Example usage for org.apache.commons.csv CSVRecord get

List of usage examples for org.apache.commons.csv CSVRecord get

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Introduction

In this page you can find the example usage for org.apache.commons.csv CSVRecord get.

Prototype

public String get(final String name)

Source Link

Document

Returns a value by name.

Usage

From source file:com.nuevebit.miroculus.mrna.cli.DatabasePopulator.java

private void parseCSV(String csv) throws IOException {
    CSVParser csvParser = CSVParser.parse(csv, CSVFormat.EXCEL);

    Iterator<CSVRecord> records = csvParser.iterator();
    // ignore headers
    records.next();//from   w ww.java  2 s.c o  m

    // read line by line
    while (records.hasNext()) {
        CSVRecord record = records.next();

        // normalize the name (remove *)
        String miRNAName = MiRNA.normalizeName(record.get(0));
        MiRNA miRNA = miRNARepository.findByName(miRNAName);

        if (miRNA == null) { // primera vez que se agrega
            miRNA = miRNARepository.save(new MiRNA(miRNAName));
        }

        String diseaseName = record.get(1).toLowerCase().trim();
        Disease disease = diseaseRepository.findByName(diseaseName);

        if (disease == null) {
            disease = diseaseRepository.save(new Disease(diseaseName));
            disease.setMortalityRate(0d);
        }

        String authorName = record.get(4).trim();
        Author author = authorRepository.findByName(authorName);

        if (author == null) {
            author = authorRepository.save(new Author(authorName));
        }

        String publicationTitle = record.get(6).trim();
        String publicationJournal = record.get(5).trim();

        Publication pub = publicationRepository.findByNameAndJournal(publicationTitle, publicationJournal);

        if (pub == null) {
            pub = new Publication(publicationTitle, publicationJournal);
            pub.setAuthor(author);
            String year = record.get(7);
            pub.setYear(Integer.valueOf(year));
            pub.setDescription(record.get(9).trim());

            pub = publicationRepository.save(pub);

        }

        String methodName = record.get(8).trim();
        DiscoveryMethod method = discoveryMethodRepository.findByName(methodName);

        if (method == null) {
            method = discoveryMethodRepository.save(new DiscoveryMethod(methodName));
        }

        CorrelationDiscovery correlation = new CorrelationDiscovery(miRNA, disease,
                Integer.valueOf(record.get(2)));

        correlation.setPublication(pub);
        correlation.setMethod(method);

        // save the found correlation
        correlationDiscoveryRepository.save(correlation);
    }
}

From source file:ColdestWeather.ColdestWeather.java

public CSVRecord checkColdest(CSVRecord currentRow, CSVRecord coldestSoFar) {
    if (coldestSoFar == null) {
        coldestSoFar = currentRow;/*from  ww w  .ja v a  2  s.  c  o m*/
    } else {
        double currentTemp = Double.parseDouble(currentRow.get("TemperatureF"));
        double coldestTemp = Double.parseDouble(coldestSoFar.get("TemperatureF"));
        //Check if currentTemp < coldestTemp
        if (currentTemp < coldestTemp && currentTemp > -9000) {
            //Update coldesSoFar to currentRow
            coldestSoFar = currentRow;
        }
    }
    return coldestSoFar;
}

From source file:com.cotrino.langnet.GenerateVisualization.java

private double[] calculateSimilarity(File logFile) throws IOException {

    int i = 0;//from  ww w . j a  va 2s .com
    double total = 0.0;
    Reader reader = new FileReader(logFile);
    CSVParser parser = new CSVParser(reader, csvFormat);
    for (CSVRecord record : parser) {
        try {
            double similarity = Double.parseDouble(record.get("Similarity"));
            total += similarity;
            i++;
        } catch (NumberFormatException e) {
            logger.error("At " + logFile.getName() + ", failed line: " + record.toString());
        }
    }
    parser.close();
    reader.close();
    return new double[] { (total / i), i };

}

From source file:com.team3637.service.ScheduleServiceMySQLImpl.java

@Override
public void importCSV(String inputFile) {
    try {//from   w w  w .j a v  a  2s  .c om
        String csvData = new String(Files.readAllBytes(FileSystems.getDefault().getPath(inputFile)));
        csvData = csvData.replaceAll("\\r", "");
        CSVParser parser = CSVParser.parse(csvData, CSVFormat.DEFAULT.withRecordSeparator("\n"));
        for (CSVRecord record : parser) {
            Schedule schedule = new Schedule();
            schedule.setId(Integer.parseInt(record.get(0)));
            schedule.setMatchNum(Integer.parseInt(record.get(1)));
            schedule.setB1(Integer.parseInt(record.get(2)));
            schedule.setB2(Integer.parseInt(record.get(3)));
            schedule.setB3(Integer.parseInt(record.get(4)));
            schedule.setR1(Integer.parseInt(record.get(5)));
            schedule.setR2(Integer.parseInt(record.get(6)));
            schedule.setR3(Integer.parseInt(record.get(7)));
            if (checkForMatch(schedule))
                update(schedule);
            else
                create(schedule);
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:assignment.CSVFileReader.java

