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Commit 10c859b

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Mark Robinson
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Dynamic DOT writing for input and output subgraphs
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4 files changed

+252
-10
lines changed

4 files changed

+252
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lines changed

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

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@@ -19,9 +19,14 @@
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package org.commonwl.viewer.domain;
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import org.commonwl.viewer.services.DotWriter;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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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 @@
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*/
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public class Workflow {
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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 {
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private Map<String, CWLElement> inputs;
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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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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) {
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logger.error("Failed to create DOT graph for workflow: " + ex.getMessage());
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}
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}
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@Override
@@ -122,4 +142,12 @@ public Date getRetrievedOn() {
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public void setRetrievedOn(Date retrievedOn) {
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this.retrievedOn = retrievedOn;
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}
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public String getDotGraph() {
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return dotGraph;
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}
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public void setDotGraph(String dotGraph) {
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this.dotGraph = dotGraph;
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}
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}

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

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@@ -0,0 +1,175 @@
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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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package org.commonwl.viewer.services;
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import org.commonwl.viewer.domain.CWLElement;
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import org.commonwl.viewer.domain.Workflow;
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import java.io.IOException;
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import java.io.Writer;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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/**
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* Writes GraphViz DOT files from Workflows
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*/
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public class DotWriter {
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private static final String EOL = System.getProperty("line.separator");
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private Writer writer;
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public DotWriter(Writer writer) {
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this.writer = writer;
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}
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/**
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* Write a graph representing a workflow to the Writer
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* @param workflow The workflow to be graphed
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* @throws IOException Any errors in writing which may have occurred
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*/
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public void writeGraph(Workflow workflow) throws IOException {
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/**
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* DOT graph styling is based on the Apache
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* Taverna workflow management system
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*/
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// Begin graph
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writeLine("digraph workflow {");
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// Overall graph style
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writeLine(" graph [");
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writeLine(" bgcolor = \"#EEEEEE\"");
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writeLine(" color = \"black\"");
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writeLine(" fontsize = \"10\"");
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writeLine(" labeljust = \"left\"");
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writeLine(" clusterrank = \"local\"");
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writeLine(" ranksep = \"0.22\"");
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writeLine(" nodesep = \"0.05\"");
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writeLine(" ]");
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// Overall node style
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writeLine(" node [");
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writeLine(" fontname = \"Helvetica\"");
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writeLine(" fontsize = \"10\"");
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writeLine(" fontcolor = \"black\"");
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writeLine(" shape = \"record\"");
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writeLine(" height = \"0\"");
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writeLine(" width = \"0\"");
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writeLine(" color = \"black\"");
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writeLine(" fillcolor = \"lightgoldenrodyellow\"");
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writeLine(" style = \"filled\"");
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writeLine(" ];");
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// Overall edge style
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writeLine(" edge [");
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writeLine(" fontname=\"Helvetica\"");
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writeLine(" fontsize=\"8\"");
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writeLine(" fontcolor=\"black\"");
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writeLine(" color=\"black\"");
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writeLine(" arrowsize=\"0.7\"");
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writeLine(" ];");
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// Write inputs as a subgraph
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writeInputs(workflow);
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// Write outputs as a subgraph
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writeOutputs(workflow);
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// End graph
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writeLine("}");
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}
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/**
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* Writes a set of inputs from a workflow to the Writer
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* @param workflow The workflow to get the inputs from
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* @throws IOException Any errors in writing which may have occurred
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*/
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private void writeInputs(Workflow workflow) throws IOException {
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// Get inputs from workflow
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Map<String, CWLElement> inputs = workflow.getInputs();
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// Start of subgraph with styling
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writeLine(" subgraph cluster_inputs {");
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writeLine(" rank = \"same\";");
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writeLine(" style = \"dashed\";");
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writeLine(" label = \"Workflow Inputs\";");
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// Write each of the inputs as a node
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for (Map.Entry<String, CWLElement> input : workflow.getInputs().entrySet()) {
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writeInputOutput(input);
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}
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// End subgraph
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writeLine(" }");
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}
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/**
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* Writes a set of outputs from a workflow to the Writer
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* @param workflow The workflow to get the outputs from
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* @throws IOException Any errors in writing which may have occurred
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*/
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private void writeOutputs(Workflow workflow) throws IOException {
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// Start of subgraph with styling
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writeLine(" subgraph cluster_outputs {");
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writeLine(" rank = \"same\";");
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writeLine(" style = \"dashed\";");
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writeLine(" label = \"Workflow Outputs\";");
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// Write each of the outputs as a node
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for (Map.Entry<String, CWLElement> output : workflow.getOutputs().entrySet()) {
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writeInputOutput(output);
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}
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// End subgraph
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writeLine(" }");
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}
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/**
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* Writes a single input or output to the Writer
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* @param inputOutput The input or output
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* @throws IOException Any errors in writing which may have occurred
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*/
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private void writeInputOutput(Map.Entry<String, CWLElement> inputOutput) throws IOException {
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// List of options for this node
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List<String> nodeOptions = new ArrayList<>();
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nodeOptions.add("fillcolor=\"#94DDF4\"");
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// Use label if it is defined
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String label = inputOutput.getValue().getLabel();
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if (label != null && !label.isEmpty()) {
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nodeOptions.add("label=\"" + label + "\";");
159+
}
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// Write the line for the node
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writeLine(" \"" + inputOutput.getKey() + "\" [" + String.join(",", nodeOptions) + "];");
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}
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/**
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* Write a single line using the Writer
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* @param line The line to be written
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* @throws IOException Any errors in writing which may have occurred
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*/
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private void writeLine(String line) throws IOException {
171+
writer.write(line);
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writer.write(EOL);
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}
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}

