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

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

  1. HOME
  2. Java
  3. org.apache.commons
  4. org.apache.commons.csv.*
  5. CSVRecord
  6. get

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:org.phenotips.vocabulary.AbstractCSVAnnotationsExtension.java

/**
 * Helper method that gets the cell on the specified column, as string, if it exists, without throwing exceptions.
 *
 * @param row the {@link CSVRecord row} currently being processed
 * @param colNumber the number of the column of interest
 * @return the value on the target column, if such value exists, {@code null} otherwise
 *///from   w  ww.j  av a2s .  c  om
protected String getRowItem(@Nonnull final CSVRecord row, final int colNumber) {
    if (colNumber < row.size()) {
        return row.get(colNumber);
    }
    return null;
}

From source file:org.phenotips.vocabulary.internal.solr.MendelianInheritanceInMan.java

private void parseOmimData(URL sourceUrl) {
    try {//  w  ww .  ja  va2 s. com
        Reader in = new InputStreamReader(sourceUrl.openConnection().getInputStream(),
                Charset.forName(ENCODING));
        for (CSVRecord row : CSVFormat.TDF.withCommentMarker('#').parse(in)) {
            // Ignore moved or removed entries
            if ("Caret".equals(row.get(0))) {
                continue;
            }

            SolrInputDocument crtTerm = new SolrInputDocument();
            // set id
            addFieldValue(ID_FIELD, row.get(1), crtTerm);

            // set symbol
            addFieldValue(SYMBOL_FIELD, SYMBOLS.get(row.get(0)), crtTerm);
            // set type (multivalued)
            for (String type : TYPES.get(row.get(0))) {
                addFieldValue(TYPE_FIELD, type, crtTerm);
            }
            // set name
            String name = StringUtils.substringBefore(row.get(2), TITLE_SEPARATOR).trim();
            addFieldValue(NAME_FIELD, name, crtTerm);
            // set short name
            String shortNameString = StringUtils.substringAfter(row.get(2), TITLE_SEPARATOR).trim();
            String[] shortNames = StringUtils.split(shortNameString, TITLE_SEPARATOR);
            for (String shortName : shortNames) {
                addFieldValue(SHORT_NAME_FIELD, shortName.trim(), crtTerm);
            }

            // set synonyms
            setListFieldValue(SYNONYM_FIELD, row.get(3), crtTerm);
            // set included name
            setListFieldValue(INCLUDED_NAME_FIELD, row.get(4), crtTerm);

            this.data.put(String.valueOf(crtTerm.get(ID_FIELD).getFirstValue()), crtTerm);
        }
    } catch (IOException ex) {
        this.logger.warn("Failed to read/parse the OMIM source: {}", ex.getMessage());
    }
}

From source file:org.phenotips.vocabulary.internal.solr.MendelianInheritanceInMan.java

private void loadGenes() {
    try (BufferedReader in = new BufferedReader(
            new InputStreamReader(new URL(GENE_ANNOTATIONS_URL).openConnection().getInputStream(), ENCODING))) {
        for (CSVRecord row : CSVFormat.TDF.withCommentMarker('#').parse(in)) {
            SolrInputDocument term = this.data.get(row.get(0).trim());
            if (term != null) {
                String gs = row.get(3).trim();
                if (StringUtils.isNotBlank(gs)) {
                    term.addField(GENE_FIELD, gs);
                }/*from w ww . ja  va2 s.  c o m*/
                String eidLine = row.get(4).trim();
                if (StringUtils.isNotBlank(eidLine)) {
                    String[] eids = StringUtils.split(eidLine, ",");
                    for (String eid : eids) {
                        term.addField(GENE_FIELD, eid.trim());
                    }
                }
            }
        }
    } catch (IOException ex) {
        this.logger.error("Failed to load OMIM-Gene links: {}", ex.getMessage(), ex);
    }
}

From source file:org.phenotips.vocabulary.internal.solr.MendelianInheritanceInMan.java

private void loadGeneReviews() {
    try (BufferedReader in = new BufferedReader(new InputStreamReader(
            new URL(GENEREVIEWS_MAPPING_URL).openConnection().getInputStream(), ENCODING))) {
        for (CSVRecord row : CSVFormat.TDF.withHeader().parse(in)) {
            SolrInputDocument term = this.data.get(row.get(2));
            if (term != null) {
                term.setField("gene_reviews_link", "https://www.ncbi.nlm.nih.gov/books/" + row.get(0));
            }/* w ww.j av  a2s .  c o  m*/
        }
    } catch (IOException ex) {
        this.logger.error("Failed to load OMIM-GeneReviews links: {}", ex.getMessage(), ex);
    }
}

