package org.isatools.isacreator.io.importisa;
import org.apache.commons.collections15.OrderedMap;
import org.apache.log4j.Logger;
import org.isatools.errorreporter.model.ErrorLevel;
import org.isatools.errorreporter.model.ErrorMessage;
import org.isatools.errorreporter.model.FileType;
import org.isatools.errorreporter.model.ISAFileErrorReport;
import org.isatools.isacreator.configuration.MappingObject;
import org.isatools.isacreator.gui.reference.DataEntryReferenceObject;
import org.isatools.isacreator.io.importisa.errorhandling.exceptions.MalformedInvestigationException;
import org.isatools.isacreator.io.importisa.investigationproperties.InvestigationFileSection;
import org.isatools.isacreator.managers.ConfigurationManager;
import org.isatools.isacreator.model.Assay;
import org.isatools.isacreator.model.Investigation;
import org.isatools.isacreator.model.Study;
import org.isatools.isacreator.settings.ISAcreatorProperties;
import org.isatools.isacreator.spreadsheet.model.TableReferenceObject;
import uk.ac.ebi.utils.collections.Pair;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
/**
* Created by the ISA team
*
* Date: 09/03/2011
* Time: 14:27
*
* @author <a href="mailto:eamonnmag@gmail.com">Eamonn Maguire</a>
* @author <a href="mailto:alejandra.gonzalez.beltran@gmail.com">Alejandra Gonzalez-Beltran</a>
*/
public class ISAtabFilesImporter extends ISAtabImporter {
private static final Logger log = Logger.getLogger(ISAtabFilesImporter.class.getName());
/**
* ImportISAFiles provides a facility for you to import ISATAB files
* and convert these files into Java Objects for you to use.
*
* This constructor can be used from the API (without accessing GUI elements).
*
* @param configDir - the directory containing the configuration files you wish to use.
*/
public ISAtabFilesImporter(String configDir) {
super();
ConfigurationManager.loadConfigurations(configDir);
}
/**
* Import an ISATAB file set!
*
* @param parentDir - Directory containing the ISATAB files. Should include a file of type
* @return boolean if successful or not!
*/
public boolean importFile(String parentDir){
return commonImportFile(parentDir);
}
}