1 package compbio.ws.server;
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3 import java.util.HashMap;
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4 import java.util.HashSet;
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5 import java.util.List;
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7 import javax.annotation.Resource;
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8 import javax.jws.WebService;
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9 import javax.xml.ws.WebServiceContext;
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11 import org.apache.log4j.Logger;
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13 import compbio.data.msa.SequenceAnnotation;
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14 import compbio.data.sequence.FastaSequence;
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15 import compbio.data.sequence.Score;
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16 import compbio.engine.AsyncExecutor;
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17 import compbio.engine.Configurator;
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18 import compbio.engine.client.ConfiguredExecutable;
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19 import compbio.metadata.ChunkHolder;
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20 import compbio.metadata.JobStatus;
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21 import compbio.metadata.JobSubmissionException;
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22 import compbio.metadata.Limit;
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23 import compbio.metadata.LimitExceededException;
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24 import compbio.metadata.LimitsManager;
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25 import compbio.metadata.Option;
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26 import compbio.metadata.Preset;
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27 import compbio.metadata.PresetManager;
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28 import compbio.metadata.ResultNotAvailableException;
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29 import compbio.metadata.RunnerConfig;
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30 import compbio.metadata.UnsupportedRuntimeException;
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31 import compbio.metadata.WrongParameterException;
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32 import compbio.runner.Util;
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33 import compbio.runner.disorder.Disembl;
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35 @WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "DisemblWS")
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36 public class DisemblWS implements SequenceAnnotation<Disembl> {
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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("DisemblWS-stats");
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44 private static Logger log = Logger.getLogger(DisemblWS.class);
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46 private static final RunnerConfig<Disembl> disemblOptions = Util
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47 .getSupportedOptions(Disembl.class);
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49 private static final PresetManager<Disembl> disemblPresets = Util
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50 .getPresets(Disembl.class);
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52 ConfiguredExecutable<Disembl> init(List<FastaSequence> sequences)
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53 throws JobSubmissionException {
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54 Disembl disembl = new Disembl();
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55 disembl.setInput("fasta.in").setOutput("disembl.out");
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56 return Configurator.configureExecutable(disembl, sequences);
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60 public HashMap<String, HashSet<Score>> getAnnotation(String jobId)
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61 throws ResultNotAvailableException {
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62 WSUtil.validateJobId(jobId);
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63 AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);
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64 ConfiguredExecutable<Disembl> disembl = (ConfiguredExecutable<Disembl>) asyncEngine
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66 HashMap<String, HashSet<Score>> mas = disembl.getResults();
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67 log.trace(jobId + " getDisorder : " + mas);
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72 public Limit<Disembl> getLimit(String presetName) {
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73 return new Disembl().getLimit(presetName);
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77 public LimitsManager<Disembl> getLimits() {
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78 return new Disembl().getLimits();
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82 public ChunkHolder pullExecStatistics(String jobId, long position) {
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83 // Execution stat is not supported
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84 return new ChunkHolder("", -1);
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88 public boolean cancelJob(String jobId) {
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89 WSUtil.validateJobId(jobId);
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90 return WSUtil.cancelJob(jobId);
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94 public JobStatus getJobStatus(String jobId) {
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95 WSUtil.validateJobId(jobId);
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96 return WSUtil.getJobStatus(jobId);
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100 public PresetManager<Disembl> getPresets() {
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101 return disemblPresets;
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105 public RunnerConfig<Disembl> getRunnerOptions() {
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106 return disemblOptions;
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109 String analize(List<FastaSequence> sequences,
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110 ConfiguredExecutable<Disembl> confExec, Logger log, String method,
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111 Limit<Disembl> limit) throws JobSubmissionException {
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112 if (limit != null && limit.isExceeded(sequences)) {
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113 throw LimitExceededException.newLimitExceeded(limit, sequences);
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116 compbio.runner.Util.writeInput(sequences, confExec);
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117 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
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118 String jobId = engine.submitJob(confExec);
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123 public String analize(List<FastaSequence> sequences)
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124 throws UnsupportedRuntimeException, LimitExceededException,
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125 JobSubmissionException {
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126 WSUtil.validateFastaInput(sequences);
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127 ConfiguredExecutable<Disembl> confDisembl = init(sequences);
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129 return analize(sequences, confDisembl, null, "analize", getLimit(""));
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133 * No options are supported, thus the result of this call will be as simple
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134 * call to analize without parameters
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137 public String customAnalize(List<FastaSequence> sequences,
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138 List<Option<Disembl>> options) throws UnsupportedRuntimeException,
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139 LimitExceededException, JobSubmissionException,
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140 WrongParameterException {
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141 return analize(sequences);
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145 * No presets are supported, thus the result of this call will be as simple
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146 * call to analize without parameters
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149 public String presetAnalize(List<FastaSequence> sequences,
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150 Preset<Disembl> preset) throws UnsupportedRuntimeException,
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151 LimitExceededException, JobSubmissionException,
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152 WrongParameterException {
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154 return analize(sequences);
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