Examples with BatchDBProcessor ambit2.db.processors.BatchDBProcessor used on opensource projects

Example 1 with BatchDBProcessor

use of ambit2.db.processors.BatchDBProcessor 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 2 with BatchDBProcessor

use of ambit2.db.processors.BatchDBProcessor in project ambit-mirror by ideaconsult.

the class BatchDBProcessorTest method setUp.

@Before
public void setUp() throws Exception {
    batch = new BatchDBProcessor();
    file = new File("src//test//resources//ambit2//db//processors//sdf//224824.sdf");
    Assert.assertTrue(file.exists());
}

Example 3 with BatchDBProcessor

use of ambit2.db.processors.BatchDBProcessor in project ambit-mirror by ideaconsult.

the class Context method parseCommandFingerprints.

public void parseCommandFingerprints(String subcommand, long now) throws Exception {
    boolean multifile = true;
    int page = parsePageParam();
    int pagesize = parsePageSizeParam();
    final boolean fp_count = parseWriteCountParam();
    final boolean fp_raw = parseWriteRawParam();
    String smiles_header = parseInputTag_Param("smiles", IteratingDelimitedFileReader.defaultSMILESHeader);
    String inchi_header = parseInputTag_Param("inchi", "InChI");
    String inchikey_header = parseInputTag_Param("inchikey", "InChIKey");
    Object tmpTag = parseSdfTitleParam();
    final String[] tags_to_keep = parsetags_to_keep();
    final String sdf_title = tmpTag == null ? null : tmpTag.toString().toLowerCase();
    final int startRecord = pagesize > 0 ? (page * pagesize + 1) : 1;
    final int maxRecord = pagesize > 0 ? ((page + 1) * pagesize + 1) : pagesize;
    final File file = getInputFile();
    FileInputState input = new FileInputState(file);
    input.setOptionalSMILESHeader(smiles_header);
    input.setOptionalInChIHeader(inchi_header);
    input.setOptionalInChIKeyHeader(inchikey_header);
    if (options.output == null)
        throw new FileNotFoundException("Output file not specified. Please use -o {file}");
    final File outfile = new File(options.output);
    logger_cli.log(Level.INFO, "MSG_INFO_READINGWRITING", new Object[] { file.getAbsoluteFile(), outfile.getAbsolutePath() });
    final List<IFingerprinter> fps = parseFingerprinterParams();
    FileOutputState out = null;
    final IChemObjectWriter awriter;
    if (multifile) {
        awriter = new MultiFingerprintsWriter(outfile, fps, tags_to_keep);
    } else {
        out = new FileOutputState(outfile);
        awriter = out.getWriter();
        if (awriter instanceof FilesWithHeaderWriter)
            ((FilesWithHeaderWriter) awriter).setAddSMILEScolumn(false);
    }
    final IChemObjectWriter writer = awriter;
    final boolean writesdf = writer instanceof SDFWriter;
    final Map<Object, Property> tags = new HashMap<>();
    Property newtag = Property.getSMILESInstance();
    newtag.setName("SMILES");
    newtag.setEnabled(false);
    tags.put(Property.opentox_SMILES, newtag);
    tags.put(Property.getSMILESInstance(), newtag);
    newtag = Property.getInChIInstance();
    newtag.setEnabled(false);
    tags.put(Property.opentox_InChI, newtag);
    tags.put("InChI", newtag);
    tags.put(Property.getInChIInstance(), newtag);
    newtag = Property.getInChIKeyInstance();
    newtag.setEnabled(true);
    newtag.setName("InChIKey");
    tags.put(Property.opentox_InChIKey, newtag);
    tags.put(Property.getInChIKeyInstance(), newtag);
    newtag = Property.getInstance(CDKConstants.TITLE, CDKConstants.TITLE);
    newtag.setEnabled(false);
    tags.put(CDKConstants.TITLE, newtag);
    tags.put(newtag, newtag);
    newtag = Property.getInstance("CHEMBL", "CHEMBL");
    newtag.setEnabled(false);
    tags.put("CHEMBL", newtag);
    tags.put(newtag, newtag);
    final BatchDBProcessor<IStructureRecord> batch = new BatchDBProcessor<IStructureRecord>() {

