/*
* Copyright (c) 2012. The Genome Analysis Centre, Norwich, UK
* MISO project contacts: Robert Davey, Mario Caccamo @ TGAC
* *********************************************************************
*
* This file is part of MISO.
*
* MISO 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.
*
* MISO 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 MISO. If not, see <http://www.gnu.org/licenses/>.
*
* *********************************************************************
*/
package uk.ac.bbsrc.tgac.miso.core.test;
import com.eaglegenomics.simlims.core.User;
import junit.framework.TestCase;
import org.junit.Test;
import org.odftoolkit.odfdom.doc.OdfTextDocument;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import uk.ac.bbsrc.tgac.miso.core.data.Sample;
import uk.ac.bbsrc.tgac.miso.core.data.impl.UserImpl;
import uk.ac.bbsrc.tgac.miso.core.factory.DataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.factory.TgacDataObjectFactory;
import uk.ac.bbsrc.tgac.miso.core.service.naming.DefaultLibraryNamingScheme;
import uk.ac.bbsrc.tgac.miso.core.util.FormUtils;
import uk.ac.bbsrc.tgac.miso.core.util.LimsUtils;
import java.io.*;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/**
* uk.ac.bbsrc.tgac.miso.core.test
* <p/>
* Info
*
* @author Rob Davey
* @date 06-Sep-2011
* @since 0.1.1
*/
public class FormUtilsTests {
protected static final Logger log = LoggerFactory.getLogger(FormUtilsTests.class);
private static File testSampleDeliveryFile;
private static File testSampleBulkInputOdsFile;
private static File testSampleBulkInputXlsFile;
static {
try {
testSampleDeliveryFile = File.createTempFile("test-sampleDeliveryForm", ".odt");
testSampleBulkInputOdsFile = File.createTempFile("test-sampleBulkInputOds", ".ods");
testSampleBulkInputXlsFile = File.createTempFile("test-sampleBulkInputXls", ".xlsx");
}
catch (IOException e) {
e.printStackTrace();
TestCase.fail();
}
}
@Test
public void testCreateSampleDeliveryForm() {
try {
uk.ac.bbsrc.tgac.miso.core.util.FormUtils.createSampleDeliveryForm(generateSamples(), testSampleDeliveryFile);
}
catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
}
@Test
public void testConvertToPdf() {
try {
OdfTextDocument oDoc = uk.ac.bbsrc.tgac.miso.core.util.FormUtils.createSampleDeliveryForm(generateSamples(), testSampleDeliveryFile);
uk.ac.bbsrc.tgac.miso.core.util.FormUtils.convertToPDF(oDoc);
}
catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
}
@Test
public void testImportSampleDeliveryForm() {
try {
List<Sample> samples = uk.ac.bbsrc.tgac.miso.core.util.FormUtils.importSampleDeliveryForm(testSampleDeliveryFile);
int numExpected = generateSamples().size();
if (samples.size() != numExpected) {
log.error("Expected samples in: " + numExpected + ". Number imported: " + samples.size());
TestCase.fail();
}
else {
log.info("Expected samples in: " + numExpected + ". Number imported: " + samples.size());
}
}
catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
finally {
testSampleDeliveryFile.delete();
}
}
@Test
public void testImportBulkInputODS() {
try {
InputStream in = FormUtilsTests.class.getClassLoader().getResourceAsStream("test-bulk_input.ods");
LimsUtils.writeFile(in, testSampleBulkInputOdsFile);
User u = new UserImpl();
u.setLoginName("testBulkImportUser");
List<Sample> samples = FormUtils.importSampleInputSpreadsheet(testSampleBulkInputOdsFile, u, new MockFormTestRequestManager(), new DefaultLibraryNamingScheme());
log.info("Imported :: " + LimsUtils.join(samples, " | "));
}
catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
finally {
testSampleBulkInputOdsFile.delete();
}
}
@Test
public void testImportBulkInputXLS() {
try {
InputStream in = FormUtilsTests.class.getClassLoader().getResourceAsStream("test-bulk_input.xlsx");
LimsUtils.writeFile(in, testSampleBulkInputXlsFile);
User u = new UserImpl();
u.setLoginName("testBulkImportUser");
List<Sample> samples = FormUtils.importSampleInputSpreadsheet(testSampleBulkInputXlsFile, u, new MockFormTestRequestManager(), new DefaultLibraryNamingScheme());
log.info("Imported :: " + LimsUtils.join(samples, " | "));
}
catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
finally {
testSampleBulkInputXlsFile.delete();
}
}
private List<Sample> generateSamples() {
List<Sample> samples = new ArrayList<Sample>();
DataObjectFactory dataObjectFactory = new TgacDataObjectFactory();
for (int i = 1; i < 6; i++) {
Sample s = dataObjectFactory.getSample();
s.setId(i);
s.setName("SAM"+i);
s.setAlias("MI_S"+i+"_TestSample");
s.setScientificName("F.bar");
s.setIdentificationBarcode(s.getName() + "::" + s.getAlias());
samples.add(s);
}
Collections.sort(samples);
return samples;
}
}