git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/application/perform-service@176830 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
decc90cccd
commit
c060f291ce
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@ -4,6 +4,9 @@
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<wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
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<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
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<wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
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<dependent-module archiveName="data-miner-manager-cl-1.6.0-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/data-miner-manager-cl/data-miner-manager-cl">
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<dependency-type>uses</dependency-type>
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</dependent-module>
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<property name="context-root" value="perform-service"/>
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<property name="java-output-path" value="/perform-service/target/classes"/>
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</wb-module>
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@ -4,6 +4,7 @@ import java.io.IOException;
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import java.sql.SQLException;
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import java.util.Map;
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import org.gcube.application.perform.service.engine.dm.DMException;
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import org.gcube.application.perform.service.engine.model.CSVExportRequest;
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import org.gcube.application.perform.service.engine.model.InternalException;
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import org.gcube.application.perform.service.engine.model.InvalidRequestException;
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@ -13,5 +14,5 @@ public interface PerformanceManager {
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public Map<String,String> generateCSV(CSVExportRequest request)throws SQLException, InvalidRequestException, InternalException, IOException;
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public void loadOutputData(ImportRoutineDescriptor desc)throws SQLException, InvalidRequestException, InternalException, IOException;
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public void loadOutputData(ImportRoutineDescriptor desc)throws SQLException, InvalidRequestException, InternalException, IOException, DMException;
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}
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@ -0,0 +1,130 @@
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package org.gcube.application.perform.service.engine.dm;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.Timer;
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import org.gcube.data.analysis.dataminermanagercl.server.dmservice.SClient;
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import org.gcube.data.analysis.dataminermanagercl.server.monitor.DMMonitor;
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import org.gcube.data.analysis.dataminermanagercl.server.monitor.DMMonitorListener;
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import org.gcube.data.analysis.dataminermanagercl.server.monitor.DMMonitorTask;
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import org.gcube.data.analysis.dataminermanagercl.shared.data.computations.ComputationId;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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public class AsynchDMMonitor extends DMMonitor {
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private static final Logger log= LoggerFactory.getLogger(AsynchDMMonitor.class);
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private int sleep = 2000; // Sleep duration in millisecond
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private int delay = 2000; // Delay on first check in millisecond
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private int period = 2000;// Interval between monitoring requests in millisecond
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private ComputationId computationId;
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private SClient sClient;
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private ArrayList<DMMonitorListener> listeners = new ArrayList<DMMonitorListener>();
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private Timer timer;
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private boolean notEnd;
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public AsynchDMMonitor(ComputationId computationId, SClient sClient) {
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super(computationId, sClient);
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this.computationId = computationId;
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this.sClient = sClient;
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}
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@Override
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public void start() {
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throw new RuntimeException("Unecpetcted call to start() method");
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}
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public void startAsynch() throws DMException {
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try {
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log.debug("Start Monitoring");
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notEnd = true;
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timer = new Timer(false);
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DMMonitorTask dmMonitorTask = new DMMonitorTask(this,
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computationId, sClient, listeners);
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log.debug("Start: " + new Date());
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timer.schedule(dmMonitorTask, delay, period);
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log.debug("Scheduled.");
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} catch (Throwable e) {
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throw new DMException(e);
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}
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}
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public void add(DMMonitorListener listener) {
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listeners.add(listener);
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}
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public void addAll(ArrayList<DMMonitorListener> listeners) {
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this.listeners.addAll(listeners);
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}
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public void cancel() {
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if (timer != null)
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timer.cancel();
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notEnd = false;
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}
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/**
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*
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* @return Sleep duration in millisecond
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*/
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public int getSleep() {
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return sleep;
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}
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/**
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*
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* @param sleep Sleep duration in millisecond
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*/
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public void setSleep(int sleep) {
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this.sleep = sleep;
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}
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/**
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*
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* @return Delay on first check in millisecond
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*/
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public int getDelay() {
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return delay;
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}
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/**
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*
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* @param delay Delay on first check in millisecond
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*/
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public void setDelay(int delay) {
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this.delay = delay;
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}
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/**
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*
