/** * Returns node color for a given DataSource. * * @param ds * DataSource * @return Color */ public static Color getColorForDataSource(DataSource ds) { String key = "DataSource.Color." + ds.getId(); if (visual.getProperty(key) != null) { return convertToColor(visual.getProperty(key)); } return defaultColor; }
public static String dataSourceToUri(String graphUri, DataSource dataSource) { return toUri(graphUri, "cv", dataSource.getId()); } public static String ccToUri(String graphUri, ConceptClass cc) {
/** * Returns a JLabel for the data source */ @Override public Object getElementAt(int index) { JLabel label = null; if (index > -1) { DataSource dataSource = dataSources.get(index); String name = dataSource.getFullname(); if (name.trim().length() == 0) name = dataSource.getId(); label = new JLabel(name); label.setName(dataSource.getId()); label.setToolTipText("(" + dataSource.getId() + ") " + dataSource.getDescription()); } return label; }
public String getValue(ONDEXEntity cOrr) throws InvalidOndexEntityException { if(AbstractConcept.class.isAssignableFrom(cOrr.getClass())){ return ((ONDEXConcept)cOrr).getElementOf().getId(); } throw new InvalidOndexEntityException(cOrr.getClass()+": is not an Ondex class for which cv is known"); }
@Override public Set<ONDEXConcept> getConceptsOfDataSource(DataSource dataSource) { Set<Integer> is = new HashSet<Integer>(); try { PreparedStatement getCofDataSource = conn .prepareStatement("select id from concept where sid = ? and DataSource = ?"); getCofDataSource.setLong(1, sid); getCofDataSource.setString(2, dataSource.getId()); ResultSet rs = getCofDataSource.executeQuery(); while (rs.next()) { is.add(rs.getInt(1)); } rs.close(); getCofDataSource.close(); } catch (SQLException e) { // TODO Auto-generated catch block e.printStackTrace(); } return BitSetFunctions.create(this, ONDEXConcept.class, is); }
/** * Generate metadata for Data Source. * @param ds * A Data Source (from the Ondex API). * @return JSONObject * JSONObject containing information about the Data Source. */ private JSONObject buildDataSource(DataSource ds) { JSONObject dsJson= new JSONObject(); dsJson.put(JSONAttributeNames.ID, ds.getId()); dsJson.put(JSONAttributeNames.FULLNAME, ds.getFullname()); dsJson.put(JSONAttributeNames.DESCRIPTION, ds.getDescription()); return dsJson; }
@Override public void start() { for (DataSource dataSource : graph.getMetaData().getDataSources()) { Set<ONDEXConcept> concepts = graph.getConceptsOfDataSource(dataSource); System.out.println("Data source C.V. id\tNumber of instances"); if (concepts.size() > 0) { System.out.println(dataSource.getId() + "\t" + concepts.size()); } } }
@Override public boolean deleteConceptAccession(String accession, DataSource elementOf) { try { PreparedStatement deleteCA = sg.getConnection().prepareStatement("delete from conceptaccession where (sid,id) = (?,?) and accession = ? and DataSource = ?"); deleteCA.setLong(1, getSID()); deleteCA.setInt(2, id); deleteCA.setString(3, accession); deleteCA.setString(4, elementOf.getId()); deleteCA.execute(); deleteCA.close(); return true; } catch (SQLException e) { // TODO Auto-generated catch block e.printStackTrace(); } return false; }
private void step() { boolean match = false; next = null; List<String> ofInterest = new ArrayList<String>(); while (!match && view.hasNext()) { ONDEXRelation r = view.next(); String[] cCvs = arrAnd(r.getFromConcept().getElementOf().getId().split(":"), r.getToConcept().getElementOf().getId().split(":"), validArgs); if (cCvs.length > 0) { match = true; next = cCvs; } } } }
/** * * @param conceptAccessions * @return */ private static final String getAccessionOfCV(Set<ConceptAccession> conceptAccessions, String cv) { for (ConceptAccession acc : conceptAccessions) { if (acc.getElementOf().getId().equals(cv)) { return acc.getAccession(); } } return null; }
