VwDictLoader.java

package org.molgenis.lifelinesresearchportal.plugins.loader.listeners;

import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

import org.molgenis.framework.db.Database;
import org.molgenis.framework.db.DatabaseException;
import org.molgenis.organization.Investigation;
import org.molgenis.pheno.Measurement;
import org.molgenis.protocol.Protocol;
import org.molgenis.util.Tuple;
import org.molgenis.util.TupleReader;

/**
 * This listener creates Measurement for each field and Protocol for each table
 * in VW_DICT
 * 
 * TABNAAM GROEP VELDNR VELD -> Measurement.name VLDTYPE -> Measurement.dataType
 * OMSCHR -> Measurement.description
 * 
 * @author jorislops
 * 
 */
public class VwDictLoader extends ImportTupleLoader
{

	private Map<String, Protocol> protocols = new LinkedHashMap<String, Protocol>();
	private List<Measurement> measurements = new ArrayList<Measurement>();
	private List<String> measurementNames = new ArrayList<String>();
	private final Investigation investigation;

	public VwDictLoader(Investigation investigation, String name, Database db)
	{
		super(name, db);
		this.investigation = investigation;
	}

	public void load(TupleReader csvIterator) throws Exception
	{

		for (Tuple tuple : csvIterator)
		{

			// BEZOEK is skipped because we use VW_BEZOEK_PIVOT, where each
			// subvisit has become a row
			if (tuple.getString("TABNAAM") != null && !tuple.getString("TABNAAM").equals("")
					&& !tuple.getString("TABNAAM").equals("BEZOEK"))
			{

				String protocolName = tuple.getString("TABNAAM");
				// rename VW_BEZOEK_PIVOT to BEZOEK
				if (protocolName.equals("VW_BEZOEK_PIVOT"))
				{
					protocolName = "BEZOEK";
				}

				// create new protocol if not yet known
				Protocol p = protocols.get(protocolName);
				if (p == null)
				{
					p = new Protocol();
					p.setName(protocolName);
					p.setInvestigation(investigation);
				}

				String measName = p.getName() + "_" + tuple.getString("VELD"); // temporarily
																				// prepend
																				// measurement
																				// name
																				// with
																				// table
																				// (protocol)
																				// name
				if (tuple.getString("VELD") != null && !measurementNames.contains(measName))
				{ // prevent duplicates
					measurementNames.add(measName);
					Measurement m = new Measurement();
					m.setName(measName);
					m.setInvestigation(investigation);
					m.setDataType(convertDataType(tuple.getString("VLDTYPE")));
					m.setDescription(tuple.getString("OMSCHR"));
					measurements.add(m);
					p.getFeatures_Name().add(m.getName()); // link to protocol
				}

				protocols.put(protocolName, p);
			}
		}
	}

	private String convertDataType(String string)
	{
		if (string == null) return "string";
		if (string.startsWith("NUMMER")) return "int";
		if (string.startsWith("DATUM")) return "datetime";
		// else
		return "string";

	}

	public void commit() throws DatabaseException
	{
		db.add(measurements);

		List<Protocol> protocolList = new ArrayList<Protocol>(protocols.values());
		db.add(protocolList);
		for (Protocol p : protocolList)
			protocols.put(p.getName(), p);
	}

	public Map<String, Protocol> getProtocols()
	{
		return protocols;
	}
}