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* @return Interval between monitoring requests in millisecond
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*/
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public int getPeriod() {
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return period;
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}
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/**
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*
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* @param period Interval between monitoring requests in millisecond
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*/
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public void setPeriod(int period) {
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this.period = period;
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}
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}
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@ -1,5 +1,7 @@
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package org.gcube.application.perform.service.engine.dm;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import org.gcube.application.perform.service.engine.model.importer.ImportRoutineDescriptor;
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@ -7,7 +9,11 @@ import org.gcube.data.analysis.dataminermanagercl.server.DataMinerService;
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import org.gcube.data.analysis.dataminermanagercl.server.dmservice.SClient;
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import org.gcube.data.analysis.dataminermanagercl.server.monitor.DMMonitor;
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import org.gcube.data.analysis.dataminermanagercl.server.monitor.DMMonitorListener;
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import org.gcube.data.analysis.dataminermanagercl.shared.data.OutputData;
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import org.gcube.data.analysis.dataminermanagercl.shared.data.computations.ComputationId;
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import org.gcube.data.analysis.dataminermanagercl.shared.data.output.FileResource;
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import org.gcube.data.analysis.dataminermanagercl.shared.data.output.MapResource;
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import org.gcube.data.analysis.dataminermanagercl.shared.data.output.Resource;
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import org.gcube.data.analysis.dataminermanagercl.shared.parameters.Parameter;
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import org.gcube.data.analysis.dataminermanagercl.shared.process.Operator;
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import org.slf4j.Logger;
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@ -17,60 +23,87 @@ import org.slf4j.LoggerFactory;
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public class DMUtils {
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private static final Logger log= LoggerFactory.getLogger(DMUtils.class);
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public static SClient getClient() throws DMException {
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try {
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return new DataMinerService().getClient();
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return new DataMinerService().getClient();
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}catch(Exception e) {
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throw new DMException(e);
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}
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}
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public static ComputationId getComputation(ImportRoutineDescriptor desc) {
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return new ComputationId(desc.getComputationId(), desc.getComputationUrl(), desc.getComputationOperator(), desc.getComputationOperatorName(), desc.getComputationRequest());
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}
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public static void monitor(SClient client,ComputationId computationId,DMMonitorListener listener) {
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DMMonitor monitor=new DMMonitor(computationId,client);
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monitor.add(listener);
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monitor.start();
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}
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public static void monitor(ComputationId computationId,DMMonitorListener listener) throws DMException {
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DMMonitor monitor=new DMMonitor(computationId,getClient());
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AsynchDMMonitor monitor=new AsynchDMMonitor(computationId,getClient());
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monitor.add(listener);
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monitor.start();
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monitor.startAsynch();
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}
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public static ComputationId submitJob(String operatorId, Map<String,String> parameters) throws DMException {
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return submitJob(getClient(),operatorId,parameters);
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}
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public static ComputationId submitJob(SClient client, String operatorId, Map<String,String> parameters) throws DMException {
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try {
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log.debug("Looking for operator by Id {} ",operatorId);
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Operator op=client.getOperatorById(operatorId);
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log.debug("Preparing parameters, values : {} ",parameters);
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for(Parameter param:op.getOperatorParameters()) {
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String paramName=param.getName();
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if(parameters.containsKey(paramName))
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param.setValue(parameters.get(paramName));
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}
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log.debug("Looking for operator by Id {} ",operatorId);
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Operator op=client.getOperatorById(operatorId);
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log.info("Submitting Operator {} to DM",op);
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return client.startComputation(op);
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List<Parameter> params=client.getInputParameters(op);
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log.debug("Preparing parameters, values : {} ",parameters);
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for(Parameter param:params) {
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String paramName=param.getName();
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if(parameters.containsKey(paramName))
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param.setValue(parameters.get(paramName));
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}
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op.setOperatorParameters(params);
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log.info("Submitting Operator {} to DM",op);
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return client.startComputation(op);
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}catch(Exception e) {
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throw new DMException(e);
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}
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}
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public static final Map<String,String> getOutputFiles(ComputationId computationId){
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throw new RuntimeException("Missing Implementation");
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public static final Map<String,String> getOutputFiles(ComputationId computationId) throws DMException{
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try{
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Map<String,String> toReturn=new HashMap<String,String>();
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SClient client=getClient();
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OutputData data=client.getOutputDataByComputationId(computationId);
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Resource resource = data.getResource();
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if (resource.isMap()) {
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MapResource mapResource = (MapResource) resource;
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for (String key : mapResource.getMap().keySet()) {
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Resource res = mapResource.getMap().get(key);
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switch (res.getResourceType()) {