        @Override
        public void onItemRead(IStructureRecord input, IBatchStatistics stats) {
            super.onItemRead(input, stats);
            if ((maxRecord > 0) && stats.getRecords(RECORDS_STATS.RECORDS_READ) >= (maxRecord))
                cancel();
        }

        @Override
        public boolean skip(IStructureRecord input, IBatchStatistics stats) {
            return (stats.getRecords(RECORDS_STATS.RECORDS_READ) < startRecord) || ((maxRecord > 0) && (stats.getRecords(RECORDS_STATS.RECORDS_READ) >= maxRecord));
        }

        @Override
        public void onItemSkipped(IStructureRecord input, IBatchStatistics stats) {
            super.onItemSkipped(input, stats);
            if (stats.isTimeToPrint(getSilentInterval() * 2))
                propertyChangeSupport.firePropertyChange(PROPERTY_BATCHSTATS, null, stats);
        }

        @Override
        public void onItemProcessing(IStructureRecord input, Object output, IBatchStatistics stats) {
        }

        @Override
        public void onError(IStructureRecord input, Object output, IBatchStatistics stats, Exception x) {
            super.onError(input, output, stats, x);
            logger_cli.log(Level.SEVERE, "MSG_ERR", new Object[] { x.getMessage() });
        }

        @Override
        public long getSilentInterval() {
            return 30000L;
        }

        @Override
        public void close() throws Exception {
            try {
                writer.close();
            } catch (Exception x) {
            } finally {
            }
            super.close();
        }
    };
    batch.setProcessorChain(new ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor>());
    batch.getProcessorChain().add(new DefaultAmbitProcessor<IStructureRecord, IStructureRecord>() {

        protected MoleculeReader molReader = new MoleculeReader(true, false);

        @Override
        public IStructureRecord process(IStructureRecord record) throws Exception {
            IAtomContainer mol;
            IAtomContainer processed = null;
            try {
                mol = molReader.process(record);
                if (mol != null) {
                    for (Property p : record.getRecordProperties()) {
                        Object v = record.getRecordProperty(p);
                        String pname = p.getName().replace("http://www.opentox.org/api/1.1#", "");
                        // already parsed
                        if (tags_to_keep != null && Arrays.binarySearch(tags_to_keep, pname) < 0)
                            continue;
                        else
                            mol.setProperty(p, v);
                    }
                    if (tags_to_keep != null) {
                        List<String> toRemove = null;
                        Iterator pi = mol.getProperties().keySet().iterator();
                        while (pi.hasNext()) {
                            Object p = pi.next();
                            if (Arrays.binarySearch(tags_to_keep, p.toString()) < 0) {
                                if (toRemove == null)
                                    toRemove = new ArrayList<String>();
                                toRemove.add(p.toString());
                            }
                        }
                        if (toRemove != null)
                            for (String propertyToRemove : toRemove) mol.removeProperty(propertyToRemove);
                    }
                } else {
                    logger_cli.log(Level.SEVERE, "MSG_FINGEPRINTGEN", new Object[] { "Empty molecule", getIds(record) });
                    return record;
                }
                AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
            } catch (Exception x) {
                logger_cli.log(Level.SEVERE, "MSG_ERR_MOLREAD", new Object[] { getIds(record), x.toString() });
                return record;
            } finally {
            }
            processed = mol;
            for (IFingerprinter fp : fps) {
                ICountFingerprint cfp = null;
                try {
                    cfp = fp.getCountFingerprint(processed);
                } catch (Exception x) {
                    logger.log(Level.FINER, x.getMessage());
                }
                IBitFingerprint bfp = null;
                try {
                    bfp = fp.getBitFingerprint(processed);
                } catch (Exception x) {
                }
                Map<String, Integer> fpraw = null;
                try {
                    if (fp_raw)
                        fpraw = fp.getRawFingerprint(processed);
                } catch (Exception x) {
                }
                try {
                    if (cfp != null) {
                        if (fp_count)
                            processed.setProperty(fp.getClass().getName() + ".count", cfp);
                        processed.setProperty(fp.getClass().getName(), cfp);
                    }
                    if (bfp != null)
                        processed.setProperty(fp.getClass().getName() + ".hashed", bfp);
                    if (fpraw != null)
                        processed.setProperty(fp.getClass().getName() + ".raw", fpraw);
                } catch (Exception x) {
                    // StringWriter w = new StringWriter();
                    // x.printStackTrace(new PrintWriter(w));
                    logger_cli.log(Level.SEVERE, "MSG_FINGEPRINTGEN", new Object[] { x.getMessage(), getIds(record) });
                    if (processed != null)
                        processed.setProperty("ERROR." + fp.getClass().getName(), x.getMessage());
                } finally {
                    if (processed != null)
                        processed.addProperties(mol.getProperties());
                }
            }
            if (processed != null)
                try {
                    if (writesdf && sdf_title != null) {
                        for (Entry<Object, Object> p : processed.getProperties().entrySet()) if (sdf_title.equals(p.getKey().toString().toLowerCase())) {
                            processed.setProperty(CDKConstants.TITLE, p.getValue());
                            break;
                        }
                    }
                    StructureStandardizer.renameTags(processed, tags, true);
                    writer.write(processed);
                } catch (Exception x) {
                    // StringWriter w = new StringWriter();
                    // x.printStackTrace(new PrintWriter(w));
                    logger_cli.log(Level.SEVERE, "MSG_FINGEPRINTGEN", new Object[] { x.getMessage(), getIds(record) });
                }
            else {
                logger_cli.log(Level.SEVERE, "MSG_FINGEPRINTGEN", new Object[] { "Empty molecule", getIds(record) });
            }
            return record;
        }
    });
    batch.addPropertyChangeListener(new PropertyChangeListener() {

