109 lines
5.5 KiB
Java
109 lines
5.5 KiB
Java
package org.gcube.dataanalysis.executor.tests;
|
|
|
|
import java.util.ArrayList;
|
|
import java.util.List;
|
|
|
|
import org.gcube.common.scope.api.ScopeProvider;
|
|
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
|
|
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
|
|
import org.gcube.dataanalysis.executor.job.management.GenericWorker;
|
|
import org.gcube.dataanalysis.executor.job.management.WPSJobManager;
|
|
import org.gcube.dataanalysis.executor.job.management.WPSJobManager.TasksWatcher;
|
|
import org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer;
|
|
import org.gcube.dataanalysis.executor.nodes.transducers.bionym.utils.YasmeenGlobalParameters;
|
|
|
|
public class TestWPSJobs {
|
|
|
|
public static AlgorithmConfiguration buildTestConfiguration(){
|
|
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
|
config.setConfigPath("./cfg/");
|
|
AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
|
|
config.setParam("DatabaseUserName", "utente");
|
|
config.setParam("DatabasePassword", "d4science");
|
|
config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
|
|
|
|
config.setParam(YasmeenGlobalParameters.parserNameParam, YasmeenGlobalParameters.BuiltinParsers.SIMPLE.name());
|
|
config.setParam(YasmeenGlobalParameters.taxaAuthorityFileParam, YasmeenGlobalParameters.BuiltinDataSources.FISHBASE.name());
|
|
config.setParam(YasmeenGlobalParameters.performanceParam, YasmeenGlobalParameters.Performance.MAX_SPEED.name());
|
|
|
|
config.setParam(YasmeenGlobalParameters.activatePreParsingProcessing, "true");
|
|
config.setParam(YasmeenGlobalParameters.useStemmedGenusAndSpecies, "false");
|
|
|
|
config.setParam(BionymFlexibleWorkflowTransducer.matcherParamPrefix + "_" + 1, YasmeenGlobalParameters.BuiltinMatchers.GSAy.name());
|
|
config.setParam(BionymFlexibleWorkflowTransducer.thresholdParamPrefix + "_" + 1, "0.6");
|
|
config.setParam(BionymFlexibleWorkflowTransducer.maxresultsParamPrefix + "_" + 1, "10");
|
|
|
|
config.setParam(BionymFlexibleWorkflowTransducer.matcherParamPrefix + "_" + 2, YasmeenGlobalParameters.BuiltinMatchers.FUZZYMATCH.name());
|
|
config.setParam(BionymFlexibleWorkflowTransducer.thresholdParamPrefix + "_" + 2, "0.6");
|
|
config.setParam(BionymFlexibleWorkflowTransducer.maxresultsParamPrefix + "_" + 2, "10");
|
|
|
|
config.setParam(BionymFlexibleWorkflowTransducer.matcherParamPrefix + "_" + 3, YasmeenGlobalParameters.BuiltinMatchers.LEVENSHTEIN.name());
|
|
config.setParam(BionymFlexibleWorkflowTransducer.thresholdParamPrefix + "_" + 3, "0.4");
|
|
config.setParam(BionymFlexibleWorkflowTransducer.maxresultsParamPrefix + "_" + 3, "10");
|
|
|
|
config.setParam(BionymFlexibleWorkflowTransducer.matcherParamPrefix + "_" + 4, YasmeenGlobalParameters.BuiltinMatchers.TRIGRAM.name());
|
|
config.setParam(BionymFlexibleWorkflowTransducer.thresholdParamPrefix + "_" + 4, "0.4");
|
|
config.setParam(BionymFlexibleWorkflowTransducer.maxresultsParamPrefix + "_" + 4, "10");
|
|
|
|
config.setParam(BionymFlexibleWorkflowTransducer.destinationTableParam, "taxamatchoutputlocal");
|
|
config.setParam(BionymFlexibleWorkflowTransducer.destinationTableLableParam, "taxamatchoutputlabel");
|
|
|
|
// 4
|
|
//config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "generic_id1ecb405c_980f_47a4_926a_3043d065fc7d");
|
|
//config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "field0");
|
|
|
|
config.setParam(BionymFlexibleWorkflowTransducer.originTableParam, "taxamatchinput1000");
|
|
config.setParam(BionymFlexibleWorkflowTransducer.rawnamesColumnParam, "rawstrings");
|
|
|
|
config.setAgent("BIONYM");
|
|
config.setPersistencePath("./");
|
|
config.setGcubeScope("/gcube/devNext/NextNext");
|
|
// config.setGcubeScope("/gcube/devsec/devVRE");
|
|
config.setParam("ServiceUserName", "gianpaolo.coro");
|
|
config.setParam("DatabaseDriver", "org.postgresql.Driver");
|
|
config.setGcubeUserName("gianpaolo.coro");
|
|
config.setGcubeToken("f9d49d76-cd60-48ed-9f8e-036bcc1fc045-98187548");
|
|
|
|
return config;
|
|
}
|
|
|
|
public static void main1(String[] args) throws Exception {
|
|
|
|
String host = "dataminer1-devnext.d4science.org";
|
|
String session = "12345";
|
|
int port = 80;
|
|
String algorithm = "org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer";
|
|
AlgorithmConfiguration config = buildTestConfiguration();
|
|
|
|
WPSJobManager manager = new WPSJobManager();
|
|
TasksWatcher taskWatcher = manager.new TasksWatcher(algorithm, config.getGcubeUserName(), config.getGcubeToken(), host, port, session, 1, config, 1, 1, 1, 1,"",1);
|
|
Thread t = new Thread(taskWatcher);
|
|
t.start();
|
|
|
|
while (taskWatcher.exitstatus.equals(GenericWorker.TASK_UNDEFINED)){
|
|
Thread.sleep(1000);
|
|
System.out.print(".");
|
|
}
|
|
|
|
AnalysisLogger.getLogger().debug("Task 1 terminated with output "+taskWatcher.exitstatus );
|
|
//taskWatcher.run();
|
|
}
|
|
|
|
public static void main(String[] args) throws Exception {
|
|
AlgorithmConfiguration config = buildTestConfiguration();
|
|
String algorithm = "org.gcube.dataanalysis.executor.nodes.transducers.bionym.BionymFlexibleWorkflowTransducer";
|
|
ScopeProvider.instance.set(config.getGcubeScope());
|
|
WPSJobManager jobmanager = new WPSJobManager();
|
|
//int nArguments = 100;
|
|
int nArguments = 20;
|
|
List<String> arguments = new ArrayList<String>();
|
|
for (int i=1;i<=nArguments;i++){
|
|
String argument = "1 1 "+i+" 1";
|
|
arguments.add(argument);
|
|
}
|
|
String sessionID ="1234";
|
|
jobmanager.uploadAndExecuteChunkized(config, algorithm, arguments,sessionID);
|
|
|
|
}
|
|
}
|