1 /* Copyright (c) 2009 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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19 package compbio.engine.client;
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21 import java.io.File;
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22 import java.security.InvalidParameterException;
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23 import java.util.Arrays;
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24 import java.util.List;
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26 import org.apache.log4j.Logger;
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28 import compbio.engine.client.CommandBuilder.Parameter;
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29 import compbio.engine.conf.PropertyHelperManager;
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30 import compbio.metadata.Limit;
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31 import compbio.metadata.LimitsManager;
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32 import compbio.util.PropertyHelper;
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33 import compbio.util.Util;
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35 public abstract class SkeletalExecutable<T> implements Executable<T> {
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37 protected static final PropertyHelper ph = PropertyHelperManager
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38 .getPropertyHelper();
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40 private static Logger log = Logger.getLogger(SkeletalExecutable.class);
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42 // Cache for Limits information
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43 private LimitsManager<T> limits;
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45 public static final String INPUT = "input.txt";
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46 public static final String OUTPUT = "result.txt";
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47 public static final String ERROR = "error.txt";
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49 protected String inputFile = INPUT;
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50 protected String outputFile = OUTPUT;
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51 protected String errorFile = ERROR;
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53 private boolean isInputSet = false;
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54 private boolean isOutputSet = false;
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55 private boolean isErrorSet = false;
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58 * This has to allow duplicate parameters as different options may have the
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59 * same value e.g. Muscle -weight1 clustalw -weight2 clustalw
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61 protected CommandBuilder<T> cbuilder;
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63 public SkeletalExecutable() {
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64 cbuilder = new CommandBuilder<T>(" ");
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67 public SkeletalExecutable(String parameterKeyValueDelimiter) {
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68 assert parameterKeyValueDelimiter != null;
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69 cbuilder = new CommandBuilder<T>(parameterKeyValueDelimiter);
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72 public SkeletalExecutable<T> setInput(String inFile) {
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73 if (compbio.util.Util.isEmpty(inFile)) {
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74 throw new IllegalArgumentException("Input file must not be NULL");
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76 this.inputFile = inFile;
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77 this.isInputSet = true;
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81 public SkeletalExecutable<T> setOutput(String outFile) {
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82 if (compbio.util.Util.isEmpty(outFile)
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83 || PathValidator.isAbsolutePath(outFile)) {
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84 throw new IllegalArgumentException(
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85 "Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "
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88 this.outputFile = outFile;
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89 this.isOutputSet = true;
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93 public SkeletalExecutable<T> setError(String errFile) {
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94 if (compbio.util.Util.isEmpty(errFile)
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95 || PathValidator.isAbsolutePath(errFile)) {
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96 throw new IllegalArgumentException(
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97 "Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "
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100 this.errorFile = errFile;
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101 this.isErrorSet = true;
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106 public CommandBuilder<T> getParameters(ExecProvider provider) {
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108 * Prevent modification of the parameters unintentionally. This is
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109 * important to preserve executable parameters intact as engine could
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110 * add things into the array as it see fit. For instance
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111 * ExecutableWrapper (part of local engines) add command line as the
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112 * first element of an array.
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114 paramValueUpdater();
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119 public Executable<T> addParameters(List<String> parameters) {
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120 cbuilder.addParams(parameters);
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124 public Executable<T> setParameter(String parameter) {
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125 cbuilder.setParam(parameter);
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130 * This is a generic method of changing values of the parameters with
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133 * This method iterates via commands for an executable finding matches from
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134 * the Executable.properties file and replacing values in CommandBuilder
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135 * with a combination of value from CommandBuilder to merge path from
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138 void paramValueUpdater() {
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139 for (Parameter command : cbuilder.getCommandList()) {
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140 if (command.value == null) {
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143 String propertyPath = compbio.engine.client.Util.getExecProperty(
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144 command.name + ".path", getType());
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145 if (Util.isEmpty(propertyPath)) {
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148 if (new File(command.value).isAbsolute()) {
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149 // Matrix can be found so no actions necessary
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150 // This method has been called already and the matrix name
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151 // is modified to contain full path // no further actions is
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155 String absMatrixPath = compbio.engine.client.Util
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156 .convertToAbsolute(propertyPath);
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157 command.value = absMatrixPath + File.separator + command.value;
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158 cbuilder.setParam(command);
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163 * This method cannot really tell whether the files has actually been
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164 * created or not. It must be overridden as required.