@Override protected boolean removeConceptAccession(String accession, DataSource elementOf) { return berkeley.deleteFromDatabase(ConceptAccession.class, new BerkeleyIntegerName(id, accession + elementOf.getId())); }
@Override protected DataSource storeDataSource(DataSource dataSource) { BerkeleyDataSource bcv = BerkeleyDataSource.FACTORY.convert(dataSource); if (berkeley.existsInDatabase(DataSource.class, dataSource.getId())) { berkeley.fireEventOccurred(new DuplicatedEntryEvent( Config.properties .getProperty("persistent.BerkeleyONDEXGraphMetaData.DuplicatedDataSource") + dataSource.getId(), "[BerkeleyONDEXGraphMetaData - storeDataSource]")); } else { berkeley.insertIntoDatabase(DataSource.class, dataSource.getId(), bcv.serialise()); } bcv.setUpdateListener(this); return bcv; }
@Override public ConceptAccession createConceptAccession(String accession, DataSource elementOf, boolean ambiguous) { try { soapGraph.createConceptAccession(graphId, id, new Holder<String>( accession), elementOf.getId(), Boolean.valueOf(ambiguous)); return new SOAPConceptAccession(parent, id, accession, elementOf.getId()); } catch (WebserviceException_Exception e) { parent.fireActionEvent(e, e.getMessage()); e.printStackTrace(); } return null; }
@Override public ConceptAccession getConceptAccession(String accession, DataSource elementOf) { try { if (soapGraph.getConceptAccession(graphId, id, accession, elementOf.getId()) != null) return new SOAPConceptAccession(parent, id, accession, elementOf.getId()); } catch (WebserviceException_Exception e) { parent.fireActionEvent(e, e.getMessage()); e.printStackTrace(); } return null; }
@Override public int compare(ConceptAccession o1, ConceptAccession o2) { // within same DataSource sort first by ambiguity, than by accession if (o1.getElementOf().equals(o2.getElementOf())) { if (!o1.isAmbiguous() && o2.isAmbiguous()) return -1; else if (o1.isAmbiguous() && !o2.isAmbiguous()) return 1; else return o1.getAccession().compareTo(o2.getAccession()); } else { // sort according to DataSource return o1.getElementOf().getId().compareTo(o2.getElementOf().getId()); } }
@Override public boolean deleteConceptAccession(String accession, DataSource elementOf) { try { return soapGraph.deleteConceptAccession(graphId, id, accession, elementOf.getId()); } catch (WebserviceException_Exception e) { parent.fireActionEvent(e, e.getMessage()); e.printStackTrace(); } return false; }
public void start() { ONDEXGraphMetaData metadata = graph.getMetaData(); for (ConceptClass cc : metadata.getConceptClasses()) { System.out.println("ConceptClass " + cc.getId() + " " + cc.getFullname()); System.out.println("\tConcepts = " + graph.getConceptsOfConceptClass(cc).size()); } for (DataSource dataSource : metadata.getDataSources()) { System.out.println("DataSource " + dataSource.getId() + " " + dataSource.getFullname()); System.out.println("\tConcepts = " + graph.getConceptsOfDataSource(dataSource).size()); } for (AttributeName att : metadata.getAttributeNames()) { System.out.println("AttributeName " + att.getId() + " " + att.getFullname()); System.out.println("\tConcepts = " + graph.getConceptsOfAttributeName(att).size()); System.out.println("\tRelations = " + graph.getRelationsOfAttributeName(att).size()); } for (RelationType rt : metadata.getRelationTypes()) { System.out.println("RelationType " + rt.getId() + " " + rt.getFullname()); System.out.println("\tRelations = " + graph.getRelationsOfRelationType(rt).size()); } }
@Override protected ConceptAccession retrieveConceptAccession(String accession, DataSource elementOf) { byte[] array = berkeley.getFromDatabase(ConceptAccession.class, new BerkeleyIntegerName(id, accession + elementOf.getId())); if (array != null) { BerkeleyConceptAccession conceptAccession = BerkeleyConceptAccession .deserialise(berkeley.getAbstractONDEXGraph(), array); array = null; conceptAccession.setUpdateListener(this); return conceptAccession; } return null; }