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MarkRobboMarkRobbo
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Merge pull request #20 from common-workflow-language/visualisation
Visualisation
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‎src/main/java/org/commonwl/viewer/domain/CWLCollection.java

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -132,7 +132,8 @@ private void findMainWorkflow() {
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// TODO: Consider relationship between run: parameters to better discover this
133133
for (int i=0; i < cwlDocs.size(); i++) {
134134
if (cwlDocs.get(i).get("class").asText().equals("Workflow")) {
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mainWorkflowIndex = i;
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mainWorkflowIndex = 0;
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return;
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}
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}
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}

‎src/main/java/org/commonwl/viewer/domain/Workflow.java

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Original file line numberDiff line numberDiff line change
@@ -19,9 +19,14 @@
1919

2020
package org.commonwl.viewer.domain;
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22+
import org.commonwl.viewer.services.DotWriter;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
2225
import org.springframework.data.annotation.Id;
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import org.springframework.format.annotation.DateTimeFormat;
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import java.io.IOException;
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import java.io.StringWriter;
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import java.nio.file.Path;
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import java.util.Date;
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import java.util.Map;
@@ -31,6 +36,8 @@
3136
*/
3237
public class Workflow {
3338

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static private final Logger logger = LoggerFactory.getLogger(Workflow.class);
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// ID for database
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@Id
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private String id;
@@ -47,11 +54,24 @@ public class Workflow {
4754
private Map<String, CWLElement> inputs;
4855
private Map<String, CWLElement> outputs;
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// DOT graph of the contents
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private String dotGraph = "test";
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5060
public Workflow(String label, String doc, Map<String, CWLElement> inputs, Map<String, CWLElement> outputs) {
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this.label = label;
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this.doc = doc;
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this.inputs = inputs;
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this.outputs = outputs;
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// Create a DOT graph for this workflow and store it
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StringWriter graphWriter = new StringWriter();
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DotWriter dotWriter = new DotWriter(graphWriter);
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try {
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dotWriter.writeGraph(this);
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this.dotGraph = graphWriter.toString();
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} catch (IOException ex) {
73+
logger.error("Failed to create DOT graph for workflow: " + ex.getMessage());
74+
}
5575
}
5676

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@Override
@@ -122,4 +142,12 @@ public Date getRetrievedOn() {
122142
public void setRetrievedOn(Date retrievedOn) {
123143
this.retrievedOn = retrievedOn;
124144
}
145+
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public String getDotGraph() {
147+
return dotGraph;
148+
}
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public void setDotGraph(String dotGraph) {
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this.dotGraph = dotGraph;
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}
125153
}

