Examples with I5_ROOT_OBJECTS net.idea.i5.io.I5_ROOT_OBJECTS used on opensource projects

Example 1 with I5_ROOT_OBJECTS

use of net.idea.i5.io.I5_ROOT_OBJECTS in project ambit-mirror by ideaconsult.

the class SubstanceDatasetResource method createXLSXReporter.

protected IProcessor<Q, Representation> createXLSXReporter(MediaType media, boolean hssf, String filenamePrefix) {
    groupProperties.add(new SubstancePublicName());
    groupProperties.add(new SubstanceName());
    groupProperties.add(new SubstanceUUID());
    groupProperties.add(new SubstanceOwner());
    String jsonpcallback = getParams().getFirstValue("jsonp");
    if (jsonpcallback == null)
        jsonpcallback = getParams().getFirstValue("callback");
    String configResource = String.format("config-%s.js", ((IFreeMarkerApplication) getApplication()).getProfile());
    return new OutputStreamConvertor(new StructureRecordXLSXReporter(getRequest().getRootRef().toString(), hssf, getTemplate(), getGroupProperties(), getBundles(), null, true, configResource) {

        @Override
        protected void configurePropertyProcessors() {
            getCompositionProcessors(getProcessors());
            getProcessors().add(getPropertyProcessors(false, false));
        }

        @Override
        protected void initColumns(int afterCol) {
            for (I5_ROOT_OBJECTS section : I5_ROOT_OBJECTS.values()) {
                if (section.isIUCLID5() && section.isScientificPart() && section.isSupported() && !section.isNanoMaterialTemplate()) {
                    int last = mergedProperties.size();
                    mergedProperties.put("http://www.opentox.org/echaEndpoints.owl#" + section.name(), last);
                    Cell hcell = sheet.getRow(0).createCell(last + afterCol);
                    hcell.setCellStyle(hstyle);
                    hcell.setCellType(CellType.STRING);
                    hcell.setCellValue(section.getNumber() + ". " + section.getTitle());
                    sheet.autoSizeColumn(hcell.getColumnIndex(), true);
                    // initially hide all columns, unhide if data is added
                    // to
                    sheet.setColumnHidden(hcell.getColumnIndex(), true);
                }
            }
        }
    }, media, filenamePrefix);
}

Example 2 with I5_ROOT_OBJECTS

use of net.idea.i5.io.I5_ROOT_OBJECTS 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;
}

Example 3 with I5_ROOT_OBJECTS

use of net.idea.i5.io.I5_ROOT_OBJECTS in project ambit-mirror by ideaconsult.

the class SubstanceCategoryProperty method createQuery.

@Override
protected Iterator<EffectRecord<String, IParams, String>> createQuery(Context context, Request request, Response response) throws ResourceException {
    try {
        Object topcategory = Reference.decode(request.getAttributes().get(SubstancePropertyResource.topcategory).toString());
        Object endpointcategory = Reference.decode(request.getAttributes().get(SubstancePropertyResource.endpointcategory).toString());
        if (topcategory == null || endpointcategory == null)
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
        I5_ROOT_OBJECTS category;
        try {
            category = I5_ROOT_OBJECTS.valueOf(endpointcategory.toString().replace("_SECTION", ""));
        } catch (Exception x) {
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage());
        }
        if (!category.getTopCategory().equals(topcategory.toString())) {
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, String.format("Expected /property/%s/%s", category.getTopCategory(), category.name()));
        }
        effects = new ArrayList<EffectRecord<String, IParams, String>>();
        if (category.getEndpoints() != null && category.getEndpoints().length > 0)
            for (String endpoint : category.getEndpoints()) {
                EffectRecord record = category.createEffectRecord();
                record.setEndpoint(endpoint);
                effects.add(record);
            }
        else
            effects.add(category.createEffectRecord());
        return effects.iterator();
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage());
    }
}