edu.harvard.med.screensaver.io.libraries.rnai.WorkbookLibraryContentsParser.java Source code

Introduction

Here is the source code for edu.harvard.med.screensaver.io.libraries.rnai.WorkbookLibraryContentsParser.java

Source

// $HeadURL:
// http://forge.abcd.harvard.edu/svn/screensaver/branches/iccbl/library-mgmt-rework/src/edu/harvard/med/screensaver/io/libraries/rnai/RNAiLibraryContentsParser.java
// $
// $Id$

// Copyright  2006, 2010, 2011, 2012 by the President and Fellows of Harvard College.
// Screensaver is an open-source project developed by the ICCB-L and NSRB labs
// at Harvard Medical School. This software is distributed under the terms of
// the GNU General Public License.

package edu.harvard.med.screensaver.io.libraries.rnai;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.util.Iterator;
import java.util.Map;

import edu.harvard.med.screensaver.db.GenericEntityDAO;
import edu.harvard.med.screensaver.io.ParseError;
import edu.harvard.med.screensaver.io.ParseException;
import edu.harvard.med.screensaver.io.libraries.LibraryContentsParser;
import edu.harvard.med.screensaver.io.workbook2.Cell;
import edu.harvard.med.screensaver.io.workbook2.Row;
import edu.harvard.med.screensaver.io.workbook2.Workbook;
import edu.harvard.med.screensaver.io.workbook2.Worksheet;
import edu.harvard.med.screensaver.model.libraries.Library;
import edu.harvard.med.screensaver.model.libraries.Reagent;
import edu.harvard.med.screensaver.model.libraries.Well;
import edu.harvard.med.screensaver.util.AlphabeticCounter;
import edu.harvard.med.screensaver.util.CSVPrintWriter;
import edu.harvard.med.screensaver.util.Pair;
import edu.harvard.med.screensaver.util.StringUtils;

import org.apache.commons.lang.math.IntRange;
import org.apache.log4j.Logger;

import com.google.common.collect.Maps;

/**
 * This class accomplishes both:
 * <ul>
 * <li>Parsing of the library input file, and
 * <li>Loading of the data into Library and related domain model objects on the
 * database.
 */
abstract public class WorkbookLibraryContentsParser<R extends Reagent> extends LibraryContentsParser<R> {
    private static final Logger log = Logger.getLogger(WorkbookLibraryContentsParser.class);

    private static final String FIELD_DELIMITER = "~~";
    public static final int FIRST_DATA_ROW = 1;

    protected final Pair<Well, R> EMPTY_PARSE_RESULT = new Pair<Well, R>(null, null);

    private BufferedReader _reader;
    private int _lineNumber;

    private Map<IntRange, String> _worksheetRecordRanges;

    public WorkbookLibraryContentsParser(GenericEntityDAO dao, InputStream stream, Library library) {
        super(dao, stream, library);
    }

    public void convert() throws IOException {
        Workbook _workbook = new Workbook("Library Contents Input Stream", getStream());
        File tmpFile = File.createTempFile("workbook", ".csv");
        tmpFile.deleteOnExit();
        log.debug("converting workbook into csv file: " + tmpFile.getAbsolutePath());
        CSVPrintWriter writer = new CSVPrintWriter(new BufferedWriter(new FileWriter(tmpFile)), "\n",
                FIELD_DELIMITER);
        Iterator<Worksheet> worksheetsIterator = _workbook.iterator();
        int prevSheetLastRecord = 0;
        int record = 0;
        _worksheetRecordRanges = Maps.newHashMap();
        while (worksheetsIterator.hasNext()) {
            Worksheet worksheet = worksheetsIterator.next().forOrigin(0, FIRST_DATA_ROW);
            Iterator<Row> rowsIterator = worksheet.iterator();
            while (rowsIterator.hasNext()) {
                for (Cell cell : rowsIterator.next()) {
                    writer.print(cell.getAsString());
                }
                writer.println();
                ++record;
            }
            IntRange worksheetRecordRange = new IntRange(prevSheetLastRecord, record);
            _worksheetRecordRanges.put(worksheetRecordRange, worksheet.getName());
            prevSheetLastRecord = record;
        }
        writer.close();
        _reader = new BufferedReader(new FileReader(tmpFile));
        log.debug("done converting workbook into csv file");
    }

    public Pair<Well, R> parseNext() throws ParseException, IOException {
        if (_reader == null) {
            convert();
        }
        String line = _reader.readLine();
        ++_lineNumber;
        if (StringUtils.isEmpty(line)) {
            return null;
        }
        String[] values = line.split(FIELD_DELIMITER);
        try {
            return parse(values);
        } catch (ParseException e) {
            throw new ParseException(new ParseError(e.getError().getErrorMessage(),
                    makeWorkbookCellLocation(_lineNumber, e.getError().getErrorLocation())));
        } catch (RuntimeException e) {
            // in case subclass throws a RuntimeException, instead of a ParseException
            throw new ParseException(new ParseError(e.toString(), _lineNumber));
        }
    }

    private String makeWorkbookCellLocation(int recordIndex, Object errorLocation) {
        try {
            for (Map.Entry<IntRange, String> worksheetRecordRangeEntry : _worksheetRecordRanges.entrySet()) {
                if (worksheetRecordRangeEntry.getKey().containsInteger(recordIndex)) {
                    String cellColumn = AlphabeticCounter.toLabel(Integer.parseInt(errorLocation.toString()) - 1);
                    int cellRow = recordIndex - worksheetRecordRangeEntry.getKey().getMinimumInteger() + 1;
                    return worksheetRecordRangeEntry.getValue() + ":(" + cellColumn + "," + cellRow + ")";
                }
            }
        } catch (Exception e) {
        }
        return "<workbook>";
    }

    abstract protected Pair<Well, R> parse(String[] values) throws ParseException;
}