Exemplo n.º 1
0
  @Override
  public boolean isBetaGTMspI(Sample s) {
    String enzymeString;
    try {
      if (s.getParentId() != null) {
        // if it has a parent sample, which means it's a facility library, use its parent sample to
        // check for library type
        s = sampleService.getSampleById(s.getParentId());
      }
      if (!s.getSampleType().getIName().equalsIgnoreCase("dna")) { // not dna, so must be library
        enzymeString =
            (String)
                MetaHelper.getMetaValue(
                    HELPTAG_LIB_AREA, RESTRICTION_ENZYME_META_KEY, s.getSampleMeta());
      } else { // genomic DNA
        enzymeString =
            (String)
                MetaHelper.getMetaValue(
                    HELPTAG_DNA_AREA, TYPE_OF_HELP_LIBRARY_REQUESTED_META_KEY, s.getSampleMeta());
      }

      if (enzymeString.equals("beta-GT-MspI")) {
        return true;
      }
    } catch (MetadataException e) {
      // not found
      logger.debug(
          "Restriction Enzyme Meta (and libraryToCreate meta) not found for Sample id = "
              + s.getId());
    }
    return false;
  }
Exemplo n.º 2
0
  @Override
  public List<SampleDraft> getAllbetaGTMspISampleDraftsFromJobDraftId(Integer id) {
    JobDraft jobDraft = jobDraftService.getJobDraftById(id);
    List<SampleDraft> sampleDrafts = jobDraft.getSampleDraft();

    List<SampleDraft> betaGTMspSampleDrafts = new ArrayList<SampleDraft>();
    String enzymeString;
    for (SampleDraft sd : sampleDrafts) {
      try {
        if (sd.getSampleType().getIName().equalsIgnoreCase("library")) {
          enzymeString =
              (String)
                  MetaHelper.getMetaValue(
                      HELPTAG_LIB_AREA, RESTRICTION_ENZYME_META_KEY, sd.getSampleDraftMeta());
        } else { // genomic DNA; 1-8-15; dubin
          enzymeString =
              (String)
                  MetaHelper.getMetaValue(
                      HELPTAG_DNA_AREA,
                      TYPE_OF_HELP_LIBRARY_REQUESTED_META_KEY,
                      sd.getSampleDraftMeta());
        }
        if (enzymeString.equals("beta-GT-MspI")) betaGTMspSampleDrafts.add(sd);
      } catch (MetadataException e) {
        // not found
        logger.debug(
            "Restriction Enzyme Meta (and libraryToCreate meta) is not found for Sample Draft id = "
                + id);
      }
    }
    return betaGTMspSampleDrafts;
  }
Exemplo n.º 3
0
 @Override
 public String getTypeOfHelpLibrary(Sample sample) {
   try {
     return (String)
         MetaHelper.getMetaValue(
             HELPTAG_LIB_AREA, RESTRICTION_ENZYME_META_KEY, sample.getSampleMeta());
   } catch (MetadataException e) {
   }
   // not found
   return null;
 }
Exemplo n.º 4
0
 @Override
 public String getTypeOfHelpLibraryRequestedForMacromolecule(Sample sample) {
   try {
     return (String)
         MetaHelper.getMetaValue(
             HELPTAG_DNA_AREA, TYPE_OF_HELP_LIBRARY_REQUESTED_META_KEY, sample.getSampleMeta());
   } catch (MetadataException e) {
   }
   // not found
   return null;
 }