/** * Constructor for a customized message with extension. * * @param message * String * @param extension * String */ public DataFileErrorEvent(String message, String extension) { super(message, extension); super.desc = "An error occurred with one or more data files."; this.setLog4jLevel(Level.ERROR); }
/** * Constructor for a customized message with extension. * * @param message * String * @param extension * String */ public NullValueEvent(String message, String extension) { super(message,extension); super.desc = "One or more values are null."; this.setLog4jLevel(Level.ERROR); }
/** * Constructor for a customized message with extension. * * @param message * String * @param extension * String */ public DatabaseErrorEvent(String message, String extension) { super(message, extension); super.desc = "An error occurred with the persistent layer."; this.setLog4jLevel(Level.ERROR); }
public CompoundTransformer(Parser parser) { super(parser); ccComp = graph.getMetaData().getConceptClass(MetaData.CC_COMPOUND); if (ccComp == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_COMPOUND, Parser.getCurrentMethodName())); } rtCofectorOf = graph.getMetaData().getRelationType(MetaData.RT_COFACTORS_BY); if (rtCofectorOf == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_COFACTORS_BY, Parser.getCurrentMethodName())); } attMolWeight = graph.getMetaData().getAttributeName(MetaData.ATR_MOLWEIGHT); if (attMolWeight == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent(MetaData.ATR_MOLWEIGHT, Parser.getCurrentMethodName())); } dataSourceSmiles = graph.getMetaData().getDataSource(MetaData.CV_SMILES); if (dataSourceSmiles == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_SMILES, Parser.getCurrentMethodName())); } }
public GeneTransformer(Parser parser) { super(parser); try { ccGene = graph.getMetaData().getConceptClass(MetaData.CC_Gene); if (ccGene == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_Gene, Parser.getCurrentMethodName())); } rtSetIsPartOf = graph.getMetaData().getRelationType(MetaData.RT_ENCODED_BY); if (rtSetIsPartOf == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_ENCODED_BY, Parser.getCurrentMethodName())); } attTaxId = graph.getMetaData().getAttributeName(MetaData.ATR_TAXID); if (attTaxId == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent(MetaData.ATR_TAXID, Parser.getCurrentMethodName())); } } catch (Exception e) { e.printStackTrace(); } }
@Override public void start() throws PluginConfigurationException { setOptionalArguements(); getInputAndStart(); GeneralOutputEvent so1 = new GeneralOutputEvent( "OXL parsing finished.", "[Parser - start]"); so1.setLog4jLevel(Level.INFO); fireEventOccurred(so1); }
private void log(String s) { fireEventOccurred(new GeneralOutputEvent(s, "")); }
private void logFail(String s) { EventType e = new InconsistencyEvent(s, ""); e.setLog4jLevel(Level.ERROR); fireEventOccurred(e); } }
@Override public void start() throws Exception { setupMetaData(); Map<Integer, Set<Integer>> taxId2CidSet = createTaxIdIndex(); int[] taxIDArray = createTaxIdArray(taxId2CidSet); setupDecipherAlignment(); if (algo != null && dcAlign != null) { runMapping(taxIDArray, taxId2CidSet); } else { fireEventOccurred(new WrongParameterEvent( "Alignment could not be initialized with these parameters. " , getCurrentMethodName())); } }
private void complain(String string) { InconsistencyEvent event = new InconsistencyEvent(string, ""); event.setLog4jLevel(Level.DEBUG); fireEventOccurred(event); }
/** * Constructor for a customized message with extension. * * @param message * String * @param extension * String */ public SerialisationFailedEvent(String message, String extension) { super(message, extension); super.desc = "An error during ONDEX object serialisation occurred."; this.setLog4jLevel(Level.ERROR); }
/** * Constructor for a customized message with extension. * * @param message * String * @param extension * String */ public DeserialisationFailedEvent(String message, String extension) { super(message, extension); super.desc = "An error during ONDEX object deserialisation occurred."; this.setLog4jLevel(Level.ERROR); }
public CompoundTransformer(Parser parser) { super(parser); ccComp = graph.getMetaData().getConceptClass(MetaData.CC_COMPOUND); if (ccComp == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_COMPOUND, Parser.getCurrentMethodName())); } rtCofectorOf = graph.getMetaData().getRelationType(MetaData.RT_COFACTORS_BY); if (rtCofectorOf == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_COFACTORS_BY, Parser.getCurrentMethodName())); } attMolWeight = graph.getMetaData().getAttributeName(MetaData.ATR_MOLWEIGHT); if (attMolWeight == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent(MetaData.ATR_MOLWEIGHT, Parser.getCurrentMethodName())); } dataSourceSmiles = graph.getMetaData().getDataSource(MetaData.CV_SMILES); if (dataSourceSmiles == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_SMILES, Parser.getCurrentMethodName())); } }
