Examples with AmbitException net.idea.modbcum.i.exceptions.AmbitException used on opensource projects

Example 11 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class AssayTemplateEntryJSONReporter method processItem.

@Override
public Object processItem(TR item) throws AmbitException {
    try {
        Writer writer = getOutput();
        if (comma != null)
            writer.write(comma);
        writer.write(item.toJSON());
        comma = ",";
    } catch (Exception x) {
        logger.log(java.util.logging.Level.SEVERE, x.getMessage(), x);
    }
    return item;
}

Example 12 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class CallableFileImport method importFile.

public TaskResult importFile(File file) throws Exception {
    try {
        // if target dataset is not defined, create new dataset
        final SourceDataset dataset = targetDataset != null ? targetDataset : datasetMeta(file);
        if (targetDataset == null)
            dataset.setId(-1);
        final BatchDBProcessor<String> batch = new BatchDBProcessor<String>() {

            /**
             */
            private static final long serialVersionUID = -7971761364143510120L;

            @Override
            public Iterator<String> getIterator(IInputState target) throws AmbitException {
                try {
                    File file = ((FileInputState) target).getFile();
                    RDFIteratingReader i = getRDFIterator(file, getReporter().getBaseReference().toString());
                    if (i == null) {
                        IIteratingChemObjectReader ni = getNanoCMLIterator(file, getReporter().getBaseReference().toString());
                        if (ni == null)
                            return super.getIterator(target);
                        else
                            return ni;
                    } else {
                        /*
			     * RDFMetaDatasetIterator datasets = null; try {
			     * datasets = new
			     * RDFMetaDatasetIterator(i.getJenaModel());
			     * datasets
			     * .setBaseReference(getReporter().getBaseReference
			     * ()); while (datasets.hasNext()) { SourceDataset d
			     * = datasets.next(); dataset.setId(d.getId());
			     * dataset.setName(d.getName());
			     * dataset.setTitle(d.getTitle());
			     * dataset.setURL(d.getURL()); } } catch (Exception
			     * x) { x.printStackTrace(); } finally { try {
			     * datasets.close();} catch (Exception x) {} }
			     */
                        return i;
                    }
                } catch (AmbitException x) {
                    throw x;
                } catch (Exception x) {
                    throw new AmbitException(x);
                }
            }

            @Override
            public void onItemProcessed(String input, Object output, IBatchStatistics stats) {
                super.onItemProcessed(input, output, stats);
                if (firstCompoundOnly && (stats.getRecords(RECORDS_STATS.RECORDS_PROCESSED) >= 1)) {
                    cancelled = true;
                    if (output != null)
                        if ((output instanceof ArrayList) && ((ArrayList) output).size() > 0) {
                            if (((ArrayList) output).get(0) instanceof IStructureRecord)
                                recordImported = (IStructureRecord) ((ArrayList) output).get(0);
                        } else if (output instanceof IStructureRecord)
                            recordImported = (IStructureRecord) output;
                }
            }
        };
        batch.setReference(dataset.getReference());
        batch.setConnection(connection);
        final RepositoryWriter writer = new RepositoryWriter();
        writer.setUseExistingStructure(isPropertyOnly());
        writer.setPropertyKey(getMatcher());
        writer.setDataset(dataset);
        final ProcessorsChain<String, IBatchStatistics, IProcessor> chain = new ProcessorsChain<String, IBatchStatistics, IProcessor>();
        chain.add(writer);
        batch.setProcessorChain(chain);
        writer.setConnection(connection);
        FileInputState fin = new FileInputState(file);
        IBatchStatistics stats = batch.process(fin);
        if (firstCompoundOnly) {
            if (recordImported == null)
                throw new Exception("No compound imported");
            if (compoundReporter == null)
                compoundReporter = new ConformerURIReporter("", null, false);
            try {
                batch.close();
            } catch (Exception xx) {
            }
            return new TaskResult(compoundReporter.getURI(recordImported));
        } else {
            ReadDataset q = new ReadDataset();
            q.setValue(dataset);
            QueryExecutor<ReadDataset> x = new QueryExecutor<ReadDataset>();
            x.setConnection(connection);
            ResultSet rs = x.process(q);
            ISourceDataset newDataset = null;
            while (rs.next()) {
                newDataset = q.getObject(rs);
                break;
            }
            x.closeResults(rs);
            x.setConnection(null);
            if (newDataset == null)
                throw new ResourceException(Status.SUCCESS_NO_CONTENT);
            if (reporter == null)
                reporter = new DatasetURIReporter<IQueryRetrieval<ISourceDataset>, ISourceDataset>();
            try {
                batch.close();
            } catch (Exception xx) {
            }
            return new TaskResult(reporter.getURI(newDataset));
        }
    } catch (ResourceException x) {
        throw x;
    } catch (Exception x) {
        throw new ResourceException(new Status(Status.SERVER_ERROR_INTERNAL, x.getMessage()));
    } finally {
        try {
            connection.close();
        } catch (Exception x) {
        }
        connection = null;
    }
}

