Examples with InvalidPluginArgumentException net.sourceforge.ondex.InvalidPluginArgumentException used on opensource projects

Example 1 with InvalidPluginArgumentException

use of net.sourceforge.ondex.InvalidPluginArgumentException in project knetbuilder by Rothamsted.

the class Export method start.

public void start() throws InvalidPluginArgumentException {
    noDuplicates = (Boolean) args.getUniqueValue(REMOVE_DUPLICATES_ARG);
    boolean useLinks = (Boolean) args.getUniqueValue(LINKS_ARG);
    boolean translateTaxID = (Boolean) args.getUniqueValue(TRANSLATE_TAXID_ARG);
    boolean zipFile = (Boolean) args.getUniqueValue(ZIP_FILE_ARG);
    Object min = args.getUniqueValue(MIN_REPORT_DEPTH_ARG);
    if (min != null) {
        cutoff = Integer.valueOf(min.toString());
    }
    try {
        om = graph.getMetaData();
        String pathDefinition = (String) args.getUniqueValue(ORDER_ARG);
        metaDataPath = parsePathDefinition(pathDefinition);
        // parse attributes
        Object[] attArgs = args.getObjectValueArray(ATTRIB_ARG);
        FieldArgumentParser parser = new FieldArgumentParser(useLinks, translateTaxID);
        for (Object arg : attArgs) {
            parser.parseArguments(arg.toString(), graph);
        }
        List<ONDEXEntityPath> paths = new ArrayList<ONDEXEntityPath>();
        if (metaDataPath.get(0).get(0) instanceof ConceptClass) {
            // indicates starts with concept
            // Set<ONDEXConcept> ov = SetImpl.create(graph, s, ONDEXConcept.class, new SparseDefaultBitSet());
            Set<ONDEXConcept> tmp = new HashSet<ONDEXConcept>();
            for (MetaData md : metaDataPath.get(0)) {
                tmp.addAll(graph.getConceptsOfConceptClass((ConceptClass) md));
            /*Set<ONDEXConcept> temp = graph.getConceptsOfConceptClass((ConceptClass)md);
                         if(temp!=null){
                             ov = Set.or(ov, temp);
                         }*/
            }
            for (ONDEXConcept concept : tmp) {
                ONDEXEntityPath route = new ONDEXEntityPath(concept);
                processEntity(concept, route, paths, 0, ProcessingType.CONCEPT, false);
            }
        } else {
            // therefore path.get(0) must be a RelationType
            Set<ONDEXRelation> tmp = new HashSet<ONDEXRelation>();
            // Set<ONDEXRelation> ov = SetImpl.create(graph, s, ONDEXRelation.class, new SparseDefaultBitSet());
            for (MetaData md : metaDataPath.get(0)) {
                tmp.addAll(graph.getRelationsOfRelationType((RelationType) md));
            /*Set<ONDEXRelation> temp = graph.getRelationsOfRelationType((RelationType)md);
                         if(temp != null){
                             ov = Set.or(ov, temp);
                         }*/
            }
            Iterator<ONDEXRelation> ov = tmp.iterator();
            while (ov.hasNext()) {
                ONDEXRelation r = ov.next();
                ONDEXEntityPath path = new ONDEXEntityPath(r);
                processEntity(r, path, paths, 0, ProcessingType.INCOMING_RELATION, false);
                processEntity(r, (ONDEXEntityPath) path.clone(), paths, 0, ProcessingType.OUTGOING_RELATION, true);
            }
        }
        int maxLength = 0;
        for (ONDEXEntityPath path : paths) {
            if (path.getLength() > maxLength) {
                maxLength = path.getLength();
            }
        }
        if (noDuplicates) {
            Set<ONDEXEntityPath> nonredundantRoutes = new HashSet<ONDEXEntityPath>(paths);
            paths = new ArrayList<ONDEXEntityPath>(nonredundantRoutes);
        }
        File file = new File((String) args.getUniqueValue(FileArgumentDefinition.EXPORT_FILE));
        OndexPathPrinter printer = new OndexPathPrinter(parser.getAttributeModel(), file, maxLength, graph, zipFile);
        for (ONDEXEntityPath path : paths) {
            printer.printPath(path);
        }
        printer.close();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 2 with InvalidPluginArgumentException

use of net.sourceforge.ondex.InvalidPluginArgumentException in project knetbuilder by Rothamsted.

the class Mapping method start.

