edu.utah.bmi.ibiomes.local.test.TestCommon.java Source code

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Here is the source code for edu.utah.bmi.ibiomes.local.test.TestCommon.java

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/*
 * iBIOMES - Integrated Biomolecular Simulations
 * Copyright (C) 2014  Julien Thibault, University of Utah
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package edu.utah.bmi.ibiomes.local.test;

import java.io.File;
import java.io.IOException;
import java.util.List;

import org.apache.commons.compress.compressors.CompressorException;

import edu.utah.bmi.ibiomes.io.IBIOMESFileReader;
import edu.utah.bmi.ibiomes.metadata.MetadataAVU;
import edu.utah.bmi.ibiomes.metadata.MetadataAVUList;

/**
 * Common variables and methods for the test suites 
 * @author Julien Thibault, University of Utah
 *
 */
public class TestCommon {

    public final static String TEST_DATA_DIR = System.getenv("IBIOMES_HOME") + "/test";
    public final static String TEST_IBIOMES_CONFIG_FILE = TEST_DATA_DIR + "/config/ibiomes-parser.properties";

    /**
     * Compare list of metadata to reference metadata
     * @param refMetadata Reference
     * @param sysMetadata
     * @return
     */
    public static boolean compareMetadata(MetadataAVUList refMetadata, MetadataAVUList sysMetadata) {
        boolean haNosError = true;
        for (MetadataAVU avu : refMetadata) {
            if (!sysMetadata.hasPair(avu) && !hasSameFloatValue(sysMetadata, avu)) {
                System.out.println("Missing AVU: " + avu.toString());
                haNosError = false;
            }
        }
        for (MetadataAVU avu : sysMetadata) {
            if (!refMetadata.hasPair(avu) && !hasSameFloatValue(refMetadata, avu)) {
                System.out.println("Extra AVU found: " + avu.toString());
                haNosError = false;
            }
        }
        return haNosError;
    }

    /**
     * 
     * @param metadata
     * @param avu
     * @return
     */
    private static boolean hasSameFloatValue(MetadataAVUList metadata, MetadataAVU avu) {

        try {
            double fValue1 = 0.0;
            fValue1 = Double.parseDouble(avu.getValue());
            fValue1 = Math.round(fValue1 * 1000) / 1000;
            List<String> values = metadata.getValues(avu.getAttribute());
            if (values != null) {
                for (String value : values) {
                    double fValue2 = Double.parseDouble(value);
                    fValue2 = Math.round(fValue2 * 1000) / 1000;
                    if (fValue2 == fValue1)
                        return true;
                }
            }
            return false;
        } catch (NumberFormatException e) {
            return false;
        }

    }

    /**
     * Compare list of metadata to reference metadata loaded from file
     * @param sysMetadata
     * @param filePath File path
     * @return
     * @throws IOException 
     * @throws CompressorException 
     */
    public static boolean compareMetadataToExpected(MetadataAVUList sysMetadata, String filePath)
            throws IOException, CompressorException {
        MetadataAVUList refMetadata = loadExpectedMetadataFromFile(filePath);
        return compareMetadata(refMetadata, sysMetadata);
    }

    /**
     * Load list of metadata from file
     * @param filePath Path to file
     * @return List of metadata
     * @throws IOException 
     * @throws CompressorException 
     */
    public static MetadataAVUList loadExpectedMetadataFromFile(String filePath)
            throws IOException, CompressorException {
        MetadataAVUList metadata = new MetadataAVUList();
        File file = new File(filePath);
        String line = null;
        IBIOMESFileReader br = new IBIOMESFileReader(file);
        while ((line = br.readLine()) != null) {
            line = line.trim();
            if (line.length() > 0) {
                MetadataAVU avu = parseLineForAVU(line);
                metadata.add(avu);
            }
        }
        br.close();
        return metadata;
    }

    /**
     * Parse AVU from file line
     * @param line
     * @return AVU
     */
    private static MetadataAVU parseLineForAVU(String line) {
        int index = line.indexOf('=');
        if (index > 0) {
            MetadataAVU avu = new MetadataAVU(line.substring(0, index), line.substring(index + 1));
            return avu;
        }
        return null;
    }
}