@Override public ConceptAccession getConceptAccession(String accession, DataSource elementOf) throws NullValueException, EmptyStringException { return parent.getConceptAccession(accession, elementOf); }
boolean ambiguous = concept.getConceptAccession(oldAccession, accession_dataSource).isAmbiguous(); concept.deleteConceptAccession(oldAccession, accession_dataSource); concept.createConceptAccession(replacements.get(oldAccession), accession_dataSource, ambiguous);
boolean ambiguous = concept.getConceptAccession(oldAccession, accession_dataSource).isAmbiguous(); concept.deleteConceptAccession(oldAccession, accession_dataSource); concept.createConceptAccession(replacements.get(oldAccession), accession_dataSource, ambiguous);
if(acDomain.getConceptAccession(domId, interPro) == null) { if(domId.length() > 1 && !domId.equalsIgnoreCase("NULL")) { acDomain.createConceptAccession(domId, interPro,false);
concept.getConceptAccession((String) pair.getFirst(), dataSource).setAmbiguous(accessions.get(pair));
private void writeSynonym(String synonym, String conceptName, ONDEXConcept c) { String check = (String) ValidatorRegistry.validators.get("cvregex").validate(synonym); if (check != null) { DataSource dataSource = aog.getMetaData().getDataSource(check); if (dataSource == null) { if (!reportedMissingCVs.contains(check)) { ONDEXEventHandler.getEventHandlerForSID(aog.getSID()).fireEventOccurred(new DataSourceMissingEvent("DataSource missing => " + check, "")); reportedMissingCVs.add(check); } } else { if (c.getConceptAccession(synonym, dataSource) == null) { c.createConceptAccession(synonym.toUpperCase(), dataSource, false); } } } else { if (!synonym.equalsIgnoreCase(conceptName)) { c.createConceptName(synonym,false); } } }
String ob = obIt.next(); if (ac.getConceptAccession(ob, elementOf) == null) ac.createConceptAccession(ob, elementOf, true); while (merIt.hasNext()) { String mer = merIt.next(); if ((obsoletes == null ||!obsoletes.contains(mer)) || ac.getConceptAccession(mer, elementOf) == null ) { ac.createConceptAccession(mer, elementOf, true); if (ac.getConceptAccession(pid, elementOf) == null) ac.createConceptAccession(pid, elementOf, false); if (loc > -1) { String fakelocus = pid.substring(0, loc); if (ac.getConceptAccession(fakelocus, elementOf) == null) ac.createConceptAccession(fakelocus, elementOf, true);
while (obIt.hasNext()) { String ob = obIt.next(); if (ac.getConceptAccession(ob, elementOf) == null) ac.createConceptAccession(ob, elementOf, true); while (merIt.hasNext()) { String mer = merIt.next(); if ((obsoletes == null || !obsoletes.contains(mer)) && ac.getConceptAccession(mer, elementOf) == null) { ac.createConceptAccession(mer, elementOf, true); if ( ac.getConceptAccession(pid, elementOf) == null) ac.createConceptAccession(pid, elementOf, false); if ( ac.getConceptAccession(locus, elementOf) == null) ac.createConceptAccession(locus, elementOf, true);
@Override public Object getCellEditorValue() { // this is value returned by default editor String newAccession = super.getCellEditorValue().toString(); if (acc == null) { // construct new CA with defaults if (newAccession.trim().length() > 0) acc = concept.createConceptAccession(newAccession, unknown, true); } else { // existing CA check accession update if (!newAccession.equals(acc.getAccession())) { // delete old one ConceptAccession old = concept.getConceptAccession(acc.getAccession(), acc.getElementOf()); concept.deleteConceptAccession(acc.getAccession(), acc.getElementOf()); // keep additional settings and create non empty accession if (newAccession.trim().length() > 0) acc = concept.createConceptAccession(newAccession, old.getElementOf(), old.isAmbiguous()); else // clear existing concept accession from table acc = null; } } // return concept accession instead of string return acc; }
/** * A unification reference is a non-ambiguous accession. * * @param c * ONDEXConcept with unification reference * @param uni * unificationXref used */ private void addUnificationXref(ONDEXConcept c, unificationXref uni) throws Exception { // sanity checks if (uni.getID() == null || uni.getID().isEmpty()) { System.err.println(uni.getRDFId() + " is empty unificationXref."); return; } // get current data source DataSource elementOf = findDataSource(uni.getDB()); if(elementOf.getId().equalsIgnoreCase("unknown")){ System.err.println("DataSource is UNKNOWN"); } if ((DEBUG || c.getConceptAccession(uni.getID(), elementOf) == null) && !(elementOf.getId().equalsIgnoreCase("unknown"))){ c.createConceptAccession(uni.getID(), elementOf, false); } }
/** * Any other relationships with entry of other data sources, marked as * ambiguous. * * @param c * ONDEXConcept with relationship reference * @param rel * relationshipXref used */ private void addRelationshipXref(ONDEXConcept c, relationshipXref rel) throws Exception { // sanity checks if (rel.getID() == null || rel.getID().isEmpty()) { System.err.println(rel.getRDFId() + " is empty relationshipXref."); return; } DataSource elementOf = findDataSource(rel.getDB()); if ((DEBUG || c.getConceptAccession(rel.getID(), elementOf) == null) && !(elementOf.getId().equalsIgnoreCase("unknown"))){ c.createConceptAccession(rel.getID(), elementOf, false); } } // get current data source
@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); }
&& c.getConceptAccession(name, ds) == null) { c.createConceptAccession(name, ds, false);