Package org.cipres.treebase.domain.taxon

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

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  /**
   * @author mjd 20081204
   */
  public void testFindStudiesByTaxon() {
    Taxon hSap = findHSapTaxon();
    Collection<Study> studies = getFixture().findStudies(hSap);
    logger.info("Query finished; results = " + studies.size() + " studies");
   
    assertTrue(studies.size() > 0);
    for (Study s : studies) {
      boolean thisStudyOK = false;
      for (TaxonLabelSet tls : s.getTaxonLabelSets()) {
        for (TaxonLabel tl : tls.getTaxonLabelsReadOnly()) {
          if (tl.getTaxonVariant() == null || tl.getTaxonVariant().getTaxon() == null) continue;
          if (tl.getTaxonVariant().getTaxon().getId() == hSap.getId()) {
            thisStudyOK = true;
            break;
          }
          if (thisStudyOK) break;
        }
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  /**
   * @author mjd 20081204
   */
  public void testFindTreesByTaxon() {
    Taxon hSap = findHSapTaxon();
    Collection<PhyloTree> trees = getFixture().findTrees(hSap);
    logger.info("Query finished; results = " + trees.size() + " studies");
   
    assertTrue(trees.size() > 0);
    for (PhyloTree t : trees) {
      boolean thisTreeOK = false;
      for (TaxonLabel tl : t.getAllTaxonLabels()) {
        if (tl.getTaxonVariant() == null || tl.getTaxonVariant().getTaxon() == null) continue;
        if (tl.getTaxonVariant().getTaxon().getId() == hSap.getId()) {
          thisTreeOK = true;
          break;
        }
      }
      assertTrue(thisTreeOK);
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  /**
   * @author mjd 20081204
   */
  public void testFindMatricesByTaxon() {
    Taxon hSap = findHSapTaxon();
    Collection<Matrix> matrices = getFixture().findMatrices(hSap);
    logger.info("Query finished; results = " + matrices.size() + " studies");
   
    assertTrue(matrices.size() > 0);
    for (Matrix t : matrices) {
      boolean thisMatrixOK = false;
      for (TaxonLabel tl : t.getAllTaxonLabels()) {
        if (tl.getTaxonVariant() == null || tl.getTaxonVariant().getTaxon() == null) continue;
        if (tl.getTaxonVariant().getTaxon().getId() == hSap.getId()) {
          thisMatrixOK = true;
          break;
        }
      }
      assertTrue(thisMatrixOK);
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    assertNotNull(expansion);
    assertEquals(14, expansion.size());
 
    // And each one of those TVs should refer to the same taxon
    for (TaxonVariant tv : expansion) {
      Taxon t = tv.getTaxon();
      assertTrue(t == tvEolphus.getTaxon() || t == tvCacatua.getTaxon());
    } 
   
    // And moreover the call should be idempotent
    // That is, the expansion of the expansion should be the same as
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    boolean bad = false;
    MergeDuplicateTaxaInterface me = (MergeDuplicateTaxaInterface) ContextManager.getBean("mergeDuplicateTaxa");

    for (String arg : args) {
      Long tId = Long.parseLong(arg);
      Taxon t = getTaxonHome().findPersistedObjectByID(Taxon.class, tId);
      if (t == null) {
        warn("No taxon with id T" + tId);
        bad = true;
      } else
        taxonClass.add(t);
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    Map<String,Set<Taxon>> taxonClasses = new HashMap<String,Set<Taxon>> ();
   
    warn("Scanning database");
    int taxonCount = 0;
    for (TBPersistable obj : getTaxonHome().findAll(Taxon.class)) {
      Taxon t = (Taxon) obj;
      String key = key(t);
      if (! taxonClasses.containsKey(key))
        taxonClasses.put(key, new HashSet<Taxon> ());
      taxonClasses.get(key).add(t);
      taxonCount++;
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  /* WARNING: This method should modify the TaxonSet and TaxonLink objects too, but doesn't.
   * At the time it was written, there were no such objects.  20090409 MJD
   */
  public void doMergeTaxonClass(Set<Taxon> taxonClass) {
    Iterator<Taxon> it = taxonClass.iterator();
    Taxon canonicalTaxon = it.next();
       
