/** * 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); } } }
/** * 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)"));
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()));
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())); } }
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())); } }
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]"));
/** * 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())); }
if (dataSourceTP == null) Parser.propagateEventOccurred(new DataSourceMissingEvent("TransPath DataSource is null", methodName)); if (dataSourcePMID == null) Parser.propagateEventOccurred(new DataSourceMissingEvent("TransPath PMID is null", methodName));
if (dataSource_go == null) { continueRun = false; fireEventOccurred(new DataSourceMissingEvent("Missing DataSource: GO", getName()));