edu.harvard.med.screensaver.io.libraries.LibraryCopyPlateListParser.java Source code

Introduction

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

Source

// $HeadURL:
// http://seanderickson1@forge.abcd.harvard.edu/svn/screensaver/branches/serickson/3014/core/src/main/java/edu/harvard/med/screensaver/io/libraries/LibraryCopyPlateListParser.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;

import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import com.google.common.base.Joiner;
import com.google.common.collect.Lists;

import edu.harvard.med.screensaver.util.Pair;

public class LibraryCopyPlateListParser {
    private static Logger log = Logger.getLogger(LibraryCopyPlateListParser.class);

    public static List<LibraryCopyPlateListParserResult> parsePlateCopiesSublists(String plateCopyLists) {
        List<LibraryCopyPlateListParserResult> results = Lists.newArrayList();
        for (String plateCopyList : plateCopyLists.split("\\n")) {
            results.add(parsePlateCopies(plateCopyList));
        }
        if (log.isDebugEnabled())
            log.debug("results: " + results);
        return results;
    }

    public static LibraryCopyPlateListParserResult parsePlateCopies(String plateCopyList) {
        LibraryCopyPlateListParserResult result = new LibraryCopyPlateListParserResult();

        if (plateCopyList == null || StringUtils.isEmpty(plateCopyList.trim())) {
            result.addError("no search terms specified");
            return result;
        }
        plateCopyList = plateCopyList.trim();

        Pattern numberCopyPattern = Pattern.compile("(^\\d+)([^\\-]*)$"); // modified, re [#2728] do not require whitespace or punctuation between plate and copy name
        Pattern numberRangePattern = Pattern.compile("^(\\d+)[-]+(\\d+)$"); // note [-]+ allows more than one dash
        // TODO: there may be other error patterns
        Pattern errorRangePattern = Pattern.compile("^(\\d+)[-]+$");

        List<String> list = edu.harvard.med.screensaver.util.StringUtils.tokenizeQuotedWordList(plateCopyList);

        if (log.isDebugEnabled())
            log.debug("parsed terms: " + Joiner.on(",").join(list));
        for (String s : list) {
            if (numberCopyPattern.matcher(s).matches()) {
                Matcher m = numberCopyPattern.matcher(s);
                if (m.matches()) { // here, allow the plate-copy to be concatenated, as in "111A"
                    result.addPlate(Integer.parseInt(m.group(1)));
                    String temp = m.group(2);
                    if (!StringUtils.isEmpty(temp)) {
                        result.addCopy(temp);
                    }
                }
            } else if (numberRangePattern.matcher(s).matches()) {
                Matcher m = numberRangePattern.matcher(s);
                if (m.matches()) {
                    Integer first = Integer.parseInt(m.group(1));
                    Integer second = Integer.parseInt(m.group(2));
                    result.addPlateRange(Pair.newPair(first, second));
                } else {/** nop **/
                }
            } else { // implied: if the other patterns don't match, then this is the "copyMatcher"
                if (errorRangePattern.matcher(s).matches()) {
                    result.addError("unparseable range: " + s);
                } else {
                    // Remove the quote chars that were left in by the top level matcher
                    s = s.replaceAll("\"|'+", "");
                    result.addCopy(s);
                }
            }
        }
        if (log.isDebugEnabled())
            log.debug("parsed: " + result);
        return result;
    }
}