gov.nih.nci.caintegrator.application.arraydata.ArrayDesignChecker.java Source code

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Here is the source code for gov.nih.nci.caintegrator.application.arraydata.ArrayDesignChecker.java

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/**
 * Copyright 5AM Solutions Inc, ESAC, ScenPro & SAIC
 *
 * Distributed under the OSI-approved BSD 3-Clause License.
 * See http://ncip.github.com/caintegrator/LICENSE.txt for details.
 */
package gov.nih.nci.caintegrator.application.arraydata;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import gov.nih.nci.caintegrator.domain.genomic.AbstractReporter;
import gov.nih.nci.caintegrator.domain.genomic.DnaAnalysisReporter;
import gov.nih.nci.caintegrator.domain.genomic.Gene;
import gov.nih.nci.caintegrator.domain.genomic.GeneExpressionReporter;
import gov.nih.nci.caintegrator.domain.genomic.Platform;
import gov.nih.nci.caintegrator.domain.genomic.PlatformConfiguration;
import gov.nih.nci.caintegrator.domain.genomic.ReporterList;
import gov.nih.nci.caintegrator.domain.genomic.ReporterTypeEnum;

import java.io.File;
import java.util.Date;
import java.util.HashSet;
import java.util.Set;

import org.apache.commons.lang3.StringUtils;

/**
 * Verifier for an array design.
 *
 * @author Abraham J. Evans-EL <aevansel@5amsolutions.com>
 */
public class ArrayDesignChecker {

    public static Platform checkLoadAffymetrixSnpArrayDesign(File[] cdfs, AffymetrixSnpPlatformSource source,
            ArrayDataService service) throws PlatformLoadingException, AffymetrixCdfReadException {
        AffymetrixCdfReader[] cdfReaders = getCdfReaders(cdfs);
        Platform platform = retrievePlatform(source, service);
        if (platform.getId() == null) {
            platform.setId(1L);
        }
        assertNotNull(platform);
        assertEquals(source.getPlatformName(), platform.getName());
        assertEquals(PlatformVendorEnum.AFFYMETRIX, platform.getVendor());
        for (ReporterList reporterList : platform.getReporterLists()) {
            assertNotNull(reporterList.getName());
            assertNotNull(reporterList.getGenomeVersion());
        }
        for (AffymetrixCdfReader affymetrixCdfReader : cdfReaders) {
            assertTrue(platform.getReporterListListing().contains(affymetrixCdfReader.getCdfData().getChipType()));
            affymetrixCdfReader.close();
        }
        checkSnpReporters(platform);
        return platform;
    }

    private static AffymetrixCdfReader[] getCdfReaders(File[] cdfs) throws AffymetrixCdfReadException {
        AffymetrixCdfReader[] readers = new AffymetrixCdfReader[cdfs.length];
        for (int i = 0; i < cdfs.length; i++) {
            readers[i] = AffymetrixCdfReader.create(cdfs[i]);
        }
        return readers;
    }

    private static void checkSnpReporters(Platform platform) {
        PlatformHelper platformHelper = new PlatformHelper(platform);
        for (AbstractReporter abstractReporter : platformHelper
                .getAllReportersByType((ReporterTypeEnum.DNA_ANALYSIS_REPORTER))) {
            DnaAnalysisReporter reporter = (DnaAnalysisReporter) abstractReporter;
            assertFalse(StringUtils.isBlank(reporter.getName()));
            assertNotNull(reporter.getAlleleA());
            assertNotNull(reporter.getAlleleB());
        }
    }

    public static Platform checkLoadAffymetrixExpressionArrayDesign(File cdfFile, File annotationFile,
            ArrayDataService service) throws PlatformLoadingException, AffymetrixCdfReadException {
        AffymetrixCdfReader cdfReader = AffymetrixCdfReader.create(cdfFile);
        AffymetrixExpressionPlatformSource source = new AffymetrixExpressionPlatformSource(annotationFile);
        Platform platform = retrievePlatform(source, service);
        if (platform.getId() == null) {
            platform.setId(1L);
        }
        checkPlatform(platform, cdfReader);
        checkProbeSetReporters(platform, cdfReader);
        checkGeneReporters(platform);
        cdfReader.close();
        return platform;
    }