@Override
public void start() throws InvalidPluginArgumentException, IOException {
    eviType = graph.getMetaData().getEvidenceType(EVIDENCE_BLAST);
    if (eviType == null) {
        ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new EvidenceTypeMissingEvent(RT_HAS_SIMILAR_SEQUENCE, Mapping.getCurrentMethodName()));
    }
    eValue = graph.getMetaData().getAttributeName(ATT_E_VALUE);
    if (eValue == null) {
        ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new AttributeNameMissingEvent(RT_HAS_SIMILAR_SEQUENCE, Mapping.getCurrentMethodName()));
    }
    bitScore = graph.getMetaData().getAttributeName(ATT_BITSCORE);
    if (bitScore == null) {
        ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new AttributeNameMissingEvent(ATT_BITSCORE, Mapping.getCurrentMethodName()));
    }
    AttributeName coverage = graph.getMetaData().getAttributeName(MetaData.ATT_COVERAGE);
    if (coverage == null) {
        coverage = graph.getMetaData().getFactory().createAttributeName(ATT_COVERAGE, Double.class);
    }
    // get the relationtypeset and evidencetype for this mapping
    rtSet = graph.getMetaData().getRelationType(RT_HAS_SIMILAR_SEQUENCE);
    if (rtSet == null) {
        RelationType rt = graph.getMetaData().getRelationType(RT_HAS_SIMILAR_SEQUENCE);
        if (rt == null) {
            ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new RelationTypeMissingEvent(RT_HAS_SIMILAR_SEQUENCE, Mapping.getCurrentMethodName()));
        }
        rtSet = graph.getMetaData().getFactory().createRelationType(RT_HAS_SIMILAR_SEQUENCE, rt);
    }
    seq_overlap = graph.getMetaData().getAttributeName(MetaData.ATT_OVERLAP);
    if (seq_overlap == null) {
        seq_overlap = graph.getMetaData().getFactory().createAttributeName(MetaData.ATT_OVERLAP, "Alignment overlap", Integer.class);
    }
    frame = graph.getMetaData().getAttributeName(MetaData.ATT_FRAME);
    if (frame == null) {
        frame = graph.getMetaData().getFactory().createAttributeName(MetaData.ATT_FRAME, "Translation fame", Integer.class);
    }
    query_length = graph.getMetaData().getAttributeName(MetaData.ATT_QUERY_LENGTH);
    if (query_length == null) {
        query_length = graph.getMetaData().getFactory().createAttributeName(MetaData.ATT_QUERY_LENGTH, "Length of query sequence", Integer.class);
    }
    target_length = graph.getMetaData().getAttributeName(MetaData.ATT_TARGET_LENGTH);
    if (target_length == null) {
        target_length = graph.getMetaData().getFactory().createAttributeName(MetaData.ATT_TARGET_LENGTH, "Length of target sequence", Integer.class);
    }
    HashSet<String> taxIds = new HashSet<String>();
    for (String taxId : (String[]) args.getObjectValueArray(TAX_ID_ARG)) {
        taxIds.add(taxId);
    }
    String sequenceType = (String) args.getUniqueValue(SEQ_TYPE_ARG);
    Integer speciesSeqSize = (Integer) args.getUniqueValue(SPECIES_SEQUENCE_SIZE_ARG);
    AttributeName att = graph.getMetaData().getAttributeName(sequenceType);
    AttributeName taxId = graph.getMetaData().getAttributeName(ATT_TAXID);
    // index for taxid -> set of conceptIDs
    Map<Integer, Set<Integer>> index = new HashMap<Integer, Set<Integer>>();
    Set<ONDEXConcept> allSequences = graph.getConceptsOfAttributeName(att);
    Set<ONDEXConcept> allTaxId = graph.getConceptsOfAttributeName(taxId);
    allSequences.retainAll(allTaxId);
    // of all TaxIDs and their assigned concepts
    System.out.println("Creating index");
    for (ONDEXConcept queryConcept : allSequences) {
        Attribute attribute = queryConcept.getAttribute(taxId);
        if (attribute != null) {
            String value = (String) attribute.getValue();
            // if a tax is specified then limit
            if (taxIds.size() == 0 || taxIds.contains(value)) {
                int taxIdVal = Integer.valueOf(value);
                Set<Integer> setCon = index.get(taxIdVal);
                if (setCon == null) {
                    setCon = new HashSet<Integer>();
                    index.put(taxIdVal, setCon);
                }
                setCon.add(queryConcept.getId());
            }
        }
    }
    System.out.println("Paralog prediction found " + index.size() + " species in the database");
    // filter out the databases too small to consider
    // keys are TaxIDs
    Iterator<Integer> taxids = index.keySet().iterator();
    while (taxids.hasNext()) {
        int taxIdVals = taxids.next();
        Set<Integer> sequences = index.get(taxIdVals);
        if (sequences.size() < speciesSeqSize) {
            index.remove(taxIdVals);
        }
    }
    System.out.println("Paralog prediction found " + index.size() + " qualifing species in the database");
    Float evalue = ((Number) args.getUniqueValue(E_VALUE_ARG)).floatValue();
    Integer bitscore = (Integer) args.getUniqueValue(BITSCORE_ARG);
    Integer cutoff = (Integer) args.getUniqueValue(CUTOFF_ARG);
    Float overlap = ((Number) args.getUniqueValue(OVERLAP_ARG)).floatValue();
    String programDir = (String) args.getUniqueValue(PROGRAM_DIR_ARG);
    System.out.println("Running paralog prediction");
