Java tutorial
/* * __________ * 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.mapping; import org.apache.commons.collections.CollectionUtils; import org.apache.commons.collections.Predicate; import org.apache.commons.lang.StringUtils; import org.isatools.isatab.ISATABLoader; import org.isatools.tablib.schema.FormatSetInstance; import org.isatools.tablib.utils.BIIObjectStore; import org.junit.Test; import uk.ac.ebi.bioinvindex.model.AssayResult; import uk.ac.ebi.bioinvindex.model.Identifiable; import uk.ac.ebi.bioinvindex.model.Study; import uk.ac.ebi.bioinvindex.model.processing.Assay; import uk.ac.ebi.bioinvindex.model.processing.Processing; import uk.ac.ebi.bioinvindex.model.term.PropertyValue; import uk.ac.ebi.bioinvindex.utils.DotGraphGenerator; import uk.ac.ebi.bioinvindex.utils.processing.ProcessingUtils; import java.util.ArrayList; import java.util.Collection; import static java.lang.System.out; import static org.junit.Assert.*; public class ISATABIntegrationTest { /** * Tests that a (almost) complete ISATAB is correctly loaded and mapped into BII. Additionally produces graphs of the * mapped experimental pipelines. The latter may be visualize by means of GraphViz, and it's stored in * target/ */ @SuppressWarnings("static-access") @Test public void testLoadingAndMapping() throws Exception { out.println("\n\n__________ ISATAB Mapping 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(); BIIObjectStore store = new BIIObjectStore(); ISATABMapper isatabMapper = new ISATABMapper(store, isatabInstance); isatabMapper.map(); assertTrue("Oh no! No mapped object! ", store.size() > 0); Study study = store.getType(Study.class, "bii:study:1"); assertNotNull("Oh no! Study lsid:bii:study:19239 not found in the results!", study); Collection<Assay> assays = study.getAssays(); Assay assay = (Assay) CollectionUtils.find(assays, new Predicate() { public boolean evaluate(Object assay) { return StringUtils.trimToEmpty(((Assay) assay).getAcc()) .startsWith("bii:study:1:assay:Study1.animal6.liver.extract1.le1.hyb1"); } }); assertNotNull("Gulp! Assay ...le1.hyb1.11 not found!", assay); Collection<AssayResult> ars = study.getAssayResults(); out.println("__ ASSAY RESULTS: __ "); for (AssayResult ar : ars) { out.println(ar); } assertEquals("Oh no! Wrong no. of AssayResult(s)", 24, ars.size()); ars = ProcessingUtils.findAssayResultsFromAssay(assay); assertEquals("Urp! Wrong no. of AssayResult(s) for assay test case", 1, ars.size()); AssayResult ar = ars.iterator().next(); out.println("__ CASCADED VALUES ON THE TEST CASE: __ "); Collection<PropertyValue> arProps = ar.filterRepeatedPropertyValues(ar.getCascadedPropertyValues()); for (PropertyValue<?> v : arProps) { out.println(" " + v); } assertEquals("Urp! Wrong number of cascaded properties returned by mapped assay!", 11, arProps.size()); out.println("\n\n__ RESULTS: __ "); out.println(store.toStringVerbose()); Collection<Identifiable> objects = new ArrayList<Identifiable>(); objects.addAll(store.values(Processing.class)); DotGraphGenerator dotter = new DotGraphGenerator(objects); String dotFileName = baseDir + "/target/isatab.dot"; dotter.createGraph(dotFileName); out.println("\n\nExperimental Graph written in " + dotFileName); out.println("\n\n__________ /end: ISATAB Mapping Test __________\n\n\n\n"); } /** * Test a case with transcriptomics only. Again, mapping and graph produced. */ @Test public void testSimpleISATAB() throws Exception { out.println("\n\n__________ ISATAB Mapping Test (TX Only) __________\n\n"); String baseDir = System.getProperty("basedir"); String filesPath = baseDir + "/target/test-classes/test-data/isatab/isatab/example_tx"; ISATABLoader loader = new ISATABLoader(filesPath); FormatSetInstance isatabInstance = loader.load(); BIIObjectStore store = new BIIObjectStore(); ISATABMapper isatabMapper = new ISATABMapper(store, isatabInstance); isatabMapper.map(); assertTrue("Oh no! No mapped object! ", store.size() > 0); out.println("__ RESULTS: __ "); out.println(store.toStringVerbose()); Collection<Identifiable> objects = new ArrayList<Identifiable>(); objects.addAll(store.values(Processing.class)); DotGraphGenerator dotter = new DotGraphGenerator(objects); String dotFileName = baseDir + "/target/isatab_tx.dot"; dotter.createGraph(dotFileName); out.println("\n\nExperimental Graph written in " + dotFileName); out.println("\n\n__________ /end: ISATAB Mapping Test (TX Only) __________\n\n\n\n"); } }