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case FILE:
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FileResource fileResource = (FileResource) res;
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toReturn.put(fileResource.getDescription(), fileResource.getUrl());
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break;
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}
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}
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}
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return toReturn;
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}catch(Exception e) {
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throw new DMException(e);
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}
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}
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}
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@ -4,7 +4,6 @@ import java.sql.Connection;
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import java.sql.PreparedStatement;
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import java.sql.Timestamp;
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import java.time.Instant;
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import java.util.Map;
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import javax.inject.Inject;
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@ -14,11 +13,9 @@ import org.gcube.application.perform.service.engine.impl.Queries;
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import org.gcube.application.perform.service.engine.model.DBField;
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import org.gcube.application.perform.service.engine.model.DBField.ImportRoutine;
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import org.gcube.application.perform.service.engine.model.DBQueryDescriptor;
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import org.gcube.application.perform.service.engine.model.ISQueryDescriptor;
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import org.gcube.application.perform.service.engine.model.importer.ImportRoutineDescriptor;
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import org.gcube.application.perform.service.engine.model.importer.ImportStatus;
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import org.gcube.data.analysis.dataminermanagercl.server.monitor.DMMonitorListener;
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import org.gcube.data.analysis.dataminermanagercl.shared.data.computations.ComputationId;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@ -27,16 +24,17 @@ public class ImporterMonitor implements DMMonitorListener {
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private static final Logger log= LoggerFactory.getLogger(ImporterMonitor.class);
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@Inject
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private PerformanceManager performance;
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public ImporterMonitor(ImportRoutineDescriptor routine) {
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super();
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this.routine = routine;
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}
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private ImportRoutineDescriptor routine;
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public ImporterMonitor(PerformanceManager performance, ImportRoutineDescriptor routine) {
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super();
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this.performance = performance;
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this.routine = routine;
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}
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@Override
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public void accepted() {
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@ -50,10 +48,12 @@ public class ImporterMonitor implements DMMonitorListener {
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@Override
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public void complete(double percentage) {
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updateStatus(ImportStatus.COMPLETE,routine);
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try{
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performance.loadOutputData(routine);
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updateStatus(ImportStatus.COMPLETE,routine);
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log.debug("Completed monitoring of {} ",routine);
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}catch(Throwable t) {
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log.error("Unable to load output data for "+routine,t);
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updateStatus(ImportStatus.FAILED,routine);
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}
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}
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@ -102,12 +102,5 @@ public class ImporterMonitor implements DMMonitorListener {
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}
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private static final void loadOutputData(ImportRoutineDescriptor routine, ISQueryDescriptor is) {
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log.debug("Loading output data for {} ",routine);
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ComputationId id=DMUtils.getComputation(routine);
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Map<String,String> outputFiles=DMUtils.getOutputFiles(id);
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// if(outputFiles.containsKey(Local))
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}
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}
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@ -11,9 +11,12 @@ import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import javax.inject.Inject;
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import org.gcube.application.perform.service.LocalConfiguration;
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import org.gcube.application.perform.service.engine.DataBaseManager;
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import org.gcube.application.perform.service.engine.Importer;
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import org.gcube.application.perform.service.engine.PerformanceManager;
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import org.gcube.application.perform.service.engine.dm.DMException;
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import org.gcube.application.perform.service.engine.dm.DMUtils;
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import org.gcube.application.perform.service.engine.dm.ImporterMonitor;
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@ -22,6 +25,7 @@ import org.gcube.application.perform.service.engine.model.DBField;
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import org.gcube.application.perform.service.engine.model.DBField.ImportRoutine;
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import org.gcube.application.perform.service.engine.model.DBQueryDescriptor;
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import org.gcube.application.perform.service.engine.model.InternalException;
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import org.gcube.application.perform.service.engine.model.InvalidRequestException;
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import org.gcube.application.perform.service.engine.model.importer.ImportRequest;
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import org.gcube.application.perform.service.engine.model.importer.ImportRoutineDescriptor;
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import org.gcube.application.perform.service.engine.model.importer.ImportStatus;
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@ -40,7 +44,8 @@ public class ImporterImpl implements Importer {
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private static final Logger log= LoggerFactory.getLogger(ImporterImpl.class);
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@Inject
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private PerformanceManager performance;
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||||
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@ -67,15 +72,15 @@ public class ImporterImpl implements Importer {
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try {
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conn.setAutoCommit(true);
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String hostname=getHostname();
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DBField lockField=ImportRoutine.fields.get(ImportRoutine.LOCK);
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PreparedStatement psOrphans=Queries.ORPHAN_IMPORTS.get(conn,new DBQueryDescriptor(lockField, hostname));
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PreparedStatement psAcquire=Queries.ACQUIRE_IMPORT_ROUTINE.prepare(conn);
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// set ps
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||||
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||||
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||||
