ubic.BAMSandAllen.NeuroNamesMappingLoader.java Source code

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Here is the source code for ubic.BAMSandAllen.NeuroNamesMappingLoader.java

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/*******************************************************************************
 * The ABAMS project
 * 
 * Copyright (c) 2012 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.BAMSandAllen;

import java.io.FileInputStream;
import java.util.HashSet;
import java.util.Set;

import org.apache.poi.hssf.usermodel.HSSFSheet;
import org.apache.poi.hssf.usermodel.HSSFWorkbook;
import org.apache.poi.poifs.filesystem.POIFSFileSystem;

import ubic.basecode.io.excel.ExcelUtil;

public class NeuroNamesMappingLoader {
    // colums in the Neuronames Excel file that list acronym and neuronames ID - this is checked
    final static short NNFULLCOL = 0; // full name
    final static short NNACROCOL = 1;
    final static short NNIDCOL = 4;
    final static short NNDEFAULTNAME = 2;
    HSSFSheet dong;
    HSSFSheet swanson;
    HSSFWorkbook neuronames;
    Set<NomenClatureEntry> dongEntries, swansonEntries;

    public NeuroNamesMappingLoader() {
        try {
            POIFSFileSystem fs2 = new POIFSFileSystem(
                    new FileInputStream(SetupParameters.config.getString("abams.neuronames.location")));
            neuronames = new HSSFWorkbook(fs2);
            dong = neuronames.getSheet("Dong");
            swanson = neuronames.getSheet("Swanson");
            dongEntries = getEntries(dong);
            swansonEntries = getEntries(swanson);
            checkCols(dong, swanson);
        } catch (Exception e) {
            e.printStackTrace();
            System.exit(1);
        }
    }

    public static void checkCols(HSSFSheet dong, HSSFSheet swanson) throws Exception {
        if (!ExcelUtil.getValue(swanson, 0, NNACROCOL).equals("Swn Acro"))
            throw new Exception("Excel columns not matching");
        ;
        if (!ExcelUtil.getValue(swanson, 0, NNIDCOL).equals("NN ID "))
            throw new Exception("Excel columns not matching");
        ;

        if (!ExcelUtil.getValue(dong, 0, NNACROCOL).equals("Dong Acro"))
            throw new Exception("Excel columns not matching");
        ;
        if (!ExcelUtil.getValue(dong, 0, NNIDCOL).equals("NN ID "))
            throw new Exception("Excel columns not matching");
    }

    public static Set<NomenClatureEntry> getEntries(HSSFSheet NNsheet) {
        Set<NomenClatureEntry> result = new HashSet<NomenClatureEntry>();
        NomenClatureEntry e;
        for (int i = 1; i < NNsheet.getLastRowNum() + 1; i++) {
            e = new NomenClatureEntry();
            e.acro = ExcelUtil.getValue(NNsheet, i, NNACROCOL);
            e.name = ExcelUtil.getValue(NNsheet, i, NNFULLCOL);
            e.NNID = ExcelUtil.getValue(NNsheet, i, NNIDCOL);
            e.NNName = ExcelUtil.getValue(NNsheet, i, NNDEFAULTNAME);
            result.add(e);
        }
        return result;
    }

    public Set<NomenClatureEntry> getDongEntries() {
        return dongEntries;
    }

    public Set<NomenClatureEntry> getSwansonEntries() {
        return swansonEntries;
    }
}