private void logFail(String s) { EventType e = new InconsistencyEvent(s, ""); e.setLog4jLevel(Level.ERROR); fireEventOccurred(e); } }
private void logFail(String s) { EventType e = new InconsistencyEvent(s, ""); e.setLog4jLevel(Level.ERROR); fireEventOccurred(e); } }
private void complain(String string) { InconsistencyEvent event = new InconsistencyEvent(string, ""); event.setLog4jLevel(Level.DEBUG); fireEventOccurred(event); }
".fs")); if (!indexFile.exists()) { fireEventOccurred(new InconsistencyEvent("No index " + indexFile.getAbsolutePath() + " was build.", getCurrentMethodName()));
/** * checks all requirements in the graph. * * @return if everything is ok. */ private boolean checkGraphRequirements() { boolean continueRun = true; if (graph.getConceptsOfConceptClass(cc_protFam).isEmpty()) { continueRun = false; fireEventOccurred(new InconsistencyEvent("Graph does not contain protein families.", getName())); } if (graph.getConceptsOfConceptClass(cc_protein).isEmpty()) { continueRun = false; fireEventOccurred(new InconsistencyEvent("Graph does not contain proteins.", getName())); } if (graph.getRelationsOfRelationType(rts_ortholog).isEmpty()) { continueRun = false; fireEventOccurred(new InconsistencyEvent("Graph does not contain ortholog relations.", getName())); } if (graph.getRelationsOfRelationType(rts_seq2pfam).isEmpty()) { continueRun = false; fireEventOccurred(new InconsistencyEvent("Graph does not contain protein to pfam mappings.", getName())); } return continueRun; }
fireEventOccurred(new InconsistencyEvent( "unknown parameter type found in " + pid, "[Parser - addKinetics]"));
private void addCompounds(Reaction r, SpeciesReference sp, ONDEXConcept reaction, RelationType rt) { // process all lists of reactants and products String id = sp.getSpecies(); // this is compound which is consumed or produced by reaction ONDEXConcept fromConcept = concepts.get(id); if (fromConcept == null) { fireEventOccurred(new InconsistencyEvent( "fromConcept is empty for " + id, "[Parser - addSubstrates]")); return; } // create relation and add kinetics ONDEXRelation relation = graph.getFactory().createRelation(fromConcept, reaction, rt, evidence); addKinetics(r, relation, id); }
fireEventOccurred(new InconsistencyEvent( "Non-CHEMBL ID found: " + id, getCurrentMethodName())); fireEventOccurred(new InconsistencyEvent( "Empty category for: " + id, getCurrentMethodName()));
fireEventOccurred(new InconsistencyEvent("toConcept is empty for " + id, "[Parser - processReactions]")); return; fireEventOccurred(new InconsistencyEvent("unknown type found in " + id, "[Parser - processReactions]"));
fireEventOccurred(new InconsistencyEvent( "Child concept with pid " + line[0] + " not found.", "[Parser - start]")); } else if (parentConcept == null) { fireEventOccurred(new InconsistencyEvent( "Parent concept with pid " + line[2] + " not found.", "[Parser - start]"));
fireEventOccurred(new InconsistencyEvent( "No concepts with attribute" + anChemicalStructure.getId() + " found.", getCurrentMethodName()));
id = (String) ac.getProperty(CHEMBL_ID); else fireEventOccurred(new InconsistencyEvent( "ChEMBLdb ID missing for: " + ac, getCurrentMethodName())); fireEventOccurred(new InconsistencyEvent( "CDK Problem constructing MOL and SMILES for: " + ac.getProperty(CHEMBL_ID), getCurrentMethodName())); cdk.printStackTrace(); } catch (IOException e) { fireEventOccurred(new InconsistencyEvent( "IO Problem constructing MOL and SMILES for: " + ac.getProperty(CHEMBL_ID), getCurrentMethodName()));
id = (String) ac.getProperty(CHEBI_ID); else fireEventOccurred(new InconsistencyEvent( "ChEBI ID missing for: " + ac.getProperty(CHEBI_NAME), getCurrentMethodName())); fireEventOccurred(new InconsistencyEvent( "Problem constructing MOL and SMILES for: " + ac.getProperty(CHEBI_ID),
ONDEXConcept from = graph.getConcept(fromId); if (from == null) { fireEventOccurred(new InconsistencyEvent("From concept for ID " + fromId + " not found.", getCurrentMethodName())); return; ONDEXConcept to = graph.getConcept(toId); if (to == null) { fireEventOccurred(new InconsistencyEvent( "To concept for ID " + toId + " not found.", getCurrentMethodName()));
for(Diff d : diffs) fireEventOccurred(new InconsistencyEvent(d.explain(), "validating counts"));
ONDEXConcept toConcept = mapping.get(to); if (toConcept == null) { fireEventOccurred(new InconsistencyEvent( "ToConcept for mapping " + from + " = " + to + " not present in graph.",
fireEventOccurred(new InconsistencyEvent( "Error with ConceptAccession Query '" + conceptAcc.getAccession()