    DecypherAlignment dcAlign = null;
    String algo = null;
    if (sequenceType.equalsIgnoreCase(AA)) {
        algo = DecypherAlignment.ALGO_BLASTP;
    } else if (sequenceType.equalsIgnoreCase(NA)) {
        algo = DecypherAlignment.ALGO_BLASTN;
    } else {
        fireEventOccurred(new WrongParameterEvent("Decypher can not Align these types of sequences :" + " " + sequenceType + "->" + sequenceType, getCurrentMethodName()));
    }
    try {
        int dcbit = 0;
        if (bitscore != null)
            dcbit = bitscore;
        dcAlign = new DecypherAlignment(net.sourceforge.ondex.config.Config.ondexDir, programDir, cutoff, overlap, evalue, dcbit, 60, true);
    } catch (Exception e) {
        e.printStackTrace();
    }
    int speciesNumber = 0;
    int totalSpecies = index.keySet().size();
    // keys are TaxIDs
    Iterator<Integer> keys = index.keySet().iterator();
    while (keys.hasNext()) {
        int taxIdVals = keys.next();
        speciesNumber++;
        Set<Integer> sequences = index.get(taxIdVals);
        fireEventOccurred(new GeneralOutputEvent("Finding paralogs for taxid: " + taxIdVals + " on " + sequences.size() + " sequences (" + speciesNumber + " of " + totalSpecies + ")", getCurrentMethodName()));
        Set<ONDEXConcept> seqToBLAST = BitSetFunctions.create(graph, ONDEXConcept.class, sequences);
        fireEventOccurred(new GeneralOutputEvent("Running " + SequenceAlignmentProgramArgumentDefinition.DECYPHER, getCurrentMethodName()));
        try {
            Collection<Match> resultList = dcAlign.query(graph, seqToBLAST, seqToBLAST, algo);
            // maps queryID -> Set of matches
            Map<Integer, Set<Match>> indexOnQueryId = new HashMap<Integer, Set<Match>>();
            System.out.println("Indexing matches");
            Iterator<Match> matches = resultList.iterator();
            while (matches.hasNext()) {
                Match match = matches.next();
                Set<Match> qMatches = indexOnQueryId.get(match.getQueryId());
                if (qMatches == null) {
                    qMatches = new HashSet<Match>();
                    indexOnQueryId.put(match.getQueryId(), qMatches);
                }
                qMatches.add(match);
            }
            // clear old results
            resultList = null;
            Iterator<Integer> querIt = indexOnQueryId.keySet().iterator();
            while (querIt.hasNext()) {
                int query = querIt.next();
                ONDEXConcept queryConcept = graph.getConcept(query);
                Iterator<Match> matchIt = indexOnQueryId.get(query).iterator();
                while (matchIt.hasNext()) {
                    Match hit = matchIt.next();
                    if (query != hit.getTargetId() && (bitscore == null || bitscore <= hit.getScore())) {
                        // check for reciprical hits
                        Set<Match> recipricalHits = indexOnQueryId.get(hit.getTargetId());
                        boolean found = false;
                        if (recipricalHits != null) {
                            // nothing to look for
                            for (Match hitr : recipricalHits) {
                                if (hitr.getTargetId() == query)
                                    found = true;
                            }
                        }
                        if (found) {
                            ONDEXConcept toConcept = graph.getConcept(hit.getTargetId());
                            ONDEXRelation relation = graph.getRelation(queryConcept, toConcept, rtSet);
                            // try if relation was already created
                            if (relation == null) {
                                // create a new relation between the two
                                // concepts
                                relation = graph.getFactory().createRelation(queryConcept, toConcept, rtSet, eviType);
                                relation.createAttribute(eValue, Double.valueOf(hit.getEValue()), false);
                                relation.createAttribute(bitScore, Double.valueOf(hit.getScore()), false);
                                relation.createAttribute(coverage, Double.valueOf(hit.geQueryCoverageSequence()), false);
                                relation.createAttribute(seq_overlap, Integer.valueOf(hit.getOverlapingLength()), false);
                                relation.createAttribute(frame, Integer.valueOf(hit.getQueryFrame()), false);
                                relation.createAttribute(query_length, Integer.valueOf(hit.getLengthOfQuerySequence()), false);
                                relation.createAttribute(target_length, Integer.valueOf(hit.getLengthOfTargetSequence()), false);
                            }
                        }
                    }
                }
            }
            System.runFinalization();
        } catch (MissingFileException e) {
            e.printStackTrace();
        } catch (AlgorithmNotSupportedException e) {
            e.printStackTrace();
        }
    }
}

