ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractor.java Source code

Introduction

Here is the source code for ubic.gemma.core.analysis.preprocess.batcheffects.AgilentScanDateExtractor.java

Source

/*
 * The Gemma project
 *
 * Copyright (c) 2011 University of British Columbia
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *       http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */

package ubic.gemma.core.analysis.preprocess.batcheffects;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;

/**
 * Because agilent makes slides that work with any scanner, the formats are not that predictable. I've seen these so
 * far:
 * <ul>
 * <li>GPR format
 * format.
 * <li>Agilent scanner files. These start with "TYPE" Example: GSE14466. The second line is "FEPARAMS", the fourth
 * column is "Scan_date". The data are in the third line.
 * </ul>
 *
 * @author paul
 */
public class AgilentScanDateExtractor extends BaseScanDateExtractor {

    private static final Log log = LogFactory.getLog(AgilentScanDateExtractor.class);

    @Override
    public Date extract(InputStream is) {
        BufferedReader reader = null;
        try {
            /*
             * Read the first three characters. IF they are ATF, it's a Axon file. If it's TYPE then it's probably an
             * agilent file.
             */
            reader = new BufferedReader(new InputStreamReader(is));

            String line = reader.readLine();

            if (line.startsWith("ATF")) {
                return this.extractGenePix(reader);
            } else if (line.startsWith("TYPE")) {
                line = reader.readLine();
                if (line.startsWith("FEPARAMS")) {
                    int dateField = -1;

                    // Agilent.
                    String[] fields = StringUtils.split(line, '\t');
                    for (int i = 0; i < fields.length; i++) {
                        if (fields[i].equalsIgnoreCase("Scan_date")) {
                            dateField = i;
                        }
                    }

                    if (dateField < 0) {
                        throw new IllegalStateException("Could not recognize the scan_date field");
                    }

                    // next line down has the data.
                    line = reader.readLine();

                    if (!line.startsWith("DATA")) {
                        throw new IllegalStateException("Could not understand Agilent scanner format");
                    }

                    fields = StringUtils.split(line, '\t');
                    String date = fields[dateField];

                    Date d;

                    DateFormat f = new SimpleDateFormat("MM-dd-yyyy hh:mm:ss"); // 10-18-2005 13:02:36
                    f.setLenient(true);
                    d = f.parse(date);

                    return d;
                }
            } else {
                throw new UnsupportedRawdataFileFormatException("Unknown agilent array file format.");
            }

        } catch (IOException | ParseException e) {
            throw new RuntimeException(e);
        } finally {
            try {
                if (reader != null)
                    reader.close();
            } catch (IOException e) {
                AgilentScanDateExtractor.log.error("Failed to close open file handle: " + e.getMessage());
            }
        }
        return null;
    }

}