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

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package org.gcube.portlets.user.databasesmanager.server;
import java.util.ArrayList;
import java.util.HashMap;
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.application.framework.core.session.ASLSession;
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 org.gcube.portlets.user.databasesmanager.server.util.WsUtil;
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 = "";
// //Hashmap that contains computationId with a uid key
// HashMap<String, String> computationIDMap = new HashMap<String, String>();
String operation = "";
// logger
private static Logger logger = Logger
.getLogger(GWTdbManagerServiceImpl.class);
public GWTdbManagerServiceImpl() {
}
private void initVariables() {
ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest()
.getSession());
// the result generated in the LoadTables method
List<Result> result = new ArrayList<Result>();
session.setAttribute("TablesResult", result);
// map that contains the submit query result and the related uid
HashMap<String, List<Result>> submitQueryResult = new HashMap<String, List<Result>>();
session.setAttribute("submitQueryResult", submitQueryResult);
// map that contains the the submit query result parsed and the related
// uid
HashMap<String, List<Row>> submitQueryResultParsed = new HashMap<String, List<Row>>();
session.setAttribute("submitQueryResultParsed", submitQueryResultParsed);
// List<Result> submitQueryResult = new ArrayList<Result>();
// session.setAttribute("submitQueryResult", submitQueryResult);
// attributes name for a result of a submit query operation
// List<String> attributeNames = new ArrayList<String>();
// session.setAttribute("attributeNames", attributeNames);
// information about a database
String currentDB = "";
session.setAttribute("currentDB", currentDB);
String previousDB = "";
session.setAttribute("previousDB", previousDB);
// information about a schema
String currentSchema = "";
session.setAttribute("currentSchema", currentSchema);
String previousSchema = "";
session.setAttribute("previousSchema", previousSchema);
// Hashmap that contains computationId with a uid key
HashMap<String, String> computationIDMap = new HashMap<String, String>();
session.setAttribute("ComputationIDList", computationIDMap);
// Hashmap that contains the job status with a uid key
HashMap<String, String> JobStatusMap = new HashMap<String, String>();
session.setAttribute("JobStatusList", JobStatusMap);
// information about query submitted
// String currentQuerySubmitted = "";
// session.setAttribute("currentQuerySubmitted", currentQuerySubmitted);
// String previousQuerySubmitted = "";
// session.setAttribute("previousQuerySubmitted",
// previousQuerySubmitted);
// HashMap<String, List<Result>> obj = new HashMap<String,
// List<Result>>();
// session.setAttribute("", obj);
}
// to get resources from IS
@Override
public List<FileModel> getResource() throws Exception {
// initialize variables with application startup
initVariables();
// 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 {
ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest()
.getSession());
List<Result> result = (List<Result>) session
.getAttribute("TablesResult");
// check on a database
String currentDB = "";
currentDB = dataInput.get("DatabaseName");
String previousDB = (String) session.getAttribute("previousDB");
if (!currentDB.equals(previousDB)) {
// result = null;
result = new ArrayList<Result>();
System.gc();
}
previousDB = currentDB;
session.setAttribute("previousDB", previousDB);
// check on a schema
String currentSchema = "";
currentSchema = dataInput.get("SchemaName");
String previousSchema = (String) session.getAttribute("previousSchema");
if (!currentSchema.equals(previousSchema)) {
// result = null;
result = new ArrayList<Result>();
System.gc();
}
previousSchema = currentSchema;
session.setAttribute("previousSchema", previousSchema);
// get tables
// if (result == null)
// result = getTables(dataInput);
if (result.size() == 0)
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);
session.setAttribute("TablesResult", result);
return loadResult;
}
// to submit a query
@Override
public List<String> submitQuery(LinkedHashMap<String, String> dataDB,
String query, boolean valueReadOnlyQuery,
boolean smartCorrectionQuery, String language, String UID)
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>();
List<Result> output = null;
// list that contains table attributes
List<String> listAttributes = null;
// 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();
try {
// computation id
String computationId = startComputation(algorithmId,
inputParameters, outputData, UID);
// 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();
if (mapValues.size() != 0) {
output = new ArrayList<Result>();
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);
}
// get the attributes list for the result table
listAttributes = new ArrayList<String>();
listAttributes = getListAttributes(output.get(0).getValue());
// remove the header in order to parse only the result
output.remove(0);
