1 package compbio.ws.server;
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4 import java.util.List;
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6 import javax.annotation.Resource;
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7 import javax.jws.WebService;
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8 import javax.xml.ws.WebServiceContext;
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10 import org.apache.log4j.Logger;
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12 import compbio.data.msa.SequenceAnnotation;
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13 import compbio.data.sequence.FastaSequence;
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14 import compbio.data.sequence.ScoreManager;
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15 import compbio.engine.AsyncExecutor;
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16 import compbio.engine.Configurator;
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17 import compbio.engine.client.ConfiguredExecutable;
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18 import compbio.metadata.ChunkHolder;
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19 import compbio.metadata.JobStatus;
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20 import compbio.metadata.JobSubmissionException;
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21 import compbio.metadata.Limit;
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22 import compbio.metadata.LimitExceededException;
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23 import compbio.metadata.LimitsManager;
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24 import compbio.metadata.Option;
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25 import compbio.metadata.Preset;
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26 import compbio.metadata.PresetManager;
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27 import compbio.metadata.ResultNotAvailableException;
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28 import compbio.metadata.RunnerConfig;
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29 import compbio.metadata.UnsupportedRuntimeException;
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30 import compbio.metadata.WrongParameterException;
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31 import compbio.runner.Util;
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32 import compbio.runner.conservation.AACon;
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33 import compbio.runner.disorder.Jronn;
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35 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")
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36 public class JronnWS implements SequenceAnnotation<Jronn> {
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38 // Ask for resource injection
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40 WebServiceContext wsContext;
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42 private static Logger statLog = Logger.getLogger("JronnWS-stats");
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44 private static Logger log = Logger.getLogger(JronnWS.class);
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46 private static final RunnerConfig<Jronn> jronnOptions = Util
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47 .getSupportedOptions(Jronn.class);
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49 private static final PresetManager<Jronn> jronnPresets = Util
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50 .getPresets(Jronn.class);
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52 private static final LimitsManager<Jronn> limitMan = compbio.runner.Util
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53 .getLimits(new Jronn().getType());
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55 ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)
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56 throws JobSubmissionException {
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57 Jronn jronn = new Jronn();
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58 jronn.setInput("fasta.in").setOutput("jronn.out");
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59 return Configurator.configureExecutable(jronn, sequences);
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63 public ScoreManager getAnnotation(String jobId)
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64 throws ResultNotAvailableException {
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65 WSUtil.validateJobId(jobId);
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66 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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67 ConfiguredExecutable<Jronn> jronn = (ConfiguredExecutable<Jronn>) asyncEngine
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69 ScoreManager mas = jronn.getResults();
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70 log.trace(jobId + " getConservation : " + mas);
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75 public Limit<Jronn> getLimit(String presetName) {
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76 if (limitMan == null) {
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79 return limitMan.getLimitByName(presetName);
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83 public LimitsManager<Jronn> getLimits() {
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88 public ChunkHolder pullExecStatistics(String jobId, long position) {
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89 WSUtil.validateJobId(jobId);
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90 String file = Configurator.getWorkDirectory(jobId) + File.separator
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91 + Jronn.getStatFile();
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92 return WSUtil.pullFile(file, position);
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96 public boolean cancelJob(String jobId) {
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97 WSUtil.validateJobId(jobId);
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98 return WSUtil.cancelJob(jobId);
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102 public JobStatus getJobStatus(String jobId) {
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103 WSUtil.validateJobId(jobId);
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104 return WSUtil.getJobStatus(jobId);
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108 public PresetManager<Jronn> getPresets() {
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109 return jronnPresets;
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113 public RunnerConfig<Jronn> getRunnerOptions() {
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114 return jronnOptions;
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117 String analize(List<FastaSequence> sequences,
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118 ConfiguredExecutable<Jronn> confExec, Logger log, String method,
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119 Limit<Jronn> limit) throws JobSubmissionException {
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120 if (limit != null && limit.isExceeded(sequences)) {
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121 throw LimitExceededException.newLimitExceeded(limit, sequences);
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124 compbio.runner.Util.writeInput(sequences, confExec);
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125 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
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126 String jobId = engine.submitJob(confExec);
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131 public String analize(List<FastaSequence> sequences)
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132 throws UnsupportedRuntimeException, LimitExceededException,
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133 JobSubmissionException {
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134 WSUtil.validateFastaInput(sequences);
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135 ConfiguredExecutable<Jronn> confJronn = init(sequences);
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137 return analize(sequences, confJronn, null, "analize", getLimit(""));
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141 public String customAnalize(List<FastaSequence> sequences,
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142 List<Option<Jronn>> options) throws UnsupportedRuntimeException,
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143 LimitExceededException, JobSubmissionException,
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144 WrongParameterException {
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145 WSUtil.validateFastaInput(sequences);
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146 ConfiguredExecutable<Jronn> confJronn = init(sequences);
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148 List<String> params = WSUtil.getCommands(options,
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149 AACon.KEY_VALUE_SEPARATOR);
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150 confJronn.addParameters(params);
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151 return analize(sequences, confJronn, null, "customAnalize",
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156 public String presetAnalize(List<FastaSequence> sequences,
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157 Preset<Jronn> preset) throws UnsupportedRuntimeException,
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158 LimitExceededException, JobSubmissionException,
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159 WrongParameterException {
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160 WSUtil.validateFastaInput(sequences);
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161 if (preset == null) {
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162 throw new WrongParameterException("Preset must be provided!");
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164 ConfiguredExecutable<Jronn> confJronn = init(sequences);
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165 confJronn.addParameters(preset.getOptions());
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166 Limit<Jronn> limit = getLimit(preset.getName());
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167 return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);
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