public GeneTransformer(Parser parser) { super(parser); try { ccGene = graph.getMetaData().getConceptClass(MetaData.CC_Gene); if (ccGene == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_Gene, Parser.getCurrentMethodName())); } rtSetIsPartOf = graph.getMetaData().getRelationType(MetaData.RT_ENCODED_BY); if (rtSetIsPartOf == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_ENCODED_BY, Parser.getCurrentMethodName())); } attTaxId = graph.getMetaData().getAttributeName(MetaData.ATR_TAXID); if (attTaxId == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent(MetaData.ATR_TAXID, Parser.getCurrentMethodName())); } } catch (Exception e) { e.printStackTrace(); } }
@Override public void start() throws Exception { GeneralOutputEvent goe = new GeneralOutputEvent("Start parsing Phytozome organism...", "[Parser - start()]"); goe.setLog4jLevel(Level.INFO); fireEventOccurred(goe); //parse FASTA, GFF3 and SYNONYM files GenomicParser genomic = new GenomicParser(genomeReg); genomic.start(graph, args, this); goe = new GeneralOutputEvent("Successfully parsed Phytozome.", "[Parser - start()]"); fireEventOccurred(goe); }
private void log(String s) { fireEventOccurred(new GeneralOutputEvent(s, "")); }
private void logFail(String s) { EventType e = new InconsistencyEvent(s, ""); e.setLog4jLevel(Level.ERROR); fireEventOccurred(e); } }
public CompoundTransformer(Parser parser) { super(parser); ccComp = graph.getMetaData().getConceptClass(MetaData.CC_COMPOUND); if (ccComp == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_COMPOUND, Parser.getCurrentMethodName())); } rtCofectorOf = graph.getMetaData().getRelationType(MetaData.RT_COFACTORS_BY); if (rtCofectorOf == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_COFACTORS_BY, Parser.getCurrentMethodName())); } attMolWeight = graph.getMetaData().getAttributeName(MetaData.ATR_MOLWEIGHT); if (attMolWeight == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent(MetaData.ATR_MOLWEIGHT, Parser.getCurrentMethodName())); } dataSourceSmiles = graph.getMetaData().getDataSource(MetaData.CV_SMILES); if (dataSourceSmiles == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_SMILES, Parser.getCurrentMethodName())); } }
public CompoundTransformer(Parser parser) { super(parser); ccComp = graph.getMetaData().getConceptClass(MetaData.CC_COMPOUND); if (ccComp == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_COMPOUND, Parser.getCurrentMethodName())); } rtCofectorOf = graph.getMetaData().getRelationType(MetaData.RT_COFACTORS_BY); if (rtCofectorOf == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_COFACTORS_BY, Parser.getCurrentMethodName())); } attMolWeight = graph.getMetaData().getAttributeName(MetaData.ATR_MOLWEIGHT); if (attMolWeight == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent(MetaData.ATR_MOLWEIGHT, Parser.getCurrentMethodName())); } dataSourceSmiles = graph.getMetaData().getDataSource(MetaData.CV_SMILES); if (dataSourceSmiles == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_SMILES, Parser.getCurrentMethodName())); } }
/** * fetches and checks the required metadata. */ private void fetchMetaData() { cc_hierarchy = graph.getMetaData().getConceptClass("HierarchyNode"); if (cc_hierarchy == null) fireEventOccurred(new ConceptClassMissingEvent("CC HierarchyNode is missing!", getName())); rts_isp = graph.getMetaData().getRelationType("member_of"); if (rts_isp == null) fireEventOccurred(new RelationTypeMissingEvent("RT is_p is missing!", getName())); an_taxid = graph.getMetaData().getAttributeName("TAXID"); if (an_taxid == null) fireEventOccurred(new AttributeNameMissingEvent("AN TAXID is missing!", getName())); an_theta = graph.getMetaData().getAttributeName("THETA"); if (an_theta == null) fireEventOccurred(new AttributeNameMissingEvent("AN THETA is missing!", getName())); an_logl = graph.getMetaData().getAttributeName("LOGL"); if (an_logl == null) fireEventOccurred(new AttributeNameMissingEvent("AN LOGL is missing!", getName())); dataSource_unknown = graph.getMetaData().getDataSource("unknown"); if (dataSource_unknown == null) fireEventOccurred(new DataSourceMissingEvent("DataSource unknown is missing", getName())); ev = graph.getMetaData().getEvidenceType("STOCHASTIC"); if (ev == null) fireEventOccurred(new EvidenceTypeMissingEvent("Evidence STOCHASTIC is missing!", getName())); }