ISATABLoaderTest.java

/*
 * __________
 * CREDITS
 * __________
 *
 * Team page: http://isatab.sf.net/
 * - Marco Brandizi (software engineer: ISAvalidator, ISAconverter, BII data management utility, BII model)
 * - Eamonn Maguire (software engineer: ISAcreator, ISAcreator configurator, ISAvalidator, ISAconverter,  BII data management utility, BII web)
 * - Nataliya Sklyar (software engineer: BII web application, BII model,  BII data management utility)
 * - Philippe Rocca-Serra (technical coordinator: user requirements and standards compliance for ISA software, ISA-tab format specification, BII model, ISAcreator wizard, ontology)
 * - Susanna-Assunta Sansone (coordinator: ISA infrastructure design, standards compliance, ISA-tab format specification, BII model, funds raising)
 *
 * Contributors:
 * - Manon Delahaye (ISA team trainee: BII web services)
 * - Richard Evans (ISA team trainee: rISAtab)
 *
 *
 * ______________________
 * Contacts and Feedback:
 * ______________________
 *
 * Project overview: http://isatab.sourceforge.net/
 *
 * To follow general discussion: isatab-devel@list.sourceforge.net
 * To contact the developers: isatools@googlegroups.com
 *
 * To report bugs: http://sourceforge.net/tracker/?group_id=215183&atid=1032649
 * To request enhancements: �http://sourceforge.net/tracker/?group_id=215183&atid=1032652
 *
 *
 * __________
 * License:
 * __________
 *
 * Reciprocal Public License 1.5 (RPL1.5)
 * [OSI Approved License]
 *
 * Reciprocal Public License (RPL)
 * Version 1.5, July 15, 2007
 * Copyright (C) 2001-2007
 * Technical Pursuit Inc.,
 * All Rights Reserved.
 *
 * http://www.opensource.org/licenses/rpl1.5.txt
 *
 * __________
 * Sponsors
 * __________
 * This work has been funded mainly by the EU Carcinogenomics (http://www.carcinogenomics.eu) [PL 037712] and in part by the
 * EU NuGO [NoE 503630](http://www.nugo.org/everyone) projects and in part by EMBL-EBI.
 */

package org.isatools.isatab;

import org.isatools.tablib.schema.FormatInstance;
import org.isatools.tablib.schema.FormatSetInstance;
import org.isatools.tablib.schema.Record;
import org.isatools.tablib.schema.SectionInstance;
import org.junit.Test;

import java.util.List;

import static java.lang.System.out;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;

public class ISATABLoaderTest {
	@Test
	public void testLoader() throws Exception {
		out.println("\n\n__________ ISATAB Loading Test __________\n\n");

		String baseDir = System.getProperty("basedir");
		String filesPath = baseDir + "/target/test-classes/test-data/isatab/isatab/example";
		ISATABLoader loader = new ISATABLoader(filesPath);
		FormatSetInstance isatabInstance = loader.load();

		assertNotNull("Oh no! No loaded format instance", isatabInstance);

		FormatInstance investigationFormatInstance = isatabInstance.getFormatInstance("investigation");
		assertNotNull("Sigh! No investigation format loaded", investigationFormatInstance);
		List<SectionInstance> investigationInstances = investigationFormatInstance.getSectionInstances("investigation");
		assertNotNull("Ouch! No investigation instances in investigation format", investigationInstances);
		assertEquals("Ouch! Bad number of investigations in investigation format ", 1, investigationInstances.size());
		SectionInstance investigationInstance = investigationInstances.get(0);
		assertEquals("Bad value for Investigation Title", "A Test Investigation, made for testing purposes",
				investigationInstance.getString(0, "Investigation Title")
		);

		List<SectionInstance> studyInstances = investigationFormatInstance.getSectionInstances("study");
		assertNotNull("Ouch! No study instances in investigation format", studyInstances);
		assertEquals("Ouch! Bad number of study in investigation format ", 1, studyInstances.size());

		List<FormatInstance> study1FormatInstances = isatabInstance.getFormatInstances("study_samples");
		assertNotNull("Sigh! No study format loaded", study1FormatInstances);
		assertEquals("Ops! Bad # of study formats loaded", 1, study1FormatInstances.size());
		SectionInstance studySampleInstance = study1FormatInstances.get(0).getSectionInstance("study_samples");
		assertNotNull("Oh no! No samples in the study instance", studySampleInstance);
		List<Record> sampleRecords = studySampleInstance.getRecords();
		assertNotNull("Arg! No records in study sample", sampleRecords);
		assertEquals("Oh no! Bad # of samples in the study instance", 12, sampleRecords.size());
		assertEquals("Oh no! Sample value retrieval failed", "Study1.animal4.liver",
				studySampleInstance.getString(3, "Sample Name")
		);


		List<FormatInstance> txInstances = isatabInstance.getFormatInstances("transcriptomics_assay");
		assertNotNull("Urp! No transcriptomics file loaded", txInstances);
		assertEquals("Ops! Bad # of TX formats loaded", 1, txInstances.size());
		SectionInstance txPipelineInstance = txInstances.get(0).getSectionInstance("transcriptomics_pipeline");
		assertNotNull("Oh no! No transcriptomics pipeline in the TX file", txPipelineInstance);
		List<Record> txRecords = txPipelineInstance.getRecords();
		assertNotNull("Arg! No records in TX file", txRecords);
		assertEquals("Oh no! Bad # of pipeline records in the TX file", 12, txRecords.size());
		assertEquals("Oh no! Pipeline value retrieval failed", "scan3.normalized",
				txPipelineInstance.getString(2, "Normalization Name")
		);


		List<FormatInstance> msInstances = isatabInstance.getFormatInstances("ms_spec_assay");
		assertNotNull("Urp! No MS/SPEC file loadd", msInstances);
		assertEquals("Ops! Bad # of MS/SPEC formats loaded", 1, msInstances.size());
		SectionInstance msPipelineInstance = msInstances.get(0).getSectionInstance("ms_spec_pipeline");
		assertNotNull("Oh no! No MS/SPEC pipeline in the TX file", msPipelineInstance);
		List<Record> msRecords = msPipelineInstance.getRecords();
		assertNotNull("Arg! No records in MAS/SPEC file", msRecords);
		assertEquals("Oh no! Bad # of pipeline records in the MS/SPEC file", 12, msRecords.size());
		assertEquals("Oh no! Pipeline value retrieval failed", "20 ppm", msPipelineInstance.getString(3, 6));


		out.println("\n\n_________ /end: ISATAB Loading Test __________\n\n\n");
	}
}