From source file:org.phenotips.vocabulary.internal.solr.OmimSourceParser.java

private void loadSymptoms(boolean positive) {
    String omimId = "";
    String previousOmimId = null;
    Set<String> ancestors = new HashSet<>();
    try (BufferedReader in = new BufferedReader(
            new InputStreamReader(new URL(positive ? POSITIVE_ANNOTATIONS_URL : NEGATIVE_ANNOTATIONS_URL)
                    .openConnection().getInputStream(), ENCODING))) {
        for (CSVRecord row : CSVFormat.TDF.parse(in)) {
            if ("OMIM".equals(row.get(0))) {
                omimId = row.get(1);// w ww  .  j a v  a 2  s. c o m
                addAncestors(previousOmimId, omimId, ancestors, positive);
                previousOmimId = omimId;
                SolrInputDocument term = this.data.get(omimId);
                if (term != null) {
                    term.addField(positive ? "actual_symptom" : "actual_not_symptom", row.get(4));
                }
                VocabularyTerm vterm = this.hpo.getTerm(row.get(4));
                if (vterm != null) {
                    for (VocabularyTerm ancestor : vterm.getAncestorsAndSelf()) {
                        ancestors.add(ancestor.getId());
                    }
                }
            }
        }
        addAncestors(omimId, null, ancestors, positive);
    } catch (IOException ex) {
        this.logger.error("Failed to load OMIM-HPO links: {}", ex.getMessage(), ex);
    }
}

From source file:org.seasr.meandre.components.transform.text.CSVTextToTokenCounts.java

@Override
public void executeCallBack(ComponentContext cc) throws Exception {
    Hashtable<String, Integer> htCounts = new Hashtable<String, Integer>();

    for (String text : DataTypeParser.parseAsString(cc.getDataComponentFromInput(IN_TEXT))) {
        //           boolean skippedHeader = false;
        //String[][] data = ... .getAllValues();
        //           CSVParser parser = new CSVParser(new StringReader(text), strategy); 
        //           CSVParser parser = new CSVParser(new StringReader(text), format); 
        //           String[] tokens = uninitialisedLine;
        //           while (tokens != null) {
        console.finer("received text:\n" + text + "\n");
        for (CSVRecord tokens : format.parse(new StringReader(text))) {
            //              tokens = parser.getLine();
            //              if (tokens == null) break;
            //               if (bHeader && !skippedHeader) {
            //                   skippedHeader = true;
            //                   continue;
            //               }
            //               String token = tokens[tokenPos];
            console.fine("processing row " + tokens.toString());
            if (tokens.size() <= tokenPos || tokens.size() <= countPos) {
                console.warning(//from  w w w . j  a  va2s  .  co  m
                        String.format("csv row %d too short (%d) for count pos %d or token pos %d - discarding",
                                tokens.getRecordNumber(), tokens.size(), countPos, tokenPos));
                continue;
            }
            String token = tokens.get(tokenPos);
            int count = 0;
            try {
                count = Integer.parseInt(tokens.get(countPos));
            } catch (NumberFormatException e) {
                console.warning(String.format("Token '%s' had malformed count '%s' - assigning zero!", token,
                        tokens.get(countPos)));
            }

            if (htCounts.containsKey(token))
                console.warning(String.format(
                        "Token '%s' occurs more than once in the dataset - replacing previous count %d with %d...",
                        token, htCounts.get(token), count));

            htCounts.put(token, count);
        }
    }
    cc.pushDataComponentToOutput(OUT_TOKEN_COUNTS, BasicDataTypesTools.mapToIntegerMap(htCounts, bOrdered));
}

From source file:org.shareok.data.documentProcessor.CsvHandler.java

/**
 * Reads out the data in an excel file and stores data in a hashmap
 * <p>Also sets the total record number and file heading</p>
 * /*from  w  w  w .  ja va2s.c  om*/
 * @throws Exception
 */
@Override
public void readData() {
    FileReader fileReader = null;
    CSVParser csvFileParser = null;
    String[] headMapping = null;
    //CSVFormat csvFileFormat = CSVFormat.DEFAULT.withHeader(FILE_HEADER_MAPPING);

    try {
        //initialize FileReader object
        fileReader = new FileReader(fileName);

        //initialize CSVParser object
        if (null == csvFormat) {
            csvFormat = CSVFormat.DEFAULT;
        }
        csvFileParser = new CSVParser(fileReader, csvFormat);

        //Get a list of CSV file records
        List csvRecords = csvFileParser.getRecords();

        int size = csvRecords.size();

        setRecordCount(size);

        data = new HashMap();

        //Read the CSV file records starting from the second record to skip the header
        for (int i = 0; i < size; i++) {
            CSVRecord record = (CSVRecord) csvRecords.get(i);
            if (null != record) {
                if (i == 0) {
                    List headMappingList = new ArrayList();
                    Iterator it = record.iterator();
                    while (it.hasNext()) {
                        String value = (String) it.next();
                        headMappingList.add(value);
                    }
                    headMapping = new String[headMappingList.size()];
                    headMapping = (String[]) headMappingList.toArray(headMapping);
                    setFileHeadMapping(headMapping);
                } else {
                    for (int j = 0; j < fileHeadMapping.length; j++) {
                        String colName = fileHeadMapping[j].trim();
                        String key = colName + "-" + i;
                        data.put(key, record.get(j));
                    }
                }
            }
        }