@Override
public List<Map<String, String>> readFile(String filePath) {
    Reader reader;/*from   w  w  w. j av  a2 s . c o m*/
    List<Map<String, String>> rows = new ArrayList<Map<String, String>>();
    try {
        reader = new BufferedReader(new InputStreamReader(new FileInputStream(filePath), "utf-8"));
        CSVParser csvParser = new CSVParser(reader, CSVFormat.DEFAULT);

        Iterator<CSVRecord> csvRecord = csvParser.iterator();
        CSVRecord headers = csvRecord.next();

        for (CSVRecord row : csvParser) {
            Map<String, String> item = new HashMap<String, String>();

            int colNr = 0;
            for (String header : headers) {
                String r = "";
                try {
                    r = row.get(colNr);
                } catch (Exception ex) {

                }
                item.put(header, r);
                colNr++;
            }
            rows.add(item);
        }
    } catch (Exception ex) {

    }
    return rows;
}

From source file:eu.fthevenet.binjr.data.codec.CsvDecoder.java

@Override
public Map<TimeSeriesInfo<T>, TimeSeriesProcessor<T>> decode(InputStream in, List<TimeSeriesInfo<T>> seriesInfo)
        throws IOException, DecodingDataFromAdapterException {
    try (Profiler ignored = Profiler.start("Building time series from csv data", logger::trace)) {
        try (BufferedReader reader = new BufferedReader(new InputStreamReader(in, encoding))) {
            CSVFormat csvFormat = CSVFormat.DEFAULT.withAllowMissingColumnNames(false).withFirstRecordAsHeader()
                    .withSkipHeaderRecord().withDelimiter(delimiter);
            Iterable<CSVRecord> records = csvFormat.parse(reader);
            Map<TimeSeriesInfo<T>, TimeSeriesProcessor<T>> series = new HashMap<>();
            final AtomicLong nbpoints = new AtomicLong(0);
            for (CSVRecord csvRecord : records) {
                nbpoints.incrementAndGet();
                ZonedDateTime timeStamp = dateParser.apply(csvRecord.get(0));
                for (TimeSeriesInfo<T> info : seriesInfo) {
                    T val = numberParser.apply(csvRecord.get(info.getBinding().getLabel()));
                    XYChart.Data<ZonedDateTime, T> point = new XYChart.Data<>(timeStamp, val);
                    TimeSeriesProcessor<T> l = series.computeIfAbsent(info, k -> timeSeriesFactory.create());
                    l.addSample(point);//from   w w  w  .  j  ava2s  . c om
                }
            }
            logger.trace(() -> String.format("Built %d series with %d samples each (%d total samples)",
                    seriesInfo.size(), nbpoints.get(), seriesInfo.size() * nbpoints.get()));
            return series;
        }
    }
}

From source file:ColdestWeather.ColdestWeather.java

public String lowestHumidityInManyFiles() {
    CSVRecord lowestSoFar = null;//from  ww  w .  j a v  a2 s .  c o m
    String lowestHumFile = "";
    DirectoryResource dr = new DirectoryResource();
    //Iterate over all the files
    for (File file : dr.selectedFiles()) {
        FileResource fr = new FileResource(file);
        //call lowestHumidityInFile to get the file with lowest Humidity
        CSVRecord currentRow = lowestHumidityInFile(fr.getCSVParser());
        if (lowestSoFar == null) {
            lowestSoFar = currentRow;
        } else {
            if (!currentRow.get("Humidity").contains("N/A")) {
                int currentHumidity = Integer.parseInt(currentRow.get("Humidity"));
                int lowestHumidity = Integer.parseInt(lowestSoFar.get("Humidity"));
                if (currentHumidity < lowestHumidity) {
                    lowestSoFar = currentRow;
                    lowestHumFile = file.getAbsolutePath();
                }
            }
        }

    }

    return lowestHumFile;
}

From source file:edu.washington.gs.skyline.model.quantification.QuantificationTest.java

private List<ReplicateData> readReplicates(String filename) throws Exception {
    Map<String, ReplicateData> replicates = new LinkedHashMap<>();
    Reader reader = new InputStreamReader(QuantificationTest.class.getResourceAsStream(filename));
    try {/* w  ww .j a  v a 2 s. c o  m*/
        CSVParser parser = new CSVParser(reader, CSVFormat.EXCEL.withHeader());
        for (CSVRecord record : parser.getRecords()) {
            String fileName = record.get("FileName");
            ReplicateData replicate = replicates.get(fileName);
            if (replicate == null) {
                replicate = new ReplicateData();
                replicates.put(fileName, replicate);
            }
        }

    } finally {
        reader.close();
    }
    throw new NotImplementedException();
}

