1 package compbio.ws.server;
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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.Annotation;
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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.conservation.AACon;
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34 import compbio.runner.disorder.Jronn;
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36 @WebService(endpointInterface = "compbio.data.msa.Annotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")
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37 public class JronnWS implements Annotation<Jronn> {
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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("JronnWS-stats");
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45 private static Logger log = Logger.getLogger(JronnWS.class);
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47 private static final RunnerConfig<Jronn> aaconOptions = Util
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48 .getSupportedOptions(Jronn.class);
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50 private static final PresetManager<Jronn> aaconPresets = Util
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51 .getPresets(Jronn.class);
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53 ConfiguredExecutable<Jronn> init(List<FastaSequence> sequences)
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54 throws JobSubmissionException {
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55 Jronn jronn = new Jronn();
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56 jronn.setInput("fasta.in").setOutput("aacon.out");
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57 return Configurator.configureExecutable(jronn, sequences);
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61 public HashSet<Score> getAnnotation(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 HashSet<Score> mas = aacon.getResults();
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68 log.trace(jobId + " getConservation : " + mas);
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73 public Limit<Jronn> getLimit(String presetName) {
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74 return new Jronn().getLimit(presetName);
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78 public LimitsManager<Jronn> getLimits() {
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79 return new Jronn().getLimits();
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83 public ChunkHolder pullExecStatistics(String jobId, long position) {
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84 WSUtil.validateJobId(jobId);
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85 String file = Configurator.getWorkDirectory(jobId) + File.separator
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86 + Jronn.getStatFile();
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87 return WSUtil.pullFile(file, position);
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91 public boolean cancelJob(String jobId) {
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92 WSUtil.validateJobId(jobId);
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93 return WSUtil.cancelJob(jobId);
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97 public JobStatus getJobStatus(String jobId) {
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98 WSUtil.validateJobId(jobId);
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99 return WSUtil.getJobStatus(jobId);
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103 public PresetManager<Jronn> getPresets() {
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104 return aaconPresets;
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108 public RunnerConfig<Jronn> getRunnerOptions() {
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109 return aaconOptions;
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112 String analize(List<FastaSequence> sequences,
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113 ConfiguredExecutable<Jronn> confExec, Logger log, String method,
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114 Limit<Jronn> limit) throws JobSubmissionException {
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115 if (limit != null && limit.isExceeded(sequences)) {
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116 throw LimitExceededException.newLimitExceeded(limit, sequences);
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119 compbio.runner.Util.writeInput(sequences, confExec);
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120 AsyncExecutor engine = Configurator.getAsyncEngine(confExec);
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121 String jobId = engine.submitJob(confExec);
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126 public String analize(List<FastaSequence> sequences)
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127 throws UnsupportedRuntimeException, LimitExceededException,
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128 JobSubmissionException {
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129 WSUtil.validateFastaInput(sequences);
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130 ConfiguredExecutable<Jronn> confAAcon = init(sequences);
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132 // set default conservation method to fastest - SHENKIN
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133 return analize(sequences, confAAcon, null, "analize", getLimit(""));
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137 public String customAnalize(List<FastaSequence> sequences,
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138 List<Option<Jronn>> options) throws UnsupportedRuntimeException,
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139 LimitExceededException, JobSubmissionException,
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140 WrongParameterException {
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141 WSUtil.validateFastaInput(sequences);
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142 ConfiguredExecutable<Jronn> confJronn = init(sequences);
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143 // Could not do that! Space separated values
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144 // will all be treated as keys! thus duplicates removed
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145 // String params = cbuilder.getCommand();
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146 List<String> params = WSUtil.getCommands(options,
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147 AACon.KEY_VALUE_SEPARATOR);
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148 confJronn.addParameters(params);
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149 return analize(sequences, confJronn, null, "customAnalize",
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154 public String presetAnalize(List<FastaSequence> sequences,
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155 Preset<Jronn> preset) throws UnsupportedRuntimeException,
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156 LimitExceededException, JobSubmissionException,
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157 WrongParameterException {
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158 WSUtil.validateFastaInput(sequences);
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159 if (preset == null) {
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160 throw new WrongParameterException("Preset must be provided!");
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162 ConfiguredExecutable<Jronn> confJronn = init(sequences);
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163 confJronn.addParameters(preset.getOptions());
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164 Limit<Jronn> limit = getLimit(preset.getName());
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165 return WSUtil.align(sequences, confJronn, null, "presetAnalize", limit);
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