@Override protected DataSource resolveExternally(String name) { return og.getMetaData().getDataSource(name); } };
public DataSource safeFetchDataSource(String id) { DataSource dataSource = metaData.getDataSource(id); if (dataSource == null) { dataSource = metaData.getFactory().createDataSource(id); } return dataSource; }
protected static DataSource createDataSource(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ DataSource dataSource = meta.getDataSource(type); if(dataSource == null)dataSource = meta.getFactory().createDataSource(type); return dataSource; }
@Override public DataSource getElementOf() { String a = EntityHelper.fetchString(sg, "concept", "DataSource", id); return sg.getMetaData().getDataSource(a); }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public DataSource requireDataSource(String id) throws DataSourceMissingException { DataSource dataSource = graph.getMetaData().getDataSource(id); if (dataSource == null) throw new DataSourceMissingException("DataSource " + id + " missing"); else return dataSource; }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public DataSource requireDataSource(String id) throws DataSourceMissingException { DataSource dataSource = graph.getMetaData().getDataSource(id); if (dataSource == null) throw new DataSourceMissingException("DataSource " + id + " missing"); else return dataSource; }
protected static DataSource createDataSource(ONDEXGraphMetaData meta, String type) throws NullValueException, EmptyStringException{ DataSource dataSource = meta.getDataSource(type); if(dataSource == null)dataSource = meta.getFactory().createDataSource(type); return dataSource; }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public DataSource requireDataSource(String id) throws DataSourceMissingException { DataSource dataSource = graph.getMetaData().getDataSource(id); if (dataSource == null) throw new DataSourceMissingException("DataSource " + id + " missing"); else return dataSource; }
/** * fetches the required metadata or throws a respective runtime * exception if it doesn't exist. * * @param id the id of the metadata object. */ public DataSource requireDataSource(String id) throws DataSourceMissingException { DataSource dataSource = graph.getMetaData().getDataSource(id); if (dataSource == null) throw new DataSourceMissingException("Data Source " + id + " missing"); else return dataSource; }
/** * Get cv * * @param graph * @param type * @return */ public static DataSource createDataSource(final ONDEXGraph graph, final String type) { ONDEXGraphMetaData meta = graph.getMetaData(); DataSource dataSource = meta.getDataSource(type); if (dataSource == null) dataSource = meta.getFactory().createDataSource(type); return dataSource; }
public Blast(String blastDir, String pfamPfad, String tmpDir, String evalue, String bitscore, String hmmThreshold, ONDEXGraph graph, AttributeName seqAtt, ConceptClass conceptType) { super(blastDir, pfamPfad, tmpDir, evalue, bitscore, hmmThreshold, graph, seqAtt, conceptType); this.ccPfam = graph.getMetaData().getConceptClass(MetaData.CC_Pfam); this.dataSourcePfam = graph.getMetaData().getDataSource( MetaData.CV_PFAM); this.blast = graph.getMetaData().getEvidenceType(EV_BLAST); }
/** * initialise Ondex meta-data */ private void initMetaData() { // basic concept meta data dsCHEMBL = graph.getMetaData().getDataSource(DS_CHEMBL); dsVO = graph.getMetaData().getDataSource(DS_VO); ccComp = graph.getMetaData().getConceptClass(CC_COMP); ccThing = graph.getMetaData().getConceptClass(CC_THING); evidencetype = graph.getMetaData().getEvidenceType(ET_IMPD); rtIsa = graph.getMetaData().getRelationType(RT_ISA); }
public void start() { FileFilter filter = setupFilters(graph.getConceptsOfConceptClass(graph .getMetaData().getConceptClass(MetaData.CC_ProtFam)), graph .getMetaData().getDataSource(MetaData.CV_PDB)); try { transformer = new ProteinTransformer(graph); ReadFiles(filter); } catch (Exception e) { e.printStackTrace(); } } }
public Decypher(String programDir, String pfamPfad, String tmpDir, String evalue, String bitscore, String hmmThreshold, ONDEXGraph graph, AttributeName seqAtt, ConceptClass conceptType) { super(programDir, pfamPfad, tmpDir, evalue, bitscore, hmmThreshold, graph, seqAtt, conceptType); this.hmmer = graph.getMetaData().getEvidenceType(EV_HMMER); this.ccPfam = graph.getMetaData().getConceptClass( MetaData.CC_Pfam); this.dataSourcePfam = graph.getMetaData().getDataSource(MetaData.CV_PFAM); }
public Hmmer(String blastDir, String pfamPfad, String tmpDir, String evalue, String bitscore, String hmmThreshold, ONDEXGraph graph, AttributeName seqAtt, ConceptClass conceptType) { super(blastDir, pfamPfad, tmpDir, evalue, bitscore, hmmThreshold, graph, seqAtt, conceptType); this.ccPfam = graph.getMetaData().getConceptClass( MetaData.CC_Pfam); this.dataSourcePfam = graph.getMetaData().getDataSource(MetaData.CV_PFAM); this.hmmer = graph.getMetaData().getEvidenceType(EV_HMMER); }
public static void initialiseMetaData(ONDEXGraph g) { graph = g; ONDEXGraphMetaData metaData = graph.getMetaData(); dataSource = metaData.getFactory().createDataSource("BCSDB", "bacterial carbohydrate structure database"); cc = metaData.getConceptClass("Taxon"); et = metaData.getEvidenceType("IMPD"); external = metaData.getDataSource("TX"); // as used by NCBI Taxonomy parser taxidAttributeName = metaData.getAttributeName("TAXID"); }
public ECNumberTransformer(Parser parser) { super(parser); ccEC = graph.getMetaData().getConceptClass(MetaData.CC_EC); if (ccEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CC_EC, Parser.getCurrentMethodName())); } dataSourceEC = graph.getMetaData().getDataSource(MetaData.CV_EC); if (dataSourceEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_EC, Parser.getCurrentMethodName())); } }
public ECNumberTransformer(Parser parser) { super(parser); ccEC = graph.getMetaData().getConceptClass(MetaData.CC_EC); if (ccEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CC_EC, Parser.getCurrentMethodName())); } dataSourceEC = graph.getMetaData().getDataSource(MetaData.CV_EC); if (dataSourceEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_EC, Parser.getCurrentMethodName())); } }
public ECNumberTransformer(Parser parser) { super(parser); ccEC = graph.getMetaData().getConceptClass(MetaData.CC_EC); if (ccEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CC_EC, Parser.getCurrentMethodName())); } dataSourceEC = graph.getMetaData().getDataSource(MetaData.CV_EC); if (dataSourceEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_EC, Parser.getCurrentMethodName())); } }
public ECNumberTransformer(Parser parser) { super(parser); ccEC = graph.getMetaData().getConceptClass(MetaData.CC_EC); if (ccEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CC_EC, Parser.getCurrentMethodName())); } dataSourceEC = graph.getMetaData().getDataSource(MetaData.CV_EC); if (dataSourceEC == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_EC, Parser.getCurrentMethodName())); } }