        @Override
        public void propertyChange(PropertyChangeEvent evt) {
            if (AbstractBatchProcessor.PROPERTY_BATCHSTATS.equals(evt.getPropertyName()))
                logger_cli.log(Level.INFO, evt.getNewValue().toString());
        }
    });
    /*
		 * standardprocessor.setCallback(new
		 * DefaultAmbitProcessor<IAtomContainer, IAtomContainer>() {
		 * 
		 * @Override public IAtomContainer process(IAtomContainer target) throws
		 * Exception { try { //writer.write(target); } catch (Exception x) {
		 * logger.log(Level.SEVERE, x.getMessage()); } return target; } });
		 */
    IBatchStatistics stats = null;
    try {
        stats = batch.process(input);
    } catch (Exception x) {
        logger_cli.log(Level.WARNING, x.getMessage(), x);
    } finally {
        try {
        } catch (Exception x) {
            logger_cli.warning(x.getMessage());
        }
        try {
            if (batch != null)
                batch.close();
        } catch (Exception x) {
            logger_cli.warning(x.getMessage());
        }
        if (stats != null)
            logger_cli.log(Level.INFO, stats.toString());
    }
}

Example 4 with BatchDBProcessor

use of ambit2.db.processors.BatchDBProcessor in project ambit-mirror by ideaconsult.

the class AmbitPipeline method parseCommandStandardize.

