public PublicationTransformer(Parser parser) { super(parser); attTitle = graph.getMetaData().getAttributeName(MetaData.ATR_PUBLICATION_TITLE); if (attTitle == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.ATR_PUBLICATION_TITLE, Parser .getCurrentMethodName())); } dataSourceNLM = graph.getMetaData().getDataSource( MetaData.CV_PubMedID); if (dataSourceNLM == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.CV_PubMedID, Parser .getCurrentMethodName())); } }
public PublicationTransformer(Parser parser) { super(parser); attTitle = graph.getMetaData().getAttributeName(MetaData.ATR_PUBLICATION_TITLE); if (attTitle == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.ATR_PUBLICATION_TITLE, Parser .getCurrentMethodName())); } dataSourceNLM = graph.getMetaData().getDataSource( MetaData.CV_PubMedID); if (dataSourceNLM == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.CV_PubMedID, Parser .getCurrentMethodName())); } }
public PublicationTransformer(Parser parser) { super(parser); attTitle = graph.getMetaData().getAttributeName(MetaData.ATR_PUBLICATION_TITLE); if (attTitle == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.ATR_PUBLICATION_TITLE, Parser .getCurrentMethodName())); } dataSourceNLM = graph.getMetaData().getDataSource( MetaData.CV_PubMedID); if (dataSourceNLM == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.CV_PubMedID, Parser .getCurrentMethodName())); } }
public PublicationTransformer(Parser parser) { super(parser); attTitle = graph.getMetaData().getAttributeName(MetaData.ATR_PUBLICATION_TITLE); if (attTitle == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.ATR_PUBLICATION_TITLE, Parser .getCurrentMethodName())); } dataSourceNLM = graph.getMetaData().getDataSource( MetaData.CV_PubMedID); if (dataSourceNLM == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.CV_PubMedID, 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())); } }
Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_IS_A, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_INHIBITED_BY, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_ACTIVATED_BY, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_PART_OF_CATALYSING_CLASS, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_CATALYSED_BY, Parser.getCurrentMethodName())); Parser.propagateEventOccurred(new RelationTypeMissingEvent(MetaData.RT_COFACTORS_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())); } }
/** * Create a RelationType, if missing in metadata. * * @param name - Name of RelationType to be contained * @return RelationType */ private RelationType getRelationType(String name) { RelationType rt = aog.getMetaData().getRelationType(name); if (rt != null) { return aog.getMetaData().getFactory().createRelationType(rt.getId(),rt); } else { Parser.propagateEventOccurred( new RelationTypeMissingEvent("Missing RelationType: "+name, "getRelationType(String name)")); } return null; }
/** * Create a RelationType, if missing in metadata. * * @param name * Name of RelationType to be contained * @return RelationType */ private RelationType getRelationType(String name) { RelationType rt = aog.getMetaData().getRelationType(name); if (rt != null) { return aog.getMetaData().getFactory().createRelationType(rt.getId(), rt); } else { Parser.propagateEventOccurred(new RelationTypeMissingEvent( "Missing RelationType: " + name, "getRelationType(String name)")); } return null; }
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(); } }
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())); } }
/** * 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())); }