databases-manager-portlet/src/main/java/org/gcube/portlets/user/databasesmanager/server/GWTdbManagerServiceImpl.java

package org.gcube.portlets.user.databasesmanager.server;

import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.net.URLConnection;
import java.net.URLStreamHandler;

import javax.servlet.http.HttpSession;
import org.apache.regexp.RE;
import org.gcube.common.scope.api.ScopeProvider;
import org.gcube.contentmanager.storageclient.model.protocol.smp.SMPURLConnection;
import org.gcube.data.analysis.statisticalmanager.proxies.StatisticalManagerDSL;
import org.gcube.data.analysis.statisticalmanager.proxies.StatisticalManagerFactory;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMAlgorithm;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMComputationConfig;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMComputationRequest;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMGroupedAlgorithms;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMListGroupedAlgorithms;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMOperationStatus;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMParameter;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMParameters;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMResourceType;
import org.gcube.data.analysis.statisticalmanager.stubs.types.SMTypeParameter;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMAbstractResource;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMComputation;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMEntries;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMFile;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMInputEntry;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMObject;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMOperationInfo;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMResource;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMTable;
import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.StatisticalServiceType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.portlets.user.databasesmanager.client.GWTdbManagerService;
import org.gcube.portlets.user.databasesmanager.client.datamodel.ComputationOutput;
import org.gcube.portlets.user.databasesmanager.client.datamodel.FileModel;
import org.gcube.portlets.user.databasesmanager.client.datamodel.Parameter;
import org.gcube.portlets.user.databasesmanager.client.datamodel.Result;
import org.gcube.portlets.user.databasesmanager.client.datamodel.Row;
import org.gcube.portlets.user.databasesmanager.server.util.SessionUtil;
import com.extjs.gxt.ui.client.data.BasePagingLoadResult;
import com.extjs.gxt.ui.client.data.PagingLoadConfig;
import com.extjs.gxt.ui.client.data.PagingLoadResult;
import com.google.gwt.user.server.rpc.RemoteServiceServlet;
import com.thoughtworks.xstream.XStream;
import org.apache.log4j.Logger;

public class GWTdbManagerServiceImpl extends RemoteServiceServlet implements
		GWTdbManagerService {

	// the result generated in the LoadTables method
	private List<Result> result = null;
	// information about a database
	private String currentDB = "";
	private String previousDB = "";
	// information about a schema
	private String currentSchema = "";
	private String previousSchema = "";
	// logger
	private static Logger logger = Logger
			.getLogger(GWTdbManagerServiceImpl.class);

	public GWTdbManagerServiceImpl() {

	}

	// to get resources from IS
	public List<FileModel> getResource() throws Exception {
		// data input
		List<Parameter> inputParameters = new ArrayList<Parameter>();
		// data output
		List<FileModel> outputParameters = new ArrayList<FileModel>();

		// get list of algorithms
		List<String> algorithms = new ArrayList<String>();
		algorithms = getDatabaseManagerAlgorithms();

		// get algorithmId
		String algorithmId = null;

		for (int i = 0; i < algorithms.size(); i++) {
			if (algorithms.get(i).equals("LISTDBNAMES")) {
				algorithmId = algorithms.get(i);

				// print check
				// logger.info("algorithmId: " + algorithmId);
			}
		}

		// get input parameters of the algorithm specified by id
		inputParameters = getParameters(algorithmId);

		if (inputParameters.size() != 0) {
			// print check
			logger.info("algorithm input parameters retrieved");
		}

		// // print check input parameters
		// for (int i = 0; i < inputParameters.size(); i++) {
		// logger.info(inputParameters.get(i).getName());
		// }

		// create data structure for data output
		ComputationOutput outputData = new ComputationOutput();
		// computationId
		String computationId = startComputation(algorithmId, inputParameters,
				outputData);

		// print check
		// retrieve data
		// logger.info("output data retrieved");

		// data output
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		mapValues = outputData.getMapValues();

		for (int i = 0; i < mapValues.size(); i++) {
			FileModel obj = new FileModel(mapValues.get(String.valueOf(i)));
			// obj.setIsLoaded(true);
			outputParameters.add(obj);
		}

		return outputParameters;
	}

	// to get information about databases of a resource
	@Override
	public LinkedHashMap<String, FileModel> getDBInfo(String resourceName)
			throws Exception {
		// data input
		List<Parameter> inputParameters = new ArrayList<Parameter>();
		// data output
		LinkedHashMap<String, FileModel> outputParameters = new LinkedHashMap<String, FileModel>();