public void parseCommandStandardize(String subcommand, long now) throws Exception {
    int page = parsePageParam();
    int pagesize = parsePageSizeParam();
    Object tmpTag = parseSdfTitleParam();
    String smiles_header = parseInputTag_Param("smiles", IteratingDelimitedFileReader.defaultSMILESHeader);
    String inchi_header = parseInputTag_Param("inchi", "InChI");
    String inchikey_header = parseInputTag_Param("inchikey", "InChIKey");
    final String sdf_title = tmpTag == null ? null : tmpTag.toString().toLowerCase();
    final StructureStandardizer standardprocessor = new StructureStandardizer(logger_cli);
    standardprocessor.setGenerate2D(parseBooleanParam(":generate2D", false));
    standardprocessor.setGenerateTautomers(parseBooleanParam(":tautomers", false));
    SMIRKSProcessor tmp = null;
    try {
        Object o = options.getParam(":smirks");
        if (o != null) {
            File smirksConfig = new File(o.toString());
            if (smirksConfig.exists()) {
                tmp = new SMIRKSProcessor(smirksConfig, logger_cli);
                tmp.setEnabled(true);
            } else
                logger_cli.log(Level.WARNING, "SMIRKS transformation file not found");
        }
    } catch (Exception x) {
        logger_cli.log(Level.SEVERE, x.getMessage());
        tmp = null;
    }
    final SMIRKSProcessor smirksProcessor = tmp;
    standardprocessor.setSplitFragments(parseBooleanParam(":splitfragments", false));
    standardprocessor.setImplicitHydrogens(parseBooleanParam(":implicith", false));
    standardprocessor.setNeutralise(parseBooleanParam(":neutralise", false));
    final String[] tags_to_keep = parsetags_to_keep();
    standardprocessor.setRankTag(parseStringParam(":tag_rank", "RANK"));
    standardprocessor.setInchiTag(parseStringParam(":tag_inchi", "InChI"));
    standardprocessor.setInchiKeyTag(parseStringParam(":tag_inchikey", "InChIKey"));
    standardprocessor.setSMILESTag(parseStringParam(":tag_smiles", "SMILES"));
    standardprocessor.setGenerateInChI(parseBooleanParam(":inchi", true));
    standardprocessor.setGenerateSMILES(parseBooleanParam(":smiles", true));
    standardprocessor.setGenerateSMILES_Canonical(parseBooleanParam(":smilescanonical", false));
    standardprocessor.setGenerateSMILES_Aromatic(parseBooleanParam(":smilesaromatic", false));
    standardprocessor.setGenerateStereofrom2D(parseBooleanParam(":generatestereofrom2d", false));
    standardprocessor.setClearIsotopes(parseBooleanParam(":setClearIsotopes", false));
    final boolean debugatomtypes = parseBooleanParam(":debugatomtypes", false);
    final int startRecord = pagesize > 0 ? (page * pagesize + 1) : 1;
    final int maxRecord = pagesize > 0 ? ((page + 1) * pagesize + 1) : pagesize;
    final File file = getInputFile();
    FileInputState in = new FileInputState(file);
    in.setOptionalInChIHeader(inchi_header);
    in.setOptionalInChIKeyHeader(inchikey_header);
    in.setOptionalSMILESHeader(smiles_header);
    if (options.output == null)
        throw new FileNotFoundException("Output file not specified. Please use -o {file}");
    final File outfile = new File(options.output);
    logger_cli.log(Level.INFO, "MSG_INFO_READINGWRITING", new Object[] { file.getAbsoluteFile(), outfile.getAbsolutePath() });
    FileOutputState out = new FileOutputState(outfile);
    final IChemObjectWriter writer = out.getWriter();
    if (writer instanceof FilesWithHeaderWriter)
        ((FilesWithHeaderWriter) writer).setAddSMILEScolumn(false);
    final BatchDBProcessor<IStructureRecord> batch = new BatchDBProcessor<IStructureRecord>() {

        @Override
        public void onItemRead(IStructureRecord input, IBatchStatistics stats) {
            super.onItemRead(input, stats);
            if ((maxRecord > 0) && stats.getRecords(RECORDS_STATS.RECORDS_READ) >= (maxRecord))
                cancel();
        }

        @Override
        public boolean skip(IStructureRecord input, IBatchStatistics stats) {
            return (stats.getRecords(RECORDS_STATS.RECORDS_READ) < startRecord) || ((maxRecord > 0) && (stats.getRecords(RECORDS_STATS.RECORDS_READ) >= maxRecord));
        }

        @Override
        public void onItemSkipped(IStructureRecord input, IBatchStatistics stats) {
            super.onItemSkipped(input, stats);
            if (stats.isTimeToPrint(getSilentInterval() * 2))
                propertyChangeSupport.firePropertyChange(PROPERTY_BATCHSTATS, null, stats);
        }

