gov.nih.nci.caarray.application.translation.geosoft.GeoSoftFileWriterUtilTest.java Source code

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Here is the source code for gov.nih.nci.caarray.application.translation.geosoft.GeoSoftFileWriterUtilTest.java

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//======================================================================================
// Copyright 5AM Solutions Inc, Yale University
//
// Distributed under the OSI-approved BSD 3-Clause License.
// See http://ncip.github.com/caarray/LICENSE.txt for details.
//======================================================================================
package gov.nih.nci.caarray.application.translation.geosoft;

import gov.nih.nci.caarray.domain.project.Experiment;
import java.io.PrintWriter;
import java.io.StringReader;
import java.io.StringWriter;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.junit.Before;
import org.junit.Test;
import static org.junit.Assert.*;

/**
 *
 * @author gax
 */
public class GeoSoftFileWriterUtilTest {
    private GeoSoftExporterBeanTest helper;

    @Before
    public void setUp() throws Exception {
        helper = new GeoSoftExporterBeanTest();
        helper.baseIntegrationSetUp();
        helper.setUp();
    }

    @Test
    public void testWriteSoftFile() throws Exception {
        Experiment experiment = helper.makeGoodExperiment();
        String permaLinkUrl = "http://example.com/my-experiment";
        StringWriter sw = new StringWriter();
        PrintWriter out = new PrintWriter(sw);
        GeoSoftFileWriterUtil.writeSoftFile(experiment, permaLinkUrl, out);
        out.close();
        @SuppressWarnings("unchecked")
        List<String> lines = IOUtils.readLines(new StringReader(sw.toString()));

        final String[] expected = { "^SAMPLE=test-hyb", "!Sample_title=test-hyb",
                "!Sample_description=test-sample1, test-sample2", "!Sample_supplementary_file=raw_file.data",
                "!Sample_table=derived_file.data", "!Sample_source_name=test-source",
                "!Sample_organism=test Organizm 1", "!Sample_organism=test Organizm 2",
                "!Sample_treatment_protocol=\"some treatment:treatment desc\"; \"another treatment:another treatment desc\"",
                "!Sample_growth_protocol=\"some growth:growth desc\"",
                "!Sample_extract_protocol=\"some extract:extract desc\"",
                "!Sample_label_protocol=\"some label:labeling desc\"",
                "!Sample_hyb_protocol=\"some hybridization:hybridization desc\"",
                "!Sample_scan_protocol=\"some scan:scan desc\"",
                "!Sample_data_processing=\"data processing:data proc desc\"", "!Sample_label=label",
                "!Sample_biomaterial_provider=Affymetrix", "!Sample_platform_id=test-ga",
                "!Sample_characteristics=test-factor:test-value growth",
                "!Sample_characteristics=OrganismPart:some tissue site",
                "!Sample_characteristics=DiseaseState:some disease state",
                "!Sample_characteristics=ExternalId:test external id",
                "!Sample_characteristics=test-cat:test-val growth",
                "!Sample_characteristics=CellType:some cell type", "!Sample_molecule=other", "^SERIES=test-exp-id",
                "!Series_title=test-title", "!Series_summary=test-title",
                "!Series_overall_design=\"test-design-type1 (MO)\"; \"test-design-type2 (MO)\"",
                "!Series_pubmed_id=test-pub", "!Series_contributor=fff,mmm,lll",
                "!Series_web_link=http://example.com/my-experiment", "!Series_sample_id=test-hyb" };

        for (int i = 0; i < expected.length; i++) {
            String result = lines.get(i);
            assertEquals("line " + (i + 1), expected[i], result);
        }

    }

}