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‎README.md

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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.
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[![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")
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[![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")
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‎src/main/java/org/commonwl/view/graphviz/DotWriter.java

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@@ -193,6 +193,16 @@ private void writeSteps(Workflow workflow) throws IOException {
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}
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}
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}
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// Workaround to force outputs to lowest ranking, see #104
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writeLine("");
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writeLine(" // Invisible links to force outputs to be at lowest rank");
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for (Map.Entry<String, CWLStep> step : workflow.getSteps().entrySet()) {
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writeLine(" \"" + step.getKey() + "\" -> \"" +
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workflow.getOutputs().keySet().iterator().next() +
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"\" [style=invis];");
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}
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}
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/**

‎src/main/java/org/commonwl/view/workflow/WorkflowService.java

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if (workflow != null) {
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// Delete the existing workflow if the cache has expired
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if (cacheExpired(workflow)) {
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// Update by trying to add a new workflow
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removeWorkflow(workflow);
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// Add the new workflow if it exists
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Workflow newWorkflow = createWorkflow(workflow.getRetrievedFrom());
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// Only replace workflow if it could be successfully parsed
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if (newWorkflow == null) {
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// Add back the old workflow if it is broken now
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logger.error("Could not parse updated workflow " + workflow.getID());
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workflowRepository.save(workflow);
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} else {
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// Delete the existing workflow
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removeWorkflow(workflow);
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// Save new workflow
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workflowRepository.save(newWorkflow);
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workflow = newWorkflow;
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}
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}

‎src/main/resources/static/css/main-20170613.css

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/*
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* Licensed to the Apache Software Foundation (ASF) under one
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* or more contributor license agreements. See the NOTICE file
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* distributed with this work for additional information
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* regarding copyright ownership. The ASF licenses this file
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* to you under the Apache License, Version 2.0 (the
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* "License"); you may not use this file except in compliance
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* with the License. You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing,
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* software distributed under the License is distributed on an
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* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
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* KIND, either express or implied. See the License for the
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* specific language governing permissions and limitations
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* under the License.
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*/
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body {
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padding-top: 61px;
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}
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.hide {
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display: none;
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}
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:target {
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padding-top: 61px;
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margin-top: -61px;
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}
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.alert-grey {
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color: #7d7d7d;
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background-color: #f8f8f8;
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}
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#logo {
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height: 61px;
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padding: 5px;
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}
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#explore {
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padding-top: 20px;
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}
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#githubURL {
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background: url("/img/GitHub-Mark-32px.png") no-repeat scroll 7px 4px;
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background-size: 25px 25px;
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padding-left: 45px;
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}
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#githubLogo {
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margin-right: 5px;
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}
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#dockerLogo {
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height: 75px;
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margin-left: 10px;
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}
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.logos {
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margin-top: 1em;
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}
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.logos img {
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height: 3em;
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align: top;
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margin-left: 1em;
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margin-right: 1em;
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}
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.graphControl {
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position: absolute;
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top: 10px;
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right: 25px;
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cursor: pointer;
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font-size: 25px;
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opacity: 0.333;
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}
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.graphControl:hover {
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opacity: 1;
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}
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#fullscreen-close {
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top: 25px;
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}
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#selectChildren, #selectParents {
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top: 8px;
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width: 30px;
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height: 35px;
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}
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#selectChildren {
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left: 25px;
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}
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#selectParents {
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left: 62px;
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height: 32px;
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width: 50px;
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}
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#fullScreenGraphModal .modal-dialog {
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width: 98%;
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height: 92%;
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padding: 0;
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}
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#fullScreenGraphModal .modal-body {
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width: 100%;
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height: 100%;
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}
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#fullScreenGraphModal .modal-content {
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height: 99%;
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}
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#graphFullscreen {
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background-color: #eeeeee;
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width: 100%;
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height: 90%;
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}
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#graph-menu {
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margin-bottom: 5px;
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}
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.icon-view {
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font-size: 20px;
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}
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.workflow-thumb {
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width:100%;
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max-height:300px;
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}
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#visualisation {
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overflow: hidden;
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padding: 0;
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height: 500px;
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}
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@media (max-width: 767px) {
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#visualisation {
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height: 300px;
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}
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}
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#graph {
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width: 100%;
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height: 100%;
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}
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#graph svg text {
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cursor: default;
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-webkit-user-select: none;
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-moz-user-select: none;
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-ms-user-select: none;
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user-select: none;
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}
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#graph svg text::selection {
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background: none;
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}
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#download-gv {
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margin-bottom: 5px;
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}
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#dot {
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margin-top: 5px;
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margin-bottom: 10px;
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}
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#modalTitle {
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margin-top: 0;
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}
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.notFound {
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color: #c30000;
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}
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tr.selected, .table-hover tbody tr.selected:hover td, .table-hover tbody tr.selected:hover th {
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background-color: #b9ffbb !important;
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}
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tr.hover, .table-hover tbody tr:hover td, .table-hover tbody tr:hover th {
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background-color: #c9ffcb !important;
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}
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polygon.selected, polygon.hover.selected {
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fill: #b9ffbb;
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}
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polygon.hover {
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fill: #c9ffcb;
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}
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#footer {
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text-align: center;
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font-style: italic;
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margin-bottom: 30px;
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}

‎src/main/resources/templates/fragments/header.html

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<nav th:fragment="navbar" class="navbar navbar-default navbar-fixed-top">
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<div class="container">
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<div class="navbar-header">
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<a class="navbar-brand" href="/">
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<a href="/" class="navbar-left">
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<img id="logo" src="/img/CWL-Logo-nofonts.svg"></img>
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</a>
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<a href="/workflows" class="button navbar-toggle">Explore</a>
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</div>
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<div class="collapse navbar-collapse">
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<ul class="nav navbar-nav navbar-right">
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<li><a href="/workflows">Explore</a></li>
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<li><a id="explore" href="/workflows">Explore</a></li>
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</ul>
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</div>
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</div>

‎src/test/resources/graphviz/testWorkflow.dot

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"input2" -> "step1";
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"default1" [label="examplefile.jar", fillcolor="#D5AEFC"]
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"default1" -> "step1";
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// Invisible links to force outputs to be at lowest rank
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"default1" -> "output" [style=invis];
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"step2" -> "output" [style=invis];
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"step1" -> "output" [style=invis];
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}

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