        @Override
        public void onItemProcessing(IStructureRecord input, Object output, IBatchStatistics stats) {
        }

        @Override
        public void onError(IStructureRecord input, Object output, IBatchStatistics stats, Exception x) {
            super.onError(input, output, stats, x);
            logger_cli.log(Level.SEVERE, x.getMessage());
        }

        @Override
        public long getSilentInterval() {
            return 30000L;
        }

        @Override
        public void close() throws Exception {
            try {
                writer.close();
            } catch (Exception x) {
            } finally {
            }
            super.close();
        }
    };
    batch.setProcessorChain(new ProcessorsChain<IStructureRecord, IBatchStatistics, IProcessor>());
    batch.getProcessorChain().add(new StdzBatchProcessor(standardprocessor, smirksProcessor, tags_to_keep, logger_cli, writer, sdf_title, debugatomtypes));
    batch.addPropertyChangeListener(new PropertyChangeListener() {

        @Override
        public void propertyChange(PropertyChangeEvent evt) {
            if (AbstractBatchProcessor.PROPERTY_BATCHSTATS.equals(evt.getPropertyName()))
                logger_cli.log(Level.INFO, evt.getNewValue().toString());
        }
    });
    /*
		 * standardprocessor.setCallback(new
		 * DefaultAmbitProcessor<IAtomContainer, IAtomContainer>() {
		 * 
		 * @Override public IAtomContainer process(IAtomContainer target) throws
		 * Exception { try { //writer.write(target); } catch (Exception x) {
		 * logger.log(Level.SEVERE, x.getMessage()); } return target; } });
		 */
    IBatchStatistics stats = null;
    try {
        stats = batch.process(in);
    } catch (Exception x) {
        StringWriter w = new StringWriter();
        x.printStackTrace(new PrintWriter(w));
        logger_cli.log(Level.WARNING, "MSG_ERR", new Object[] { x.getMessage() });
        logger_cli.log(Level.FINE, "MSG_ERR_DEBUG", new Object[] { x.getMessage(), w.toString() });
    } finally {
        try {
            if (batch != null)
                batch.close();
        } catch (Exception x) {
            logger_cli.log(Level.WARNING, "MSG_ERR", new Object[] { x.getMessage() });
        }
        if (stats != null)
            logger_cli.log(Level.INFO, "MSG_INFO", new Object[] { stats.toString() });
    }
}

Example 5 with BatchDBProcessor

use of ambit2.db.processors.BatchDBProcessor in project ambit-mirror by ideaconsult.

the class CallableSubstanceImporter method createBatch.

@Override
protected AbstractBatchProcessor createBatch(FileInputState target) throws Exception {
    if (target == null)
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
    final BatchDBProcessor<String> batch = new BatchDBProcessor<String>() {

        /**
         */
        private static final long serialVersionUID = 5712170806359764006L;

