How to use

createConceptAccession

method

in

net.sourceforge.ondex.core.ONDEXConcept

public ONDEXConcept lookupPublication(String id) {
  Holder h = lookupConcept(pubIndex, publication, id);
  ONDEXConcept c = h.concept;
  if (h.isNew)
    c.createConceptAccession(id, pmid, false);
  return c;
}

public synchronized ConceptAccession getAccession ( String accession, DataSource dataSrc, boolean isAmbiguous, ONDEXConcept concept )
{
  // TODO: is the ID unique? Is it concept-unique? 
  return this.cacheGet ( 
    ConceptAccession.class, accession,
    () -> concept.createConceptAccession ( accession, dataSrc, isAmbiguous )
  );        
}

private void assignAccessions(ONDEXConcept c, Set<String> accs) {
  for (String acc : accs) {
    String[] split = dataSourceLookup.recognize(acc);
    if (split != null) {
      String cvStr = split[0], value = split[1];
      DataSource dataSource = dataSourceLookup.get(cvStr);
      if (dataSource != null) {
        c.createConceptAccession(value, dataSource, false);
      }
    } else {
      unmatchedKeys.add(acc);
    }
  }
}

private void assignAccessions(ONDEXConcept c, Set<String> accs) {
  for (String acc : accs) {
    String[] split = dataSourceLookup.recognize(acc);
    if (split != null) {
      String cvStr = split[0], value = split[1];
      DataSource dataSource = dataSourceLookup.get(cvStr);
      if (dataSource != null) {
        c.createConceptAccession(value, dataSource, false);
      }
    } else {
      unmatchedKeys.add(acc);
    }
  }
}

  /**
   * Creates the corresponding ONDEXConcept on the given graph.
   * 
   * @return created publication ONDEXConcept
   */
  public ONDEXConcept createONDEXConcept(int index) {

    if (!taxids[index].isEmpty()) {
      ONDEXConcept c = graph.getFactory().createConcept(taxids[index], dataSource, cc, et);

      // publication associated Attribute
      c.createAttribute(taxidAttributeName, taxids[index], false);
      c.createConceptAccession(taxids[index], external, false);
      
      return c;
    }
    else { throw new RuntimeException("Organism without valid taxid tag!"); } 
  }
}

/**
 * Extracts all target information and creats a new Ondex concept
 * 
 * @param eElement
 * @return
 */
private ONDEXConcept createTarget(Element eElement) {
  // check for existing targets
  String key = getTagValue("target__chemblid", eElement);
  if (!targets.containsKey(key)) {
    // new target concept
    ONDEXConcept c = graph.getFactory().createConcept(key, dsCHEMBL,
        ccTarget, evidencetype);
    c.createConceptName(getTagValue("target__name", eElement), true);
    c.createConceptAccession(key, dsTARGET, false);
    targets.put(key, c);
  }
  return targets.get(key);
}

/**
 * Copies all accessions from old concept to new concept.
 * 
 * @param oldC
 *            old ONDEXConcept
 * @param newC
 *            new ONDEXConcept
 */
private void copyAccessions(ONDEXConcept oldC, ONDEXConcept newC) {
  // iterate over all old accessions
  for (ConceptAccession acc : oldC.getConceptAccessions()) {
    // clone old accession on new concept
    newC.createConceptAccession(acc.getAccession(), acc.getElementOf(), acc.isAmbiguous());
  }
}

@Override
public void nodeToConcept(AbstractNode node) {
  Protein protein = (Protein) node;
  ConceptClass cc = null;
  if (protein.isComplex())
    cc = ccProteinComplex;
  else
    cc = ccProtein;
  ONDEXConcept concept = graph.getFactory().createConcept(protein.getUniqueId(), dataSourceAraC,
      cc, etIMPD);
  
  concept.createAttribute( attTaxId, MetaData.TAXID, false);
  int monomerPos = protein.getUniqueId().indexOf("-MONOMER");
  if (monomerPos != -1){
    concept.createConceptAccession(protein.getUniqueId().subSequence(0, monomerPos).toString(), super.dataSourceTAIR, true);
    String nameWithoutMonomer = protein.getUniqueId().subSequence(0, monomerPos).toString();
    if ( !protein.getSynonym().contains(nameWithoutMonomer))
      concept.createConceptName(nameWithoutMonomer,false );
  }
  protein.setConcept(concept);
}

public static void correctUniprotAccession(OVTK2PropertiesAggregator viewer) {
  ONDEXGraph graph = viewer.getONDEXJUNGGraph();
  ConceptClass prot = graph.getMetaData().getConceptClass("Protein");
  DataSource nc_np = graph.getMetaData().getDataSource("NC_NP");
  for (ONDEXConcept p : graph.getConceptsOfConceptClass(prot)) {
    List<String> newAcc = new ArrayList<String>();
    for (ConceptAccession ca : p.getConceptAccessions()) {
      if (ca.getElementOf().equals(nc_np)) {
        if (ca.getAccession().contains(".")) {
          newAcc.add(ca.getAccession().split("\\.")[0]);
        }
      }
    }
    for (String str : newAcc) {
      p.createConceptAccession(str, nc_np, true);
    }
  }
}

@Override
public void nodeToConcept(AbstractNode node) {
  ECNumber ecNumber = (ECNumber) node;
  ONDEXConcept concept = graph.getFactory().createConcept(ecNumber.getUniqueId(), dataSourceMetaC,
      ccEC, etIMPD);
  concept.createConceptAccession(ecNumber.getUniqueId(), dataSourceEC, false);
  ecNumber.setConcept(concept);    
}