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166 * @see compbio.engine.client.Executable#getCreatedFiles()
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169 public List<String> getCreatedFiles() {
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170 return Arrays.asList(getOutput(), getError());
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174 public String getInput() {
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178 protected boolean isInputSet() {
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182 protected boolean isOutputSet() {
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183 return isOutputSet;
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186 protected boolean isErrorSet() {
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191 public String getOutput() {
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196 public String getError() {
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201 public String toString() {
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202 String value = "Input: " + this.getInput() + "\n";
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203 value += "Output: " + this.getOutput() + "\n";
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204 value += "Error: " + this.getError() + "\n";
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205 value += "Class: " + this.getClass() + "\n";
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206 value += "Params: " + cbuilder + "\n";
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211 public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {
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212 if (!compbio.util.Util.isEmpty(rconfig.getOutput())) {
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213 setOutput(rconfig.getOutput());
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215 if (!compbio.util.Util.isEmpty(rconfig.getError())) {
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216 setError(rconfig.getError());
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218 if (!compbio.util.Util.isEmpty(rconfig.getInput())) {
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219 setInput(rconfig.getInput());
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221 this.cbuilder = (CommandBuilder<T>) rconfig.getParameters();
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226 public boolean equals(Object obj) {
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230 if (!(obj instanceof SkeletalExecutable<?>)) {
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233 SkeletalExecutable<?> exec = (SkeletalExecutable<?>) obj;
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234 if (!Util.isEmpty(this.inputFile) && !Util.isEmpty(exec.inputFile)) {
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235 if (!this.inputFile.equals(exec.inputFile)) {
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239 if (!Util.isEmpty(this.outputFile) && !Util.isEmpty(exec.outputFile)) {
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240 if (!this.outputFile.equals(exec.outputFile)) {
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244 if (!Util.isEmpty(this.errorFile) && !Util.isEmpty(exec.errorFile)) {
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245 if (!this.errorFile.equals(exec.errorFile)) {
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249 if (!this.cbuilder.equals(exec.cbuilder)) {
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256 public int hashCode() {
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257 int code = inputFile.hashCode();
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258 code += outputFile.hashCode();
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259 code += errorFile.hashCode();
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260 code *= this.cbuilder.hashCode();
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265 public String getClusterJobSettings() {
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266 String settings = ph.getProperty(getType().getSimpleName()
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267 .toLowerCase() + ".cluster.settings");
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268 return settings == null ? "" : settings;
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273 * @return number of cpus to use on the cluster or 0 if the value is
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276 public static int getClusterCpuNum(Class<? extends Executable<?>> type) {
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278 String cpuNum = ph.getProperty(type.getSimpleName().toLowerCase()
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279 + ".cluster.cpunum");
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280 if (compbio.util.Util.isEmpty(cpuNum)) {
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284 cpus = Integer.parseInt(cpuNum);
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285 } catch (NumberFormatException e) {
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287 log.debug("Number of cpus to use for cluster execution is defined but could not be parsed as integer! Given value is: "
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291 if (cpus < 1 || cpus > 100) {
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292 throw new InvalidParameterException(
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293 "Number of cpu for cluster execution must be within 1 and 100! "
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294 + "Look at the value of 'tcoffee.cluster.cpunum' property. Given value is "
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301 public synchronized Limit<T> getLimit(String presetName) {
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302 // Assume this function is called for the first time and thus need
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304 if (limits == null) {
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305 limits = getLimits();
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307 // Either the initialization failed or limits were not configured.
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308 if (limits == null) {
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312 Limit<T> limit = null;
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313 if (limits != null) {
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314 // this returns default limit if preset is undefined!
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315 limit = limits.getLimitByName(presetName);
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317 // If limit is not defined for a particular preset, then return default
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319 if (limit == null) {
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320 log.debug("Limit for the preset " + presetName
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321 + " is not found. Using default");
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322 limit = limits.getDefaultLimit();
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328 public LimitsManager<T> getLimits() {
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329 synchronized (SkeletalExecutable.class) {
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330 if (limits == null) {
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331 limits = compbio.engine.client.Util.getLimits(this.getType());
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339 * @return subclasses must return their type
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341 public abstract Class<T> getType();
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