Package org.cipres.treebase.domain.taxon

Examples of org.cipres.treebase.domain.taxon.TaxonVariant

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      }
//      getTaxonHome().reattachUnmodified(t);
    }
   
//    Transaction transaction = getTransaction();
    TaxonVariant tv = new TaxonVariant(ubio, name, fullName, lexicalQualifier);
    tv.setTaxon(t);
    taxonHome.save(tv);
//    transaction.commit();
  }
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  /**
   *
   * @see org.cipres.treebase.domain.taxon.TaxonHome#findTaxonVariantByFullName(java.lang.String)
   */
  public TaxonVariant findTaxonVariantByFullName(String pFullName) {
    TaxonVariant returnVal = null;

    if (!TreebaseUtil.isEmpty(pFullName)) {
      Criteria c = getSession().createCriteria(TaxonVariant.class);
      c.add(Expression.eq("fullName", pFullName));

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   * @see org.cipres.treebase.domain.taxon.TaxonLabelService#findTaxonVariant(org.cipres.treebase.domain.taxon.TaxonLabel)
   */
  public TaxonVariant findTaxonVariant(TaxonLabel pTaxonLabel) {
    String alabel = pTaxonLabel.getTaxonLabel();

    TaxonVariant taxonVariant = getTaxonHome().findTaxonVariantByFullName(alabel);
    if (taxonVariant != null) {
      return taxonVariant;
    }

    String[] parts = null;
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    if (canonicalF != null) {
      returnVal.put("canonicalFormNBO", canonicalF.getTextContent());
    }
    // For this particular element, canonical form is treated as nameString and
    // nameString as fullNameString.
    firstVariant = new TaxonVariant(
      TreebaseUtil.parseLong(id.getTextContent(), null),
      returnVal.get("canonicalFormNBO"),
      returnVal.get("nameStringNBO"),
      null);
    ubioDataList.add(firstVariant);   
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      ncbiPreferredName = null, preferredVariant = null, mNameBankID = null,
      nameString = null, nameStringNBO = null, canonicalFormNBO = null;
    boolean ncbiStringFromTF = false;
    booleanplaceholder bph = new booleanplaceholder();
    longplaceholder lph = new longplaceholder();
    TaxonVariant firstVariant = null;
   
    // XXX 1. Turn label into tri- or binomial, no var./ex./etc.
    testString = normalizeLabelString(pTaxonLabel.getTaxonLabel());

    // XXX 2. Run TaxonFinder query on URL-escaped, normalized label
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    if (pNewVariants == null || pNewVariants.isEmpty()) {
      return pCurrentVariant;
    }

    // default the return value to be current variant. Need to merge
    TaxonVariant returnVal = pCurrentVariant;

    Collection<TaxonVariant> currentVariants = getTaxonHome().findVariantsByTaxon(pTaxon);
    Collection<TaxonVariant> newVariants = new ArrayList<TaxonVariant>();

    // match the namebankid AND the fullname.
    for (TaxonVariant taxonVariant : pNewVariants) {

      boolean matched = false;
      Iterator<TaxonVariant> variantIter = currentVariants.iterator();
      while (variantIter.hasNext() && !matched) {
        TaxonVariant currentVariant = variantIter.next();

        // TODO: move the code to TaxonVariant.equals() method. define hashcode()
        if (TreebaseUtil.isEqual(taxonVariant.getFullName(), currentVariant.getFullName())
          && TreebaseUtil.isEqual(taxonVariant.getNamebankID(), currentVariant
            .getNamebankID())) {

