Examples with IChemObjectReaderErrorHandler org.openscience.cdk.io.IChemObjectReaderErrorHandler used on opensource projects

Example 1 with IChemObjectReaderErrorHandler

use of org.openscience.cdk.io.IChemObjectReaderErrorHandler in project ambit-mirror by ideaconsult.

the class I5ParserTest method testi5z.

@Test
public void testi5z() throws Exception {
    URL url = getClass().getClassLoader().getResource("ambit2/core/data/i5z/RefSub_030913110311.i5z");
    IIteratingChemObjectReader ireader = FileInputState.getReader(new File(url.getFile()));
    ireader.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) {
            exception.printStackTrace();
        }

        @Override
        public void handleError(String message) {
        }
    });
    int count = 0;
    int foundCas = 0;
    int foundName = 0;
    RawIteratingFolderReader reader = (RawIteratingFolderReader) ireader;
    while (reader.hasNext()) {
        IStructureRecord record = reader.nextRecord();
        /*
			for (Property p : record.getProperties())
				System.out.println(String.format("%s [%s] = %s",p.getName(),p.getReference().getTitle(),record.getProperty(p)));
			System.out.println();
			*/
        count++;
        for (Property p : record.getRecordProperties()) {
            foundCas += record.getRecordProperty(p).equals("59-87-0") ? 1 : 0;
            foundName += record.getRecordProperty(p).equals("5-nitro-2-furaldehyde semicarbazone") ? 1 : 0;
            System.out.println(p.getName() + " = " + record.getRecordProperty(p));
        }
    // Assert.assertNotNull(record.getSmiles());
    // Assert.assertNotNull(record.getInchi());
    // Assert.assertNotNull(record.getProperty(Property.getI5UUIDInstance()));
    }
    reader.close();
    Assert.assertEquals(10, count);
    Assert.assertEquals(1, foundCas);
    Assert.assertEquals(1, foundName);
}

Example 2 with IChemObjectReaderErrorHandler

use of org.openscience.cdk.io.IChemObjectReaderErrorHandler in project ambit-mirror by ideaconsult.

the class DataSet method getReader.

public static IIteratingChemObjectReader<IAtomContainer> getReader(InputStream in, String extension) throws CDKException, AmbitIOException {
    FileInputState instate = new FileInputState();
    IIteratingChemObjectReader<IAtomContainer> reader;
    if (extension.endsWith(FileInputState._FILE_TYPE.SDF_INDEX.getExtension())) {
        reader = new InteractiveIteratingMDLReader(in, SilentChemObjectBuilder.getInstance());
        ((InteractiveIteratingMDLReader) reader).setSkip(true);
    } else
        reader = instate.getReader(in, extension);
    reader.setReaderMode(Mode.RELAXED);
    reader.setErrorHandler(new IChemObjectReaderErrorHandler() {

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

        @Override
        public void handleError(String message, int row, int colStart, int colEnd) {
            System.out.println(message);
        }

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

        @Override
        public void handleError(String message) {
            System.out.println(message);
        }
    });
    return reader;
}

Example 3 with IChemObjectReaderErrorHandler

use of org.openscience.cdk.io.IChemObjectReaderErrorHandler in project ambit-mirror by ideaconsult.

the class SLNCli method getReader.

public IIteratingChemObjectReader<IAtomContainer> getReader(InputStream in, String extension) throws CDKException, AmbitIOException {
    FileInputState instate = new FileInputState();
    IIteratingChemObjectReader<IAtomContainer> reader;
    if (extension.endsWith(FileInputState._FILE_TYPE.SDF_INDEX.getExtension())) {
        reader = new InteractiveIteratingMDLReader(in, SilentChemObjectBuilder.getInstance());
        ((InteractiveIteratingMDLReader) reader).setSkip(true);
    } else
        reader = instate.getReader(in, extension);
    reader.setReaderMode(Mode.RELAXED);
    reader.setErrorHandler(new IChemObjectReaderErrorHandler() {

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

        @Override
        public void handleError(String message, int row, int colStart, int colEnd) {
            System.out.println(message);
        }

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

        @Override
        public void handleError(String message) {
            System.out.println(message);
        }
    });
    return reader;
}

Example 4 with IChemObjectReaderErrorHandler

use of org.openscience.cdk.io.IChemObjectReaderErrorHandler in project ambit-mirror by ideaconsult.

the class CallableSubstanceI5Query method getReader.

private IZReader getReader(File i5z) throws Exception {
    IChemObjectReaderErrorHandler errhandler = new IChemObjectReaderErrorHandler() {

        @Override
        public void handleError(String message, int row, int colStart, int colEnd, Exception exception) {
            localLogger.log(Level.WARNING, String.format("%s [row %d colStart %d colEnd %d] %s", message, row, colStart, colEnd, exception.getMessage()));
        }

        @Override
        public void handleError(String message, int row, int colStart, int colEnd) {
            localLogger.log(Level.WARNING, String.format("%s [row %d colStart %d colEnd %d]", message, row, colStart, colEnd));
        }

        @Override
        public void handleError(String message, Exception exception) {
            localLogger.log(Level.WARNING, exception.getMessage());
        }

        @Override
        public void handleError(String message) {
            localLogger.log(Level.WARNING, message);
        }
    };
    IZReader reader = iuclidversion.getReader(i5z, errhandler);
    reader.setErrorHandler(errhandler);
    return reader;
}

Example 5 with IChemObjectReaderErrorHandler

use of org.openscience.cdk.io.IChemObjectReaderErrorHandler 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;
}