/*
* #%L
* org.gitools.analysis
* %%
* Copyright (C) 2013 - 2014 Universitat Pompeu Fabra - Biomedical Genomics group
* %%
* This program 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.
*
* This program 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 this program. If not, see
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package org.gitools.analysis;
import org.gitools.api.matrix.IMatrix;
import org.gitools.api.resource.IResourceFormat;
import org.gitools.api.resource.IResourceLocator;
import org.gitools.api.resource.ResourceReference;
import org.gitools.persistence.locators.UrlResourceLocator;
import org.junit.Before;
import org.junit.runner.RunWith;
import java.io.File;
import java.io.IOException;
import static org.gitools.api.ApplicationContext.getPersistenceManager;
import static org.gitools.api.ApplicationContext.getProgressMonitor;
@RunWith(WeldRunner.class)
public abstract class AbstractProcessorTest<A extends Analysis> {
private Class<A> analysisClass;
private String resourceUrl;
private A analysis;
public AbstractProcessorTest(Class<A> analysisClass, String resourceUrl) {
this.analysisClass = analysisClass;
this.resourceUrl = resourceUrl;
}
protected A getAnalysis() {
return analysis;
}
@Before
public void setUp() throws Exception {
analysis = new ResourceReference<>(
new UrlResourceLocator(getClass().getResource(resourceUrl)),
analysisClass
).get();
}
protected IMatrix storeAndLoadMatrix(IMatrix matrixToStore) throws IOException {
// Write the results to a temporal file
File tmpFile = File.createTempFile(getClass().getSimpleName(), ".tdm.gz");
tmpFile.deleteOnExit();
IResourceLocator tmpLocator = getPersistenceManager().applyFilters(new UrlResourceLocator(tmpFile));
IResourceFormat<IMatrix> format = getPersistenceManager().getFormat("tdm", IMatrix.class);
getPersistenceManager().store(tmpLocator, matrixToStore, format, getProgressMonitor());
File indexFile = new File(tmpFile.getAbsolutePath() + ".mtabix");
indexFile.deleteOnExit();
// Load the results from the temporal file
return new ResourceReference<>(tmpLocator, format).get();
}
}