		// get list of algorithms
		List<String> algorithms = new ArrayList<String>();
		algorithms = getDatabaseManagerAlgorithms();

		// get algorithmId
		String algorithmId = null;

		for (int i = 0; i < algorithms.size(); i++) {
			if (algorithms.get(i).equals("LISTDBINFO")) {
				algorithmId = algorithms.get(i);

				// print check
				// logger.info("algorithmId: " + algorithmId);
			}
		}

		// get input parameters of the algorithm specified by id
		inputParameters = getParameters(algorithmId);

		if (inputParameters.size() != 0) {
			// print check
			logger.info("algorithm input parameters retrieved");
		}

		inputParameters.get(0).setValue(resourceName);

		// print check
		// logger.info(inputParameters.get(0).getName());

		// create data structure
		ComputationOutput outputData = new ComputationOutput();
		// computation id
		String computationId = startComputation(algorithmId, inputParameters,
				outputData);

		// print check
		// retrieve data
		// logger.info("output data retrieved");

		// data output values
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		// data output keys
		LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();

		mapValues = outputData.getMapValues();
		mapKeys = outputData.getmapKeys();

		for (int i = 0; i < mapValues.size(); i++) {
			FileModel obj = new FileModel(mapValues.get(String.valueOf(i)));
			// obj.setIsLoaded(true);

			// print check
			// logger.info("value: " + mapValues.get(String.valueOf(i)));
			// logger.info("key: " + mapKeys.get(String.valueOf(i)));
			outputParameters.put(mapKeys.get(String.valueOf(i)), obj);
		}
		return outputParameters;
	}

	// to get schema for a database
	@Override
	public List<FileModel> getDBSchema(LinkedHashMap<String, String> dataInput)
			throws Exception {
		// data input
		List<Parameter> inputParameters = new ArrayList<Parameter>();
		// data output
		List<FileModel> outputParameters = new ArrayList<FileModel>();

		// get list of algorithms
		List<String> algorithms = new ArrayList<String>();
		algorithms = getDatabaseManagerAlgorithms();

		// get algorithmId
		String algorithmId = null;

		for (int i = 0; i < algorithms.size(); i++) {
			if (algorithms.get(i).equals("LISTDBSCHEMA")) {
				algorithmId = algorithms.get(i);
				// print check
				// logger.info("algorithmId: " + algorithmId);
			}
		}

		// get input parameters of the algorithm specified by id
		inputParameters = getParameters(algorithmId);

		if (inputParameters.size() != 0) {
			// print check
			logger.info("algorithm input parameters retrieved");
		}

		// print check algorithm input parameters
		// for (int i = 0; i < inputParameters.size(); i++) {
		// logger.info(inputParameters.get(i).getName());
		// }

		inputParameters.get(0).setValue(dataInput.get("ResourceName"));
		inputParameters.get(1).setValue(dataInput.get("DatabaseName"));

		// print check
		logger.info("ResourceName: " + dataInput.get("ResourceName"));
		logger.info("DatabaseName: " + dataInput.get("DatabaseName"));

		// create data structure
		ComputationOutput outputData = new ComputationOutput();
		// computation id
		String computationId = startComputation(algorithmId, inputParameters,
				outputData);

		// print check
		// retrieve data
		logger.info("output data retrieved");

		// data output values
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		// data output keys
		LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();

		mapValues = outputData.getMapValues();
		mapKeys = outputData.getmapKeys();

		for (int i = 0; i < mapValues.size(); i++) {
			FileModel obj = new FileModel(mapValues.get(String.valueOf(i)));
			// obj.setIsSchema(true);
			// obj.setIsLoaded(true);
			outputParameters.add(obj);
		}
		return outputParameters;
	}

	// to get tables
	private List<Result> getTables(LinkedHashMap<String, String> dataInput)
			throws Exception {
		// data input
		List<Parameter> inputParameters = new ArrayList<Parameter>();
		// data output
		List<Result> outputParameters = new ArrayList<Result>();

