Examples with LineIterator org.apache.commons.io.LineIterator used on opensource projects

Example 26 with LineIterator

use of org.apache.commons.io.LineIterator in project opennms by OpenNMS.

the class JmxRrdMigratorOffline method fixJmxConfigurationFile.

/**
     * Fixes a JMX configuration file.
     *
     * @param jmxConfigFile the JMX configuration file
     * @throws OnmsUpgradeException the OpenNMS upgrade exception
     */
private void fixJmxConfigurationFile(File jmxConfigFile) throws OnmsUpgradeException {
    try {
        log("Updating JMX metric definitions on %s\n", jmxConfigFile);
        zipFile(jmxConfigFile);
        backupFiles.add(new File(jmxConfigFile.getAbsolutePath() + ZIP_EXT));
        File outputFile = new File(jmxConfigFile.getCanonicalFile() + ".temp");
        FileWriter w = new FileWriter(outputFile);
        Pattern extRegex = Pattern.compile("import-mbeans[>](.+)[<]");
        Pattern aliasRegex = Pattern.compile("alias=\"([^\"]+\\.[^\"]+)\"");
        List<File> externalFiles = new ArrayList<File>();
        LineIterator it = FileUtils.lineIterator(jmxConfigFile);
        while (it.hasNext()) {
            String line = it.next();
            Matcher m = extRegex.matcher(line);
            if (m.find()) {
                externalFiles.add(new File(jmxConfigFile.getParentFile(), m.group(1)));
            }
            m = aliasRegex.matcher(line);
            if (m.find()) {
                String badDs = m.group(1);
                String fixedDs = getFixedDsName(badDs);
                log("  Replacing bad alias %s with %s on %s\n", badDs, fixedDs, line.trim());
                line = line.replaceAll(badDs, fixedDs);
                if (badMetrics.contains(badDs) == false) {
                    badMetrics.add(badDs);
                }
            }
            w.write(line + "\n");
        }
        LineIterator.closeQuietly(it);
        w.close();
        FileUtils.deleteQuietly(jmxConfigFile);
        FileUtils.moveFile(outputFile, jmxConfigFile);
        if (!externalFiles.isEmpty()) {
            for (File configFile : externalFiles) {
                fixJmxConfigurationFile(configFile);
            }
        }
    } catch (Exception e) {
        throw new OnmsUpgradeException("Can't fix " + jmxConfigFile + " because " + e.getMessage(), e);
    }
}

Example 27 with LineIterator

use of org.apache.commons.io.LineIterator in project Asqatasun by Asqatasun.

the class CodeGeneratorMojo method getCsv.

/**
     *
     * @return
     */
private Iterable<CSVRecord> getCsv() {
    // we parse the csv file to extract the first line and get the headers 
    LineIterator lineIterator;
    try {
        lineIterator = FileUtils.lineIterator(dataFile, Charset.defaultCharset().name());
    } catch (IOException ex) {
        Logger.getLogger(CodeGeneratorMojo.class.getName()).log(Level.SEVERE, null, ex);
        lineIterator = null;
    }
    String[] csvHeaders = lineIterator != null ? lineIterator.next().split(String.valueOf(delimiter)) : new String[0];
    isCriterionPresent = extractCriterionFromCsvHeader(csvHeaders);
    try {
        extractAvailableLangsFromCsvHeader(csvHeaders);
    } catch (I18NLanguageNotFoundException ex) {
        Logger.getLogger(CodeGeneratorMojo.class.getName()).log(Level.SEVERE, null, ex);
        return null;
    }
    // from here we just add each line to a build to re-create the csv content
    // without the first line.
    StringBuilder strb = new StringBuilder();
    while (lineIterator.hasNext()) {
        strb.append(lineIterator.next());
        strb.append("\n");
    }
    Reader in;
    try {
        in = new StringReader(strb.toString());
        CSVFormat csvf = CSVFormat.newFormat(delimiter).withHeader(csvHeaders);
        return csvf.parse(in);
    } catch (FileNotFoundException ex) {
        Logger.getLogger(CodeGeneratorMojo.class.getName()).log(Level.SEVERE, null, ex);
        return null;
    } catch (IOException ex) {
        Logger.getLogger(CodeGeneratorMojo.class.getName()).log(Level.SEVERE, null, ex);
        return null;
    }
}

Example 28 with LineIterator

use of org.apache.commons.io.LineIterator in project Asqatasun by Asqatasun.

the class ExtractCsvAndCopy method getCsv.

public Iterable<CSVRecord> getCsv() throws IOException {
    // we parse the csv file to extract the first line and get the headers 
    LineIterator lineIterator;
    lineIterator = FileUtils.lineIterator(DATA_FILE);
    csvHeaders = lineIterator.next().split(String.valueOf(DELIMITER));
    StringBuilder strb = new StringBuilder();
    while (lineIterator.hasNext()) {
        strb.append(lineIterator.next());
        strb.append("\n");
    }
    Reader in;
    try {
        in = new StringReader(strb.toString());
        CSVFormat csvf = CSVFormat.newFormat(DELIMITER).withHeader(csvHeaders);
        return csvf.parse(in);
    } catch (FileNotFoundException ex) {
        return null;
    } catch (IOException ex) {
        return null;
    }
}

Example 29 with LineIterator

use of org.apache.commons.io.LineIterator in project goci by EBISPOT.

the class GwasJsonController method getJsonFromFile.