    // Find the taxon in the set with the lowest ID number
    while (it.hasNext()) {
      Taxon t = it.next();
      if (t.getId() < canonicalTaxon.getId()) canonicalTaxon = t;
    }
   
    {
      StringBuilder s = new StringBuilder ("Merging taxon class : ");
      for (Taxon t : taxonClass) s.append(t.getId()).append(" ");
      s.append("\n");
      warn(s.toString());
    }
    warn("  Canonical taxon for this set is T" + canonicalTaxon.getId());
   
    // Map all the other taxa to the canonical one
    for (Taxon t : taxonClass) {
      if (t.equals(canonicalTaxon)) continue;
      for (TaxonVariant tv : getTaxonHome().findVariantsByTaxon(t)) {
        tv.setTaxon(canonicalTaxon); 
        getTaxonHome().merge(tv);
      }
      getCurrentSession().flush();
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  public void createTaxon(String[] args) {
    String name = args[0];
    Long ubio = Long.decode(args[1]);
    Integer ncbi = Integer.decode(args[2]);

    Taxon t = new Taxon(name, ubio, ncbi);
    getTaxonHome().save(t);
  }
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    Map<String,Taxon> knownTaxon = new HashMap<String, Taxon> ();
    Map<String,Set<Taxon>> duplicateTaxa = new HashMap<String, Set<Taxon>> ();

    warn("Building knownTaxon cache...");
    for (TBPersistable tX : taxonHome.findAll(Taxon.class)) {
      Taxon t = (Taxon) tX;
      Integer legacyID = t.getTB1LegacyId();
      Integer ncbiID = t.getNcbiTaxId();
      String name = t.getName();
      if (ncbiID != null || name != null) {
        String uniqueKey = name + "," + ncbiID;
        if (knownTaxon.containsKey(uniqueKey)) {
          warn("Duplicate taxa with key '" + uniqueKey + "': " + idListString(t.getId(), knownTaxon.get(uniqueKey).getId()));
          if (mergeDuplicates) {
            if (! duplicateTaxa.containsKey(uniqueKey))
              duplicateTaxa.put(uniqueKey, new HashSet<Taxon>());
            duplicateTaxa.get(uniqueKey).add(t);
            duplicateTaxa.get(uniqueKey).add(knownTaxon.get(uniqueKey));
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      String tvFullName = rec.get("fullNameString");
      String nameBankID = rec.get("uBIO");

      TaxonVariant tv = knownTaxonVariant.get(oldID);

      Taxon t = taxon.get(rec.get("tID"));
      if (t == null) {
        warn("taxonVariant " + oldID + " calls for unknown taxon " +
            rec.get("tID") + "; skipping");
        continue;
      }

      if (tv == null) {
        Long uBioID = TreebaseUtil.parseLong(rec.get("uBIO"), null);

        tv = new TaxonVariant(
            uBioID,
            rec.get("nameString"),
            rec.get("fullNameString"),
            rec.get("lexQual")
        );

        tv.setTaxon(t);
        tv.setTB1LegacyId(oldIDInteger);
        sess.save(tv);
        knownTaxonVariant.put(oldID, tv);
        uncommittedTaxonVariants++;
        warn("Made new TV '" + tvFullName + "'");
      }

      if (tv.getTaxon() == null || tv.getTaxon().equals(t)) {
        Long oldId = tv.getTaxon() == null ? null : tv.getTaxon().getId();
        warn("Mapping TaxonVariant " + tvFullName + " to Taxon " + t.getId() + "; was " + oldId);
        tv.setTaxon(t);
        sess.update(tv);
        uncommittedTaxonVariants++;
      }
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Related Classes of org.cipres.treebase.domain.taxon.Taxon

  • 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.util.CreateTaxon
  • 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.TaxonSearchController
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