/** * gets the set of data sources as from in restrictions, if empty return * than map to anything * * @return */ private Set<DataSource> getExclusiveDataSources() throws InvalidPluginArgumentException { Set<DataSource> dataSources = new HashSet<DataSource>(); if (args.getOptions().get(ArgumentNames.DS_ACCESSION_RESTRICTION_ARG) != null) { List<String> valueList = args.getObjectValueList( ArgumentNames.DS_ACCESSION_RESTRICTION_ARG, String.class); for (String value : valueList) { DataSource dataSource = graph.getMetaData() .getDataSource(value); if (dataSource != null) dataSources.add(dataSource); else fireEventOccurred(new DataSourceMissingEvent( value.toString(), getCurrentMethodName())); } return dataSources; } return null; }
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())); } }
DataSource dataSource = graph.getMetaData().getDataSource(dsname); if (dataSource == null) { fireEventOccurred(new DataSourceMissingEvent(dataSource + " not found: ignoring", getCurrentMethodName())); continue;
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); } } }
fireEventOccurred(new DataSourceMissingEvent(CV, "[Parser - start]")); return;
fireEventOccurred(new DataSourceMissingEvent( "Mapping: " + key + " to " + dataSourceMapping.get(key),
DataSource ds = graph.getMetaData().getDataSource(dsId); if (ds == null) { fireEventOccurred(new DataSourceMissingEvent("DataSource " + dsId + " not found.", "[Transformer - start]")); } else { DataSource elementOf = graph.getMetaData().getDataSource(typeId); if (elementOf == null) { fireEventOccurred(new DataSourceMissingEvent("DataSource " + typeId + " not found.", "[Transformer - start]")); return;
fireEventOccurred(new DataSourceMissingEvent(cvName + " does not exist : creating", getCurrentMethodName())); dataSource = graph.getMetaData().getFactory().createDataSource(cvName); fireEventOccurred(new DataSourceMissingEvent(cvaName + " does not exist", getCurrentMethodName())); return;
/** * sets the ONDEXGraph and starts the parser */ public void start() throws InvalidPluginArgumentException { if (args.getUniqueValue(ArgumentNames.CV_ARG) != null) { cvToUse = (String) args.getUniqueValue(ArgumentNames.CV_ARG); if (graph.getMetaData().getDataSource(cvToUse) == null) { graph.getMetaData().getFactory().createDataSource(cvToUse); fireEventOccurred(new DataSourceMissingEvent( "The specified DataSource is not part of the metadata, therefore creating new one.", "[Parser - start]")); } } taxidToUse = (String) args.getUniqueValue(ArgumentNames.TAXID_TO_USE_ARG); try { ReadAllFiles(); // clean up to enable execute from scratch SinkFactory.getInstance().clearCache(); TransformerFactory.instanceRegister.clear(); } catch (Exception e) { e.printStackTrace(); } }
DataSource dataSource = aog.getMetaData().getDataSource(link.getCv()); if (dataSource == null) { Parser.propagateEventOccurred(new DataSourceMissingEvent("DataSource " + link.getCv() + " not detected", "createGene(GeneObject g)"));
fireEventOccurred(new DataSourceMissingEvent( "Mapping: " + key + " to " + dataSourceMapping.get(key),
net.sourceforge.ondex.parser.ec.MetaData.DS_EC); if (dataSourceEC == null) fireEventOccurred(new DataSourceMissingEvent( net.sourceforge.ondex.parser.ec.MetaData.DS_EC, getCurrentMethodName())); MetaData.cvGO); if (dataSourceGO == null) fireEventOccurred(new DataSourceMissingEvent(MetaData.cvGO, getCurrentMethodName()));
DataSource ds = graph.getMetaData().getDataSource(dsId); if (ds == null) { fireEventOccurred(new DataSourceMissingEvent("DataSource " + dsId + " not found.", getCurrentMethodName())); } else {
Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_AraC, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_NCBIGene, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_ECOCYC, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_METACYC, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_CAS, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_KNAPSACK, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_PUBCHEM, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_REFSEQGene, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_UniProt, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_PIR, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_PID, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_KEGG, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_CHEBI, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_TAIR, Parser.getCurrentMethodName()));
Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_EcoC, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_NCBIGene, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_ECOCYC, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_CAS, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_REFSEQGene, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_UniProt, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_PIR, Parser.getCurrentMethodName()));
Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_MetaC, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_NCBIGene, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_ECOCYC, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_CAS, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_REFSEQGene, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_UniProt, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_PIR, Parser.getCurrentMethodName()));
Parser.propagateEventOccurred(new DataSourceMissingEvent(Parser.cvToUse, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_NCBIGene, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_ECOCYC, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_CAS, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_REFSEQGene, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_UniProt, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new DataSourceMissingEvent(MetaData.CV_PIR, Parser.getCurrentMethodName()));