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1 package edu.unc.genomics;
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2
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3 import java.io.StringWriter;
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4 import java.util.ArrayList;
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5 import java.util.HashMap;
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6 import java.util.Iterator;
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7 import java.util.List;
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8 import java.util.Map;
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9
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10 import org.apache.log4j.Logger;
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11 import org.apache.log4j.PatternLayout;
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12 import org.apache.log4j.WriterAppender;
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13
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14 import com.beust.jcommander.JCommander;
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15 import com.beust.jcommander.ParameterDescription;
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16
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17 /**
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18 * A Job represents an instance of a tool configured with specific arguments
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19 * Attempting to run a Job with invalid arguments will throw a RuntimeException
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20 * If tool execution fails, a RuntimeException will also be thrown
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21 * UncheckedExceptions should be managed by setting the Job's UncheckedExceptionManager
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22 * or providing a ThreadGroup / default UncheckedExceptionManager
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23 *
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24 * @author timpalpant
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25 *
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26 */
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27 public class Job implements Iterable<ParameterDescription>, Runnable {
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28
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29 private static final Logger log = Logger.getLogger(Job.class);
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30
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31 private final Class<? extends CommandLineTool> tool;
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32 private final CommandLineTool app;
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33 private final List<ParameterDescription> parameters;
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34 private final String usageText;
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35 private boolean isRunning = false;
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36 private StringWriter writer = new StringWriter();
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37
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38 /**
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39 * Arguments for running this Job
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40 */
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41 private Map<ParameterDescription,String> args = new HashMap<>();
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42
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43 /**
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44 * Creates a new Job model for the specified tool
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45 * @param tool
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46 * @throws IllegalAccessException
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47 * @throws InstantiationException
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48 */
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49 public Job(final Class<? extends CommandLineTool> tool) throws InstantiationException, IllegalAccessException {
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50 this.tool = tool;
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51
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52 // Attempt to instantiate the tool and extract parameter information
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53 app = tool.newInstance();
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54 JCommander jc = new JCommander(app);
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55 jc.setProgramName(tool.getSimpleName());
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56 parameters = jc.getParameters();
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57 StringBuilder sbuilder = new StringBuilder();
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58 jc.usage(sbuilder);
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59 usageText = sbuilder.toString();
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60
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61 // Set default arguments
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62 for (ParameterDescription param : parameters) {
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63 if (param.getDefault() != null) {
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64 setArgument(param, String.valueOf(param.getDefault()));
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65 }
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66 }
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67 }
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68
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69 /**
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70 * Copy-constructor
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71 * @param job
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72 */
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73 public Job(final Job job) {
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74 this.tool = job.tool;
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75 this.app = job.app;
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76 this.parameters = job.parameters;
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77 this.args = job.args;
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78 this.usageText = job.usageText;
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79 }
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80
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81 @Override
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82 public void run() {
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83 // Load the arguments for running the tool
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84 String[] args;
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85 try {
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86 args = getArguments();
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87 } catch (JobException e) {
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88 // TODO Auto-generated catch block
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89 e.printStackTrace();
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90 throw new CommandLineToolException("Job arguments are not valid");
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91 }
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92
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93 // Attempt to instantiate and run the tool
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94 WriterAppender appender = new WriterAppender(new PatternLayout(), writer);
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95 appender.addFilter(new ThreadFilter(Thread.currentThread().getName()));
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96 Logger.getRootLogger().addAppender(appender);
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97 isRunning = true;
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98 app.toolRunnerMain(args);
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99 isRunning = false;
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100 Logger.getRootLogger().removeAppender(appender);
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101 }
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102
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103 /**
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104 * Render the arguments for running an instance of this Job
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105 * @return
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106 * @throws JobException
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107 */
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108 public String[] getArguments() throws JobException {
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109 if (!validateArguments()) {
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110 throw new JobException("Job Arguments are not valid");
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111 }
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112
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113 List<String> cmdArgs = new ArrayList<>();
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114 for (ParameterDescription p : args.keySet()) {
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115 cmdArgs.add(p.getLongestName());
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116 cmdArgs.add(args.get(p));
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117 }
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118
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119 String[] ret = new String[cmdArgs.size()];
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120 return cmdArgs.toArray(ret);
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121 }
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122
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123 public String getArgument(final ParameterDescription p) {
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124 return args.get(p);
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125 }
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126
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127 /**
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128 * Set a value for the given parameter
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129 * @param p
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130 * @param value
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131 */
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132 public void setArgument(final ParameterDescription p, final String value) {
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133 if (value.length() == 0) {
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134 args.remove(p);
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135 } else {
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136 args.put(p, value);
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137 }
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138 }
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139
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140 /**
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141 * Remove all set arguments for this Job
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142 */
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143 public void resetArguments() {
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144 args.clear();
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145 }
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146
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147 /**
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148 * Is this parameter set?
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149 * @param p
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150 * @return
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151 */
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152 public boolean isSet(final ParameterDescription p) {
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153 return args.containsKey(p);
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154 }
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155
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156 /**
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157 * Validate that this job has all of its parameters set
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158 * and that they are all valid
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159 * @return
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160 */
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161 public boolean validateArguments() {
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162 // TODO: Better validation based on parameter type
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163 boolean hasAllRequiredParams = true;
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164 for (ParameterDescription param : parameters) {
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165 if (param.getParameter().required() && !isSet(param)) {
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166 log.debug("Job is missing required argument: " + param.getLongestName());
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167 hasAllRequiredParams = false;
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168 }
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169 }
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170
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171 return hasAllRequiredParams;
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172 }
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173
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174 public int numParameters() {
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175 return parameters.size();
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176 }
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177
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178 @Override
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179 public Iterator<ParameterDescription> iterator() {
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180 return parameters.iterator();
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181 }
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182
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183 public String getName() {
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184 return tool.getSimpleName();
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185 }
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186
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187 public boolean isRunning() {
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188 return isRunning;
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189 }
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190
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191 /**
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192 * @return the usageText
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193 */
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194 public String getUsageText() {
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195 return usageText;
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196 }
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197
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198 @Override
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199 public String toString() {
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200 return getName();
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201 }
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202
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203 public String getOutput() {
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204 return writer.toString();
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205 }
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206
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207 }
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