    public static Platform checkLoadAgilentExpressionArrayDesign(String platformName, File annotationFile,
            ArrayDataService service) throws PlatformLoadingException {
        AgilentExpressionPlatformSource source = new AgilentExpressionPlatformSource(annotationFile, platformName,
                annotationFile.getName());
        Platform platform = retrievePlatform(source, service);
        if (platform.getId() == null) {
            platform.setId(1L);
        }
        checkGeneReporters(platform);
        return platform;
    }

    public static Platform checkLoadAgilentCopyNumberArrayDesign(String platformName, File annotationFile,
            ArrayDataService service) throws PlatformLoadingException {
        AgilentCnPlatformSource source = new AgilentCnPlatformSource(annotationFile, platformName,
                annotationFile.getName());
        Platform platform = retrievePlatform(source, service);
        if (platform.getId() == null) {
            platform.setId(1L);
        }
        checkDnaReporters(platform);
        return platform;
    }

    private static void checkDnaReporters(Platform platform) {
        PlatformHelper platformHelper = new PlatformHelper(platform);
        for (AbstractReporter abstractReporter : platformHelper
                .getAllReportersByType((ReporterTypeEnum.DNA_ANALYSIS_REPORTER))) {
            DnaAnalysisReporter reporter = (DnaAnalysisReporter) abstractReporter;
            assertFalse(StringUtils.isBlank(reporter.getName()));
        }
    }

    private static void checkGeneReporters(Platform platform) {
        PlatformHelper platformHelper = new PlatformHelper(platform);
        Set<ReporterList> geneReporters = platformHelper.getReporterLists(ReporterTypeEnum.GENE_EXPRESSION_GENE);
        for (ReporterList reporterList : geneReporters) {
            assertEquals(platform, reporterList.getPlatform());
            Set<String> geneSymbols = new HashSet<String>();
            for (AbstractReporter reporter : reporterList.getReporters()) {
                assertEquals(1, reporter.getGenes().size());
                Gene gene = reporter.getGenes().iterator().next();
                assertEquals(reporter.getName(), gene.getSymbol());
                geneSymbols.add(gene.getSymbol());
            }
            assertEquals(reporterList.getReporters().size(), geneSymbols.size());
        }
    }

    private static void checkProbeSetReporters(Platform platform, AffymetrixCdfReader cdfReader) {
        PlatformHelper platformHelper = new PlatformHelper(platform);
        Set<ReporterList> probeSetReporters = platformHelper
                .getReporterLists(ReporterTypeEnum.GENE_EXPRESSION_PROBE_SET);
        for (ReporterList reporterList : probeSetReporters) {
            assertEquals(platform, reporterList.getPlatform());
            assertEquals(cdfReader.getCdfData().getHeader().getNumProbeSets(), reporterList.getReporters().size());
            for (AbstractReporter abstractReporter : reporterList.getReporters()) {
                GeneExpressionReporter reporter = (GeneExpressionReporter) abstractReporter;
                assertFalse(StringUtils.isBlank(reporter.getName()));
            }
        }
    }

    private static void checkPlatform(Platform platform, AffymetrixCdfReader cdfReader) {
        assertNotNull(platform);
        assertEquals(cdfReader.getCdfData().getChipType(), platform.getName());
        assertEquals(PlatformVendorEnum.AFFYMETRIX, platform.getVendor());
        assertEquals(2, platform.getReporterLists().size());
    }

    private static Platform retrievePlatform(AbstractPlatformSource source, ArrayDataService service) {
        PlatformConfiguration configuration = new PlatformConfiguration(source);
        configuration.setDeploymentStartDate(new Date());
        service.savePlatformConfiguration(configuration);
        return service.loadArrayDesign(configuration).getPlatform();
    }
}