‎src/main/resources/static/css/main.css

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@@ -55,6 +55,10 @@ body {
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stroke-width: 0;
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}
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#graph .subgraph path {
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stroke-dasharray: 1, 5;
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}
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#loading {
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width: 150px;
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margin: 0 auto;

‎src/main/resources/templates/workflow.html

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@@ -41,19 +41,54 @@ <h4 class="modal-title" id="dotGraphLabel">Workflow DOT Graph</h4>
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<div class="modal-body">
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<a id="download-link-gv" href="" download="workflow.gv"></a>
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<button id="download-gv" class="btn btn-primary" type="button">Download as .gv File</button>
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<textarea id="dot" class="form-control" rows="15">
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<textarea id="dot" class="form-control" rows="15" th:field="${workflow.dotGraph}">
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digraph G {
46-
bgcolor="#eeeeee";
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subgraph cluster_c0 {
48-
a0 -> a1 -> a2 -> a3;
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graph [
47+
bgcolor="#eeeeee"
48+
color="black"
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fontsize="10"
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labeljust="left"
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clusterrank="local"
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ranksep="0.22"
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nodesep="0.05"
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];
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node [
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fontname="Helvetica"
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fontsize="10"
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fontcolor="black"
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shape="record"
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height="0"
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width="0"
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color="black"
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fillcolor="lightgoldenrodyellow"
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style="filled"
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];
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edge [
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fontname="Helvetica"
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fontsize="8"
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fontcolor="black"
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color="black"
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arrowsize="0.7"
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];
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subgraph cluster_inputs {
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rank = same;
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style = "dashed";
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label = "Workflow Inputs";
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input1 [fillcolor="#94DDF4"];
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input2 [fillcolor="#94DDF4"];
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input3 [fillcolor="#94DDF4"];
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}
50-
subgraph cluster_c1 {
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b0 -> b1 -> b2 -> b3;
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subgraph cluster_outputs {
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rank = same;
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style = "dotted";
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label = "Workflow Outputs";
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output1 [fillcolor="#94DDF4"];
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output2 [fillcolor="#94DDF4"];
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output3 [fillcolor="#94DDF4"];
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}
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x -> a0;
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x -> b0;
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a1 -> b3;
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b1 -> a3;
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input1->step1->step4->output1;
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input2->step2->output2;
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input3->step3->output3;
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}
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</textarea>
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</div>

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