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())); } }
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()));
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()));
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())); } }
/** * 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(); } }
MetaData.RT_CONSUMED_BY); if (rtCsBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_CONSUMED_BY, Parser.getCurrentMethodName())); MetaData.RT_PRODUCED_BY); if (rtPdBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_PRODUCED_BY, Parser.getCurrentMethodName())); MetaData.RT_MEMBER_IS_PART_OF); if (rtMemberIsPart == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_MEMBER_IS_PART_OF, Parser .getCurrentMethodName()));
MetaData.RT_CONSUMED_BY); if (rtCsBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_CONSUMED_BY, Parser.getCurrentMethodName())); MetaData.RT_PRODUCED_BY); if (rtPdBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_PRODUCED_BY, Parser.getCurrentMethodName())); MetaData.RT_MEMBER_IS_PART_OF); if (rtMemberIsPart == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_MEMBER_IS_PART_OF, Parser .getCurrentMethodName()));
MetaData.RT_CONSUMED_BY); if (rtCsBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_CONSUMED_BY, Parser.getCurrentMethodName())); MetaData.RT_PRODUCED_BY); if (rtPdBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_PRODUCED_BY, Parser.getCurrentMethodName())); MetaData.RT_MEMBER_IS_PART_OF); if (rtMemberIsPart == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_MEMBER_IS_PART_OF, Parser .getCurrentMethodName()));
MetaData.RT_CONSUMED_BY); if (rtCsBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_CONSUMED_BY, Parser.getCurrentMethodName())); MetaData.RT_PRODUCED_BY); if (rtPdBy == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_PRODUCED_BY, Parser.getCurrentMethodName())); MetaData.RT_MEMBER_IS_PART_OF); if (rtMemberIsPart == null) { Parser.propagateEventOccurred(new RelationTypeMissingEvent( MetaData.RT_MEMBER_IS_PART_OF, Parser .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(); } }