Examples with CSVReader au.com.bytecode.opencsv.CSVReader used on opensource projects

Example 46 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project molgenis by molgenis.

the class OmimRepository method getEntitiesByGeneSymbol.

private Map<String, List<Entity>> getEntitiesByGeneSymbol() {
    if (entitiesByGeneSymbol == null) {
        Map<String, List<List<String>>> omimEntriesByGeneSymbol = new HashMap<>();
        entitiesByGeneSymbol = new LinkedHashMap<>();
        try (CSVReader csvReader = new CSVReader(new InputStreamReader(new FileInputStream(file), forName("UTF-8")), SEPARATOR, DEFAULT_QUOTE_CHARACTER, 1)) {
            String[] values = csvReader.readNext();
            while (values != null) {
                addLineToMap(omimEntriesByGeneSymbol, values);
                values = csvReader.readNext();
            }
            for (String geneSymbol : omimEntriesByGeneSymbol.keySet()) {
                addEntityToGeneEntityList(omimEntriesByGeneSymbol, geneSymbol);
            }
        } catch (IOException e) {
            throw new UncheckedIOException(e);
        }
    }
    return entitiesByGeneSymbol;
}

Example 47 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project ma-modules-public by infiniteautomation.

the class DataImportController method parseFile.

/* (non-Javadoc)
	 * @see com.serotonin.m2m2.web.mvc.controller.FileUploadController#parseFile(java.io.InputStream, java.util.Map, com.serotonin.m2m2.i18n.Translations, javax.servlet.http.HttpServletRequest)
	 */
@Override
protected void parseFile(InputStream input, Map<String, Object> model, Translations translations, HttpServletRequest request) {
    // Setup for error tracking
    List<String> errorMessages = new ArrayList<String>();
    model.put("errorMessages", errorMessages);
    CSVReader csvReader = new CSVReader(new InputStreamReader(input));
    try {
        importCsv(csvReader, model, translations, errorMessages);
    } catch (Exception e) {
        if (e instanceof TranslatableException)
            errorMessages.add(((TranslatableException) e).getTranslatableMessage().translate(translations));
        else
            errorMessages.add(e.getMessage());
    } finally {
        model.put("hasImportErrors", errorMessages.size() > 0);
        try {
            csvReader.close();
        } catch (IOException e) {
            errorMessages.add(e.getMessage());
        }
    }
}

Example 48 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project cu-kfs by CU-CommunityApps.

the class CsvBatchInputFileTypeBase method validateCSVFileInput.

/**
 * Validates the CSV file content against the CSVEnum items as header
 * 1. content header must match CSVEnum order/value
 * 2. each data row should have same size as the header
 *
 * @param expectedHeaderList        expected CSV header String list
 * @param fileContents              contents to validate
 *
 * @throws IOException
 */
private void validateCSVFileInput(final List<String> expectedHeaderList, InputStream fileContents) throws IOException {
    // use csv reader to parse the csv content
    CSVReader csvReader = new CSVReader(new InputStreamReader(fileContents));
    List<String> inputHeaderList = Arrays.asList(csvReader.readNext());
    String errorMessage = null;
    // validate
    if (!CollectionUtils.isEqualCollection(expectedHeaderList, inputHeaderList)) {
        errorMessage = "CSV Batch Input File contains incorrect number of headers";
    // collection has same elements, now check the exact content orders by looking at the toString comparisons
    } else if (!expectedHeaderList.equals(inputHeaderList)) {
        errorMessage = "CSV Batch Input File headers are different";
    } else {
        // check the content size as well if headers are validated
        int line = 1;
        List<String> inputDataList = null;
        while ((inputDataList = Arrays.asList(csvReader.readNext())) != null && errorMessage != null) {
            // if the data list size does not match header list (its missing data)
            if (inputDataList.size() != expectedHeaderList.size()) {
                errorMessage = "line " + line + " layout does not match the header";
            }
            line++;
        }
    }
    if (errorMessage != null) {
        LOG.error(errorMessage);
        throw new RuntimeException(errorMessage);
    }
}

Example 49 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project incubator-sdap-mudrod by apache.

the class DataGenerator method parseFile.

/**
 * Parses the original user-specified CSV file, storing the contents for future calculations
 * and formatting.
 */
public static void parseFile() {
    String[][] dataArr = null;
    try {
        String sourceDir = mySourceDir;
        if (// Case where multiple files have to be processed
        isMultFiles) {
            // Iterate over files in directory
            File directory = new File(sourceDir);
            File[] directoryListing = directory.listFiles();
            if (directoryListing != null) {
                for (File child : directoryListing) {
                    CSVReader csvReader = new CSVReader(new FileReader(child));
                    List<String[]> list = csvReader.readAll();
                    // Store into 2D array by transforming array list to normal array
                    dataArr = new String[list.size()][];
                    dataArr = list.toArray(dataArr);
                    calculateVec(dataArr);
                    csvReader.close();
                }
                // Store the header
                storeHead(dataArr);
            }
        } else // Process only one file
        {
            File file = new File(sourceDir);
            if (file != null) {
                CSVReader csvReader = new CSVReader(new FileReader(file));
                List<String[]> list = csvReader.readAll();
                // Store into 2D array by transforming array list to normal array
                dataArr = new String[list.size()][];
                dataArr = list.toArray(dataArr);
                // Store the header
                storeHead(dataArr);
                calculateVec(dataArr);
                csvReader.close();
            }
        }
    } catch (FileNotFoundException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 50 with CSVReader

use of au.com.bytecode.opencsv.CSVReader in project dkpro-tc by dkpro.

the class TcFlexTable method getCsvReader.

public StreamReader getCsvReader() {
    return new StreamReader() {

        @Override
        public void read(InputStream aStream) throws IOException {
            try {
                CSVReader reader = new CSVReader(new InputStreamReader(aStream, "UTF-8"));
                String[] headers = reader.readNext();
                Method converter = TcFlexTable.this.dataClass.getMethod("valueOf", String.class);
                String[] data;
                while ((data = reader.readNext()) != null) {
                    Map<String, V> row = new LinkedHashMap<String, V>();
                    for (int i = 1; i < headers.length; i++) {
                        @SuppressWarnings("unchecked") V value = (V) converter.invoke(null, data[i]);
                        row.put(headers[i], value);
                    }
                    addRow(data[0], row);
                }
                reader.close();
            } catch (IOException e) {
                throw e;
            } catch (NoSuchMethodException e) {
                throw new IOException("Data class " + TcFlexTable.this.dataClass.getName() + " does not have a " + "public static Object valueOf(String) method - unable unmarshall the " + "data.");
            } catch (Exception e) {
                throw new IOException(e);
            }
        }
    };
}