Examples with CSV12Reader net.idea.loom.nm.csv.CSV12Reader used on opensource projects

Example 1 with CSV12Reader

use of net.idea.loom.nm.csv.CSV12Reader in project ambit-mirror by ideaconsult.

the class ProteinCoronaPaperReaderTest method test.

@Test
public void test() throws Exception {
    RawIteratingWrapper reader = null;
    try {
        LiteratureEntry entry = new LiteratureEntry("Protein Corona", "http://dx.doi.org/10.1021/nn406018q");
        entry.setType(_type.Dataset);
        File baseDir = new File(System.getProperty("java.io.tmpdir"));
        File datafile = new File(baseDir, "MergedSheets.csv");
        if (!datafile.exists()) {
            URL url = new URL("https://raw.githubusercontent.com/ideaconsult/Protein_Corona/master/MergedSheets.csv");
            DownloadTool.download(url, datafile);
        }
        CSV12Reader chemObjectReader = new CSV12Reader(new FileReader(datafile), entry, "PRCR-");
        reader = new CSV12SubstanceReader(chemObjectReader);
        int r = 0;
        while (reader.hasNext()) {
            IStructureRecord mol = reader.nextRecord();
            Assert.assertTrue(mol instanceof SubstanceRecord);
            System.out.println(((SubstanceRecord) mol).getPublicName());
            System.out.println(((SubstanceRecord) mol).getMeasurements());
            r++;
        }
        Assert.assertTrue(r >= 120);
    } finally {
        reader.close();
    }
}

Example 2 with CSV12Reader

use of net.idea.loom.nm.csv.CSV12Reader in project ambit-mirror by ideaconsult.

the class ProteinCoronaPaperReaderTest method testRDFExport.

@Test
public void testRDFExport() throws Exception {
    CSV12SubstanceReader reader = null;
    Request hack = new Request();
    hack.setRootRef(new Reference("http://localhost/ambit2"));
    File baseDir = new File(System.getProperty("java.io.tmpdir"));
    File datafile = new File(baseDir, "MergedSheets.csv");
    if (!datafile.exists()) {
        URL url = new URL("https://raw.githubusercontent.com/ideaconsult/Protein_Corona/master/MergedSheets.csv");
        DownloadTool.download(url, datafile);
    }
    SubstanceRDFReporter r = new SubstanceRDFReporter(hack, MediaType.TEXT_RDF_N3);
    Model model = ModelFactory.createDefaultModel();
    r.header(model, null);
    r.setOutput(model);
    LiteratureEntry entry = new LiteratureEntry("Protein Corona", "http://dx.doi.org/10.1021/nn406018q");
    entry.setType(_type.Dataset);
    try {
        CSV12Reader chemObjectReader = new CSV12Reader(new FileReader(datafile), entry, "PRCR-");
        reader = new CSV12SubstanceReader(chemObjectReader);
        while (reader.hasNext()) {
            IStructureRecord record = reader.nextRecord();
            Assert.assertTrue(record instanceof SubstanceRecord);
            r.processItem((SubstanceRecord) record);
        }
        r.footer(model, null);
        File output = new File(System.getProperty("java.io.tmpdir") + "/" + "protein_export.ttl");
        System.out.println("Exported to " + output.getAbsolutePath());
        OutputStream writer = new FileOutputStream(output);
        RDFDataMgr.write(writer, model, RDFFormat.TURTLE);
    } finally {
        if (reader != null)
            reader.close();
    }
}

Example 3 with CSV12Reader

use of net.idea.loom.nm.csv.CSV12Reader in project ambit-mirror by ideaconsult.

the class ProteinCoronaPaperReaderTest method testWriteProteinCoronaData.

@Test
public void testWriteProteinCoronaData() throws Exception {
    setUpDatabaseFromResource("ambit2/db/processors/test/empty-datasets.xml");
    IDatabaseConnection c = getConnection();
    IRawReader<IStructureRecord> parser = null;
    try {
        LiteratureEntry entry = new LiteratureEntry("Protein Corona", "http://dx.doi.org/10.1021/nn406018q");
        entry.setType(_type.Dataset);
        File baseDir = new File(System.getProperty("java.io.tmpdir"));
        File datafile = new File(baseDir, "MergedSheets.csv");
        if (!datafile.exists()) {
            URL url = new URL("https://raw.githubusercontent.com/ideaconsult/Protein_Corona/master/MergedSheets.csv");
            DownloadTool.download(url, datafile);
        }
        CSV12Reader chemObjectReader = new CSV12Reader(new FileReader(datafile), entry, "PRCR-");
        parser = new CSV12SubstanceReader(chemObjectReader);
        write(parser, c.getConnection(), new ReferenceSubstanceUUID(), false);
    } finally {
        parser.close();
        c.close();
    }
}

Example 4 with CSV12Reader

use of net.idea.loom.nm.csv.CSV12Reader 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;
}