		// get list of algorithms
		List<String> algorithms = new ArrayList<String>();
		algorithms = getDatabaseManagerAlgorithms();

		// get algorithmId
		String algorithmId = null;

		for (int i = 0; i < algorithms.size(); i++) {
			if (algorithms.get(i).equals("LISTTABLES")) {
				algorithmId = algorithms.get(i);

				// print check
				// logger.info("algorithmId: " + algorithmId);
			}
		}

		// get input parameters of the algorithm
		inputParameters = getParameters(algorithmId);

		if (inputParameters.size() != 0) {
			// print check
			logger.info("algorithm input parameters retrieved");
		}

		// print check algorithm input parameters
		// for (int i = 0; i < inputParameters.size(); i++) {
		// logger.info(inputParameters.get(i).getName());
		// }

		inputParameters.get(0).setValue(dataInput.get("ResourceName"));
		inputParameters.get(1).setValue(dataInput.get("DatabaseName"));
		inputParameters.get(2).setValue(dataInput.get("SchemaName"));

		// print check
		logger.info("ResourceName: " + dataInput.get("ResourceName"));
		logger.info("DatabaseName: " + dataInput.get("DatabaseName"));
		logger.info("SchemaName: " + dataInput.get("SchemaName"));

		// create data structure
		ComputationOutput outputData = new ComputationOutput();
		// computation id
		String computationId = startComputation(algorithmId, inputParameters,
				outputData);

		// print check on retrieving data
		// logger.info("output data retrieved");

		// data output values
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		// data output keys
		LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();

		mapValues = outputData.getMapValues();
		mapKeys = outputData.getmapKeys();

		for (int i = 0; i < mapValues.size(); i++) {
			Result row = new Result(String.valueOf(i), mapValues.get(String
					.valueOf(i)));
			outputParameters.add(row);
		}
		return outputParameters;
	}

	// to load tables
	@Override
	public PagingLoadResult<Result> LoadTables(PagingLoadConfig config,
			LinkedHashMap<String, String> dataInput, boolean SearchTable,
			String keyword) throws Exception {

		// check on a database
		currentDB = dataInput.get("DatabaseName");
		if (!currentDB.equals(previousDB)) {
			result = null;
			System.gc();
		}

		previousDB = currentDB;

		// check on a schema
		currentSchema = dataInput.get("SchemaName");
		if (!currentSchema.equals(previousSchema)) {
			result = null;
			System.gc();
		}

		previousSchema = currentSchema;

		// get tables
		if (result == null)
			result = getTables(dataInput);

		// Create a sublist and add data to list according
		// to the limit and offset value of the config
		List<Result> sublist = new ArrayList<Result>();
		BasePagingLoadResult loadResult = null;

		// print check on the search
		// logger.info("Searching in the table: " + SearchTable);
		// logger.info("Keyword to search: " + keyword);

		int start = config.getOffset();
		int limit = result.size();

		if (config.getLimit() > 0) {
			limit = Math.min(start + config.getLimit(), limit);
		}

		int totalNumber = result.size();

		if ((SearchTable == false) || keyword == null || keyword.length() == 0) {
			sublist = new ArrayList<Result>(result.subList(start, limit));
		} else {
			// print check
			// logger.info("searching the table");

			// search the table
			for (int i = 0; i < result.size(); i++) {
				if ((result.get(i).getValue().toLowerCase()).startsWith(keyword
						.toLowerCase())) {
					sublist.add(result.get(i));
				}
			}

			limit = sublist.size();
			int sublen = sublist.size();
			totalNumber = sublen;

			if (start < sublen - 1) {
				limit = Math.min(sublen, limit);
				totalNumber = sublist.size();
				sublist = new ArrayList<Result>(sublist.subList(start, limit));
			}
		}

		// print check
		// logger.info("result size: " + totalNumber);
		// logger.info("limit: " + limit);
		// logger.info("offset: " + config.getOffset());
		// logger.info("start: " + start);

		loadResult = new BasePagingLoadResult<Result>(sublist,
				config.getOffset(), totalNumber);

		return loadResult;
	}

	// to submit a query
	@Override
	public List<Result> submitQuery(LinkedHashMap<String, String> dataDB,
			String query, boolean valueReadOnlyQuery,
			boolean smartCorrectionQuery, String language) throws Exception {

		logger.info("Dialect used for smart correction: " + language);

