408 lines
12 KiB
Java
408 lines
12 KiB
Java
package org.gcube.dataaccess.algorithms.drmalgorithms;
|
|
|
|
import java.io.File;
|
|
import java.io.IOException;
|
|
import java.io.UnsupportedEncodingException;
|
|
import java.net.URLDecoder;
|
|
import java.net.URLEncoder;
|
|
import java.util.ArrayList;
|
|
import java.util.HashMap;
|
|
import java.util.Iterator;
|
|
import java.util.LinkedHashMap;
|
|
import java.util.List;
|
|
import java.util.UUID;
|
|
|
|
import org.gcube.common.scope.api.ScopeProvider;
|
|
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
|
import org.gcube.dataaccess.databases.access.DatabasesDiscoverer;
|
|
import org.gcube.dataaccess.databases.resources.DBResource;
|
|
import org.gcube.dataaccess.databases.utils.DatabaseManagement;
|
|
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
|
|
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
|
|
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
|
|
import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
|
|
import org.gcube.resources.discovery.client.api.DiscoveryException;
|
|
import org.gcube.resources.discovery.client.api.InvalidResultException;
|
|
import org.hibernate.HibernateException;
|
|
import org.hibernate.SessionFactory;
|
|
|
|
/**
|
|
* Class that allows to perform a sample operation on a table of a chosen
|
|
* database. It retrieves the first 100 rows of a table.
|
|
*/
|
|
public class SampleOnTable extends StandardLocalExternalAlgorithm {
|
|
|
|
private LinkedHashMap<String, StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
|
|
|
|
// object that allows to manage some operations on a database
|
|
private DatabaseManagement mgt;
|
|
// database's parameters specified by the user
|
|
private String resourceName = null;
|
|
private String databaseName = null;
|
|
private String schemaName = null;
|
|
private String tableName = null;
|
|
|
|
private SessionFactory sf;
|
|
// variable that keeps track of the driver information
|
|
private String driverInfo;
|
|
|
|
@Override
|
|
public void init() throws Exception {
|
|
|
|
mgt = new DatabaseManagement(config.getConfigPath());
|
|
AnalysisLogger.getLogger().debug("In SampleOnTable->Initialization");
|
|
|
|
String scope = config.getGcubeScope();
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->scope set by config object: " + scope);
|
|
|
|
if (scope == null || scope.length() == 0) {
|
|
scope = ScopeProvider.instance.get();
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->scope set by ScopeProvider: " + scope);
|
|
} else {
|
|
ScopeProvider.instance.set(scope);
|
|
}
|
|
}
|
|
|
|
@Override
|
|
public String getDescription() {
|
|
return "Algorithm that allows to perform a sample operation on a table";
|
|
}
|
|
|
|
@Override
|
|
protected void process() throws Exception {
|
|
AnalysisLogger.getLogger().debug("In SampleOnTable->Processing");
|
|
|
|
try {
|
|
// retrieve information
|
|
List<String> Info = retrieveInfo();
|
|
|
|
// check on table name field
|
|
tableName = getInputParameter("TableName");
|
|
if(tableName != null){
|
|
tableName = getInputParameter("TableName").trim();
|
|
}
|
|
if ((tableName == null) || (tableName.equals(""))) {
|
|
throw new Exception("Warning: insert the table name");
|
|
}
|
|
|
|
// check on schema name field
|
|
if (driverInfo.toLowerCase().contains("postgres")) {
|
|
schemaName = getInputParameter("SchemaName");
|
|
if(schemaName != null){
|
|
schemaName = getInputParameter("SchemaName").trim();
|
|
}
|
|
if ((schemaName == null) || (schemaName.equals(""))) {
|
|
throw new Exception("Warning: insert the schema name");
|
|
}
|
|
}
|
|
|
|
// create the connection
|
|
getConnection(Info);
|
|
|
|
// sample operation on table
|
|
map = sampleOnTable();
|
|
|
|
} catch (HibernateException h) {
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable-> ERROR " + h.getMessage());
|
|
throw h;
|
|
}
|
|
|
|
catch (IllegalStateException e) {
|
|
// e.printStackTrace();
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable-> ERROR " + e.getMessage());
|
|
throw e;
|
|
|
|
} catch (DiscoveryException e1) {
|
|
// e1.printStackTrace();
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable-> ERROR " + e1.getMessage());
|
|
throw e1;
|
|
|
|
} catch (InvalidResultException e2) {
|
|
// e2.printStackTrace();