Example 3 with InvalidPluginArgumentException

use of net.sourceforge.ondex.InvalidPluginArgumentException in project knetbuilder by Rothamsted.

the class Mapping method getMethod.

/**
 * Returns the method which is definied by <code>METHOD_ARG<code> PluginArgument.
 *
 * @return IMethod - an implementation of the IMethod interface
 * @throws MethodNotFoundException - if the method can't be found
 */
public IMethod getMethod(ONDEXGraph graph) throws MethodNotFoundException, InvalidPluginArgumentException {
    String methodName = (String) args.getUniqueValue(ArgumentNames.METHOD_ARG);
    IMethod method = null;
    try {
        Class<?> c = Class.forName(this.getClass().getPackage().getName() + ".method." + methodName);
        if (c.getConstructors().length != 1) {
            throw new MethodNotFoundException();
        }
        method = (IMethod) c.getConstructors()[0].newInstance(new Object[] { super.args.getUniqueValue(ArgumentNames.PROGRAM_DIR_ARG).toString(), super.args.getUniqueValue(ArgumentNames.PFAM_PATH_ARG).toString(), fastaFile.getAbsolutePath(), (String) super.args.getUniqueValue(ArgumentNames.EVALUE_ARG).toString(), (String) super.args.getUniqueValue(ArgumentNames.BIT_SCORE_ARG).toString(), (String) super.args.getUniqueValue(ArgumentNames.HMM_THRESHOLDS_ARG), graph, atSource, ccSource });
    } catch (Exception e) {
        e.printStackTrace();
    }
    return method;
}

Example 4 with InvalidPluginArgumentException

use of net.sourceforge.ondex.InvalidPluginArgumentException in project knetbuilder by Rothamsted.

the class Mapping method start.