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||||
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||||
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||||
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ResultSet rsOrphans=psOrphans.executeQuery();
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long monitoredCount=0l;
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while(rsOrphans.next()) {
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@ -127,13 +132,13 @@ public class ImporterImpl implements Importer {
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private void monitor(ImportRoutineDescriptor desc) throws DMException {
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log.debug("Monitoring {} ",desc);
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DMUtils.monitor(DMUtils.getComputation(desc), new ImporterMonitor(desc));
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DMUtils.monitor(DMUtils.getComputation(desc), new ImporterMonitor(performance,desc));
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}
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||||
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||||
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||||
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||||
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private ComputationId submit(ImportRequest request) throws DMException {
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private ComputationId submit(ImportRequest request) throws DMException, InvalidRequestException {
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/**
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* dataminer-prototypes.d4science.org/wps/WebProcessingService?
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* request=Execute&service=WPS&Version=1.0.0&gcube-token=***REMOVED***&lang=en-US&
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@ -145,11 +150,15 @@ public class ImporterImpl implements Importer {
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* FarmID=ID
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*/
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log.debug("Preparing DM Parameters from request : {} ",request);
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Map<String,String> parameters=new HashMap<>();
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parameters.put("InputData", request.getSource());
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parameters.put("BatchType", request.getBatchType());
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parameters.put("FarmID", request.getFarmId().toString());
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||||
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||||
try {
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parameters.put("InputData", request.getSource());
|
||||
parameters.put("BatchType", request.getBatchType());
|
||||
parameters.put("FarmID", request.getFarmId().toString());
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}catch(Throwable t) {
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throw new InvalidRequestException("Invalid request : "+request,t);
|
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}
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return DMUtils.submitJob(LocalConfiguration.getProperty(LocalConfiguration.IMPORTER_COMPUTATION_ID), parameters);
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}
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||||
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||||
|
|
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@ -1,8 +1,11 @@
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package org.gcube.application.perform.service.engine.impl;
|
||||
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||||
import java.io.BufferedReader;
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||||
import java.io.FileReader;
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||||
import java.io.IOException;
|
||||
import java.io.InputStreamReader;
|
||||
import java.io.Reader;
|
||||
import java.net.URL;
|
||||
import java.sql.Connection;
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||||
import java.sql.PreparedStatement;
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||||
import java.sql.ResultSet;
|
||||
|
|
@ -10,6 +13,7 @@ import java.sql.SQLException;
|
|||
import java.sql.Statement;
|
||||
import java.sql.Timestamp;
|
||||
import java.sql.Types;
|
||||
import java.time.Instant;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
|
|
@ -23,6 +27,7 @@ import org.apache.commons.csv.CSVRecord;
|
|||
import org.gcube.application.perform.service.LocalConfiguration;
|
||||
import org.gcube.application.perform.service.engine.DataBaseManager;
|
||||
import org.gcube.application.perform.service.engine.PerformanceManager;
|
||||
import org.gcube.application.perform.service.engine.dm.DMException;
|
||||
import org.gcube.application.perform.service.engine.dm.DMUtils;
|
||||
import org.gcube.application.perform.service.engine.model.CSVExportRequest;
|
||||
import org.gcube.application.perform.service.engine.model.DBField;
|
||||
|
|
@ -39,16 +44,16 @@ import org.slf4j.LoggerFactory;
|
|||
|
||||
public class PerformanceManagerImpl implements PerformanceManager{
|
||||
|
||||
|
||||
|
||||
private static final Logger log= LoggerFactory.getLogger(PerformanceManagerImpl.class);
|
||||
|
||||
|
||||
private static Map<AnalysisType,Set<ImportedTable>> analysisConfiguration=new HashMap<>();
|
||||
|
||||
|
||||
public static Map<AnalysisType, Set<ImportedTable>> getAnalysisConfiguration() {
|
||||
return analysisConfiguration;
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public Map<String, String> generateCSV(CSVExportRequest request) throws SQLException, InvalidRequestException, InternalException, IOException {
|
||||
log.trace("Serving {} ",request);
|
||||
|
|
@ -66,7 +71,7 @@ public class PerformanceManagerImpl implements PerformanceManager{
|
|||
}
|
||||
|
||||
@Override
|
||||
public void loadOutputData(ImportRoutineDescriptor desc) throws SQLException, InvalidRequestException, InternalException, IOException{
|
||||
public void loadOutputData(ImportRoutineDescriptor desc) throws SQLException, InvalidRequestException, InternalException, IOException, DMException{
|
||||
log.info("Importing output for {} ",desc);
|
||||
ComputationId computation=DMUtils.getComputation(desc);
|
||||
Map<String,String> outputs=DMUtils.getOutputFiles(computation);
|
||||
|
|
@ -75,10 +80,12 @@ public class PerformanceManagerImpl implements PerformanceManager{
|
|||
for(Entry<String,String> entry:outputs.entrySet()) {
|
||||
parse(entry.getValue(),entry.getKey(),desc,conn);
|
||||
}
|
||||
log.info("IMPORTED ALL FILES for {}, gonna clean previous routines output. ",desc);
|
||||
|
||||
log.debug("IMPORTED ALL FILES for {}, gonna clean previous routines output. ",desc);
|
||||
|
||||
removeOlderEquivalents(desc, conn);
|
||||
log.debug("COMMITTING...");
|
||||
conn.commit();
|
||||
log.info("Successfully imported data for {} ",desc);
|
||||
}finally {
|
||||
conn.close();
|
||||
}
|
||||
|
|
@ -99,19 +106,19 @@ public class PerformanceManagerImpl implements PerformanceManager{
|
|||
if(Boolean.parseBoolean(LocalConfiguration.getProperty(LocalConfiguration.COMMIT_SCHEMA)))
|
||||
conn.commit();
|
||||
}
|
||||
|
||||
|
||||
|
||||
public static void importSchema(SchemaDefinition schema,String csvBasePath) throws IOException, SQLException, InternalException {
|
||||
log.info("Loading schema {} ",schema);
|
||||
|
||||
String actualCSVPath=csvBasePath+"/"+schema.getCsvPath();
|
||||
|
||||
|
||||
log.debug("CSV path : {} ",actualCSVPath);
|
||||
|
||||
ArrayList<DBField> csvFieldsDefinition=getCSVFieldsDefinition(actualCSVPath);
|
||||
|
||||
|
||||
ArrayList<DBField> csvFieldsDefinition=getCSVFieldsDefinition(actualCSVPath,schema);
|
||||
|
||||
AnalysisType analysisType=schema.getRelatedAnalysis();
|
||||
|
||||
|
||||
String tablename=(analysisType.getId()+"_"+schema.getRelatedDescription()).toLowerCase().replaceAll(" ", "_");
|
||||
|
||||
|
||||
|
|
@ -127,7 +134,7 @@ public class PerformanceManagerImpl implements PerformanceManager{
|
|||
}
|
||||
|
||||
|
||||
|
||||
|
||||
static Set<ImportedTable> getAnalysisSet(CSVExportRequest request) throws InvalidRequestException{
|
||||
AnalysisType type=request.getType();
|
||||
if(!analysisConfiguration.containsKey(type))
|
||||
|
|
@ -137,15 +144,16 @@ public class PerformanceManagerImpl implements PerformanceManager{
|
|||
|
||||
private static final void removeOlderEquivalents(ImportRoutineDescriptor last,Connection conn) throws SQLException, InvalidRequestException {
|
||||
log.debug("Removing imports replaced by {} ",last);
|
||||
|
||||
|
||||
DBQueryDescriptor desc=new DBQueryDescriptor().
|
||||
add(DBField.ImportRoutine.fields.get(ImportRoutine.BATCH_TYPE),last.getBatch_type()).
|
||||
add(DBField.ImportRoutine.fields.get(ImportRoutine.SOURCE_URL),last.getSourceUrl()).
|
||||
add(DBField.ImportRoutine.fields.get(ImportRoutine.END),new Timestamp(last.getEndTime().toEpochMilli()));
|
||||
|
||||
|
||||
add(DBField.ImportRoutine.fields.get(ImportRoutine.BATCH_TYPE),last.getBatch_type()).
|
||||
add(DBField.ImportRoutine.fields.get(ImportRoutine.SOURCE_URL),last.getSourceUrl()).
|
||||
add(DBField.ImportRoutine.fields.get(ImportRoutine.ID),last.getId()).