From source file:gov.ornl.stucco.stix_extractors.MetasploitExtractor.java

private STIXPackage extract(String metasploitInfo) {
    List<CSVRecord> records;
    try {/*from  w  w  w. j  ava 2  s.co  m*/
        records = getCSVRecordsList(HEADERS, metasploitInfo);
    } catch (IOException e) {
        e.printStackTrace();
        return null;
    }
    if (records.isEmpty()) {
        return null;
    }

    CSVRecord record = records.get(0);
    int start;
    if (record.get(0).equals(ID)) {
        if (records.size() == 1) {
            return null;
        } else {
            start = 1;
        }
    } else {
        start = 0;
    }

    ExploitTargetsType ets = new ExploitTargetsType();
    TTPsType ttps = new TTPsType();

    for (int i = start; i < records.size(); i++) {
        try {
            record = records.get(i);

            /* exploit */
            ExploitType exploit = new ExploitType();
            BehaviorType behavior = new BehaviorType();
            boolean withExploit = false;

            if (!record.get(FULLNAME).isEmpty()) {
                exploit.withTitle(record.get(FULLNAME));
                withExploit = true;
            }

            if (!record.get(MTYPE).isEmpty()) {
                exploit.withId(new QName("gov.ornl.stucco",
                        record.get(MTYPE) + "-" + UUID.randomUUID().toString(), "stucco"));
                withExploit = true;

            }

            if (!record.get(NAME).isEmpty()) {
                exploit.withShortDescriptions(new StructuredTextType() //list
                        .withValue(record.get(NAME)));
                withExploit = true;
            }

            if (!record.get(DESCRIPTION).isEmpty()) {
                exploit.withDescriptions(new StructuredTextType() //list
                        .withValue(record.get(DESCRIPTION)));
                withExploit = true;
            }

            if (withExploit) {
                behavior.withExploits(new ExploitsType().withExploits(exploit));
            }

            /* vulnerability */
            List<RelatedExploitTargetType> relatedEt = new ArrayList<RelatedExploitTargetType>();
            Pattern pattern = Pattern.compile("CVE-\\d{4}-\\d{4,7}");
            Matcher matcher = pattern.matcher(record.get(REF_NAMES));

            while (matcher.find()) {
                ExploitTarget et = new ExploitTarget().withId(
                        new QName("gov.ornl.stucco", "vulnerability-" + UUID.randomUUID().toString(), "stucco"))
                        .withTitle("Vulnerability").withVulnerabilities(new VulnerabilityType() //list
                                .withCVEID(matcher.group()).withTitle(matcher.group())
                                .withDescriptions(new StructuredTextType() //list
                                        .withValue(matcher.group()))
                                .withSource("Metasploit"));
                ets.withExploitTargets(et);

                relatedEt.add(new RelatedExploitTargetType()
                        .withExploitTarget(new ExploitTarget().withIdref(et.getId()))
                        .withRelationship(new ControlledVocabularyStringType().withValue("exploit")));
            }

            //if malware exists, then packing it and adding references to vulnerabilities
            if (withExploit) {
                TTP ttp = initTTP("Exploit", "Metasploit").withBehavior(behavior);
                if (!relatedEt.isEmpty()) {
                    ttp.withExploitTargets(
                            new org.mitre.stix.ttp_1.ExploitTargetsType().withExploitTargets(relatedEt));
                }

                ttps.withTTPS(ttp);
            }
        } catch (RuntimeException e) {
            e.printStackTrace();
        }
    }

    if (!ets.getExploitTargets().isEmpty()) {
        try {
            stixPackage = initStixPackage("Vulnerability and Malware Description", "Metasploit")
                    .withExploitTargets(ets);
        } catch (DatatypeConfigurationException e) {
            e.printStackTrace();
        }
    }
    if (!ttps.getTTPS().isEmpty()) {
        if (stixPackage == null) {
            try {
                stixPackage = initStixPackage("Vulnerability and Malware Description", "Metasploit")
                        .withTTPs(ttps);
            } catch (DatatypeConfigurationException e) {
                e.printStackTrace();
            }
        } else {
            stixPackage.withTTPs(ttps);
        }
    }

    return stixPackage;
}

From source file:com.mycompany.couchdb.CsvManage.java

public boolean hello() throws FileNotFoundException, IOException {
    int count = 0;
    String filename = "src/main/resources/GeoLiteCity-Location.csv";
    City city;//from   www.j  a v  a 2s  . c o  m
    DataDealer cityDao;

    cityDao = new DataDealer();

    Reader in = new FileReader(filename); //read file
    CSVParser parser = new CSVParser(in, CSVFormat.EXCEL.withHeader()); //create parser
    city = new City();
    for (CSVRecord record : parser) {
        //parse file and create objects

        //city.setLocId(Integer.parseInt(record.get("locId")));
        //city.setCountry(record.get("country"));
        city.setCity(record.get("city"));
        //city.setRegion(record.get("region"));
        city.setLatitude(Float.parseFloat(record.get("latitude")));
        city.setLongitude(Float.parseFloat(record.get("longitude")));

        //

        try {
            cityDao.save(city);

        } finally {
            cityDao.finalize();
        }

    }
    return true;
}