‎src/main/java/org/commonwl/viewer/services/DotWriter.java

Lines changed: 175 additions & 0 deletions
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@@ -0,0 +1,175 @@
1+
/*
2+
* Licensed to the Apache Software Foundation (ASF) under one
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* or more contributor license agreements. See the NOTICE file
4+
* 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
8+
* 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
14+
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
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* KIND, either express or implied. See the License for the
16+
* specific language governing permissions and limitations
17+
* under the License.
18+
*/
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20+
package org.commonwl.viewer.services;
21+
22+
import org.commonwl.viewer.domain.CWLElement;
23+
import org.commonwl.viewer.domain.Workflow;
24+
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import java.io.IOException;
26+
import java.io.Writer;
27+
import java.util.ArrayList;
28+
import java.util.List;
29+
import java.util.Map;
30+
31+
/**
32+
* Writes GraphViz DOT files from Workflows
33+
*/
34+
public class DotWriter {
35+
36+
private static final String EOL = System.getProperty("line.separator");
37+
private Writer writer;
38+
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public DotWriter(Writer writer) {
40+
this.writer = writer;
41+
}
42+
43+
/**
44+
* Write a graph representing a workflow to the Writer
45+
* @param workflow The workflow to be graphed
46+
* @throws IOException Any errors in writing which may have occurred
47+
*/
48+
public void writeGraph(Workflow workflow) throws IOException {
49+
50+
/**
51+
* DOT graph styling is based on the Apache
52+
* Taverna workflow management system
53+
*/
54+
// Begin graph
55+
writeLine("digraph workflow {");
56+
57+
// Overall graph style
58+
writeLine(" graph [");
59+
writeLine(" bgcolor = \"#EEEEEE\"");
60+
writeLine(" color = \"black\"");
61+
writeLine(" fontsize = \"10\"");
62+
writeLine(" labeljust = \"left\"");
63+
writeLine(" clusterrank = \"local\"");
64+
writeLine(" ranksep = \"0.22\"");
65+
writeLine(" nodesep = \"0.05\"");
66+
writeLine(" ]");
67+
68+
// Overall node style
69+
writeLine(" node [");
70+
writeLine(" fontname = \"Helvetica\"");
71+
writeLine(" fontsize = \"10\"");
72+
writeLine(" fontcolor = \"black\"");
73+
writeLine(" shape = \"record\"");
74+
writeLine(" height = \"0\"");
75+
writeLine(" width = \"0\"");
76+
writeLine(" color = \"black\"");
77+
writeLine(" fillcolor = \"lightgoldenrodyellow\"");
78+
writeLine(" style = \"filled\"");
79+
writeLine(" ];");
80+
81+
// Overall edge style
82+
writeLine(" edge [");
83+
writeLine(" fontname=\"Helvetica\"");
84+
writeLine(" fontsize=\"8\"");
85+
writeLine(" fontcolor=\"black\"");
86+
writeLine(" color=\"black\"");
87+
writeLine(" arrowsize=\"0.7\"");
88+
writeLine(" ];");
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90+
// Write inputs as a subgraph
91+
writeInputs(workflow);
92+
93+
// Write outputs as a subgraph
94+
writeOutputs(workflow);
95+
96+
// End graph
97+
writeLine("}");
98+
}
99+
100+
/**
101+
* Writes a set of inputs from a workflow to the Writer
102+
* @param workflow The workflow to get the inputs from
103+
* @throws IOException Any errors in writing which may have occurred
104+
*/
105+
private void writeInputs(Workflow workflow) throws IOException {
106+
// Get inputs from workflow
107+
Map<String, CWLElement> inputs = workflow.getInputs();
108+
109+
// Start of subgraph with styling
110+
writeLine(" subgraph cluster_inputs {");
111+
writeLine(" rank = \"same\";");
112+
writeLine(" style = \"dashed\";");
113+
writeLine(" label = \"Workflow Inputs\";");
114+
115+
// Write each of the inputs as a node
116+
for (Map.Entry<String, CWLElement> input : workflow.getInputs().entrySet()) {
117+
writeInputOutput(input);
118+
}
119+
120+
// End subgraph
121+
writeLine(" }");
122+
}
123+
124+
/**
125+
* Writes a set of outputs from a workflow to the Writer
126+
* @param workflow The workflow to get the outputs from
127+
* @throws IOException Any errors in writing which may have occurred
128+
*/
129+
private void writeOutputs(Workflow workflow) throws IOException {
130+
// Start of subgraph with styling
131+
writeLine(" subgraph cluster_outputs {");
132+
writeLine(" rank = \"same\";");
133+
writeLine(" style = \"dashed\";");
134+
writeLine(" label = \"Workflow Outputs\";");
135+
136+
// Write each of the outputs as a node
137+
for (Map.Entry<String, CWLElement> output : workflow.getOutputs().entrySet()) {
138+
writeInputOutput(output);
139+
}
140+
141+
// End subgraph
142+
writeLine(" }");
143+
}
144+
145+
/**
146+
* Writes a single input or output to the Writer
147+
* @param inputOutput The input or output
148+
* @throws IOException Any errors in writing which may have occurred
149+
*/
150+
private void writeInputOutput(Map.Entry<String, CWLElement> inputOutput) throws IOException {
151+
// List of options for this node
152+
List<String> nodeOptions = new ArrayList<>();
153+
nodeOptions.add("fillcolor=\"#94DDF4\"");
154+
155+
// Use label if it is defined
156+
String label = inputOutput.getValue().getLabel();
157+
if (label != null && !label.isEmpty()) {
158+
nodeOptions.add("label=\"" + label + "\";");
159+
}
160+
161+
// Write the line for the node
162+
writeLine(" \"" + inputOutput.getKey() + "\" [" + String.join(",", nodeOptions) + "];");
163+
}
164+
165+
/**
166+
* Write a single line using the Writer
167+
* @param line The line to be written
168+
* @throws IOException Any errors in writing which may have occurred
169+
*/
170+
private void writeLine(String line) throws IOException {
171+
writer.write(line);
172+
writer.write(EOL);
173+
}
174+
175+
}