		// data input
		List<Parameter> inputParameters = new ArrayList<Parameter>();
		// data output
		List<Result> output = new ArrayList<Result>();

		// get list of algorithms
		List<String> algorithms = new ArrayList<String>();
		algorithms = getDatabaseManagerAlgorithms();

		// get algorithmId
		String algorithmId = null;

		for (int i = 0; i < algorithms.size(); i++) {
			if (algorithms.get(i).equals("SUBMITQUERY")) {
				algorithmId = algorithms.get(i);

				// print check
				// logger.info("algorithmId: " + algorithmId);
			}
		}

		// get input parameters of the algorithm
		inputParameters = getParameters(algorithmId);

		if (inputParameters.size() != 0) {
			// print check
			logger.info("algorithm input parameters retrieved");
		}

		// print check
		// for (int i = 0; i < inputParameters.size(); i++) {
		// logger.info(inputParameters.get(i).getName());
		// }

		// print check
		logger.info("ResourceName: " + dataDB.get("ResourceName"));
		logger.info("DatabaseName: " + dataDB.get("DatabaseName"));
		logger.info("Query: " + query);
		logger.info("SmartCorrections check: " + smartCorrectionQuery);

		inputParameters.get(0).setValue(dataDB.get("ResourceName"));
		inputParameters.get(1).setValue(dataDB.get("DatabaseName"));
		inputParameters.get(2).setValue(String.valueOf(valueReadOnlyQuery));
		inputParameters.get(3).setValue(String.valueOf(smartCorrectionQuery));
		inputParameters.get(4).setValue(language);
		inputParameters.get(5).setValue(query);

		// create data structure
		ComputationOutput outputData = new ComputationOutput();
		// computation id
		String computationId = startComputation(algorithmId, inputParameters,
				outputData);

		// print check on retrieving data
		// logger.info("output data retrieved");

		// data output values
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		// data output keys
		LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();

		mapValues = outputData.getMapValues();
		mapKeys = outputData.getmapKeys();

		for (int i = 0; i < mapValues.size(); i++) {
			Result row = new Result(mapKeys.get(String.valueOf(i)),
					mapValues.get(String.valueOf(i)));
			output.add(row);
		}

		return output;
	}

	@Override
	public List<Result> sample(LinkedHashMap<String, String> dataInput)
			throws Exception {
		// data input
		List<Parameter> inputParameters = new ArrayList<Parameter>();
		// output sample result
		List<Result> output = new ArrayList<Result>();

		// get list of algorithms
		List<String> algorithms = new ArrayList<String>();
		algorithms = getDatabaseManagerAlgorithms();

		// get algorithmId
		String algorithmId = null;

		for (int i = 0; i < algorithms.size(); i++) {
			if (algorithms.get(i).equals("SAMPLEONTABLE")) {
				algorithmId = algorithms.get(i);

				// print check
				// logger.info("algorithmId: " + algorithmId);
			}
		}

		// get input parameters of the algorithm specified by id
		inputParameters = getParameters(algorithmId);

		if (inputParameters.size() != 0) {
			// print check
			logger.info("algorithm input parameters retrieved");
		}

		// print check
		// for (int i = 0; i < inputParameters.size(); i++) {
		// logger.info(inputParameters.get(i).getName());
		// }

		// print check
		logger.info("ResourceName: " + dataInput.get("ResourceName"));
		logger.info("DatabaseName: " + dataInput.get("DatabaseName"));
		logger.info("SchemaName: " + dataInput.get("SchemaName"));
		logger.info("TableName: " + dataInput.get("TableName"));

		inputParameters.get(0).setValue(dataInput.get("ResourceName"));
		inputParameters.get(1).setValue(dataInput.get("DatabaseName"));
		inputParameters.get(2).setValue(dataInput.get("SchemaName"));
		inputParameters.get(3).setValue(dataInput.get("TableName"));

		// create data structure
		ComputationOutput outputData = new ComputationOutput();
		// computation id
		String computationId = startComputation(algorithmId, inputParameters,
				outputData);

		// print check on retrieving data
		// logger.info("output data retrieved");