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable-> ERROR " + e2.getMessage());
|
|
throw e2;
|
|
|
|
} catch (IOException e3) {
|
|
// e3.printStackTrace();
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable-> ERROR " + e3.getMessage());
|
|
throw e3;
|
|
}
|
|
|
|
catch (Exception e4) {
|
|
// e4.printStackTrace();
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable-> Exception " + e4.getMessage());
|
|
throw e4;
|
|
|
|
} finally {
|
|
// close the connection
|
|
mgt.closeConnection();
|
|
}
|
|
}
|
|
|
|
@Override
|
|
protected void setInputParameters() {
|
|
// parameters specified by the user
|
|
addStringInput("ResourceName", "The name of the resource", "");
|
|
addStringInput("DatabaseName", "The name of the database", "");
|
|
addStringInput("SchemaName", "The name of the schema", "");
|
|
addStringInput("TableName", "The name of the table", "");
|
|
}
|
|
|
|
public StatisticalType getOutput() {
|
|
|
|
AnalysisLogger.getLogger()
|
|
.debug("In SampleOnTable->retrieving outputs");
|
|
|
|
// generate a primitive type for the collection
|
|
PrimitiveType output = new PrimitiveType(LinkedHashMap.class.getName(),
|
|
map, PrimitiveTypes.MAP, "ResultsMap"+UUID.randomUUID(), "Results Map");
|
|
|
|
return output;
|
|
}
|
|
|
|
@Override
|
|
public void shutdown() {
|
|
AnalysisLogger.getLogger().debug("In SampleOnTable->Shutdown");
|
|
|
|
}
|
|
|
|
// Method that recovers the info useful for the connection
|
|
private List<String> retrieveInfo() throws Exception,
|
|
IllegalStateException, DiscoveryException, InvalidResultException {
|
|
|
|
resourceName = getInputParameter("ResourceName");
|
|
|
|
if (resourceName != null) {
|
|
resourceName = getInputParameter("ResourceName").trim();
|
|
}
|
|
|
|
if ((resourceName == null) || (resourceName.equals(""))) {
|
|
throw new Exception("Warning: insert the resource name");
|
|
}
|
|
|
|
databaseName = getInputParameter("DatabaseName");
|
|
|
|
if (databaseName != null) {
|
|
databaseName = getInputParameter("DatabaseName").trim();
|
|
}
|
|
if ((databaseName == null) || (databaseName.equals(""))) {
|
|
throw new Exception("Warning: insert the database name");
|
|
}
|
|
|
|
// retrieve the chosen resource
|
|
DatabasesDiscoverer discovery = new DatabasesDiscoverer();
|
|
List<DBResource> resources = discovery.discover();
|
|
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->number of elements: " + resources.size());
|
|
|
|
// list that contains information useful for the connection
|
|
List<String> info = new ArrayList<String>();
|
|
|
|
check: for (int i = 0; i < resources.size(); i++) {
|
|
if (resources.get(i).getResourceName().toLowerCase()
|
|
.equals(resourceName.toLowerCase())) {
|
|
normalizeDBInfo(resources.get(i));
|
|
for (int j = 0; j < resources.get(i).getAccessPoints().size(); j++) {
|
|
|
|
if (resources.get(i).getAccessPoints().get(j)
|
|
.getDatabaseName().toLowerCase()
|
|
.equals(databaseName.toLowerCase())) {
|
|
|
|
info.add(resources.get(i).getAccessPoints().get(j)
|
|
.getUsername());
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->username: "
|
|
+ resources.get(i).getAccessPoints()
|
|
.get(j).getUsername());
|
|
|
|
info.add(resources.get(i).getAccessPoints().get(j)
|
|
.getPassword());
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->password: "
|
|
+ resources.get(i).getAccessPoints()
|
|
.get(j).getPassword());
|
|
|
|
info.add(resources.get(i).getAccessPoints().get(j)
|
|
.getDriver());
|
|
driverInfo = resources.get(i).getAccessPoints().get(j)
|
|
.getDriver();
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->driver: "
|
|
+ resources.get(i).getAccessPoints()
|
|
.get(j).getDriver());
|
|
|
|
// driverInfo =
|
|
// resources.get(i).getAccessPoints().get(j)
|
|
// .getDriver();
|
|
|
|
info.add(resources.get(i).getAccessPoints().get(j)
|
|
.getDialect());
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->dialect: "
|
|
+ resources.get(i).getAccessPoints()
|
|
.get(j).getDialect());
|
|
|
|
info.add(resources.get(i).getAccessPoints().get(j)
|
|
.address());
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->url: "
|
|
+ resources.get(i).getAccessPoints()
|
|
.get(j).address());
|
|
|
|
info.add(databaseName);
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->databasename: "
|
|
+ resources.get(i).getAccessPoints()
|
|
.get(j).getDatabaseName());
