**WARNING**: Please ensure that your MongoDB installation is not exposed to the world on port `27017`
-
 If you have modified the source code, then you may want to build the docker image locally first:
 
     docker build -t commonworkflowlanguage/cwlviewer .
@@ -117,17 +107,17 @@ There are a variety of configuration options detailed in the [application config
 When deploying with docker, these can be overriden externally by creating/modifying `docker-compose.override.yml` as follows:
 
 ```yaml
-version: '2'
+version: '3.2'
 services:
   spring:
     environment:
-            githubAPI.authentication: oauth
-            githubAPI.oauthToken: abcdefghhijklmnopqrstuvwxyz
+            applicationName: Common Workflow Language Viewer
+            applicationURL: https://view.commonwl.org
+            cacheDays: 1
 ```
 
 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)
+command line, e.g. `-DcacheDays=1` 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)
 
 # Thanks
 

docker-compose.yml

@@ -1,27 +1,53 @@
-version: '2'
+version: '3.2'
+volumes:
+  bundle:
+  git:
+  graphviz:
+  mongo:
+  sparql:
 services:
   spring:
     # To run from this source code instead of Docker hub,
     # disable "image:"" and enable "build:" below
-    image: commonworkflowlanguage/cwlviewer    
+    image: commonworkflowlanguage/cwlviewer:v1.1.0
     #build: .
     ports:
      - "8080:8080"
     links:
      - mongo
      - sparql
+    volumes:
+     - type: volume
+       source: bundle
+       target: /data/bundle
+     - type: volume
+       source: git
+       target: /data/git
+     - type: volume
+       source: graphviz
+       target: /data/graphviz
     environment:
      - SPARQL_ENDPOINT=http://sparql:3030/cwlviewer/
      - SPRING_DATA_MONGODB_HOST=mongo
      - SPRING_DATA_MONGODB_PORT=27017
+     - BUNDLESTORAGE=/data/bundle
+     - GITSTORAGE=/data/git
+     - GRAPHVIZSTORAGE=/data/graphviz
   mongo:
-    image: mongo
+    image: mongo:3.4
+    volumes:
+      - type: volume
+        source: mongo
+        target: /data/db
   sparql:
 ## For debugging, expose the Fuseki port by enabling:
 #    ports:
 #     - "3030:3030"
 ## To find the admin password, try:
 ##   docker-compose exec sparql grep admin /fuseki/shiro.ini
-    image: stain/jena-fuseki
-    # FIXME: --loc=/fuseki/databases/cwlviewer fails as it needs empty dir
-    command: "/jena-fuseki/fuseki-server --loc=/fuseki/databases /cwlviewer"
+    image: stain/jena-fuseki:3.4.0
+    volumes:
+    - type: volume
+      source: sparql
+      target: /fuseki/databases
+    command: "/jena-fuseki/fuseki-server --loc=/fuseki/databases/cwlviewer /cwlviewer"

src/main/resources/templates/index.html

@@ -53,8 +53,7 @@ <h2>Workflow URL</h2>
                         <strong>Don't know what to view?</strong> Try these from <i>common-workflow-language/workflows</i>:
                         <a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/compile/compile1.cwl">compile</a>,
                         <a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/make-to-cwl/dna.cwl">make-to-cwl</a>,
-                        <a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/lobSTR/lobSTR-workflow.cwl">lobSTR</a>,
-                        <a class="example" href="https://github.com/common-workflow-language/workflows/tree/master/workflows/scidap/bam-genomecov-bigwig-rna-dutp.cwl">scidap</a>
+                        <a class="example" href="https://github.com/common-workflow-language/workflows/tree/lobstr-v1/workflows/lobSTR/lobSTR-workflow.cwl">lobSTR</a>
                         or <a href="/workflows">explore the collection</a>
                     </div>
                     <form id="add" action="#" th:action="@{/workflows}" th:object="${workflowForm}" method="POST">