Package uk.ac.bbsrc.tgac.miso.core.util

Examples of uk.ac.bbsrc.tgac.miso.core.util.UnicodeReader

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    try {
      if (statusXml != null && !"".equals(statusXml)) {
        String runDirRegex = "([A-z0-9\\-]+)_([0-9]{8})_(.*)";
        Pattern runRegex = Pattern.compile(runDirRegex);
        Document statusDoc = SubmissionUtils.emptyDocument();
        SubmissionUtils.transform(new UnicodeReader(statusXml), statusDoc);

        String runName;
        if (statusDoc.getDocumentElement().getTagName().equals("error")) {
          runName = (statusDoc.getElementsByTagName("RunName").item(0).getTextContent());
        }
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  }

  public void parseStatusXml(String statusXml) {
    try {
      Document statusDoc = SubmissionUtils.emptyDocument();
      SubmissionUtils.transform(new UnicodeReader(statusXml), statusDoc);
      String runDirRegex = "([A-Za-z0-9]+)_([0-9]{8})_(.*)";
      Pattern runRegex = Pattern.compile(runDirRegex);

      if (statusDoc.getDocumentElement().getTagName().equals("error")) {
        String runName = statusDoc.getElementsByTagName("RunName").item(0).getTextContent();
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  public IlluminaRun(String statusXml, User user) {
    try {
      Document statusDoc = SubmissionUtils.emptyDocument();
      if (statusXml != null && !"".equals(statusXml)) {
        SubmissionUtils.transform(new UnicodeReader(statusXml), statusDoc);

        String runName = (statusDoc.getElementsByTagName("RunName").item(0).getTextContent());
        setPairedEnd(false);

        if (!statusDoc.getDocumentElement().getTagName().equals("error")) {
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  }

  public void parseStatusXml(String statusXml) {
    try {
      Document statusDoc = SubmissionUtils.emptyDocument();
      SubmissionUtils.transform(new UnicodeReader(statusXml), statusDoc);

      if (statusDoc.getDocumentElement().getTagName().equals("error")) {
        String runName = statusDoc.getElementsByTagName("RunName").item(0).getTextContent();
        String runDirRegex = "(\\d{6})_([A-z0-9]+)_(\\d+)_[A-z0-9_]*";
        Matcher m = Pattern.compile(runDirRegex).matcher(runName);
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              if (r.getSequencerReference() != null) {
                if (run.has("runparams")) {
                  try {
                    Document paramsDoc = SubmissionUtils.emptyDocument();
                    SubmissionUtils.transform(new UnicodeReader(run.getString("runparams")), paramsDoc);

                    Element runInfo = (Element)paramsDoc.getElementsByTagName("run").item(0);
                    String runDesc = runInfo.getElementsByTagName("shortName").item(0).getTextContent();
                    r.setDescription(runDesc);
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            else {
              status.setHealth(HealthType.Running);
            }

            Document statusDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
            SubmissionUtils.transform(new UnicodeReader(j.getString("xml")), statusDoc);
            String runStarted = statusDoc.getElementsByTagName("RunStarted").item(0).getTextContent();
            status.setStartDate(new SimpleDateFormat("EEEE, MMMMM dd, yyyy h:mm aaa").parse(runStarted));
            status.setInstrumentName(statusDoc.getElementsByTagName("InstrumentName").item(0).getTextContent());
            status.setRunName(statusDoc.getElementsByTagName("RunName").item(0).getTextContent());
            s.add(status);
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            else {
              status.setHealth(HealthType.Running);
            }

            Document statusDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
            SubmissionUtils.transform(new UnicodeReader(j.getString("xml")), statusDoc);
            String runStarted = statusDoc.getElementsByTagName("RunStarted").item(0).getTextContent();
            status.setStartDate(new SimpleDateFormat("EEEE, MMMMM dd, yyyy h:mm aaa").parse(runStarted));
            status.setInstrumentName(statusDoc.getElementsByTagName("InstrumentName").item(0).getTextContent());
            status.setRunName(runName);
            return status;
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            else {
              status.setHealth(HealthType.Running);
            }

            Document statusDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
            SubmissionUtils.transform(new UnicodeReader(j.getString("xml")), statusDoc);
            String runStarted = statusDoc.getElementsByTagName("date").item(0).getTextContent();
            status.setStartDate(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'").parse(runStarted));
            status.setInstrumentName(statusDoc.getElementsByTagName("serialNumber").item(0).getTextContent());
            Node n = statusDoc.getElementsByTagName("run").item(0);
            for (int i = 0; i < n.getChildNodes().getLength(); i++) {
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            }
            else {
              status.setHealth(HealthType.Running);
            }
            Document statusDoc = DocumentBuilderFactory.newInstance().newDocumentBuilder().newDocument();
            SubmissionUtils.transform(new UnicodeReader(j.getString("xml")), statusDoc);
            String runStarted = statusDoc.getElementsByTagName("date").item(0).getTextContent();
            status.setStartDate(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss'Z'").parse(runStarted));
            status.setInstrumentName(statusDoc.getElementsByTagName("serialNumber").item(0).getTextContent());
            Node n = statusDoc.getElementsByTagName("run").item(0);
            for (int i = 0; i < n.getChildNodes().getLength(); i++) {
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            RunArray ra = solidService.getSolidPort().getRun(runName, machineName);
            if (ra != null && !ra.getItem().isEmpty()) {
              try {
                String statusXml = ra.getItem().get(0).getXml();
                Document statusDoc = SubmissionUtils.emptyDocument();
                SubmissionUtils.transform(new UnicodeReader(statusXml), statusDoc);

                run.put("runName", runName);
                run.put("fullPath", rootFile.getAbsolutePath());
                run.put("status", statusXml);
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Related Classes of uk.ac.bbsrc.tgac.miso.core.util.UnicodeReader

  • uk.ac.bbsrc.tgac.miso.core.data.impl.illumina.IlluminaRun
  • uk.ac.bbsrc.tgac.miso.core.data.impl.illumina.IlluminaStatus
  • uk.ac.bbsrc.tgac.miso.core.data.impl.solid.SolidRun
  • uk.ac.bbsrc.tgac.miso.core.data.impl.solid.SolidStatus
  • uk.ac.bbsrc.tgac.miso.core.service.integration.strategy.interrogator.IlluminaSequencerInterrogationStrategy
  • uk.ac.bbsrc.tgac.miso.core.service.integration.strategy.interrogator.LS454SequencerInterrogationStrategy
  • uk.ac.bbsrc.tgac.miso.notification.consumer.service.mechanism.LS454NotificationMessageConsumerMechanism
  • uk.ac.bbsrc.tgac.miso.notification.service.SolidTransformer
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