/** * gets the set of concept classes as from in restrictions, if empty return * than map to anything * * @return */ private Set<ConceptClass> getExclusiveConceptClasses() throws InvalidPluginArgumentException { Set<ConceptClass> ccs = new HashSet<ConceptClass>(); if (args.getOptions().get(ArgumentNames.CONCEPTCLASS_RESTRICTION_ARG) != null) { List<String> valueList = args.getObjectValueList( ArgumentNames.CONCEPTCLASS_RESTRICTION_ARG, String.class); for (String value : valueList) { ConceptClass cc0; // optional could contain a pair of concept classes for (String s : value.split(",")) { cc0 = graph.getMetaData().getConceptClass(s); if (cc0 != null) ccs.add(cc0); else fireEventOccurred(new ConceptClassMissingEvent( value.toString(), getCurrentMethodName())); } } } return ccs; }
ConceptClass cc = graph.getMetaData().getConceptClass(ccName); if (cc == null) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new ConceptClassMissingEvent( ccName, getCurrentMethodName())); else
args.getUniqueValue(TAG_ARG).toString()); if (classContext == null) { fireEventOccurred(new ConceptClassMissingEvent( "Given ConceptClass not found. " + args.getUniqueValue(TAG_ARG).toString(),
ConceptClass cc = graph.getMetaData().getConceptClass(ccName); if (cc == null) ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new ConceptClassMissingEvent( ccName, getCurrentMethodName())); else
ConceptClass cc = graph.getMetaData().getConceptClass(ccId); if (cc == null) { fireEventOccurred(new ConceptClassMissingEvent( "ConceptClass " + ccId + " not found.", "[Transformer - start]"));
ConceptClass cc = graph.getMetaData().getConceptClass(ccId); if (cc == null) { fireEventOccurred(new ConceptClassMissingEvent( "ConceptClass " + ccId + " not found.", 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(); } }
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(); } }
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(); } }
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(); } }
Parser.propagateEventOccurred(new ConceptClassMissingEvent( MetaData.CC_Protein, Parser.getCurrentMethodName())); MetaData.CC_PROTEIN_COMPLEX); if (ccProteinComplex == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent( MetaData.CC_PROTEIN_COMPLEX, Parser .getCurrentMethodName()));
MetaData.CC_Protein); if (ccProtein == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent( MetaData.CC_Protein, Parser.getCurrentMethodName())); MetaData.CC_PROTEIN_COMPLEX); if (ccProteinComplex == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent( MetaData.CC_PROTEIN_COMPLEX, Parser .getCurrentMethodName()));
MetaData.CC_Protein); if (ccProtein == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent( MetaData.CC_Protein, Parser.getCurrentMethodName())); MetaData.CC_PROTEIN_COMPLEX); if (ccProteinComplex == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent( MetaData.CC_PROTEIN_COMPLEX, Parser .getCurrentMethodName()));
MetaData.CC_Protein); if (ccProtein == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent( MetaData.CC_Protein, Parser.getCurrentMethodName())); MetaData.CC_PROTEIN_COMPLEX); if (ccProteinComplex == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent( MetaData.CC_PROTEIN_COMPLEX, Parser .getCurrentMethodName()));
public PathwayTransformer(Parser parser) { super(parser); ccPathway = graph.getMetaData().getConceptClass(MetaData.CC_PATHWAY); if (ccPathway == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_PATHWAY, Parser.getCurrentMethodName())); } rtMemberIsPart = graph.getMetaData() .getRelationType(MetaData.RT_MEMBER_IS_PART_OF); if (rtMemberIsPart == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_MEMBER_IS_PART_OF, Parser.getCurrentMethodName())); } rtPrecededBy = graph.getMetaData() .getRelationType(MetaData.RT_PRECEDED_BY); if (rtPrecededBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_PRECEDED_BY, Parser.getCurrentMethodName())); } }
public PathwayTransformer(Parser parser) { super(parser); ccPathway = graph.getMetaData().getConceptClass(MetaData.CC_PATHWAY); if (ccPathway == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_PATHWAY, Parser.getCurrentMethodName())); } rtMemberIsPart = graph.getMetaData() .getRelationType(MetaData.RT_MEMBER_IS_PART_OF); if (rtMemberIsPart == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_MEMBER_IS_PART_OF, Parser.getCurrentMethodName())); } rtPrecededBy = graph.getMetaData() .getRelationType(MetaData.RT_PRECEDED_BY); if (rtPrecededBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_PRECEDED_BY, Parser.getCurrentMethodName())); } }
public PathwayTransformer(Parser parser) { super(parser); ccPathway = graph.getMetaData().getConceptClass(MetaData.CC_PATHWAY); if (ccPathway == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_PATHWAY, Parser.getCurrentMethodName())); } rtMemberIsPart = graph.getMetaData() .getRelationType(MetaData.RT_MEMBER_IS_PART_OF); if (rtMemberIsPart == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_MEMBER_IS_PART_OF, Parser.getCurrentMethodName())); } rtPrecededBy = graph.getMetaData() .getRelationType(MetaData.RT_PRECEDED_BY); if (rtPrecededBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_PRECEDED_BY, Parser.getCurrentMethodName())); } }
public PathwayTransformer(Parser parser) { super(parser); ccPathway = graph.getMetaData().getConceptClass(MetaData.CC_PATHWAY); if (ccPathway == null) { Parser.propagateEventOccurred(new ConceptClassMissingEvent(MetaData.CC_PATHWAY, Parser.getCurrentMethodName())); } rtMemberIsPart = graph.getMetaData() .getRelationType(MetaData.RT_MEMBER_IS_PART_OF); if (rtMemberIsPart == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_MEMBER_IS_PART_OF, Parser.getCurrentMethodName())); } rtPrecededBy = graph.getMetaData() .getRelationType(MetaData.RT_PRECEDED_BY); if (rtPrecededBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_PRECEDED_BY, 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())); } }