@Override
public void start() throws InvalidPluginArgumentException {
    EvidenceType etIMPD = graph.getMetaData().getEvidenceType("IMPD");
    ConceptClass ccProteinFamily = graph.getMetaData().getConceptClass(MetaData.CC_ProteinFamily);
    DataSource dataSource = graph.getMetaData().getDataSource("Seq2Pfam");
    if (dataSource == null) {
        dataSource = graph.getMetaData().createDataSource("Seq2Pfam", "Sequence to Pfam Mapping", "Concepts created on the fly by sequence to pfam");
    }
    ccSource = graph.getMetaData().getConceptClass(args.getUniqueValue(ArgumentNames.CONCEPT_CLASS_ARG).toString());
    atSource = graph.getMetaData().getAttributeName(args.getUniqueValue(ArgumentNames.ATTRIBUTE_ARG).toString());
    rtMemberIsPartOf = graph.getMetaData().getRelationType(MetaData.RT_MEMBER_IS_PART_OF);
    atrEvalue = graph.getMetaData().getAttributeName(MetaData.ATT_EVALUE);
    atrBitscore = graph.getMetaData().getAttributeName(MetaData.ATT_BITSCORE);
    atrDomainEvalue = graph.getMetaData().getFactory().createAttributeName("BD_Evalue", "Bestdomain EValue", Double.class);
    atrDomainBitscore = graph.getMetaData().getFactory().createAttributeName("BD_Score", "Best domain Score", Double.class);
    atrTranslationFrame = graph.getMetaData().getFactory().createAttributeName("TranslationFrame", "TranslationFrame", Integer.class);
    fastaFile = new File(super.args.getUniqueValue("TmpDir").toString());
    if (!((String) args.getUniqueValue(ArgumentNames.METHOD_ARG)).equalsIgnoreCase("decypher")) {
        // create a fasta styled database
        try {
            fastaFile = File.createTempFile("fasta_" + new Date(System.currentTimeMillis()).toString().replaceAll(" ", "_").replaceAll(":", "_"), ".tmp", fastaFile);
            fastaFile.mkdirs();
            Set<ONDEXConcept> allConcepts = graph.getConceptsOfConceptClass(ccSource);
            if (((String) args.getUniqueValue(ArgumentNames.METHOD_ARG)).equalsIgnoreCase("Hmmer") && atSource.getId().equalsIgnoreCase("NA")) {
                try {
                    translateToFASTAFile(fastaFile, allConcepts, graph);
                } catch (Exception e) {
                    // To change body of catch statement use File | Settings | File Templates.
                    e.printStackTrace();
                }
            } else {
                BufferedWriter b = new BufferedWriter(new FileWriter(fastaFile));
                int writtenSequences = 0;
                for (ONDEXConcept c : allConcepts) {
                    if (this.addEntryToFastaDatabase(b, c, graph))
                        writtenSequences++;
                }
                b.close();
                ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Found " + writtenSequences + " sequences", Mapping.class.toString()));
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
    // resolve the method class
    IMethod method;
    try {
        method = this.getMethod(graph);
    } catch (MethodNotFoundException e1) {
        ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Unknown method (" + args.getUniqueValue(ArgumentNames.METHOD_ARG).toString() + "), check " + ArgumentNames.METHOD_ARG + " parameter. Using blast instead", Mapping.class.toString()));
        super.args.addOption(ArgumentNames.METHOD_ARG, "Blast");
        try {
            method = getMethod(graph);
        } catch (MethodNotFoundException e) {
            ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("There are serious problems in locating the right mapping method", Mapping.class.toString()));
            e.printStackTrace();
            return;
        }
    }
    LuceneEnv lenv = LuceneRegistry.sid2luceneEnv.get(graph.getSID());
    try {
        // get the machtes
        Collection<HMMMatch> results = method.execute();
        ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Found " + results.size() + " theoretical matches", Mapping.class.toString()));
        // create relations between protein and family
        for (HMMMatch result : results) {
            Set<ONDEXConcept> itResults = method.searchMatchingConceptsInLuceneEnvironment(lenv, // lenv.searchConceptByConceptAccessionExact(s,result.getTargetAccession());
            result);
            if (itResults == null || itResults.size() == 0) {
                ONDEXEventHandler.getEventHandlerForSID(graph.getSID()).fireEventOccurred(new GeneralOutputEvent("Pfam family " + result + " was not found:  creating new one", Mapping.class.toString()));
                ONDEXConcept concept = graph.getFactory().createConcept(result.getHmmAccession(), dataSource, ccProteinFamily, etIMPD);
                BitSet sbs = new BitSet();
                sbs.set(concept.getId());
                itResults = BitSetFunctions.create(graph, ONDEXConcept.class, sbs);
            }
            for (ONDEXConcept pfamConcept : itResults) {
                if (pfamConcept instanceof LuceneConcept) {
                    pfamConcept = ((LuceneConcept) pfamConcept).getParent();
                }
                ONDEXConcept from = graph.getConcept(result.getTargetId());
                ONDEXRelation relation = graph.getRelation(from, pfamConcept, rtMemberIsPartOf);
                if (relation == null) {
                    relation = graph.getFactory().createRelation(from, pfamConcept, rtMemberIsPartOf, method.getEvidenceType());
                    relation.createAttribute(atrEvalue, result.getEValue(), false);
                    if (result.getScore() != -1)
                        relation.createAttribute(atrBitscore, result.getScore(), false);
                    if (result.getBestDomainEvalue() != null)
                        relation.createAttribute(atrDomainEvalue, result.getBestDomainEvalue(), false);
                    if (result.getBestDomainScore() != null)
                        relation.createAttribute(atrDomainBitscore, result.getBestDomainScore(), false);
                    if (result.getQueryFrame() != null)
                        relation.createAttribute(atrTranslationFrame, result.getQueryFrame(), false);
                } else {
                    Attribute evalue = relation.getAttribute(atrEvalue);
                    Attribute bitscore = relation.getAttribute(atrBitscore);
                    Attribute domain_evalue = relation.getAttribute(atrDomainEvalue);
                    Attribute domain_bitscore = relation.getAttribute(atrDomainBitscore);
                    Attribute frame = relation.getAttribute(atrTranslationFrame);
                    if (evalue == null || result.getEValue() < ((Number) (evalue.getValue())).doubleValue()) {
                        evalue.setValue(result.getEValue());
                        if (bitscore == null) {
                            if (result.getScore() > -1) {
                                relation.createAttribute(atrBitscore, result.getScore(), false);
                            }
                        } else {
                            if (result.getScore() > -1) {
                                // remove
                                relation.deleteAttribute(atrBitscore);
                            // to
                            // avoid
                            // confusion
                            } else {
                                bitscore.setValue(result.getScore());
                            }
                        }
                        addAttribute(result.getBestDomainEvalue(), domain_evalue, relation, atrDomainEvalue);
                        addAttribute(result.getBestDomainScore(), domain_bitscore, relation, atrDomainBitscore);
                        addAttribute(result.getQueryFrame(), frame, relation, atrTranslationFrame);
                    }
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 5 with InvalidPluginArgumentException