// store the result of the submit query operation
updateSubmitQueryResultMap(UID, output);
}
} catch (Exception e) {
// TODO: handle exception
// e.printStackTrace();
}
return listAttributes;
}
@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 result for Submit query
public PagingLoadResult<Row> loadSubmitResult(PagingLoadConfig config,
List<String> listAttributes, String UID) throws Exception {
// check to verify if the submit query result has been already parsed
// boolean checkOnDataParsed = checkOnSubmitQueryResultParsed(UID);
// data parsed
List<Row> data = new ArrayList<Row>();
// submit query result
List<Result> result = new ArrayList<Result>();
//get parsed data
data = getSubmitQueryResultParsed(UID);
if ((data == null)) {
// parse the submit query result
result = getSubmitQueryResult(UID);
if ((result != null) && (result.size() != 0)) {
data = parseCVSString(result, listAttributes);
updateSubmitQueryResultParsed(UID, data);
}
}
// Create a sublist and add data to list according
// to the limit and offset value of the config
List<Row> sublist = new ArrayList<Row>();
BasePagingLoadResult loadResult = null;
int start = config.getOffset();
int limit = data.size();
if (config.getLimit() > 0) {
limit = Math.min(start + config.getLimit(), limit);
}
int totalNumber = data.size();
sublist = new ArrayList<Row>(data.subList(start, limit));
loadResult = new BasePagingLoadResult<Row>(sublist, config.getOffset(),
totalNumber);
// System.out.println("start: " + start);
// System.out.println("limit: " + limit);
// System.out.println("sublist size: " + sublist.size());
return loadResult;
}
// get attributes list for display the result in a table
private List<String> getListAttributes(String value) {
List<String> listAttributes = new ArrayList<String>();
// recover attribute fields for the result table
String headers = value;
// logger.info("Headers fields table: " + headers);
listAttributes = parseAttributesTableResult(headers);
// logger.info("attributes number: " + listAttributes.size());
// logger.info("attributes list: ");
// print check
// for (int i = 0; i < listAttributes.size(); i++) {
// logger.info("attribute: " + listAttributes.get(i));
// }
return listAttributes;
}
private List<String> parseAttributesTableResult(String phrase) {
String delimiter = ",";
List<String> elements = new ArrayList<String>();
int idxdelim = -1;
phrase = phrase.trim();
while ((idxdelim = phrase.indexOf(delimiter)) >= 0) {
elements.add(phrase.substring(0, idxdelim));
phrase = phrase.substring(idxdelim + 1).trim();
}
elements.add(phrase);
return elements;
}
// 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 synchronized List<Result> getSubmitQueryResult(String submitQueryUID) {
ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest()
.getSession());
HashMap<String, List<Result>> submitQueryResult = (HashMap<String, List<Result>>) session
.getAttribute("submitQueryResult");
if (submitQueryResult.containsKey(submitQueryUID)) {
return submitQueryResult.get(submitQueryUID);
} else {
return null;
}
}
private synchronized List<Row> getSubmitQueryResultParsed(
String submitQueryUID) {
ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest()
.getSession());
HashMap<String, List<Row>> submitQueryResultParsed = (HashMap<String, List<Row>>) session
.getAttribute("submitQueryResultParsed");
if (submitQueryResultParsed.containsKey(submitQueryUID)) {
return submitQueryResultParsed.get(submitQueryUID);
} else {
return null;
}
}
private synchronized void updateSubmitQueryResultParsed(
String submitQueryUID, List<Row> data) {
ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest()
.getSession());
HashMap<String, List<Row>> submitQueryResultParsed = (HashMap<String, List<Row>>) session
.getAttribute("submitQueryResultParsed");
// add data
if (data.size() != 0) {
submitQueryResultParsed.put(submitQueryUID, data);
session.setAttribute("submitQueryResultParsed",
submitQueryResultParsed);
}
}
private synchronized void removeResultParsed(String submitQueryUID) {
ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest()
.getSession());
HashMap<String, List<Row>> submitQueryResultParsed = (HashMap<String, List<Row>>) session
.getAttribute("submitQueryResultParsed");
if (submitQueryResultParsed.containsKey(submitQueryUID)) {
// remove data parsed
submitQueryResultParsed.remove(submitQueryUID);
// update
session.setAttribute("submitQueryResultParsed",
submitQueryResultParsed);
}
}
private synchronized void updateSubmitQueryResultMap(String submitQueryUID,
List<Result> result) {
if (submitQueryUID != null) {
ASLSession session = WsUtil.getAslSession(this
.getThreadLocalRequest().getSession());
HashMap<String, List<Result>> submitQueryResult = (HashMap<String, List<Result>>) session
.getAttribute("submitQueryResult");
submitQueryResult.put(submitQueryUID, result);
session.setAttribute("submitQueryResult", submitQueryResult);
}
}
private synchronized void removeResult(String submitQueryUID) {
ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest()
.getSession());
HashMap<String, List<Result>> submitQueryResult = (HashMap<String, List<Result>>) session
