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]")); } } }
fireEventOccurred(new AttributeNameMissingEvent(TAXID, "[Parser - start]")); return; fireEventOccurred(new AttributeNameMissingEvent(RANK, "[Parser - start]")); return;
i++; if (anGDS == null) { fireEventOccurred(new AttributeNameMissingEvent( "Given AttributeName not found. " + o.toString(), "[Export - start]"));
AttributeName att = graph.getMetaData().getAttributeName(attName); if (att == null) { fireEventOccurred(new AttributeNameMissingEvent(attName + " not found", getCurrentMethodName())); } else { HashMap<Object, Integer> objectsToValues = new HashMap<Object, Integer>();
ATT_TAXID); if (taxIdAttr == null) { fireEventOccurred(new AttributeNameMissingEvent(ATT_TAXID + " does not exist", getCurrentMethodName())); return; (String) args.getUniqueValue(CORRELATION_ATTRIBUTENAME_ARG)); if (att == null) { fireEventOccurred(new AttributeNameMissingEvent(args .getUniqueValue(CORRELATION_ATTRIBUTENAME_ARG) + " does not exist", getCurrentMethodName())); .getAttributeName(values[0]); if (patt == null) { fireEventOccurred(new AttributeNameMissingEvent(values[0] + " does not exist ignoring attribute value pair :" + valuePair, getCurrentMethodName()));
fireEventOccurred(new AttributeNameMissingEvent( "Given AttributeName for sequences not found. " + seqAttr, "[Mapping - start]")); MetaData.evalueHit); if (hitAn == null) { fireEventOccurred(new AttributeNameMissingEvent(MetaData.evalueHit, getCurrentMethodName())); ready = false; MetaData.BLAST_BITSCORE); if (attBitScore == null) { fireEventOccurred(new AttributeNameMissingEvent( MetaData.BLAST_BITSCORE, getCurrentMethodName())); ready = false; MetaData.BLAST_PSI); if (attPSI == null) { fireEventOccurred(new AttributeNameMissingEvent(MetaData.BLAST_PSI, getCurrentMethodName())); ready = false;
fireEventOccurred(new AttributeNameMissingEvent( "Given AttributeName for sequences not found. " + seqAttr, getCurrentMethodName())); fireEventOccurred(new AttributeNameMissingEvent(atTaxid, getCurrentMethodName())); ready = false; atCONF); if (attributeConf == null) { fireEventOccurred(new AttributeNameMissingEvent(atCONF, getCurrentMethodName())); ready = false; atBITSCORE); if (attributeBitscore == null) { fireEventOccurred(new AttributeNameMissingEvent(atBITSCORE, getCurrentMethodName())); ready = false;
getCurrentMethodName())); } else { fireEventOccurred(new AttributeNameMissingEvent( "Specified Attribute AttributeName is unrecognized in metadata " + gds, 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(); } }
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 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())); }
(String) args.getUniqueValue(ATTRIBUTE_EQUALS_ARG)); if (anEQUAL == null) { fireEventOccurred(new AttributeNameMissingEvent( "AttributeName " + args.getUniqueValue(ATTRIBUTE_EQUALS_ARG)
this.fireEventOccurred(new AttributeNameMissingEvent( MetaData.ATT_TAXID, getCurrentMethodName())); return;
(String) gdsArg); if (att == null) { fireEventOccurred(new AttributeNameMissingEvent( (String) gdsArg, Mapping.getCurrentMethodName())); } else {
if (an_taxid == null) { continueRun = false; fireEventOccurred(new AttributeNameMissingEvent("Missing AttributeName: TAXID", getName())); if (an_pfamhits == null) { continueRun = false; fireEventOccurred(new AttributeNameMissingEvent("Missing AttributeName: PFAMHITS", getName())); if (an_goscore == null) { continueRun = false; fireEventOccurred(new AttributeNameMissingEvent("Missing AttributeName: GOMATCHSCORE", getName())); if (an_conf == null) { continueRun = false; fireEventOccurred(new AttributeNameMissingEvent("Missing AttributeName: CONF", getName()));
"[Mapping - setONDEXGraph]")); if (hitAttr == null) fireEventOccurred(new AttributeNameMissingEvent(MetaData.accHit, "[Mapping - setONDEXGraph]"));
fireEventOccurred(new AttributeNameMissingEvent(MetaData.accHit, getCurrentMethodName())); hitAttr = graph.getMetaData().getFactory()