@Override
public void nodeToConcept(AbstractNode node) {
  ECNumber ecNumber = (ECNumber) node;
  ONDEXConcept concept = graph.getFactory().createConcept(ecNumber.getUniqueId(), dataSourceAraC,
      ccEC, etIMPD);
  concept.createConceptAccession(ecNumber.getUniqueId(), dataSourceEC, false);
  ecNumber.setConcept(concept);    
}

@Override
public void nodeToConcept(AbstractNode node) {
  ECNumber ecNumber = (ECNumber) node;
  ONDEXConcept concept = graph.getFactory().createConcept(ecNumber.getUniqueId(), dataSourceMetaC,
      ccEC, etIMPD);
  concept.createConceptAccession(ecNumber.getUniqueId(), dataSourceEC, false);
  ecNumber.setConcept(concept);    
}

@Override
public void nodeToConcept(AbstractNode node) {
  ECNumber ecNumber = (ECNumber) node;
  ONDEXConcept concept = graph.getFactory().createConcept(ecNumber.getUniqueId(), dataSourceBioC,
      ccEC, etIMPD);
  concept.createConceptAccession(ecNumber.getUniqueId(), dataSourceEC, false);
  ecNumber.setConcept(concept);    
}

  @Override
  public void actionPerformed(ActionEvent e) {
    this.setVisible(false);
    editor.acc.setAmbiguous(box.isSelected());

    // has the DataSource of accession changed?
    DataSource dataSource = (DataSource) selection.getSelectedItem();
    if (!editor.acc.getElementOf().equals(dataSource)) {
      // delete old one
      ConceptAccession old = editor.concept.getConceptAccession(editor.acc.getAccession(), editor.acc.getElementOf());
      editor.concept.deleteConceptAccession(editor.acc.getAccession(), editor.acc.getElementOf());
      // create one with new DataSource
      editor.acc = editor.concept.createConceptAccession(old.getAccession(), dataSource, old.isAmbiguous());
    }
  }
}

/**
 * Creates an accession on concept only if it does not already exists
 * 
 * @param target
 *            - relation
 * @param newAcc
 *            - attribute to create
 * @throws AccessDeniedException
 * @throws EmptyStringException
 * @throws NullValueException
 */
public static void addNewAccession(ONDEXConcept target,
    ConceptAccession newAcc) throws NullValueException,
    EmptyStringException, AccessDeniedException {
  if (target.getConceptAccession(newAcc.getAccession(),
      newAcc.getElementOf()) == null)
    target.createConceptAccession(newAcc.getAccession(),
        newAcc.getElementOf(), true);
}

@Override
public void nodeToConcept(AbstractNode node) {
  Publication pub = (Publication) node;
  if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD))
    return;
  ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD);
  
  if (pub.getPubMedId() != 0){
    concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false);
  }
  if (pub.getTitle() != null &&  !pub.getTitle().equals("")){
    concept.createAttribute(attTitle, pub.getTitle(), false);
  }
  pub.setConcept(concept);
}

@Override
public void nodeToConcept(AbstractNode node) {
  Publication pub = (Publication) node;
  if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceBioC, ccPublication, etIMPD))
    return;
  ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceBioC, ccPublication, etIMPD);
  
  if (pub.getPubMedId() != 0){
    concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false);
  }
  if (pub.getTitle() != null &&  !pub.getTitle().equals("")){
    concept.createAttribute(attTitle, pub.getTitle(), false);
  }
  pub.setConcept(concept);
}

@Override
public void nodeToConcept(AbstractNode node) {
  Publication pub = (Publication) node;
  if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceAraC, ccPublication, etIMPD))
    return;
  ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceAraC, ccPublication, etIMPD);
  
  if (pub.getPubMedId() != 0){
    concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false);
  }
  if (pub.getTitle() != null &&  !pub.getTitle().equals("")){
    concept.createAttribute(attTitle, pub.getTitle(), false);
  }
  pub.setConcept(concept);
}

@Override
public void nodeToConcept(AbstractNode node) {
  Publication pub = (Publication) node;
  if(StandardFunctions.nullChecker(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD))
    return;
  ONDEXConcept concept = this.graph.getFactory().createConcept(pub.getUniqueId(), dataSourceMetaC, ccPublication, etIMPD);
  
  if (pub.getPubMedId() != 0){
    concept.createConceptAccession(new String(pub.getPubMedId() + ""), dataSourceNLM, false);
  }
  if (pub.getTitle() != null &&  !pub.getTitle().equals("")){
    concept.createAttribute(attTitle, pub.getTitle(), false);
  }
  pub.setConcept(concept);
}

public int getOrCreateGeneID(String geneId) {
  if (poplarReg.containsGene(geneId)) {
    return poplarReg.getGene(geneId);
  } else {
    ONDEXConcept gene = og.getFactory().createConcept(geneId, dataSourcePHYTOZOME, ccGene, etIMPD);
    gene.createConceptAccession(geneId, dataSourcePHYTOZOME, false);
    gene.createConceptName(geneId, false);
    Integer ondexGeneId = gene.getId();
    gene.createAttribute(anTaxID, Parser.POPLAR_TAX_ID, false);
    poplarReg.addGene(geneId, ondexGeneId);
    return ondexGeneId;
  }
}