.getAttribute("submitQueryResult");
if (submitQueryResult.containsKey(submitQueryUID)) {
// remove data parsed
submitQueryResult.remove(submitQueryUID);
// update
session.setAttribute("submitQueryResult", submitQueryResult);
}
}
// update job with the related status
private synchronized void updateJobStatus(String jobID, String status) {
if (jobID != null) {
// add the job status
ASLSession session = WsUtil.getAslSession(this
.getThreadLocalRequest().getSession());
HashMap<String, String> JobStatusMap = (HashMap<String, String>) session
.getAttribute("JobStatusList");
JobStatusMap.put(jobID, status);
session.setAttribute("JobStatusList", JobStatusMap);
}
}
// remove job with the related status
private synchronized void removeJobStatus(String jobID) {
ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest()
.getSession());
HashMap<String, String> JobStatusMap = (HashMap<String, String>) session
.getAttribute("JobStatusList");
String status = JobStatusMap.get(jobID);
if (status != null) {
JobStatusMap.remove(jobID);
session.setAttribute("JobStatusList", JobStatusMap);
}
}
// get job status
private synchronized String getJobStatus(String jobID) {
ASLSession session = WsUtil.getAslSession(this.getThreadLocalRequest()
.getSession());
HashMap<String, String> JobStatusMap = (HashMap<String, String>) session
.getAttribute("JobStatusList");
String status = JobStatusMap.get(jobID);
return status;
}
// update job with the computation id
private synchronized void updateJob(String jobID, String computationId) {
if (jobID != null) {
// add the computation in the map
ASLSession session = WsUtil.getAslSession(this
.getThreadLocalRequest().getSession());
HashMap<String, String> computationIDMap = (HashMap<String, String>) session
.getAttribute("ComputationIDList");
computationIDMap.put(jobID, computationId);
session.setAttribute("ComputationIDList", computationIDMap);
}
}
// remove job with the computation id
private synchronized String removeJob(String jobID) {
if (jobID != null) {
// System.out.println("remove jobID " + job);
// add the computation in the map
ASLSession session = WsUtil.getAslSession(this
.getThreadLocalRequest().getSession());
HashMap<String, String> computationIDMap = (HashMap<String, String>) session
.getAttribute("ComputationIDList");
String computationId = computationIDMap.get(jobID);
if (computationId != null) {
computationIDMap.remove(jobID);
session.setAttribute("ComputationIDList", computationIDMap);
return computationId;
}
}
return null;
}
private String startComputation(String algorithmName,
List<Parameter> parameters, ComputationOutput outputData)
throws Exception {
return startComputation(algorithmName, parameters, outputData, null);
}
private String startComputation(String algorithmName,
List<Parameter> parameters, ComputationOutput outputData,
String jobID) 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();
updateJobStatus(jobID, "computation started");
updateJob(jobID, computationId);
logger.info("startComputation->The computation has started!");
while (percentage < 100) {
percentage = checkComputationStatus(scope, computationId,
username, outputData);
Thread.sleep(3000);
}
logger.info("startComputation->The computation has finished!");
updateJobStatus(jobID, "computation finished");
removeJob(jobID);
return computationId;
} catch (Exception e) {
logger.info("startComputation->The job submit has failed!");
// e.printStackTrace();
throw e;
}
}
private float checkComputationStatus(String scope, String computationId,
String user, ComputationOutput outputData) throws Exception {
// System.out.println("checkComputation " + computationId);
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);
}
// remove the computation
public Boolean removeComputation(String uidSubmitQuery) throws Exception {
// System.out.println("server UID: " + uidSubmitQuery);
String computationId = null;
if ((uidSubmitQuery != null) && (!(uidSubmitQuery.equals("")))) {
// get job status
// ASLSession session = WsUtil.getAslSession(this
// .getThreadLocalRequest().getSession());
// HashMap<String, String> JobStatusMap = (HashMap<String, String>)
// session
// .getAttribute("JobStatusList");
// String status = JobStatusMap.get(uidSubmitQuery);
String status = getJobStatus(uidSubmitQuery);
if (status == null) {
// the computation has not started
while (computationId == null) {
computationId = removeJob(uidSubmitQuery);
}
} else if (status.equals("computation started")) {
// the computation has started
computationId = removeJob(uidSubmitQuery);
}
}
if (computationId != null) {
StatisticalManagerFactory factory = getFactory();
try {
factory.removeComputation(computationId);
} catch (Exception e) {
e.printStackTrace();
logger.info("Could not remove the computation ID "
+ computationId + " corresponding to jobID "
+ uidSubmitQuery);
logger.error(e);
}
}
// remove job status
removeJobStatus(uidSubmitQuery);
return (new Boolean(true));
}
public void refreshDataOnServer(String submitQueryUID) {
if ((submitQueryUID != null) && (!submitQueryUID.equals(""))) {
removeResultParsed(submitQueryUID);
removeResult(submitQueryUID);
}
}
}