private void setOptionalArguements() throws InvalidPluginArgumentException { EventType so = new GeneralOutputEvent("Starting OXL parsing...", "[Parser - start]"); so.setLog4jLevel(Level.INFO); fireEventOccurred(so); String[] gdss = (String[]) args .getObjectValueArray(ArgumentNames.IGNORE_ATTRIBUTE_ARG); for (String gds : gdss) { AttributeName attname = graph.getMetaData().getAttributeName(gds); if (attname != null) { if (ignoreGDSAttributeGDS == null) { ignoreGDSAttributeGDS = new HashSet<AttributeName>(); } ignoreGDSAttributeGDS.add(attname); } else { fireEventOccurred(new AttributeNameMissingEvent(gds + " is not found in the metadata (ignoring parameter)", "[Parser - start]")); } } }
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(); } }
/** * 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())); }
fireEventOccurred(new AttributeNameMissingEvent(MetaData.accHit, getCurrentMethodName())); hitAttr = graph.getMetaData().getFactory()
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())); } }
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new AttributeNameMissingEvent( RT_HAS_SIMILAR_SEQUENCE, Mapping.getCurrentMethodName())); ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new AttributeNameMissingEvent( ATT_BITSCORE, Mapping.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())); } }
MetaData.ATR_TAXID); if (attTaxId == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent( MetaData.ATR_TAXID, Parser.getCurrentMethodName()));
MetaData.ATR_TAXID); if (attTaxId == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent( MetaData.ATR_TAXID, Parser.getCurrentMethodName()));
MetaData.ATR_TAXID); if (attTaxId == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent( MetaData.ATR_TAXID, Parser.getCurrentMethodName()));
MetaData.ATR_TAXID); if (attTaxId == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent( MetaData.ATR_TAXID, Parser.getCurrentMethodName()));
MetaData.ATR_DELTAGO); if (deltaGo == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent( MetaData.CV_PubMedID, Parser.getCurrentMethodName()));
MetaData.ATR_DELTAGO); if (deltaGo == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent( MetaData.CV_PubMedID, Parser.getCurrentMethodName()));
MetaData.ATR_DELTAGO); if (deltaGo == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent( MetaData.CV_PubMedID, Parser.getCurrentMethodName()));
MetaData.ATR_DELTAGO); if (deltaGo == null) { Parser.propagateEventOccurred(new AttributeNameMissingEvent( MetaData.CV_PubMedID, Parser.getCurrentMethodName()));