|
||||
add(DBField.ImportRoutine.fields.get(ImportRoutine.END),new Timestamp(Instant.now().toEpochMilli()));
|
||||
|
||||
|
||||
ResultSet rsEquivalents=Queries.GET_OLDER_EQUIVALENT_IMPORT_ROUTINE.get(conn, desc).executeQuery();
|
||||
|
||||
|
||||
while(rsEquivalents.next()) {
|
||||
ImportRoutineDescriptor older=Queries.rowToDescriptor(rsEquivalents);
|
||||
log.debug("Removing outputs from {} ",older);
|
||||
|
|
@ -155,17 +163,19 @@ public class PerformanceManagerImpl implements PerformanceManager{
|
|||
table.cleanByImportRoutine(older,conn);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
private static final long parse(String path, String description, ImportRoutineDescriptor routine, Connection conn) throws IOException, SQLException, InvalidRequestException {
|
||||
Reader in = new FileReader(path);
|
||||
URL csvUrl = new URL(path);
|
||||
BufferedReader in = new BufferedReader(new InputStreamReader(csvUrl.openStream()));
|
||||
|
||||
CSVParser parser= CSVFormat.DEFAULT.withFirstRecordAsHeader().parse(in);
|
||||
|
||||
|
||||
AnalysisType type=new AnalysisType(routine);
|
||||
|
||||
|
||||
try {
|
||||
log.debug("Parsing file {} : {} ",description,path);
|
||||
// Extract CSV Schema
|
||||
|
|
@ -205,11 +215,22 @@ public class PerformanceManagerImpl implements PerformanceManager{
|
|||
private static final String INTEGER_REGEX="\\d*";
|
||||
|
||||
|
||||
private static ArrayList<DBField> getCSVFieldsDefinition(String csvFile) throws IOException{
|
||||
private static ArrayList<DBField> getCSVFieldsDefinition(String csvFile,SchemaDefinition schema) throws IOException{
|
||||
|
||||
Reader in = null;
|
||||
CSVParser parser= null;
|
||||
try {
|
||||
HashSet<String> deanonimizationLabels=new HashSet<>();
|
||||
if(schema.getAssociationUUIDField()!=null)
|
||||
deanonimizationLabels.add(schema.getAssociationUUIDField());
|
||||
if(schema.getFarmUUIDField()!=null)
|
||||
deanonimizationLabels.add(schema.getFarmUUIDField());
|
||||
if(schema.getBatchUUIDField()!=null)
|
||||
deanonimizationLabels.add(schema.getBatchUUIDField());
|
||||
if(schema.getCompanyUUIDField()!=null)
|
||||
deanonimizationLabels.add(schema.getCompanyUUIDField());
|
||||
|
||||
|
||||
in=new FileReader(csvFile);
|
||||
parser=CSVFormat.DEFAULT.withFirstRecordAsHeader().parse(in);
|
||||
Map<String,Integer> headers=parser.getHeaderMap();
|
||||
|
|
@ -219,10 +240,15 @@ public class PerformanceManagerImpl implements PerformanceManager{
|
|||
|
||||
for(Entry<String,Integer> header:headers.entrySet()) {
|
||||
String value=record.get(header.getKey());
|
||||
String name=header.getKey();
|
||||
int type=Types.VARCHAR;
|
||||
if(value.matches(FLOAT_REGEX)) type=Types.REAL;
|
||||
else if(value.matches(INTEGER_REGEX)) type=Types.BIGINT;
|
||||
toReturn.add(new DBField(type, header.getKey()));
|
||||
|
||||
//Deanonimized fields will always contain strings
|
||||
if(!deanonimizationLabels.contains(name)) {
|
||||
//NB INT will be managed as real in order to deal with Dataminer output format
|
||||
if(value.matches(FLOAT_REGEX)||value.matches(INTEGER_REGEX)) type=Types.REAL;
|
||||
}
|
||||
toReturn.add(new DBField(type, name));
|
||||
}
|
||||
return toReturn;
|
||||
|
||||
|
|
@ -231,6 +257,6 @@ public class PerformanceManagerImpl implements PerformanceManager{
|
|||
if(parser!=null) parser.close();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -39,9 +39,11 @@ public class Queries {
|
|||
public static final Query GET_OLDER_EQUIVALENT_IMPORT_ROUTINE=new Query("Select * from "+ImportRoutine.TABLE+" WHERE "
|
||||
+ImportRoutine.BATCH_TYPE+"=? AND "
|
||||
+ImportRoutine.SOURCE_URL+"=? AND "
|
||||
+ImportRoutine.END+"<?",
|
||||
+ImportRoutine.ID+"<>? AND "
|
||||
+"("+ImportRoutine.END+"<? OR "+ImportRoutine.END+" IS NULL) ",
|
||||
new DBField[]{DBField.ImportRoutine.fields.get(ImportRoutine.BATCH_TYPE),
|
||||
DBField.ImportRoutine.fields.get(ImportRoutine.SOURCE_URL),
|
||||
DBField.ImportRoutine.fields.get(ImportRoutine.ID),
|
||||
DBField.ImportRoutine.fields.get(ImportRoutine.END)});
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -48,6 +48,13 @@ public class ImportRequest {
|
|||
public void setFarmId(Long farmId) {
|
||||
this.farmId = farmId;
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return "ImportRequest [source=" + source + ", version=" + version + ", batchType=" + batchType + ", farmId="
|
||||
+ farmId + "]";