        @Override
        public Iterator<String> getIterator(IInputState target) throws AmbitException {
            try {
                IRawReader<IStructureRecord> reader = null;
                File file = ((FileInputState) target).getFile();
                String ext = file.getName().toLowerCase();
                if (ext.endsWith(FileInputState._FILE_TYPE.I5Z_INDEX.getExtension())) {
                    if (writer instanceof DBSubstanceWriter)
                        if (writer instanceof DBSubstanceWriter) {
                            ((DBSubstanceWriter) writer).setSplitRecord(true);
                            ((DBSubstanceWriter) writer).setI5mode(true);
                        }
                    reader = new I5ZReader(file);
                    ((I5ZReader) reader).setQASettings(getQASettings());
                } else if (ext.endsWith(FileInputState._FILE_TYPE.I6Z_INDEX.getExtension())) {
                    if (writer instanceof DBSubstanceWriter)
                        if (writer instanceof DBSubstanceWriter) {
                            ((DBSubstanceWriter) writer).setSplitRecord(true);
                            ((DBSubstanceWriter) writer).setI5mode(true);
                        }
                    reader = new I6ZReader(file);
                    ((I6ZReader) reader).setQASettings(getQASettings());
                } else if (ext.endsWith(FileInputState._FILE_TYPE.CSV_INDEX.getExtension())) {
                    if (writer instanceof DBSubstanceWriter)
                        ((DBSubstanceWriter) writer).setSplitRecord(false);
                    LiteratureEntry reference = new LiteratureEntry(originalname, originalname);
                    reader = new CSV12SubstanceReader(new CSV12Reader(new FileReader(file), reference, "FCSV-"));
                } else if (ext.endsWith(".rdf")) {
                    if (writer instanceof DBSubstanceWriter) {
                        ((DBSubstanceWriter) writer).setSplitRecord(false);
                        ((DBSubstanceWriter) writer).setImportBundles(true);
                    }
                    reader = new NanoWikiRDFReader(new InputStreamReader(new FileInputStream(file), "UTF-8"), null, "RDF/XML");
                } else if (ext.endsWith(".ttl")) {
                    if (writer instanceof DBSubstanceWriter) {
                        ((DBSubstanceWriter) writer).setSplitRecord(false);
                        ((DBSubstanceWriter) writer).setImportBundles(true);
                    }
                    reader = new ENanoMapperRDFReader(new InputStreamReader(new FileInputStream(file), "UTF-8"), "ENM3");
                } else if (FileInputState._FILE_TYPE.XLSX_INDEX.hasExtension(ext) || FileInputState._FILE_TYPE.XLS_INDEX.hasExtension(ext)) {
                    if (configFile == null)
                        throw new AmbitException("XLSX/XLSX file import requires a JSON configuration file");
                    final StructureRecordValidator validator = new StructureRecordValidator(file.getName(), true, "XLSX");
                    reader = new GenericExcelParser(new FileInputStream(file), configFile, FileInputState._FILE_TYPE.XLSX_INDEX.hasExtension(ext)) {

                        public Object next() {
                            Object record = super.next();
                            try {
                                if (record instanceof IStructureRecord)
                                    record = validator.process((IStructureRecord) record);
                            } catch (Exception x) {
                            }
                            return record;
                        }
                    };
                    if (writer instanceof DBSubstanceWriter) {
                        ((DBSubstanceWriter) writer).setSplitRecord(false);
                    /*
							 * ((DBSubstanceWriter) writer)
							 * .setClearComposition(false); ((DBSubstanceWriter)
							 * writer) .setClearMeasurements(false);
							 */
                    }
                } else if (ext.endsWith(".json")) {
                    if (writer instanceof DBSubstanceWriter)
                        ((DBSubstanceWriter) writer).setSplitRecord(false);
                    reader = new SubstanceStudyParser(new InputStreamReader(new FileInputStream(file), "UTF-8")) {

                        protected EffectRecord createEffectRecord(Protocol protocol) {
                            try {
                                I5_ROOT_OBJECTS category = I5_ROOT_OBJECTS.valueOf(protocol.getCategory() + "_SECTION");
                                return category.createEffectRecord();
                            } catch (Exception x) {
                                return super.createEffectRecord(protocol);
                            }
                        }
                    };
                    if (writer instanceof DBSubstanceWriter) {
                        ((DBSubstanceWriter) writer).setClearComposition(false);
                        ((DBSubstanceWriter) writer).setClearMeasurements(false);
                    }
                } else {
                    throw new AmbitException("Unsupported format " + file);
                }
                reader.setErrorHandler(new IChemObjectReaderErrorHandler() {

                    @Override
                    public void handleError(String message, int row, int colStart, int colEnd, Exception exception) {
                    }

                    @Override
                    public void handleError(String message, int row, int colStart, int colEnd) {
                    }

                    @Override
                    public void handleError(String message, Exception exception) {
                    }

                    @Override
                    public void handleError(String message) {
                    }
                });
                return reader;
            } catch (AmbitException x) {
                throw x;
            } catch (Exception x) {
                throw new AmbitException(x);
            }
        }
    };
    return batch;
}