		// data output values
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		// data output keys
		LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();

		mapValues = outputData.getMapValues();
		mapKeys = outputData.getmapKeys();

		for (int i = 0; i < mapValues.size(); i++) {
			Result row = new Result(mapKeys.get(String.valueOf(i)),
					mapValues.get(String.valueOf(i)));
			output.add(row);
		}

		return output;
	}

	@Override
	public List<Result> smartSample(LinkedHashMap<String, String> dataInput)
			throws Exception {
		// data input
		List<Parameter> inputParameters = new ArrayList<Parameter>();
		// output sample result
		List<Result> output = new ArrayList<Result>();

		// get list of algorithms
		List<String> algorithms = new ArrayList<String>();
		algorithms = getDatabaseManagerAlgorithms();

		// get algorithmId
		String algorithmId = null;

		for (int i = 0; i < algorithms.size(); i++) {
			if (algorithms.get(i).equals("SMARTSAMPLEONTABLE")) {
				algorithmId = algorithms.get(i);
				// print check
				// logger.info("algorithmId: " + algorithmId);
			}
		}

		// get input parameters of the algorithm
		inputParameters = getParameters(algorithmId);

		if (inputParameters.size() != 0) {
			// print check
			logger.info("algorithm input parameters retrieved");
		}

		// print check
		// for (int i = 0; i < inputParameters.size(); i++) {
		// logger.info(inputParameters.get(i).getName());
		// }

		// print check
		logger.info("ResourceName: " + dataInput.get("ResourceName"));
		logger.info("DatabaseName: " + dataInput.get("DatabaseName"));
		logger.info("SchemaName: " + dataInput.get("SchemaName"));
		logger.info("TableName: " + dataInput.get("TableName"));

		inputParameters.get(0).setValue(dataInput.get("ResourceName"));
		inputParameters.get(1).setValue(dataInput.get("DatabaseName"));
		inputParameters.get(2).setValue(dataInput.get("SchemaName"));
		inputParameters.get(3).setValue(dataInput.get("TableName"));

		// create data structure
		ComputationOutput outputData = new ComputationOutput();
		// computation id
		String computationId = startComputation(algorithmId, inputParameters,
				outputData);

		// print check on retrieving data
		logger.info("output data retrieved");

		// data output values
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		// data output keys
		LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();

		mapValues = outputData.getMapValues();
		mapKeys = outputData.getmapKeys();

		for (int i = 0; i < mapValues.size(); i++) {
			Result row = new Result(mapKeys.get(String.valueOf(i)),
					mapValues.get(String.valueOf(i)));
			output.add(row);
		}
		return output;
	}

	@Override
	public List<Result> randomSample(LinkedHashMap<String, String> dataInput)
			throws Exception {

		// data input
		List<Parameter> inputParameters = new ArrayList<Parameter>();
		// output sample result
		List<Result> output = new ArrayList<Result>();

		// get list of algorithms
		List<String> algorithms = new ArrayList<String>();
		algorithms = getDatabaseManagerAlgorithms();

		// get algorithmId
		String algorithmId = null;

		for (int i = 0; i < algorithms.size(); i++) {
			if (algorithms.get(i).equals("RANDOMSAMPLEONTABLE")) {
				algorithmId = algorithms.get(i);
				// print check
				// logger.info("algorithmId: " + algorithmId);
			}
		}

		// get input parameters of the algorithm specified by id
		inputParameters = getParameters(algorithmId);

		if (inputParameters.size() != 0) {
			// print check
			logger.info("algorithm input parameters retrieved");
		}

		// print check algorithm input parameters
		// for (int i = 0; i < inputParameters.size(); i++) {
		// logger.info(inputParameters.get(i).getName());
		// }

		// print check
		logger.info("ResourceName: " + dataInput.get("ResourceName"));
		logger.info("DatabaseName: " + dataInput.get("DatabaseName"));
		logger.info("SchemaName: " + dataInput.get("SchemaName"));
		logger.info("TableName: " + dataInput.get("TableName"));

		inputParameters.get(0).setValue(dataInput.get("ResourceName"));
		inputParameters.get(1).setValue(dataInput.get("DatabaseName"));
		inputParameters.get(2).setValue(dataInput.get("SchemaName"));
		inputParameters.get(3).setValue(dataInput.get("TableName"));

		// create data structure
		ComputationOutput outputData = new ComputationOutput();
		// computation id
		String computationId = startComputation(algorithmId, inputParameters,
				outputData);

		// print check on retrieving data
		logger.info("output data retrieved");

		// data output values
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		// data output keys
		LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();

		mapValues = outputData.getMapValues();
		mapKeys = outputData.getmapKeys();

		for (int i = 0; i < mapValues.size(); i++) {
			Result row = new Result(mapKeys.get(String.valueOf(i)),
					mapValues.get(String.valueOf(i)));
			output.add(row);
		}
		return output;
	}

	@Override
	public LinkedHashMap<String, FileModel> getTableDetails(
			LinkedHashMap<String, String> dataInput) throws Exception {
		// data input
		List<Parameter> inputParameters = new ArrayList<Parameter>();
		// data ouptut
		LinkedHashMap<String, FileModel> outputParameters = new LinkedHashMap<String, FileModel>();

		// get list of algorithms
		List<String> algorithms = new ArrayList<String>();
		algorithms = getDatabaseManagerAlgorithms();

		// get algorithmId
		String algorithmId = null;

		for (int i = 0; i < algorithms.size(); i++) {
			if (algorithms.get(i).equals("GETTABLEDETAILS")) {
				algorithmId = algorithms.get(i);
				// print check
				// logger.info("algorithmId: " + algorithmId);
			}
		}

		// get input parameters of the algorithm specified by id
		inputParameters = getParameters(algorithmId);

		if (inputParameters.size() != 0) {
			// print check
			logger.info("algorithm input parameters retrieved");
		}

		// print check algorithm input parameters
		// for (int i = 0; i < inputParameters.size(); i++) {
		// logger.info(inputParameters.get(i).getName());
		// }

		// print check
		logger.info("ResourceName: " + dataInput.get("ResourceName"));
		logger.info("DatabaseName: " + dataInput.get("DatabaseName"));
		logger.info("SchemaName: " + dataInput.get("SchemaName"));
		logger.info("TableName: " + dataInput.get("TableName"));

		inputParameters.get(0).setValue(dataInput.get("ResourceName"));
		inputParameters.get(1).setValue(dataInput.get("DatabaseName"));
		inputParameters.get(2).setValue(dataInput.get("SchemaName"));
		inputParameters.get(3).setValue(dataInput.get("TableName"));

		// create data structure
		ComputationOutput outputData = new ComputationOutput();
		// computation id
		String computationId = startComputation(algorithmId, inputParameters,
				outputData);

		// print check on retrieving data
		// logger.info("output data retrieved");

		// output data values
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		// output data keys
		LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();

		mapValues = outputData.getMapValues();
		mapKeys = outputData.getmapKeys();

		for (int i = 0; i < mapValues.size(); i++) {
			FileModel obj = new FileModel(mapValues.get(String.valueOf(i)));
			// obj.setIsLoaded(true);
			outputParameters.put(mapKeys.get(String.valueOf(i)), obj);

			// print check
			// logger.info("value: " + outputMap.get(String.valueOf(i)));
			// logger.info("key: " + outputKey.get(String.valueOf(i)));
		}
		return outputParameters;
	}

	// parse a csv row in a list of values
	public List<Row> parseCVSString(List<Result> result, List<String> attrNames)
			throws Exception {

		List<Row> rows = new ArrayList<Row>();

		if (result != null) {
			for (int i = 0; i < result.size(); i++) {
				List<String> attrValues = parse(result.get(i).getValue());
				Row element = new Row(attrNames, attrValues, i);
				rows.add(element);
			}
		}
		return rows;
	}

	private List<String> parse(String row) throws Exception {

		String delimiter = ",";

		// print check
		// logger.info("row: " + row);

		List<String> elements = new ArrayList<String>();
		String phrase = row;
		int idxdelim = -1;
		boolean quot = false;
		phrase = phrase.trim();
		while ((idxdelim = phrase.indexOf(delimiter)) >= 0) {
			quot = phrase.startsWith("\"");
			if (quot) {
				phrase = phrase.substring(1);
				String quoted = "";
				if (phrase.startsWith("\""))
					phrase = phrase.substring(1);
				else {
					RE regexp = new RE("[^\\\\]\"");
					boolean matching = regexp.match(phrase);

					if (matching) {
						int i0 = regexp.getParenStart(0);
						quoted = phrase.substring(0, i0 + 1).trim();
						phrase = phrase.substring(i0 + 2).trim();
					}
				}

				if (phrase.startsWith(delimiter))
					phrase = phrase.substring(1);

				elements.add(quoted);

			} else {
				elements.add(phrase.substring(0, idxdelim));
				phrase = phrase.substring(idxdelim + 1).trim();
			}

			// logger.info("server token: " + phrase);
		}
		if (phrase.startsWith("\""))
			phrase = phrase.substring(1);

		if (phrase.endsWith("\""))
			phrase = phrase.substring(0, phrase.length() - 1);

		elements.add(phrase);

		// logger.info("size: " + elements.size());

		return elements;
	}

	private List<String> getDatabaseManagerAlgorithms() {

		ArrayList<String> dbAlg = new ArrayList<String>();
		StatisticalManagerFactory factory = getFactory();

		// get and print algorithms
		SMListGroupedAlgorithms groups = factory.getAlgorithms();

		if (groups == null)
			logger.info("GROUPS OF ALGORITHMS IS NULL!");
		else
			logger.info("GROUPS OF ALGORITHMS IS NOT NULL!");

		// get list categories
		for (SMGroupedAlgorithms group : groups.thelist()) {
			for (SMAlgorithm algorithm : group.thelist()) {
				dbAlg.add(algorithm.name());
			}
		}
		return dbAlg;
	}

	private List<Parameter> getParameters(String algorithmId) {

		StatisticalManagerFactory factory = getFactory();
		SMParameters smParams = factory.getAlgorithmParameters(algorithmId);
		List<Parameter> params = new ArrayList<Parameter>();

		for (SMParameter smParam : smParams.list()) {
			SMTypeParameter smType = smParam.type();
			StatisticalServiceType smTypeName = smType.name();

			String paramName = smParam.name();
			String paramDescription = smParam.description();
			String defaultValue = smParam.defaultValue();
			String objectType = smType.values().get(0);

			// print CHECK
			// logger.info("parameters: ");
			// logger.info(paramName);
			// logger.info(paramDescription);
			// logger.info(objectType);
			// logger.info(defaultValue);

			Parameter objectParam = new Parameter(paramName, paramDescription,
					objectType, defaultValue);
			params.add(objectParam);
		}
		return params;
	}

	private String startComputation(String algorithmName,
			List<Parameter> parameters, ComputationOutput outputData)
			throws Exception {

		SMComputationConfig config = new SMComputationConfig();
		SMInputEntry[] list = new SMInputEntry[parameters.size()];
		int i = 0;

		for (Parameter p : parameters)
			list[i++] = new SMInputEntry(p.getName(), p.getValue());
		config.parameters(new SMEntries(list));
		config.algorithm(algorithmName);

		// create a computation request
		SMComputationRequest request = new SMComputationRequest();
		request.user(getUsername());
		request.config(config);

		try {
			StatisticalManagerFactory factory = getFactory();
			String computationId = factory.executeComputation(request);

			float percentage = 0;
			String scope = getScope();
			String username = getUsername();

			while (percentage < 100) {
				percentage = checkComputationStatus(scope, computationId,
						username, outputData);
				Thread.sleep(3000);
			}
			return computationId;
		} catch (Exception e) {
			// e.printStackTrace();
			throw e;
		}
	}

	private float checkComputationStatus(String scope, String computationId,
			String user, ComputationOutput outputData) throws Exception {

		ScopeProvider.instance.set(scope);

		StatisticalManagerFactory factory = StatisticalManagerDSL
				.createStateful().build();

		SMComputation computation = factory.getComputation(computationId);

		SMOperationStatus status = SMOperationStatus.values()[computation
				.operationStatus()];

		float percentage = 0;

		if (status == SMOperationStatus.RUNNING) {

			// logger.info("RUNNING");
			SMOperationInfo infos = factory.getComputationInfo(computationId,
					user);
			// percentage = Float.parseFloat(infos.percentage());
			// logger.info("Percentage:" +
			// percentage);
			// computation = factory.getComputation(computationId);

			status = SMOperationStatus.values()[computation.operationStatus()];
		} else if ((status == SMOperationStatus.COMPLETED)
				|| (status == SMOperationStatus.FAILED)) {

			// logger.info("COMPLETED OR FAILED");