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -146,6 +146,17 @@ public class ImportRoutineDescriptor {
|
|||
public void setComputationRequest(String computationRequest) {
|
||||
this.computationRequest = computationRequest;
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
return "ImportRoutineDescriptor [id=" + id + ", farmId=" + farmId + ", batch_type=" + batch_type
|
||||
+ ", sourceUrl=" + sourceUrl + ", sourceVersion=" + sourceVersion + ", startTime=" + startTime
|
||||
+ ", endTime=" + endTime + ", status=" + status + ", lock=" + lock + ", caller=" + caller
|
||||
+ ", computationId=" + computationId + ", computationUrl=" + computationUrl + ", computationOperator="
|
||||
+ computationOperator + ", computationOperatorName=" + computationOperatorName + ", computationRequest="
|
||||
+ computationRequest + "]";
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -149,13 +149,18 @@ public class ImportedTable {
|
|||
for(Entry<String,String> csvField:csvRow.entrySet()) {
|
||||
DBField toSetField=labels.get(csvField.getKey());
|
||||
|
||||
Object value=csvField.getValue();
|
||||
Object value=csvField.getValue();
|
||||
if(value!=null)
|
||||
switch(toSetField.getType()) {
|
||||
case Types.BIGINT : value=Long.parseLong((String) value);
|
||||
break;
|
||||
case Types.REAL : value=Double.parseDouble((String) value);
|
||||
break;
|
||||
try {
|
||||
switch(toSetField.getType()) {
|
||||
case Types.BIGINT : value=Long.parseLong((String) value);
|
||||
break;
|
||||
case Types.REAL : value=Double.parseDouble((String) value);
|
||||
break;
|
||||
}
|
||||
}catch(NumberFormatException e) {
|
||||
log.error("Unable to parse field {} value was {} ",csvField.getKey(),csvField.getValue());
|
||||
throw e;
|
||||
}
|
||||
desc.add(toSetField, value);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ import org.slf4j.LoggerFactory;
|
|||
@ManagedBy(PerformServiceManager.class)
|
||||
public class Import {
|
||||
|
||||
private static final Logger log= LoggerFactory.getLogger(Mappings.class);
|
||||
private static final Logger log= LoggerFactory.getLogger(Import.class);
|
||||
|
||||
@Inject
|
||||
private Importer importer;
|
||||
|
|
@ -44,15 +44,23 @@ public class Import {
|
|||
* @param farmid
|
||||
* @param sourceFile
|
||||
*/
|
||||
@POST
|
||||
public void importExcel(@QueryParam(ServiceConstants.Import.BATCH_TYPE_PARAMETER)String batchType,
|
||||
@POST
|
||||
@Produces(MediaType.APPLICATION_JSON)
|
||||
public ImportRoutineDescriptor importExcel(@QueryParam(ServiceConstants.Import.BATCH_TYPE_PARAMETER)String batchType,
|
||||
@QueryParam(ServiceConstants.Import.FARM_ID_PARAMETER)Long farmid,
|
||||
@QueryParam(ServiceConstants.Import.EXCEL_FILE_PARAMETER)String sourceFile,
|
||||
@QueryParam(ServiceConstants.Import.EXCEL_FILE_VERSION_PARAMETER)String sourceVersion) {
|
||||
|
||||
InterfaceCommons.checkMandatory(batchType, ServiceConstants.Import.BATCH_TYPE_PARAMETER);
|
||||
InterfaceCommons.checkMandatory(farmid, ServiceConstants.Import.FARM_ID_PARAMETER);
|
||||
InterfaceCommons.checkMandatory(sourceFile, ServiceConstants.Import.EXCEL_FILE_PARAMETER);
|
||||
InterfaceCommons.checkMandatory(sourceVersion, ServiceConstants.Import.EXCEL_FILE_VERSION_PARAMETER);
|
||||
|
||||
ImportRequest req=new ImportRequest(sourceFile, sourceVersion, batchType, farmid);
|
||||
try {
|
||||
importer.importExcel(new ImportRequest(sourceFile, sourceVersion, batchType, farmid));
|
||||
return importer.importExcel(req);
|
||||
}catch(Throwable t) {
|
||||
log.warn("Unexpected Exception on IMPORT ",t);
|
||||
log.warn("Unexpected Exception on IMPORT "+req,t);
|
||||
throw new WebApplicationException("Unexpected Exception.", t,Response.Status.INTERNAL_SERVER_ERROR);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1 @@
|
|||
,fabio,pc-fabio,25.01.2019 16:45,file:///home/fabio/.config/libreoffice/4;
|
||||
|
|
@ -0,0 +1,68 @@
|
|||
package org.gcube.application.perform.service;
|
||||
|
||||
import java.net.MalformedURLException;
|
||||
import java.nio.file.Paths;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
import java.util.concurrent.Semaphore;
|
||||
|
||||
import org.gcube.application.perform.service.engine.dm.DMException;
|
||||
import org.gcube.application.perform.service.engine.dm.DMUtils;
|
||||
import org.gcube.data.analysis.dataminermanagercl.server.monitor.DMMonitorListener;
|
||||
import org.gcube.data.analysis.dataminermanagercl.shared.data.computations.ComputationId;
|
||||
|