          // already in the list
          matched = true;
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        lexicalQualifier = element.getElementsByTagName("lexicalQualifier").item(0).getTextContent();
        if (LOGGER.isDebugEnabled()) {
          LOGGER.debug("B lexicalQualifier: " + lexicalQualifier); //$NON-NLS-1$
        }
      }
      txnVariantList.add(new TaxonVariant(
        nameBankID,
        nameString,
        fullNameString,
        lexicalQualifier));     
      if (LOGGER.isDebugEnabled()) {
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  public Collection<TaxonVariant> findTaxonVariantByFullName(String s) {
    return getTaxonLabelHome().findTaxonVariantByFullName(s);
  }
 
  public TaxonVariant findTaxonVariantByID(Long id) {
    TaxonVariant variant = getTaxonLabelHome().findPersistedObjectByID(TaxonVariant.class, id);
    return variant;
  }
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          } catch ( NumberFormatException e ) {
            addMessage(request, "Ignoring malformed TreeBASE1 ID string '" + identifier + "', because: " + e.getMessage());
            LOGGER.error("Couldn't parse legacy ID: "+e.getMessage());
          }
          if ( null != tb1LegacyId && null != index && index.matches(".*taxonVariant.*") ) {
            TaxonVariant tv = getTaxonHome().findVariantByTB1LegacyId(tb1LegacyId);
            LOGGER.debug("Found taxon variant: " + tv.getId());
            if ( null != tv.getTaxon() ) {
              taxaFound.add(tv.getTaxon());
            }
          }
          else if ( null != tb1LegacyId ){
            Taxon taxon = getTaxonHome().findByTB1LegacyId(tb1LegacyId);
            LOGGER.debug("Found taxon: " + taxon.getId());
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            break FINDID;
          }
        }
        if ( validateMe ) {
          Collection<TaxonVariant> variants = getTaxonLabelService().findTaxonVariants(taxonlabel);
          TaxonVariant variant = null;
         
          // one variant, no homonyms
          if ( variants.size() == 1 ) {
            variant = variants.iterator().next();
          }
         
          // homonyms
          else if ( variants.size() > 1 ){
            homonyms.put(taxonlabel.getId(), taxonlabel.getTaxonLabel());
            variant = variants.iterator().next();     
          }
         
          // no variants were found locally in the db
          else {
            variant = getTaxonLabelService().createFromUBIOService(taxonlabel);
           
            // no variants were found by uBio
            if ( variant == null ) {
              if (getTaxonLabelService().getuBioTimeOutError()) {
                ubioResultMessages.add("uBio service was unavailable when checking " + taxonlabel.getTaxonLabel() + ".");
                ubioResultErrors.add("uBio service was unavailable when checking " + taxonlabel.getTaxonLabel() +
                    " try <a href=" + UBIOSEARCHTAXONLABEL
                  + taxonlabel.getTaxonLabel().replace(EMPTYSPACE, "%20")
                  + " target=_blank>UBIO</a> site.");
              }
              else {
                ubioResultMessages.add(taxonlabel.getTaxonLabel() + " is **UNRECOGNIZED**.");
                ubioResultErrors.add(taxonlabel.getTaxonLabel()
                  + " is **UNRECOGNIZED** try <a href=" + UBIOSEARCHTAXONLABEL
                  + taxonlabel.getTaxonLabel().replace(EMPTYSPACE, "%20")
                  + " target=_blank>UBIO</a> site.");
              }
            }
           
            // variants stored by uBio,TODO now check for homonyms
            else {
              ubioResultErrors.add(taxonlabel.getTaxonLabel()
                + " was located in uBio, see: <a href=" + UBIOTAXONRECORD
                + variant.getNamebankID()
                + " target=_blank>UBIO</a> site.");             
            }
          }
          setStoreTaxonVariant(variant,taxonlabel);
          ubioResultMessages.add("Validated "+taxonlabel.getTaxonLabel());
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Related Classes of org.cipres.treebase.domain.taxon.TaxonVariant

  • org.cipres.treebase.dao.taxon.TaxonDAO
  • org.cipres.treebase.domain.Annotation
  • org.cipres.treebase.service.taxon.TaxonLabelServiceImpl
  • org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest
  • org.cipres.treebase.service.tree.PhyloTreeServiceImplTest
  • org.cipres.treebase.util.CreateTaxonVariant
  • org.cipres.treebase.util.LoadTaxonData
  • org.cipres.treebase.util.MergeDuplicateTaxa
  • org.cipres.treebase.web.controllers.EditTaxonLabelController
  • org.cipres.treebase.web.controllers.ListTaxaController
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