‎src/main/resources/static/bower_components/bootstrap/.bower.json

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{
2+
"name": "bootstrap",
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"description": "The most popular front-end framework for developing responsive, mobile first projects on the web.",
4+
"keywords": [
5+
"css",
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"js",
7+
"less",
8+
"mobile-first",
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"responsive",
10+
"front-end",
11+
"framework",
12+
"web"
13+
],
14+
"homepage": "http://getbootstrap.com",
15+
"license": "MIT",
16+
"moduleType": "globals",
17+
"main": [
18+
"less/bootstrap.less",
19+
"dist/js/bootstrap.js"
20+
],
21+
"ignore": [
22+
"/.*",
23+
"_config.yml",
24+
"CNAME",
25+
"composer.json",
26+
"CONTRIBUTING.md",
27+
"docs",
28+
"js/tests",
29+
"test-infra"
30+
],
31+
"dependencies": {
32+
"jquery": "1.9.1 - 3"
33+
},
34+
"version": "3.3.7",
35+
"_release": "3.3.7",
36+
"_resolution": {
37+
"type": "version",
38+
"tag": "v3.3.7",
39+
"commit": "0b9c4a4007c44201dce9a6cc1a38407005c26c86"
40+
},
41+
"_source": "https://github.com/twbs/bootstrap.git",
42+
"_target": "^3.3.7",
43+
"_originalSource": "bootstrap",
44+
"_direct": true
45+
}

‎src/main/resources/static/bower_components/bootstrap/CHANGELOG.md

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Bootstrap uses [GitHub's Releases feature](https://github.com/blog/1547-release-your-software) for its changelogs.
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See [the Releases section of our GitHub project](https://github.com/twbs/bootstrap/releases) for changelogs for each release version of Bootstrap.
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5+
Release announcement posts on [the official Bootstrap blog](http://blog.getbootstrap.com) contain summaries of the most noteworthy changes made in each release.

‎src/main/resources/static/bower_components/bootstrap/Gemfile

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source 'https://rubygems.org'
2+
3+
group :development, :test do
4+
gem 'jekyll', '~> 3.1.2'
5+
gem 'jekyll-sitemap', '~> 0.11.0'
6+
end

‎src/main/resources/static/bower_components/bootstrap/Gemfile.lock

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GEM
2+
remote: https://rubygems.org/
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specs:
4+
addressable (2.4.0)
5+
colorator (0.1)
6+
ffi (1.9.14-x64-mingw32)
7+
jekyll (3.1.6)
8+
colorator (~> 0.1)
9+
jekyll-sass-converter (~> 1.0)
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jekyll-watch (~> 1.1)
11+
kramdown (~> 1.3)
12+
liquid (~> 3.0)
13+
mercenary (~> 0.3.3)
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rouge (~> 1.7)
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safe_yaml (~> 1.0)
16+
jekyll-sass-converter (1.4.0)
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sass (~> 3.4)
18+
jekyll-sitemap (0.11.0)
19+
addressable (~> 2.4.0)
20+
jekyll-watch (1.4.0)
21+
listen (~> 3.0, < 3.1)
22+
kramdown (1.11.1)
23+
liquid (3.0.6)
24+
listen (3.0.8)
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rb-fsevent (~> 0.9, >= 0.9.4)
26+
rb-inotify (~> 0.9, >= 0.9.7)
27+
mercenary (0.3.6)
28+
rb-fsevent (0.9.7)
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rb-inotify (0.9.7)
30+
ffi (>= 0.5.0)
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rouge (1.11.1)
32+
safe_yaml (1.0.4)
33+
sass (3.4.22)
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PLATFORMS
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x64-mingw32
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DEPENDENCIES
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jekyll (~> 3.1.2)
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jekyll-sitemap (~> 0.11.0)
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BUNDLED WITH
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1.12.5

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