Example 13 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class PropertyAnnotationRDFReporter method annotation2RDF.

public static void annotation2RDF(PropertyAnnotation item, OntModel jenaModel, Individual feature, String rootReference) throws AmbitException {
    Property predicate = null;
    if (item.getPredicate().startsWith("http")) {
        // there is a chance this
        // is an URI
        predicate = jenaModel.createProperty(item.getPredicate());
    } else {
        predicate = jenaModel.createProperty(String.format("http://www.opentox.org/api/1.1#%s", Reference.encode(item.getPredicate().replace(" ", "_"))));
    }
    String object = item.getObject().toString();
    if (item.getType().startsWith("^^")) {
        // xsd:string.
        try {
            // ot:ToxicCategory a rdfs:Datatype; rdfs:subClassOf xsd:string.
            String ctype = item.getType().replace("^^", "");
            Resource rdfDataType = jenaModel.createResource(OT.NS + ctype);
            jenaModel.add(rdfDataType, RDF.type, RDFS.Datatype);
            feature.addProperty(predicate, jenaModel.createTypedLiteral(object, rdfDataType.getURI()));
            try {
                ICategory.CategoryType.valueOf(ctype);
                jenaModel.add(rdfDataType, RDFS.subClassOf, jenaModel.getResource(OT.NS + "ToxicityCategory"));
            } catch (Exception x) {
                // x.printStackTrace();
                jenaModel.add(rdfDataType, RDFS.subClassOf, XSD.xstring);
            }
            return;
        } catch (Exception x) {
            x.printStackTrace();
        }
    // fallback to string
    } else if (item.getType().equals(OT.OTClass.ModelConfidenceFeature)) {
        feature.addOntClass(OT.OTClass.ModelConfidenceFeature.getOntClass(jenaModel));
        if (!object.startsWith("http"))
            object = String.format("%s%s", rootReference, object);
    }
    feature.addProperty(predicate, object);
}

Example 14 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class SubstanceCompositionJSONReporter method processItem.

/**
 * <pre>
 * 		{"source":0,	"target":2,	"value":0.28,	"value2":0.82},
 * </pre>
 */
@Override
public Object processItem(CompositionRelation item) throws AmbitException {
    try {
        if (item == null)
            return null;
        if (item.getFirstStructure() == null)
            return null;
        if (item.getSecondStructure() == null)
            return null;
        if (comma != null)
            getOutput().write(comma);
        StringWriter w = new StringWriter();
        cmpReporter.setOutput(w);
        cmpReporter.setComma(null);
        cmpReporter.processItem(item.getSecondStructure());
        getOutput().write(item.toJSON(substanceReporter.getURI(item.getFirstStructure()), w.toString()));
        comma = ",";
    } catch (Exception x) {
        logger.log(Level.WARNING, x.getMessage(), x);
    }
    return item;
}

Example 15 with AmbitException

use of net.idea.modbcum.i.exceptions.AmbitException in project ambit-mirror by ideaconsult.

the class CallableFingerprintsModelCreator method createProcessors.

protected ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor> createProcessors() throws Exception {
    ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor> p1 = new ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor>();
    p1.add(new ProcessorStructureRetrieval());
    p1.add(new MoleculeReader());
    p1.add(new FingerprintGenerator(new Fingerprinter()));
    p1.add(new DefaultAmbitProcessor<BitSet, BitSet>() {

        /**
         */
        private static final long serialVersionUID = -2978697147490545478L;

        public BitSet process(BitSet target) throws AmbitException {
            builder.getTrainingData().add(target);
            return target;
        }
    });
    p1.setAbortOnError(true);
    return p1;
}