|
|
break check;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
AnalysisLogger
|
|
.getLogger()
|
|
.debug("In SampleOnTable->information useful for connection: retrieved");
|
|
|
|
return info;
|
|
}
|
|
|
|
// to normalize the information related to a database
|
|
private void normalizeDBInfo(DBResource resource) throws Exception {
|
|
|
|
try{
|
|
int ap = resource.getAccessPoints().size();
|
|
|
|
for (int i = 0; i < ap; i++) {
|
|
resource.normalize(i);
|
|
}
|
|
|
|
}catch (Exception e) {
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->: Error in normalization process"
|
|
+ e.getMessage());
|
|
|
|
throw e;
|
|
}
|
|
|
|
// int ap = resource.getAccessPoints().size();
|
|
// for (int i = 0; i < ap; i++) {
|
|
// try {
|
|
// resource.normalize(i);
|
|
// } catch (IOException e) {
|
|
// // e.printStackTrace();
|
|
// AnalysisLogger.getLogger().debug(
|
|
// "In SampleOnTable->: Error in normalization process"
|
|
// + e.getMessage());
|
|
// throw e;
|
|
// }
|
|
// }
|
|
}
|
|
|
|
// create the database's connection
|
|
private void getConnection(List<String> Info) throws IOException {
|
|
|
|
// create the connection
|
|
Iterator<String> iterator = Info.iterator();
|
|
|
|
String DatabaseUserName = iterator.next();
|
|
String DatabasePassword = iterator.next();
|
|
String DatabaseDriver = iterator.next();
|
|
String DatabaseDialect = iterator.next();
|
|
String DatabaseURL = iterator.next();
|
|
String DatabaseName = iterator.next();
|
|
|
|
mgt.createConnection(DatabaseUserName,
|
|
DatabasePassword, DatabaseDriver, DatabaseDialect, DatabaseURL,
|
|
DatabaseName);
|
|
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->database " + DatabaseName + ": connected");
|
|
}
|
|
|
|
// to perform the sample operation on the table
|
|
private LinkedHashMap<String, StatisticalType> sampleOnTable()
|
|
throws Exception {
|
|
|
|
LinkedHashMap<String, StatisticalType> mapResults = new LinkedHashMap<String, StatisticalType>();
|
|
AnalysisLogger.getLogger().debug(
|
|
"In SampleOnTable->starting the sample operation on table");
|
|
|
|
// sample on table operation
|
|
// List<Object> resultSet = null;
|
|
|
|
if (driverInfo.toLowerCase().contains("postgres")) {
|
|
// for a postgres database the second parameter is the schema name
|
|
// resultSet = mgt.sampleOnTable(tableName, schemaName,
|
|
// config.getPersistencePath());
|
|
mgt.sampleOnTable(tableName, schemaName,
|
|
config.getPersistencePath());
|
|
}
|
|
|
|
if (driverInfo.toLowerCase().contains("mysql")) {
|
|
// for a mysql database the second parameter is the database name
|
|
// resultSet = mgt.sampleOnTable(tableName, databaseName,
|
|
// config.getPersistencePath());
|
|
mgt.sampleOnTable(tableName, databaseName,
|
|
config.getPersistencePath());
|
|
}
|
|
|
|
AnalysisLogger.getLogger().debug("In SampleOnTable->result retrieved");
|
|
|
|
// to add the results to the variable map
|
|
// to add the map
|
|
|
|
HashMap<String, String> mapResult = new HashMap<String, String>();
|
|
mapResult = mgt.getMapSampleTableResult();
|
|
|
|
String encoded = null;
|
|
encoded = new String(mapResult.get("HEADERS").getBytes(), "UTF-8");
|
|
|
|
// // check encoded value
|
|
//
|
|
// AnalysisLogger.getLogger().debug(
|
|
// "In SampleOnTable->string encoded: " + encoded);
|
|
|
|
PrimitiveType val = new PrimitiveType(String.class.getName(), encoded,
|
|
PrimitiveTypes.STRING, "Row", "Row");
|
|
mapResults.put("HEADERS", val);
|
|
|
|
for (int i = 0; i < mapResult.size() - 1; i++) {
|
|
encoded = new String(mapResult.get(String.valueOf(i)).getBytes(),
|
|
"UTF-8");
|
|
|
|
// // check encoded value
|
|
// AnalysisLogger.getLogger().debug(
|
|
// "In SampleOnTable->string encoded: " + encoded);
|
|
|
|
PrimitiveType val1 = new PrimitiveType(String.class.getName(),
|
|
encoded, PrimitiveTypes.STRING, "Row", "Row");
|
|
mapResults.put(String.valueOf(i), val1);
|
|
// //check value contained in the map
|
|
// String value = (String) val1.getContent();
|
|
//
|
|
// AnalysisLogger.getLogger().debug(
|
|
// "In SampleOnTable->value: " + value);
|
|
|
|
}
|
|
|
|
// to add the file
|
|
PrimitiveType fileResult = new PrimitiveType(File.class.getName(),
|
|
mgt.getFile(), PrimitiveTypes.FILE, "File",
|
|
"File");
|
|
mapResults.put("File", fileResult);
|
|
|
|
return mapResults;
|
|
|
|
}
|
|
}
|