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.conservation.Method;
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13 import compbio.data.msa.Annotation;
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14 import compbio.data.sequence.FastaSequence;
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15 import compbio.data.sequence.JalviewAnnotation;
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16 import compbio.data.sequence.MultiAnnotatedSequence;
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17 import compbio.engine.AsyncExecutor;
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18 import compbio.engine.Configurator;
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19 import compbio.engine.client.ConfiguredExecutable;
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20 import compbio.metadata.ChunkHolder;
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21 import compbio.metadata.JobStatus;
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22 import compbio.metadata.JobSubmissionException;
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23 import compbio.metadata.Limit;
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24 import compbio.metadata.LimitExceededException;
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25 import compbio.metadata.LimitsManager;
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26 import compbio.metadata.Option;
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27 import compbio.metadata.Preset;
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28 import compbio.metadata.PresetManager;
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29 import compbio.metadata.ResultNotAvailableException;
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30 import compbio.metadata.RunnerConfig;
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31 import compbio.metadata.UnsupportedRuntimeException;
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32 import compbio.metadata.WrongParameterException;
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33 import compbio.runner.Util;
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34 import compbio.runner.conservation.AACon;
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36 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")
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37 public class AAConWS implements Annotation<AACon> {
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39 // Ask for resource injection
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41 WebServiceContext wsContext;
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43 private static Logger statLog = Logger.getLogger("AAConWS-stats");
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45 private static Logger log = Logger.getLogger(AAConWS.class);
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47 private static final RunnerConfig<AACon> aaconOptions = Util
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48 .getSupportedOptions(AACon.class);
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50 private static final PresetManager<AACon> aaconPresets = Util
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51 .getPresets(AACon.class);
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53 ConfiguredExecutable<AACon> init(List<FastaSequence> sequences)
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54 throws JobSubmissionException {
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55 AACon aacon = new AACon();
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56 aacon.setInput("fasta.in").setOutput("fasta.out");
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57 return Configurator.configureExecutable(aacon, sequences);
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60 @SuppressWarnings("unchecked")
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61 public MultiAnnotatedSequence<Method> getResult(String jobId)
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62 throws ResultNotAvailableException {
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63 WSUtil.validateJobId(jobId);
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64 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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65 ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine
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67 MultiAnnotatedSequence<Method> mas = aacon.getResults();
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68 // log(jobId, "getResults");
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72 @SuppressWarnings("unchecked")
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73 public JalviewAnnotation getJalviewAnnotation(String jobId)
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74 throws ResultNotAvailableException {
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75 MultiAnnotatedSequence<Method> result = getResult(jobId);
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77 // log(jobId, "getResults");
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78 return result.toJalviewAnnotation();
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81 public Limit<AACon> getLimit(String presetName) {
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82 return new AACon().getLimit(presetName);
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85 public LimitsManager<AACon> getLimits() {
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86 return new AACon().getLimits();
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89 public ChunkHolder pullExecStatistics(String jobId, long position) {
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90 WSUtil.validateJobId(jobId);
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91 String file = Configurator.getWorkDirectory(jobId) + File.separator
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92 + AACon.getStatFile();
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93 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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101 public JobStatus getJobStatus(String jobId) {
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102 WSUtil.validateJobId(jobId);
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103 return WSUtil.getJobStatus(jobId);
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106 public PresetManager<AACon> getPresets() {
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107 return aaconPresets;
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110 public RunnerConfig<AACon> getRunnerOptions() {
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111 return aaconOptions;
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115 public String analize(List<FastaSequence> sequences)
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116 throws UnsupportedRuntimeException, LimitExceededException,
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117 JobSubmissionException {
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118 // TODO Auto-generated method stub
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123 public String customAnalize(List<FastaSequence> sequences,
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124 List<Option<AACon>> options) throws UnsupportedRuntimeException,
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125 LimitExceededException, JobSubmissionException,
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126 WrongParameterException {
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127 // TODO Auto-generated method stub
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132 public String presetAnalize(List<FastaSequence> sequences,
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133 Preset<AACon> preset) throws UnsupportedRuntimeException,
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134 LimitExceededException, JobSubmissionException,
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135 WrongParameterException {
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136 // TODO Auto-generated method stub
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