    } catch (Exception e) {
        System.out.println("Error in CsvFileReader !!!");
        e.printStackTrace();
    } finally {
        try {
            fileReader.close();
            csvFileParser.close();
        } catch (IOException e) {
            System.out.println("Error while closing fileReader/csvFileParser !!!");
            e.printStackTrace();
        }
    }
}

From source file:org.softinica.maven.jmeter.report.parser.CSVReportParser.java

@Override
public Input parseInput(InputDefinition definition) {
    CSVParser parser = null;/*from w  ww  .ja v a  2 s.c o m*/
    Input input = new Input();
    try {
        Reader reader = new InputStreamReader(new FileInputStream(definition.getInputFile()));
        parser = new CSVParser(reader, CSVFormat.DEFAULT);
        Iterator<CSVRecord> it = parser.iterator();
        while (it.hasNext()) {
            Sample sample = new Sample();
            CSVRecord record = it.next();
            sample.setTimestamp(Long.valueOf(record.get(0)));
            sample.setLabel(record.get(2));
            sample.setValue(Double.valueOf(record.get(4)) * definition.getScale());
            sample.setSuccess(Boolean.parseBoolean(record.get(7)));
            input.getSamples().add(sample);
        }
    } catch (IOException e) {
        throw new RuntimeException(e);
    } finally {
        Utils.close(parser);
    }
    return input;
}

From source file:org.softinica.maven.jmeter.report.parser.SimpleCSVParser.java

@Override
public Input parseInput(InputDefinition definition) {
    CSVParser parser = null;/*from www.j  av  a 2s .c o m*/
    List<String> headers = new LinkedList<String>();
    Input input = new Input();
    try {
        Reader reader = new InputStreamReader(new FileInputStream(definition.getInputFile()));
        parser = new CSVParser(reader, CSVFormat.DEFAULT);
        Iterator<CSVRecord> it = parser.iterator();
        if (it.hasNext()) {
            CSVRecord header = it.next();
            for (String value : header) {
                headers.add(value);
            }
            while (it.hasNext()) {
                Sample sample = new Sample();
                CSVRecord record = it.next();
                for (int i = 0; i < record.size(); i++) {
                    sample.put(headers.get(i), record.get(i));
                }
                input.getSamples().add(sample);
            }
        }
    } catch (IOException e) {
        throw new RuntimeException(e);
    } finally {
        Utils.close(parser);
    }
    return input;
}

From source file:org.sonar.db.version.v51.FeedFileSourcesBinaryData.java

private byte[] toBinary(Long fileSourceId, @Nullable String data) {
    DbFileSources.Data.Builder dataBuilder = DbFileSources.Data.newBuilder();
    CSVParser parser = null;/*from  ww w .  jav a 2  s  . c  o m*/
    try {
        if (data != null) {
            parser = CSVParser.parse(data, CSVFormat.DEFAULT);
            Iterator<CSVRecord> rows = parser.iterator();
            int line = 1;
            while (rows.hasNext()) {
                CSVRecord row = rows.next();
                if (row.size() == 16) {

                    DbFileSources.Line.Builder lineBuilder = dataBuilder.addLinesBuilder();
                    lineBuilder.setLine(line);
                    String s = row.get(0);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setScmRevision(s);
                    }
                    s = row.get(1);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setScmAuthor(s);
                    }
                    Date scmDate = DateUtils.parseDateTimeQuietly(row.get(2));
                    if (scmDate != null) {
                        lineBuilder.setScmDate(scmDate.getTime());
                    }
                    s = row.get(3);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setUtLineHits(Integer.parseInt(s));
                    }
                    s = row.get(4);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setUtConditions(Integer.parseInt(s));
                    }
                    s = row.get(5);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setUtCoveredConditions(Integer.parseInt(s));
                    }
                    s = row.get(6);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setItLineHits(Integer.parseInt(s));
                    }
                    s = row.get(7);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setItConditions(Integer.parseInt(s));
                    }
                    s = row.get(8);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setItCoveredConditions(Integer.parseInt(s));
                    }
                    s = row.get(9);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setOverallLineHits(Integer.parseInt(s));
                    }
                    s = row.get(10);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setOverallConditions(Integer.parseInt(s));
                    }
                    s = row.get(11);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setOverallCoveredConditions(Integer.parseInt(s));
                    }
                    s = row.get(12);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setHighlighting(s);
                    }
                    s = row.get(13);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.setSymbols(s);
                    }
                    s = row.get(14);
                    if (StringUtils.isNotEmpty(s)) {
                        lineBuilder.addAllDuplication(splitIntegers(s));
                    }
                    s = row.get(15);
                    if (s != null) {
                        lineBuilder.setSource(s);
                    }
                }
                line++;
            }
        }
        return FileSourceDto.encodeSourceData(dataBuilder.build());
    } catch (Exception e) {
        throw new IllegalStateException(
                "Invalid FILE_SOURCES.DATA on row with ID " + fileSourceId + ": " + data, e);
    } finally {
        IOUtils.closeQuietly(parser);
    }
}