use of net.sourceforge.ondex.InvalidPluginArgumentException in project knetbuilder by Rothamsted.

the class Export method start.

// parameter to exclude all of selected feature
/*    private static final String ALL = "ALL";

    // export concepts that do not have relations, default true
    private boolean writeIsolatedConcepts = true;

    // mapping concepts to relation counts
    private Map<Integer, Integer> conIdToRelationCounts = null;

    // A list of the Attributes of Attribute values to exclude. String ALL =>
    // Excludes all attributes.
    private Set<String> excludeGDSSet = new HashSet<String>();

    // A list of the ConceptClasses to be excluded in the export.
    private Set<String> excludeCCSet = new HashSet<String>();

    // A list of the RelationTypes to be excluded in the export.
    private Set<String> excludeRt = new HashSet<String>();
*/
/**
 * Other application dependent annotation data for this export, can be null.
 */
// protected Map<String, String> annotations = null;
/**
 * Builds a file with Ondex Graph data exported to JSON variables for concepts (nodes), relations (edges)
 * and other Item Info.
 *
 * @throws IOException
 * @throws InvalidPluginArgumentException
 */
@Override
public void start() throws IOException, InvalidPluginArgumentException {
    setOptionalArguments();
    fireEventOccurred(new GeneralOutputEvent("Ready to Export.", "[Export - start]"));
    // A jsimple-json object (JSONObject) for the node, edge data for cytoscapeJS.
    JSONObject graphJson = new JSONObject();
    /* Another jsimple-json object (JSONObject) to store all graph data (including metadata, concepts & 
      * relations' information). */
    JSONObject allDataJson = new JSONObject();
    // JSONArray objects to store all the ceoncepts (nodes) & relations (edges) to.
    JSONArray conceptNodes = new JSONArray();
    JSONArray relationEdges = new JSONArray();
    // Set output File location for writing network graph JSON data & other graph metadata to.
    graphFileWriter = getOutputFileForGraphJson();
    try {
        // Retrieving all the concepts & relations from the graph (the ONDEXGraph object).
        if (graph != null) {
            concepts = graph.getConcepts();
            relations = graph.getRelations();
        }
        // Generate all graph metadata in JSON format.
        JSONObject allGraphDataJson = getJsonMetadata();
        allDataJson.put(JSONAttributeNames.ONDEXMETADATA, allGraphDataJson);
        // Generate necessary node(s) data in JSON format for CytoscapeJS graph.
        graphJson = getNodesJsonData(graphJson, conceptNodes, relations);
        // Generate necessary edge(s) data in JSON format for CytoscapeJS graph.
        graphJson = getEdgesJsonData(graphJson, relationEdges);
        // Write graph JSON & metadata JSON to output file.
        writeJSONToFile(graphJson, allDataJson, graphFileWriter);
    } catch (Exception ex) {
        throw new IOException("Failed to write Attribute values", ex);
    }
    fireEventOccurred(new GeneralOutputEvent("Finished JSON Export.", "[Export - start]"));
}