||||
public class DMTests {
|
||||
|
||||
public static void main(String[] args) throws DMException, MalformedURLException {
|
||||
Map<String,String> params=new HashMap<String,String>();
|
||||
TokenSetter.set("/gcube/preprod/preVRE");
|
||||
LocalConfiguration.init(Paths.get("src/main/webapp/WEB-INF/config.properties").toUri().toURL());
|
||||
|
||||
|
||||
|
||||
ComputationId compId=DMUtils.submitJob(LocalConfiguration.getProperty(LocalConfiguration.IMPORTER_COMPUTATION_ID), params);
|
||||
|
||||
final Semaphore sem=new Semaphore(0);
|
||||
|
||||
DMUtils.monitor(compId, new DMMonitorListener() {
|
||||
|
||||
@Override
|
||||
public void running(double percentage) {
|
||||
System.out.println("RUN");
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public void failed(String message, Exception exception) {
|
||||
System.out.println("FAIL");
|
||||
sem.release();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void complete(double percentage) {
|
||||
System.out.println("DONE");
|
||||
sem.release();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void cancelled() {
|
||||
System.out.println("CANC");
|
||||
sem.release();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void accepted() {
|
||||
System.out.println("ACCEPTED");
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
System.out.println("WAITING FOR MONITOR");
|
||||
try {
|
||||
sem.acquire();
|
||||
} catch (InterruptedException e) {
|
||||
}
|
||||
System.out.println("WOKE UP");
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,40 @@
|
|||
package org.gcube.application.perform.service;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.net.MalformedURLException;
|
||||
import java.nio.file.Paths;
|
||||
import java.sql.Connection;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.Map.Entry;
|
||||
import java.util.Set;
|
||||
|
||||
import org.gcube.application.perform.service.engine.DataBaseManager;
|
||||
import org.gcube.application.perform.service.engine.impl.PerformanceManagerImpl;
|
||||
import org.gcube.application.perform.service.engine.model.InternalException;
|
||||
import org.gcube.application.perform.service.engine.model.importer.AnalysisType;
|
||||
import org.gcube.application.perform.service.engine.model.importer.ImportedTable;
|
||||
|
||||
public class DeleteSchema {
|
||||
|
||||
public static void main(String[] args) throws SQLException, IOException, InternalException {
|
||||
|
||||
LocalConfiguration.init(Paths.get("src/main/webapp/WEB-INF/config.properties").toUri().toURL());
|
||||
|
||||
PerformServiceLifecycleManager.initSchema("src/main/webapp/WEB-INF");
|
||||
|
||||
TokenSetter.set("/gcube/preprod/preVRE");
|
||||
|
||||
Connection conn=DataBaseManager.get().getConnection();
|
||||
Statement stmt=conn.createStatement();
|
||||
for(Entry<AnalysisType,Set<ImportedTable>> entry:PerformanceManagerImpl.getAnalysisConfiguration().entrySet()) {
|
||||
for(ImportedTable t:entry.getValue()) {
|
||||
stmt.execute("DROP TABLE "+t.getTableName());
|
||||
}
|
||||
}
|
||||
|
||||
conn.commit();
|
||||
// throw new RuntimeException("Uncomment commit to really perform cleanup");
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -7,18 +7,33 @@ import org.junit.Test;
|
|||
|
||||
public class ImportTests extends CommonTest{
|
||||
|
||||
Long farmid=12682101l;
|
||||
|
||||
@Test
|
||||
public void submit() {
|
||||
/**
|
||||
* http://perform.dev.d4science.org/perform-service/gcube/service/import?
|
||||
* batch_type=HATCHERY_INDIVIDUAL&
|
||||
* farmid=12682101&
|
||||
* source=https://data1-d.d4science.org/shub/E_aUJUbDNzeUlLL29KL2xlZUloWFQ5TEdlZ0ZnZzlNNTVLNUEzeDVRNFVoVHlLMW5DVG5RbVVXVzlYeUUzZWFXRA==
|
||||
* source_version=1.1
|
||||
*/
|
||||
|
||||
WebTarget target=
|
||||
target(ServiceConstants.Import.PATH).
|
||||
queryParam(ServiceConstants.Import.BATCH_TYPE_PARAMETER, "pino").
|
||||
queryParam(ServiceConstants.Import.FARM_ID_PARAMETER, 12682549).
|
||||
queryParam(ServiceConstants.Import.EXCEL_FILE_PARAMETER, "gino").
|
||||
queryParam(ServiceConstants.Import.EXCEL_FILE_VERSION_PARAMETER, "gino2.1");
|
||||
queryParam(ServiceConstants.Import.BATCH_TYPE_PARAMETER, "HATCHERY_INDIVIDUAL").
|
||||
queryParam(ServiceConstants.Import.FARM_ID_PARAMETER, farmid).
|
||||
queryParam(ServiceConstants.Import.EXCEL_FILE_PARAMETER, "https://data1-d.d4science.org/shub/E_aUJUbDNzeUlLL29KL2xlZUloWFQ5TEdlZ0ZnZzlNNTVLNUEzeDVRNFVoVHlLMW5DVG5RbVVXVzlYeUUzZWFXRA==").
