etname.toString()); if (et == null) { fireEventOccurred(new EvidenceTypeMissingEvent(et + " not found: ignoring", getCurrentMethodName())); continue; etname.toString()); if (et == null) { fireEventOccurred(new EvidenceTypeMissingEvent(et + " not found: ignoring", getCurrentMethodName())); continue;
fireEventOccurred(new EvidenceTypeMissingEvent(ET, "[Parser - start]")); return;
EvidenceType et = graph.getMetaData().getEvidenceType(name.trim()); if (et == null) { fireEventOccurred(new EvidenceTypeMissingEvent( "Specified EvidenceType not found: " + name, getCurrentMethodName()));
EvidenceType et = graph.getMetaData().getEvidenceType(etName); if (et == null) { fireEventOccurred(new EvidenceTypeMissingEvent(etName + " does not exist", getCurrentMethodName())); return; .getEvidenceType(MetaData.IMPD); if (etIMPD == null) { fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.IMPD, Parser.getCurrentMethodName()));
.getEvidenceType(MetaData.evidence); if (et == null) fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.evidence, getCurrentMethodName()));
.getEvidenceType(MetaData.evidence); if (et == null) { fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.evidence, getCurrentMethodName())); ready = false;
etINPARANOID); if (evidencetype == null) { fireEventOccurred(new EvidenceTypeMissingEvent(etINPARANOID, getCurrentMethodName())); ready = false;
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new EvidenceTypeMissingEvent( RT_HAS_SIMILAR_SEQUENCE, Mapping.getCurrentMethodName()));
.getEvidenceType(MetaData.ET); if (et == null) { this.fireEventOccurred(new EvidenceTypeMissingEvent( MetaData.ET, getCurrentMethodName())); return;
fireEventOccurred(new EvidenceTypeMissingEvent(EVI_GDSEQUAL, Mapping.getCurrentMethodName())); eviType = graph
fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.evidence, getCurrentMethodName())); eviType = graph.getMetaData().getFactory()
"[Mapping - setONDEXGraph]")); if (eviType == null) fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.evidence, "[Mapping - setONDEXGraph]")); if (hitAttr == null)
private void setupMetaData() throws InvalidPluginArgumentException { eviType_blast = graph.getMetaData().getEvidenceType(EVIDENCE_BLAST); if (eviType_blast == null) { ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new EvidenceTypeMissingEvent( RT_HAS_SIMILAR_SEQUENCE, Mapping.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())); }
fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.at_taxID, Parser.getCurrentMethodName())); fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.at_YEAR, Parser.getCurrentMethodName())); fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.at_AUTH, Parser.getCurrentMethodName())); fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.at_TITLE_JOURNAL, Parser.getCurrentMethodName())); fireEventOccurred(new EvidenceTypeMissingEvent(ET, Parser.getCurrentMethodName()));
fireEventOccurred(new EvidenceTypeMissingEvent("IMPD missing", "[Parser - start]")); return;
ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new EvidenceTypeMissingEvent(MetaData.EVIDENCE_BLAST, Mapping.getCurrentMethodName()));
Parser.propagateEventOccurred(new EvidenceTypeMissingEvent(MetaData.IMPD, Parser.getCurrentMethodName()));
Parser.propagateEventOccurred(new EvidenceTypeMissingEvent(MetaData.IMPD, Parser.getCurrentMethodName()));
Parser.propagateEventOccurred(new EvidenceTypeMissingEvent(MetaData.IMPD, Parser.getCurrentMethodName()));