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.ws.client;
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21 import java.io.File;
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22 import java.net.URL;
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23 import java.util.Set;
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25 import javax.xml.namespace.QName;
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26 import javax.xml.ws.Service;
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28 import compbio.data.msa.JABAService;
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29 import compbio.data.msa.MsaWS;
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30 import compbio.data.msa.SequenceAnnotation;
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31 import compbio.engine.client.ConfExecutable;
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32 import compbio.engine.client.Executable;
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33 import compbio.runner.conservation.AACon;
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34 import compbio.runner.disorder.Disembl;
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35 import compbio.runner.disorder.GlobPlot;
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36 import compbio.runner.disorder.IUPred;
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37 import compbio.runner.disorder.Jronn;
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38 import compbio.runner.msa.ClustalW;
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39 import compbio.runner.msa.Mafft;
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40 import compbio.runner.msa.Muscle;
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41 import compbio.runner.msa.Probcons;
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42 import compbio.runner.msa.Tcoffee;
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45 * List of web services currently supported by JABAWS version 2
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48 public enum Services {
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49 MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS;
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51 public static Services getService(String servName) {
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52 servName = servName.trim().toLowerCase();
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53 for (Services service : Services.values()) {
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54 if (service.toString().equalsIgnoreCase(servName)) {
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61 public static Services getServiceByRunner(
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62 Class<Executable<?>> runnerClassName) {
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63 assert runnerClassName != null;
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64 String sname = runnerClassName.getSimpleName().toLowerCase();
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65 for (Services service : Services.values()) {
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66 if (service.toString().toLowerCase().contains(sname)) {
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73 public Class<? extends Executable<?>> getServiceImpl() {
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78 return ClustalW.class;
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82 return Muscle.class;
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84 return Tcoffee.class;
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86 return Probcons.class;
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88 return Disembl.class;
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90 return GlobPlot.class;
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94 return IUPred.class;
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96 throw new RuntimeException(
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97 "Unknown web service implementation class for service: "
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102 public static Class<? extends Executable<?>> getRunnerByJobDirectory(
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104 Services service = getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));
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105 return service.getServiceImpl();
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108 private static String getRunnerNameByJobDirectory(File jobdir) {
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109 String name = jobdir.getName().split("#")[0];
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111 if (name.startsWith(ConfExecutable.CLUSTER_TASK_ID_PREFIX)) {
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112 assert ConfExecutable.CLUSTER_TASK_ID_PREFIX.length() == 1;
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113 name = name.substring(1);
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118 public static Services getServiceByJobDirectory(File jobdir) {
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119 return getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));
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122 private static Services getServiceByRunnerName(String name) {
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123 for (Services service : Services.values()) {
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124 String runnerName = service.getServiceImpl().getSimpleName()
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126 name = name.trim().toLowerCase();
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127 if (name.startsWith(runnerName)) {
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134 Service getService(URL url, String sqname) {
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135 QName qname = new QName(sqname, this.toString());
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136 return Service.create(url, qname);
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139 public static String toString(Set<Services> services) {
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140 if (services == null || services.isEmpty()) {
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144 String delim = ", ";
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145 for (Services serv : services) {
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146 value += serv.toString() + delim;
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148 value = value.substring(0, value.length() - delim.length());
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152 Class<? extends JABAService> getServiceType() {
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154 // deliberate leaking
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160 return SequenceAnnotation.class;
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162 // deliberate leaking
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169 return MsaWS.class;
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171 throw new RuntimeException("Unrecognised Web Service Type "
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172 + this + " - Should never happened!");
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176 JABAService getInterface(Service service) {
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177 assert service != null;
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179 QName portName = new QName(service.getServiceName().getNamespaceURI(),
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180 this.toString() + "Port");
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181 return service.getPort(portName, this.getServiceType());
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