Merge branch 'nested-workflows'

# Conflicts:
#	src/main/java/org/commonwl/view/researchobject/ROBundleService.java

Author: Mark Robinson

.travis.yml

@@ -4,3 +4,7 @@ dist: trusty
 language: java
 
 services: mongodb
+
+before_install:
+  - sudo apt-get -qq update
+  - sudo apt-get install graphviz

Dockerfile

@@ -29,7 +29,7 @@ ADD pom.xml LICENSE.md NOTICE.md README.md /usr/src/app/
 # add src/ (which often change)
 ADD src /usr/src/app/src
 # Skip tests while building as that requires a local mongodb
-RUN mvn clean package -DskipTests && cp target/cwlvisualiser-*.jar /usr/lib/cwlvisualizer.jar && rm -rf target
+RUN mvn clean package -DskipTests && cp target/cwlviewer-*.jar /usr/lib/cwlviewer.jar && rm -rf target
 
 # NOTE: ~/.m2/repository is a VOLUME and so will be deleted anyway
 # This also means that every docker build downloads all of it..
@@ -41,4 +41,4 @@ EXPOSE 8080
 # Expects mongodb on port 27017
 ENV SPRING_DATA_MONGODB_HOST=mongo
 ENV SPRING_DATA_MONGODB_PORT=27017
-CMD ["/usr/bin/java", "-jar", "/usr/lib/cwlvisualizer.jar"]
+CMD ["/usr/bin/java", "-jar", "/usr/lib/cwlviewer.jar"]

README.md

@@ -98,6 +98,19 @@ If you run cwlviewer in production, you are likely to hit the GitHub API's rate
 
 OAuth tokens can be obtained using the [Github authorizations API](https://developer.github.com/v3/oauth_authorizations/).
 
+## Private Repositories
+
+If you wish to use cwlviewer to view private Github repositories, set
+
+```
+githubAPI.useForDownloads = true
+singleFileSizeLimit = 1048575
+```
+
+Along with an authentication method which has the privileges necessary to access the repository (see above).
+
+**WARNING**: This uses the [Github Contents API](https://developer.github.com/v3/repos/contents/) to download files instead of [Rawgit](https://rawgit.com/) which will increase API calls significantly.
+
 ## 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`),
@@ -118,11 +131,11 @@ You can create an executable JAR file by using:
 
 Afterwards, run:
 
-    java -jar target/cwlvisualizer*.jar
+    java -jar target/cwlviewer*.jar
 
 (The exact filename will vary per version)
 
-Once CWL Visualizer is running, you should see log output somewhat like:
+Once CWL Viewer is running, you should see log output somewhat like:
 
 ```
 ()..)

pom.xml

@@ -3,13 +3,13 @@
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
-	<groupId>org.commonwl</groupId>
-	<artifactId>cwlvisualiser</artifactId>
+	<groupId>org.commonwl.view</groupId>
+	<artifactId>cwlviewer</artifactId>
 	<version>0.0.1-SNAPSHOT</version>
 	<packaging>jar</packaging>
 
-	<name>CWLVisualiser</name>
-	<description>Gets a workflow from Github and displays details of it</description>
+	<name>CWLViewer</name>
+	<description>Web application to visualise and enable easy sharing of Common Workflow Language workflows</description>
 
 	<parent>
 		<groupId>org.springframework.boot</groupId>

…ommonwl/viewer/CwlViewerApplication.java …/commonwl/view/CwlViewerApplication.javasrc/main/java/org/commonwl/viewer/CwlViewerApplication.java renamed to src/main/java/org/commonwl/view/CwlViewerApplication.java src/main/java/org/commonwl/viewer/CwlViewerApplication.java renamed to src/main/java/org/commonwl/view/CwlViewerApplication.java

@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer;
+package org.commonwl.view;
 
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;

…ava/org/commonwl/viewer/MongoConfig.java …/java/org/commonwl/view/MongoConfig.javasrc/main/java/org/commonwl/viewer/MongoConfig.java renamed to src/main/java/org/commonwl/view/MongoConfig.java src/main/java/org/commonwl/viewer/MongoConfig.java renamed to src/main/java/org/commonwl/view/MongoConfig.java

@@ -17,9 +17,9 @@
  * under the License.
  */
 
-package org.commonwl.viewer.web;
+package org.commonwl.view;
 
-import org.commonwl.viewer.domain.WorkflowForm;
+import org.commonwl.view.workflow.WorkflowForm;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.GetMapping;

…/commonwl/viewer/web/PageController.java …va/org/commonwl/view/PageController.javasrc/main/java/org/commonwl/viewer/web/PageController.java renamed to src/main/java/org/commonwl/view/PageController.java src/main/java/org/commonwl/viewer/web/PageController.java renamed to src/main/java/org/commonwl/view/PageController.java

@@ -17,7 +17,7 @@
  * under the License.
  */
 
-package org.commonwl.viewer.domain;
+package org.commonwl.view.cwl;
 
 import java.util.ArrayList;
 import java.util.List;

…g/commonwl/viewer/domain/CWLElement.java …va/org/commonwl/view/cwl/CWLElement.javasrc/main/java/org/commonwl/viewer/domain/CWLElement.java renamed to src/main/java/org/commonwl/view/cwl/CWLElement.java src/main/java/org/commonwl/viewer/domain/CWLElement.java renamed to src/main/java/org/commonwl/view/cwl/CWLElement.java

@@ -0,0 +1,35 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 permissions and limitations
+ * under the License.
+ */
+
+package org.commonwl.view.cwl;
+
+/**
+ * Enum for possible CWL processes
+ */
+public enum CWLProcess {
+    WORKFLOW,
+    COMMANDLINETOOL,
+    EXPRESSIONTOOL;
+
+    @Override
+    public String toString() {
+        String defaultString = super.toString();
+        return defaultString.substring(0, 1) + defaultString.substring(1).toLowerCase();
+    }
+}