/**
     * Return as a string the content of the gwas.json file pointed out by Constants.JSON_FILE_PATH
     *
     * @return the content of the gwas.json
     * @throws IOException
     */
public String getJsonFromFile() throws IOException {
    String json = "";
    File jsonFile = new File(Constants.JSON_FILE_PATH);
    LineIterator it = FileUtils.lineIterator(jsonFile, "UTF-8");
    try {
        while (it.hasNext()) {
            json = json + it.nextLine();
        // do something with line
        }
    } finally {
        LineIterator.closeQuietly(it);
    }
    return json;
}

Example 30 with LineIterator

use of org.apache.commons.io.LineIterator in project ice by JBEI.

the class BulkCSVUpload method getBulkUploadDataFromFile.

// NOTE: this also validates the part data (with the exception of the actual files)
List<PartWithSample> getBulkUploadDataFromFile(InputStream inputStream) throws IOException {
    List<PartWithSample> partDataList = new LinkedList<>();
    // initialize parser to null; when not-null in the loop below, then the header has been parsed
    CSVParser parser = null;
    HashMap<Integer, HeaderValue> headers = null;
    // parse CSV file
    try {
        LineIterator it = IOUtils.lineIterator(inputStream, "UTF-8");
        int index = 0;
        while (it.hasNext()) {
            String line = it.nextLine().trim();
            // check if first time parsing (first line)
            if (parser == null) {
                // to indicate the type of parser to use (tab or comma separated)
                if (line.contains("\t") && !line.contains(","))
                    parser = new CSVParser('\t');
                else
                    parser = new CSVParser();
                // get column headers
                String[] fieldStrArray = parser.parseLine(line);
                headers = processColumnHeaders(fieldStrArray);
                continue;
            }
            // skip any empty lines (holes) in the csv file
            if (StringUtils.isBlank(line) || line.replaceAll(",", "").trim().isEmpty())
                continue;
            // at this point we must have headers since that should be the first item in the file
            if (headers == null)
                throw new IOException("Could not parse file headers");
            // parser != null; process line contents with available headers
            String[] valuesArray = parser.parseLine(line);
            PartData partData = new PartData(addType);
            PartSample partSample = null;
            if (subType != null) {
                partData.getLinkedParts().add(new PartData(subType));
            }
            // for each column
            for (int i = 0; i < valuesArray.length; i += 1) {
                HeaderValue headerForColumn = headers.get(i);
                // process sample information
                if (headerForColumn.isSampleField()) {
                    // todo : move to another method
                    if (partSample == null)
                        partSample = new PartSample();
                    setPartSampleData(((SampleHeaderValue) headerForColumn).getSampleField(), partSample, valuesArray[i]);
                } else {
                    EntryHeaderValue entryHeaderValue = (EntryHeaderValue) headerForColumn;
                    EntryField field = entryHeaderValue.getEntryField();
                    PartData data;
                    String value = valuesArray[i];
                    boolean isSubType = entryHeaderValue.isSubType();
                    if (isSubType)
                        data = partData.getLinkedParts().get(0);
                    else
                        data = partData;
                    // get the data for the field
                    switch(field) {
                        case ATT_FILENAME:
                            ArrayList<AttachmentInfo> attachments = data.getAttachments();
                            if (attachments == null) {
                                attachments = new ArrayList<>();
                                data.setAttachments(attachments);
                            }
                            attachments.clear();
                            attachments.add(new AttachmentInfo(value));
                            break;
                        case SEQ_FILENAME:
                            data.setSequenceFileName(value);
                            break;
                        case SEQ_TRACE_FILES:
                            // todo
                            break;
                        case EXISTING_PART_NUMBER:
                            Entry entry = DAOFactory.getEntryDAO().getByPartNumber(value);
                            if (entry == null)
                                throw new IOException("Could not locate part number \"" + value + "\" for linking");
                            PartData toLink = entry.toDataTransferObject();
                            data.getLinkedParts().add(toLink);
                            break;
                        default:
                            partData = EntryUtil.setPartDataFromField(partData, value, field, isSubType);
                    }
                }
            }
            // validate
            List<EntryField> fields = EntryUtil.validates(partData);
            if (!fields.isEmpty()) {
                invalidFields.clear();
                invalidFields.addAll(fields);
                return null;
            }
            partData.setIndex(index);
            PartWithSample partWithSample = new PartWithSample(partSample, partData);
            partDataList.add(partWithSample);
            index += 1;
        }
    } finally {
        IOUtils.closeQuietly(inputStream);
    }
    return partDataList;
}