|
||||
queryParam(ServiceConstants.Import.EXCEL_FILE_VERSION_PARAMETER, "1.1");
|
||||
|
||||
System.out.println(target.getUri());
|
||||
Response resp=target.request().post(null);
|
||||
System.out.println("Status : "+resp.getStatus() );
|
||||
System.out.println("Status : "+resp.getStatus() );
|
||||
try {
|
||||
Thread.sleep(1000*60*10);
|
||||
} catch (InterruptedException e) {
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -3,19 +3,23 @@ package org.gcube.application.perform.service;
|
|||
import java.io.IOException;
|
||||
import java.net.MalformedURLException;
|
||||
import java.nio.file.Paths;
|
||||
import java.sql.ResultSet;
|
||||
import java.sql.SQLException;
|
||||
import java.util.Arrays;
|
||||
|
||||
import org.gcube.application.perform.service.engine.DataBaseManager;
|
||||
import org.gcube.application.perform.service.engine.PerformanceManager;
|
||||
import org.gcube.application.perform.service.engine.impl.ExportCSVQuery;
|
||||
import org.gcube.application.perform.service.engine.dm.DMException;
|
||||
import org.gcube.application.perform.service.engine.impl.ImporterImpl;
|
||||
import org.gcube.application.perform.service.engine.impl.PerformanceManagerImpl;
|
||||
import org.gcube.application.perform.service.engine.model.CSVExportRequest;
|
||||
import org.gcube.application.perform.service.engine.impl.Queries;
|
||||
import org.gcube.application.perform.service.engine.model.DBField;
|
||||
import org.gcube.application.perform.service.engine.model.DBQueryDescriptor;
|
||||
import org.gcube.application.perform.service.engine.model.InternalException;
|
||||
import org.gcube.application.perform.service.engine.model.importer.AnalysisType;
|
||||
import org.gcube.application.perform.service.engine.model.importer.ImportRoutineDescriptor;
|
||||
|
||||
public class LoadSchemaTest {
|
||||
|
||||
public static void main(String[] args) throws MalformedURLException, IOException, SQLException, InternalException {
|
||||
public static void main(String[] args) throws MalformedURLException, IOException, SQLException, InternalException, DMException {
|
||||
LocalConfiguration.init(Paths.get("src/main/webapp/WEB-INF/config.properties").toUri().toURL());
|
||||
|
||||
PerformServiceLifecycleManager.initSchema("src/main/webapp/WEB-INF");
|
||||
|
|
@ -25,13 +29,32 @@ public class LoadSchemaTest {
|
|||
|
||||
|
||||
PerformanceManager mng =new PerformanceManagerImpl();
|
||||
CSVExportRequest req=new CSVExportRequest(new AnalysisType("GROW_OUT_AGGREGATED", "GROW_OUT_AGGREGATED"));
|
||||
req.addAreas(Arrays.asList("A1","A2"));
|
||||
req.addFarmId(12682549l);
|
||||
req.addPeriods(Arrays.asList("p1"));
|
||||
req.addSpecies(Arrays.asList("Gadidae"));
|
||||
|
||||
System.out.println(mng.generateCSV(req));
|
||||
/**
|
||||
* [id=26,
|
||||
* farmId=12682101,
|
||||
* batch_type=HATCHERY_INDIVIDUAL,
|
||||
* sourceUrl=https://data1-d.d4science.org/shub/E_aUJUbDNzeUlLL29KL2xlZUloWFQ5TEdlZ0ZnZzlNNTVLNUEzeDVRNFVoVHlLMW5DVG5RbVVXVzlYeUUzZWFXRA==, sourceVersion=1.1, startTime=2019-01-25T14:52:31.442Z, endTime=null, status=ACCEPTED, lock=localhost, caller=MSgXVCkHb0SDoQLlCLQV9Kj8dPJlJ6gY+XicZJhenQkyuxA11kGUIdhxKs3jUdGK, computationId=7c6f5d7e-b778-42be-af20-b99229fa99ee, computationUrl=http://dataminer1-pre.d4science.org:80//wps/RetrieveResultServlet?id=7c6f5d7e-b778-42be-af20-b99229fa99ee, computationOperator=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.PERFORMFISH_DATA_EXTRACTOR, computationOperatorName=Performfish Data Extractor, computationRequest=https://dataminer1-pre.d4science.org/wps/WebProcessingService?request=Execute&service=WPS&Version=1.0.0&gcube-token=***REMOVED***&lang=en-US&Identifier=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.PERFORMFISH_DATA_EXTRACTOR&DataInputs=InputData=https%3A%2F%2Fdata1-d.d4science.org%2Fshub%2FE_aUJUbDNzeUlLL29KL2xlZUloWFQ5TEdlZ0ZnZzlNNTVLNUEzeDVRNFVoVHlLMW5DVG5RbVVXVzlYeUUzZWFXRA%3D%3D;BatchType=HATCHERY_INDIVIDUAL;FarmID=12682101;]
|
||||
*/
|
||||
|
||||
|
||||
ResultSet rs=Queries.GET_IMPORT_ROUTINE_BY_ID.get(DataBaseManager.get().getConnection(), new DBQueryDescriptor(DBField.ImportRoutine.fields.get(DBField.ImportRoutine.ID),26l)).executeQuery();
|
||||
rs.next();
|
||||
Queries.rowToDescriptor(rs);
|
||||
ImportRoutineDescriptor desc=Queries.rowToDescriptor(rs);
|
||||
|
||||
mng.loadOutputData(desc);
|
||||
|
||||
|
||||
|
||||
//
|
||||
// CSVExportRequest req=new CSVExportRequest(new AnalysisType("GROW_OUT_AGGREGATED", "GROW_OUT_AGGREGATED"));
|
||||
// req.addAreas(Arrays.asList("A1","A2"));
|
||||
// req.addFarmId(12682549l);
|
||||
// req.addPeriods(Arrays.asList("p1"));
|
||||
// req.addSpecies(Arrays.asList("Gadidae"));
|
||||
//
|
||||
// System.out.println(mng.generateCSV(req));
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue