1381 lines
42 KiB
Java
1381 lines
42 KiB
Java
package org.gcube.portlets.user.databasesmanager.server;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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import java.io.IOException;
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import java.io.InputStream;
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import java.net.URL;
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import java.net.URLConnection;
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import java.net.URLStreamHandler;
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import javax.servlet.http.HttpSession;
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import org.apache.regexp.RE;
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import org.gcube.application.framework.core.session.ASLSession;
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import org.gcube.common.scope.api.ScopeProvider;
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import org.gcube.contentmanager.storageclient.model.protocol.smp.SMPURLConnection;
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import org.gcube.data.analysis.statisticalmanager.proxies.StatisticalManagerDSL;
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import org.gcube.data.analysis.statisticalmanager.proxies.StatisticalManagerFactory;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMAlgorithm;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMComputationConfig;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMComputationRequest;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMGroupedAlgorithms;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMListGroupedAlgorithms;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMOperationStatus;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMParameter;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMParameters;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMResourceType;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.SMTypeParameter;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMAbstractResource;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMComputation;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMEntries;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMFile;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMInputEntry;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMObject;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMOperationInfo;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMResource;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.SMTable;
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import org.gcube.data.analysis.statisticalmanager.stubs.types.schema.StatisticalServiceType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
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import org.gcube.portlets.user.databasesmanager.client.GWTdbManagerService;
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import org.gcube.portlets.user.databasesmanager.client.datamodel.ComputationOutput;
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import org.gcube.portlets.user.databasesmanager.client.datamodel.FileModel;
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import org.gcube.portlets.user.databasesmanager.client.datamodel.Parameter;
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import org.gcube.portlets.user.databasesmanager.client.datamodel.Result;
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import org.gcube.portlets.user.databasesmanager.client.datamodel.Row;
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import org.gcube.portlets.user.databasesmanager.server.util.SessionUtil;
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import org.gcube.portlets.user.databasesmanager.server.util.WsUtil;
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import com.extjs.gxt.ui.client.data.BasePagingLoadResult;
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import com.extjs.gxt.ui.client.data.PagingLoadConfig;
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import com.extjs.gxt.ui.client.data.PagingLoadResult;
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import com.google.gwt.user.server.rpc.RemoteServiceServlet;
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import com.thoughtworks.xstream.XStream;
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import org.apache.log4j.Logger;
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public class GWTdbManagerServiceImpl extends RemoteServiceServlet implements
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GWTdbManagerService {
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// // the result generated in the LoadTables method
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// private List<Result> result = null;
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// information about a database
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// private String currentDB = "";
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// private String previousDB = "";
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// information about a schema
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// private String currentSchema = "";
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// private String previousSchema = "";
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//Hashmap that contains computationId
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// HashMap<UUID, String> computationIDMap = new HashMap<UUID, String>();
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// logger
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private static Logger logger = Logger
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.getLogger(GWTdbManagerServiceImpl.class);
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public GWTdbManagerServiceImpl() {
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}
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private void initVariables(){
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ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest().getSession());
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// the result generated in the LoadTables method
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List<Result> result = new ArrayList<Result>();
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session.setAttribute("TablesResult", result);
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// information about a database
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String currentDB = "";
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session.setAttribute("currentDB", currentDB);
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String previousDB = "";
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session.setAttribute("previousDB", previousDB);
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// information about a schema
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String currentSchema = "";
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session.setAttribute("currentSchema", currentSchema);
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String previousSchema = "";
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session.setAttribute("previousSchema", previousSchema);
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}
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// to get resources from IS
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@Override
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public List<FileModel> getResource() throws Exception {
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//initialize variables with application startup
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initVariables();
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// data input
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List<Parameter> inputParameters = new ArrayList<Parameter>();
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// data output
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List<FileModel> outputParameters = new ArrayList<FileModel>();
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// get list of algorithms
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List<String> algorithms = new ArrayList<String>();
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algorithms = getDatabaseManagerAlgorithms();
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// get algorithmId
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String algorithmId = null;
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for (int i = 0; i < algorithms.size(); i++) {
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if (algorithms.get(i).equals("LISTDBNAMES")) {
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algorithmId = algorithms.get(i);
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// print check
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// logger.info("algorithmId: " + algorithmId);
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}
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}
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// get input parameters of the algorithm specified by id
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inputParameters = getParameters(algorithmId);
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if (inputParameters.size() != 0) {
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// print check
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logger.info("algorithm input parameters retrieved");
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}
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// // print check input parameters
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// for (int i = 0; i < inputParameters.size(); i++) {
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// logger.info(inputParameters.get(i).getName());
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// }
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// create data structure for data output
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ComputationOutput outputData = new ComputationOutput();
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// computationId
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String computationId = startComputation(algorithmId, inputParameters,
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outputData);
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// print check
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// retrieve data
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// logger.info("output data retrieved");
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// data output
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LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
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mapValues = outputData.getMapValues();
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for (int i = 0; i < mapValues.size(); i++) {
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FileModel obj = new FileModel(mapValues.get(String.valueOf(i)));
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// obj.setIsLoaded(true);
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outputParameters.add(obj);
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}
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return outputParameters;
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}
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// to get information about databases of a resource
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@Override
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public LinkedHashMap<String, FileModel> getDBInfo(String resourceName)
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throws Exception {
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// data input
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List<Parameter> inputParameters = new ArrayList<Parameter>();
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// data output
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LinkedHashMap<String, FileModel> outputParameters = new LinkedHashMap<String, FileModel>();
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// get list of algorithms
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List<String> algorithms = new ArrayList<String>();
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algorithms = getDatabaseManagerAlgorithms();
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// get algorithmId
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String algorithmId = null;
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for (int i = 0; i < algorithms.size(); i++) {
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if (algorithms.get(i).equals("LISTDBINFO")) {
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algorithmId = algorithms.get(i);
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// print check
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// logger.info("algorithmId: " + algorithmId);
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}
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}
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// get input parameters of the algorithm specified by id
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inputParameters = getParameters(algorithmId);
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if (inputParameters.size() != 0) {
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// print check
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logger.info("algorithm input parameters retrieved");
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}
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inputParameters.get(0).setValue(resourceName);
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// print check
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// logger.info(inputParameters.get(0).getName());
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// create data structure
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ComputationOutput outputData = new ComputationOutput();
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// computation id
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String computationId = startComputation(algorithmId, inputParameters,
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outputData);
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// print check
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// retrieve data
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// logger.info("output data retrieved");
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// data output values
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LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
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// data output keys
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LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();
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mapValues = outputData.getMapValues();
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mapKeys = outputData.getmapKeys();
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for (int i = 0; i < mapValues.size(); i++) {
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FileModel obj = new FileModel(mapValues.get(String.valueOf(i)));
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// obj.setIsLoaded(true);
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// print check
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// logger.info("value: " + mapValues.get(String.valueOf(i)));
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// logger.info("key: " + mapKeys.get(String.valueOf(i)));
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outputParameters.put(mapKeys.get(String.valueOf(i)), obj);
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}
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return outputParameters;
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}
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// to get schema for a database
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@Override
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public List<FileModel> getDBSchema(LinkedHashMap<String, String> dataInput)
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throws Exception {
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// data input
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List<Parameter> inputParameters = new ArrayList<Parameter>();
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// data output
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List<FileModel> outputParameters = new ArrayList<FileModel>();
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// get list of algorithms
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List<String> algorithms = new ArrayList<String>();
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algorithms = getDatabaseManagerAlgorithms();
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// get algorithmId
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String algorithmId = null;
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for (int i = 0; i < algorithms.size(); i++) {
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if (algorithms.get(i).equals("LISTDBSCHEMA")) {
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algorithmId = algorithms.get(i);
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// print check
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// logger.info("algorithmId: " + algorithmId);
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}
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}
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// get input parameters of the algorithm specified by id
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inputParameters = getParameters(algorithmId);
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if (inputParameters.size() != 0) {
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// print check
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logger.info("algorithm input parameters retrieved");
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}
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// print check algorithm input parameters
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// for (int i = 0; i < inputParameters.size(); i++) {
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// logger.info(inputParameters.get(i).getName());
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// }
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inputParameters.get(0).setValue(dataInput.get("ResourceName"));
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inputParameters.get(1).setValue(dataInput.get("DatabaseName"));
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// print check
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logger.info("ResourceName: " + dataInput.get("ResourceName"));
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logger.info("DatabaseName: " + dataInput.get("DatabaseName"));
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// create data structure
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ComputationOutput outputData = new ComputationOutput();
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// computation id
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String computationId = startComputation(algorithmId, inputParameters,
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outputData);
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// print check
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// retrieve data
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logger.info("output data retrieved");
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// data output values
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LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
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// data output keys
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LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();
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mapValues = outputData.getMapValues();
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mapKeys = outputData.getmapKeys();
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for (int i = 0; i < mapValues.size(); i++) {
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FileModel obj = new FileModel(mapValues.get(String.valueOf(i)));
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// obj.setIsSchema(true);
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// obj.setIsLoaded(true);
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outputParameters.add(obj);
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}
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return outputParameters;
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}
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// to get tables
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private List<Result> getTables(LinkedHashMap<String, String> dataInput)
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throws Exception {
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// data input
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List<Parameter> inputParameters = new ArrayList<Parameter>();
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// data output
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List<Result> outputParameters = new ArrayList<Result>();
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// get list of algorithms
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List<String> algorithms = new ArrayList<String>();
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algorithms = getDatabaseManagerAlgorithms();
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// get algorithmId
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String algorithmId = null;
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for (int i = 0; i < algorithms.size(); i++) {
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if (algorithms.get(i).equals("LISTTABLES")) {
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algorithmId = algorithms.get(i);
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// print check
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// logger.info("algorithmId: " + algorithmId);
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}
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}
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// get input parameters of the algorithm
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inputParameters = getParameters(algorithmId);
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if (inputParameters.size() != 0) {
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// print check
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logger.info("algorithm input parameters retrieved");
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}
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// print check algorithm input parameters
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// for (int i = 0; i < inputParameters.size(); i++) {
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// logger.info(inputParameters.get(i).getName());
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// }
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inputParameters.get(0).setValue(dataInput.get("ResourceName"));
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inputParameters.get(1).setValue(dataInput.get("DatabaseName"));
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inputParameters.get(2).setValue(dataInput.get("SchemaName"));
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// print check
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logger.info("ResourceName: " + dataInput.get("ResourceName"));
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logger.info("DatabaseName: " + dataInput.get("DatabaseName"));
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logger.info("SchemaName: " + dataInput.get("SchemaName"));
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// create data structure
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ComputationOutput outputData = new ComputationOutput();
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// computation id
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String computationId = startComputation(algorithmId, inputParameters,
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outputData);
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// print check on retrieving data
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// logger.info("output data retrieved");
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// data output values
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LinkedHashMap<String, String> mapValues = new LinkedHashMap<String, String>();
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// data output keys
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LinkedHashMap<String, String> mapKeys = new LinkedHashMap<String, String>();
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mapValues = outputData.getMapValues();
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mapKeys = outputData.getmapKeys();
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for (int i = 0; i < mapValues.size(); i++) {
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Result row = new Result(String.valueOf(i), mapValues.get(String
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.valueOf(i)));
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outputParameters.add(row);
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}
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return outputParameters;
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}
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// to load tables
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@Override
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public PagingLoadResult<Result> LoadTables(PagingLoadConfig config,
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LinkedHashMap<String, String> dataInput, boolean SearchTable,
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String keyword) throws Exception {
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ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest().getSession());
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List<Result> result = (List<Result>) session.getAttribute("TablesResult");
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// check on a database
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String currentDB = "";
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currentDB = dataInput.get("DatabaseName");
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String previousDB = (String) session.getAttribute("previousDB");
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if (!currentDB.equals(previousDB)) {
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// result = null;
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result = new ArrayList<Result>();
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System.gc();
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}
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previousDB = currentDB;
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session.setAttribute("previousDB", previousDB);
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// check on a schema
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String currentSchema = "";
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currentSchema = dataInput.get("SchemaName");
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String previousSchema = (String) session.getAttribute("previousSchema");
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if (!currentSchema.equals(previousSchema)) {
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// result = null;
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result = new ArrayList<Result>();
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System.gc();
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}
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previousSchema = currentSchema;
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session.setAttribute("previousSchema", previousSchema);
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// get tables
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// if (result == null)
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// result = getTables(dataInput);
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if (result.size()==0)
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result = getTables(dataInput);
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// Create a sublist and add data to list according
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// to the limit and offset value of the config
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List<Result> sublist = new ArrayList<Result>();
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BasePagingLoadResult loadResult = null;
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// print check on the search
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// logger.info("Searching in the table: " + SearchTable);
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// logger.info("Keyword to search: " + keyword);
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int start = config.getOffset();
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int limit = result.size();
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if (config.getLimit() > 0) {
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limit = Math.min(start + config.getLimit(), limit);
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}
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int totalNumber = result.size();
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if ((SearchTable == false) || keyword == null || keyword.length() == 0) {
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sublist = new ArrayList<Result>(result.subList(start, limit));
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} else {
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// print check
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// logger.info("searching the table");
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// search the table
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for (int i = 0; i < result.size(); i++) {
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if ((result.get(i).getValue().toLowerCase()).startsWith(keyword
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.toLowerCase())) {
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sublist.add(result.get(i));
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}
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}
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limit = sublist.size();
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int sublen = sublist.size();
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totalNumber = sublen;
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if (start < sublen - 1) {
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limit = Math.min(sublen, limit);
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totalNumber = sublist.size();
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sublist = new ArrayList<Result>(sublist.subList(start, limit));
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}
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}
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// print check
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// logger.info("result size: " + totalNumber);
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// logger.info("limit: " + limit);
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// logger.info("offset: " + config.getOffset());
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// logger.info("start: " + start);
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loadResult = new BasePagingLoadResult<Result>(sublist,
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config.getOffset(), totalNumber);
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session.setAttribute("TablesResult", result);
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return loadResult;
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}
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// to submit a query
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@Override
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public List<Result> submitQuery(LinkedHashMap<String, String> dataDB,
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String query, boolean valueReadOnlyQuery,
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boolean smartCorrectionQuery, String language) throws Exception {
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logger.info("Dialect used for smart correction: " + language);
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// data input
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List<Parameter> inputParameters = new ArrayList<Parameter>();
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// data output
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List<Result> output = new ArrayList<Result>();
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// get list of algorithms
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List<String> algorithms = new ArrayList<String>();
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algorithms = getDatabaseManagerAlgorithms();
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// get algorithmId
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String algorithmId = null;
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for (int i = 0; i < algorithms.size(); i++) {
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if (algorithms.get(i).equals("SUBMITQUERY")) {
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algorithmId = algorithms.get(i);
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// print check
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// logger.info("algorithmId: " + algorithmId);
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}
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}
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// get input parameters of the algorithm
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inputParameters = getParameters(algorithmId);
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if (inputParameters.size() != 0) {
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// print check
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logger.info("algorithm input parameters retrieved");
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}
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// print check
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// for (int i = 0; i < inputParameters.size(); i++) {
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// logger.info(inputParameters.get(i).getName());
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// }
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// print check
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logger.info("ResourceName: " + dataDB.get("ResourceName"));
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logger.info("DatabaseName: " + dataDB.get("DatabaseName"));
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logger.info("Query: " + query);
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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);
|
|
|
|
// computationIDMap.put(id, computationId);
|
|
|
|
// 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;
|
|
}
|
|
|
|
// // to submit a query
|
|
// public String startSubmitQueryComputation(
|
|
// LinkedHashMap<String, String> dataDB, String query,
|
|
// boolean valueReadOnlyQuery, boolean smartCorrectionQuery,
|
|
// String language) {
|
|
//
|
|
// 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();
|
|
//
|
|
// // get computation id
|
|
//
|
|
// SMComputationConfig config = new SMComputationConfig();
|
|
// SMInputEntry[] list = new SMInputEntry[inputParameters.size()];
|
|
// int i = 0;
|
|
//
|
|
// for (Parameter p : inputParameters)
|
|
// list[i++] = new SMInputEntry(p.getName(), p.getValue());
|
|
// config.parameters(new SMEntries(list));
|
|
// config.algorithm(algorithmId);
|
|
//
|
|
// // create a computation request
|
|
// SMComputationRequest request = new SMComputationRequest();
|
|
// request.user(getUsername());
|
|
// request.config(config);
|
|
//
|
|
// // execute computation
|
|
// StatisticalManagerFactory factory = getFactory();
|
|
// String computationId = factory.executeComputation(request);
|
|
//
|
|
// return computationId;
|
|
// }
|
|
|
|
// public float startCheckSubmitQueryComputation(String computationId) {
|
|
//
|
|
// String scope = getScope();
|
|
// String user = getUsername();
|
|
//
|
|
// 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;
|
|
//
|
|
// }
|
|
|
|
// public List<Result> getSubmitQueryOutput(String computationId)
|
|
// throws Exception {
|
|
//
|
|
// String scope = getScope();
|
|
//
|
|
// ScopeProvider.instance.set(scope);
|
|
//
|
|
// StatisticalManagerFactory factory = StatisticalManagerDSL
|
|
// .createStateful().build();
|
|
//
|
|
// SMComputation computation = factory.getComputation(computationId);
|
|
//
|
|
// SMAbstractResource abstractResource = computation.abstractResource();
|
|
// SMResource smResource = abstractResource.resource();
|
|
// int resourceTypeIndex = smResource.resourceType();
|
|
// SMResourceType smResType = SMResourceType.values()[resourceTypeIndex];
|
|
//
|
|
// // create data structure
|
|
// ComputationOutput outputData = new ComputationOutput();
|
|
//
|
|
// displayOutput(smResource, smResType, outputData);
|
|
//
|
|
// // print check on retrieving data
|
|
// logger.info("output data retrieved");
|
|
//
|
|
// // data output
|
|
// List<Result> output = new ArrayList<Result>();
|
|
//
|
|
// // 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
|
|
@Override
|
|
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);
|
|
|
|
}
|
|
|
|
public void removeComputation(String computationId) throws Exception {
|
|
StatisticalManagerFactory factory = getFactory();
|
|
factory.removeComputation(computationId);
|
|
}
|
|
|
|
|
|
|
|
}
|