Examples of TaxonVariant

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

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    BindException bindExp) throws Exception {
    List<String> ubioResultErrors = new ArrayList<String>();
    TaxonLabel taxonLabel = (TaxonLabel) command;
    taxonLabel.setTaxonVariant(null);
    processRedirection(request, "onSubmit");
    TaxonVariant variant = getTaxonVariant(request, taxonLabel, ubioResultErrors);
    if ( variant != null ) {
      Map<Long,String> homonyms = (Map<Long,String>)request.getSession().getAttribute("homonyms");
      if ( homonyms != null ) {
        homonyms.remove(taxonLabel.getId());
        request.getSession().setAttribute("homonyms", homonyms);
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Examples of org.cipres.treebase.domain.taxon.TaxonVariant

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    TaxonLabel taxonLabel,
    List<String> ubioResultErrors) {
    String tvId = request.getParameter("taxonvariantid");
    String manualIdString = request.getParameter("manualid");
    Long manualId = null;
    TaxonVariant variant = null;
    if ( ! manualIdString.equals("") ) {
      try {
        manualId = Long.parseLong(manualIdString);
      } catch ( NumberFormatException e ) {
        ubioResultErrors.add("Not a valid ID: "+manualIdString);
        return variant;
      }
    } 
    if ( manualId == null ) {
      // 1a or 1b depending whether findTaxonVariantByID returns a variant or null
      try {
        variant = getTaxonLabelService().findTaxonVariantByID(Long.parseLong(tvId));
      } catch ( NumberFormatException e ) {
        LOGGER.info("NumberFormatException, user supplied taxon variant id was probably null: "+tvId);
      }
    }
    else {
      Taxon taxon = null;
      taxon = getTaxonHome().findByUBIOTaxId(manualId);
      if ( taxon != null ) {
        // 2a
        Collection<TaxonVariant> variants = getTaxonHome().findVariantsByTaxon(taxon);
        variant = variants.iterator().next();
      }
      else {
        // 2b
        TaxonLabelService taxonLabelService = getTaxonLabelService();
        Integer ncbiId = taxonLabelService.findNcbiTaxIdByUBIOTaxId(manualId); 
        Taxon newTaxon = null;
        TaxonVariant newVariant = null;
        if ( null != ncbiId ) {
          String ncbiPreferredName = taxonLabelService.getNCBIPreferredName(ncbiId.toString());
          newTaxon = new Taxon(ncbiPreferredName,manualId,ncbiId);
          newVariant = new TaxonVariant(manualId,taxonLabel.getTaxonLabel(),ncbiPreferredName,"canonical form");         
        }       
        else {
          newTaxon = new Taxon();
          newTaxon.setName(taxonLabel.getTaxonLabel());
          newTaxon.setUBioNamebankId(manualId);         
          newVariant = new TaxonVariant(manualId,taxonLabel.getTaxonLabel(),taxonLabel.getTaxonLabel(),"canonical form");
        }
        newVariant.setTaxon(newTaxon);
        getTaxonHome().store(newTaxon);
        getTaxonHome().store(newVariant);
        variant = newVariant;
      }
    }
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Examples of org.cipres.treebase.domain.taxon.TaxonVariant

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    TaxonLabel txnLabel = getTaxonLabelService().findByID(Long.parseLong(taxonlabelid));
    if (LOGGER.isDebugEnabled()) {
      LOGGER.debug("VALUE OF Taxon Label ID in FORM BACKING =" + taxonlabelid);
    }
    Collection<TaxonVariant> variants = getTaxonLabelService().findTaxonVariants(txnLabel);   
    TaxonVariant currentVariant = txnLabel.getTaxonVariant();
    if ( currentVariant != null ) {
      request.getSession().setAttribute("currentVariantId", currentVariant.getId());   
      if ( ! variants.contains(currentVariant) ) {
        variants.add(currentVariant);
      }
    }
    request.getSession().setAttribute("variants", variants);
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