Package com.eaglegenomics.simlims.core

Examples of com.eaglegenomics.simlims.core.SecurityProfile

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   * Construct a new Submission with a SecurityProfile owned by the given User
   *
   * @param user of type User
   */
  public SubmissionImpl(User user) {
    setSecurityProfile(new SecurityProfile(user));
  }
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  }

  public LS454Run(User user) {
    setPlatformType(PlatformType.LS454);
    setStatus(new StatusImpl());
    setSecurityProfile(new SecurityProfile(user));
  }
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  /**
   * Construct a new LibraryDilution with a default empty SecurityProfile
   */
  public LibraryDilution() {
    setSecurityProfile(new SecurityProfile());
  }
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   * Construct a new LibraryDilution with a SecurityProfile owned by the given User
   *
   * @param user of type User
   */
  public LibraryDilution(User user) {
    setSecurityProfile(new SecurityProfile(user));
  }
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  /**
   * Construct a new Lane with a default empty SecurityProfile
   */
  public Lane() {
    setSecurityProfile(new SecurityProfile());
  }
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   * Construct a new Lane with a SecurityProfile owned by the given User
   *
   * @param user of type User
   */
  public Lane(User user) {
    setSecurityProfile(new SecurityProfile(user));
  }
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public class IlluminaRun extends RunImpl {

  public IlluminaRun() {
    setPlatformType(PlatformType.ILLUMINA);
    setStatus(new StatusImpl());
    setSecurityProfile(new SecurityProfile());
  }
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        setFilePath(runName);
        setDescription(m.group(3));
        setPlatformType(PlatformType.ILLUMINA);
        setStatus(new IlluminaStatus(statusXml));
        if (user != null) {
          setSecurityProfile(new SecurityProfile(user));
        }
        else {
          setSecurityProfile(new SecurityProfile());
        }
      }
      else {
        log.error("No status XML for this run");
      }
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  }

  public IlluminaRun(User user) {
    setPlatformType(PlatformType.ILLUMINA);
    setStatus(new StatusImpl());
    setSecurityProfile(new SecurityProfile(user));
  }
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        JSONArray a = JSONArray.fromObject(json.get("libraries"));
        Set<Library> saveSet = new HashSet<Library>();

        for (JSONObject j : (Iterable<JSONObject>) a) {
          try {
            SecurityProfile sp = null;
            Sample sample = null;
            //String libAlias = null;
            String sampleAlias = j.getString("parentSample");

            for (Sample s : p.getSamples()) {
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Related Classes of com.eaglegenomics.simlims.core.SecurityProfile

  • uk.ac.bbsrc.tgac.miso.core.data.impl.emPCR
  • uk.ac.bbsrc.tgac.miso.core.data.impl.emPCRDilution
  • uk.ac.bbsrc.tgac.miso.core.data.impl.emPCRPool
  • uk.ac.bbsrc.tgac.miso.core.data.impl.ExperimentImpl
  • uk.ac.bbsrc.tgac.miso.core.data.impl.illumina.IlluminaPool
  • uk.ac.bbsrc.tgac.miso.core.data.impl.illumina.IlluminaRun
  • uk.ac.bbsrc.tgac.miso.core.data.impl.Lane
  • uk.ac.bbsrc.tgac.miso.core.data.impl.LibraryDilution
  • uk.ac.bbsrc.tgac.miso.core.data.impl.LibraryImpl
  • uk.ac.bbsrc.tgac.miso.core.data.impl.ls454.LS454Pool
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