			SMAbstractResource abstractResource = computation
					.abstractResource();
			SMResource smResource = abstractResource.resource();
			int resourceTypeIndex = smResource.resourceType();
			SMResourceType smResType = SMResourceType.values()[resourceTypeIndex];

			displayOutput(smResource, smResType, outputData);

			// print check
			// logger.info("SM resource Name: " + smResource.name());
			// logger.info("SM resource Name: " + smResource.name());
			// logger.info("SM resource ID: " + smResource.resourceId());
			// logger.info("SM resource ID: " + smResource.resourceId());
			// logger.info("SM resource Description: " +
			// smResource.description());

			percentage = 100;
		}
		return percentage;
	}

	private void displayOutput(SMResource smResource, SMResourceType smResType,
			ComputationOutput outputData) throws Exception {

		if (smResType.equals(SMResourceType.OBJECT)) {

			// switch (smResType) {
			// case FILE:
			// SMFile fileRes = (SMFile) smResource;
			// System.out.println("Output is a file");
			// break;
			// case OBJECT:
			SMObject objRes = (SMObject) smResource;
			if (objRes.name().contentEquals(PrimitiveTypes.MAP.toString())) {
				logger.info("Output is a map");
				getMap(objRes, outputData);

			} else if (objRes.name().contentEquals(
					PrimitiveTypes.IMAGES.toString())) {
				// logger.info("Output are images");
			}
			// else
			// System.out.println("Output is other");
			// rootLogger.log(Level.SEVERE, "Output is other");
		}

		// EXCEPTION MANAGEMENT
		if (smResType.equals(SMResourceType.ERROR)) {

			Exception e = new Exception(smResource.description());
			// e.printStackTrace();
			logger.error(e);
			throw e;
		}
	}

	//get output result
	private void getMap(SMObject objRes, ComputationOutput outputData)
			throws Exception {

		// output data values
		LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
		// output data keys
		LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();

		InputStream is = getStorageClientInputStream(objRes.url());
		// object serializer
		XStream xstream = new XStream();
		xstream.alias(
				"org.gcube_system.namespaces.data.analysis.statisticalmanager.types.SMObject",
				SMObject.class);
		xstream.alias(
				"org.gcube_system.namespaces.data.analysis.statisticalmanager.types.SMFile",
				SMFile.class);
		xstream.alias(
				"org.gcube_system.namespaces.data.analysis.statisticalmanager.types.SMResource",
				SMResource.class);
		xstream.alias(
				"org.gcube_system.namespaces.data.analysis.statisticalmanager.types.SMTable",
				SMTable.class);

		@SuppressWarnings("unchecked")
		Map<String, SMResource> smMap = (Map<String, SMResource>) (xstream
				.fromXML(is));
		is.close();

		int i = 0;
		for (String key : smMap.keySet()) {
			// add key value
			mapKeys.put(String.valueOf(i), key);

			SMResource smres = smMap.get(key);
			int resourceTypeIndex = smres.resourceType();
			SMResourceType smsubResType = SMResourceType.values()[resourceTypeIndex];

			// logger.info("ResourceType: " + smsubResType);

			if (smsubResType == SMResourceType.OBJECT) {
				SMObject obje = (SMObject) smres;
				String outstring = obje.url();
                
				// logger.info("key: " + smsubResType);
				// logger.info("object: " + outstring);
				mapValues.put(String.valueOf(i), outstring);

				i++;
			}
		}

		outputData.setMapValues(mapValues);
		outputData.setmapKeys(mapKeys);
	}

	private InputStream getStorageClientInputStream(String url)
			throws Exception {
		URL u = new URL(null, url, new URLStreamHandler() {
			@Override
			protected URLConnection openConnection(URL u) throws IOException {
				return new SMPURLConnection(u);
			}
		});
		return u.openConnection().getInputStream();
	}

	private StatisticalManagerFactory getFactory() {
		HttpSession httpSession = this.getThreadLocalRequest().getSession();
		return SessionUtil.getFactory(httpSession);
	}

	private String getUsername() {
		HttpSession httpSession = this.getThreadLocalRequest().getSession();
		return SessionUtil.getUsername(httpSession);
	}

	private String getScope() {
		HttpSession httpSession = this.getThreadLocalRequest().getSession();
		return SessionUtil.getScope(httpSession);

	}

}