ref 20971: ShortLink - Check for obsolete short urls
https://support.d4science.org/issues/20971 Fixed ShortLink urls.
This commit is contained in:
parent
2d982938ce
commit
dbb87e55f7
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@ -48,10 +48,15 @@ import org.n52.wps.server.AbstractAnnotatedAlgorithm;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm implements Observable, Cancellable{
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public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm implements Observable, Cancellable {
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/**
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* Deploying procedure: 1 - modify configuration files 2 - modify resource file: resources/templates/setup.cfg 3 - generate classes with ClassGenerator 4 - add new classes in the wps_config.xml on the wps web app config folder 5 - produce the Jar file of this project 6 - copy the jar file in the lib folder of the wps web app change the server parameters in the wps_config.xml file
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* Deploying procedure: 1 - modify configuration files 2 - modify resource
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* file: resources/templates/setup.cfg 3 - generate classes with
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* ClassGenerator 4 - add new classes in the wps_config.xml on the wps web
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* app config folder 5 - produce the Jar file of this project 6 - copy the
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* jar file in the lib folder of the wps web app change the server
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* parameters in the wps_config.xml file
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*/
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private static final Logger LOGGER = LoggerFactory.getLogger(AbstractEcologicalEngineMapper.class);
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@ -59,11 +64,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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private Observer observer = null;
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private boolean cancelled = false;
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private TokenManager tokenm = null;
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private EnvironmentVariableManager env = null;
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// inputs and outputs
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public LinkedHashMap<String, Object> inputs = new LinkedHashMap<String, Object>();
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public LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>();
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@ -205,7 +210,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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LOGGER.debug("Could not drop Temporary Table: " + table + " table is null");
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}
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} catch (Exception e) {
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LOGGER.error("error deleting temporary table",e);
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LOGGER.error("error deleting temporary table", e);
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} finally {
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DatabaseUtils.closeDBConnection(dbConnection);
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}
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@ -248,14 +253,16 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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float previousStatus = -3;
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String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
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public void updateStatus(float status, boolean canWrite) {
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if (agent != null) {
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if (status != previousStatus) {
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LOGGER.debug("STATUS update to: {} ", status );
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LOGGER.debug("STATUS update to: {} ", status);
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previousStatus = status;
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super.update(new Integer((int) status));
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try {
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if (canWrite) updateComputationOnWS(status, null);
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if (canWrite)
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updateComputationOnWS(status, null);
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} catch (Exception e) {
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LOGGER.warn("error updating compution on WS");
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}
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@ -267,17 +274,18 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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public void setEnvironmentVariableManager(EnvironmentVariableManager env) {
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this.env = env;
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}
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public void updateComputationOnWS(float status, String exception) {
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updateComputationOnWS(status, exception, null, null);
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}
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class RunDataspaceManager implements Runnable{
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class RunDataspaceManager implements Runnable {
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List<StoredData> inputData;
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List<File> generatedData;
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public RunDataspaceManager(List<StoredData> inputData, List<File> generatedData){
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this.inputData=inputData;
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this.generatedData=generatedData;
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public RunDataspaceManager(List<StoredData> inputData, List<File> generatedData) {
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this.inputData = inputData;
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this.generatedData = generatedData;
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}
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public void run() {
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@ -286,36 +294,35 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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LOGGER.debug("Dataspace->Status updater->Writing computational info on the WS asyncronously");
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manager.writeRunningComputationData();
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} catch (Exception ez) {
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LOGGER.error("Dataspace->Status updater->Impossible to write computation information on the Workspace",ez);
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LOGGER.error("Dataspace->Status updater->Impossible to write computation information on the Workspace",
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ez);
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}
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}
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};
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public void updateComputationOnWS(float status, String exception, List<StoredData> inputData, List<File> generatedData) {
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public void updateComputationOnWS(float status, String exception, List<StoredData> inputData,
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List<File> generatedData) {
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if (currentComputation != null) {
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currentComputation.setStatus("" + status);
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if (exception != null && exception.length() > 0)
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currentComputation.setException(exception);
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LOGGER.debug("RunDataspaceManager: [inputData="+inputData+", generatedData="+generatedData+"]");
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RunDataspaceManager rundm = new RunDataspaceManager(inputData,generatedData);
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LOGGER.debug("RunDataspaceManager: [inputData=" + inputData + ", generatedData=" + generatedData + "]");
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RunDataspaceManager rundm = new RunDataspaceManager(inputData, generatedData);
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rundm.run();
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/*
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Thread t = new Thread(rundm);
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t.start();
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* Thread t = new Thread(rundm); t.start();
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*/
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}
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}
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@Execute
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public void run() throws Exception {
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if (observer!=null)
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if (observer != null)
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observer.isStarted(this);
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LOGGER.info("classloader context in this thread is {}",Thread.currentThread().getContextClassLoader());
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LOGGER.info("classloader context in this thread is {}", Thread.currentThread().getContextClassLoader());
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long startTimeLong = System.currentTimeMillis();
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OperationResult operationResult = null;
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@ -324,7 +331,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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List<String> generatedInputTables = null;
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List<String> generatedOutputTables = null;
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List<File> generatedFiles = null;
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//String date = new java.text.SimpleDateFormat("dd_MM_yyyy_HH:mm:ss").format(System.currentTimeMillis());
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// String date = new
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// java.text.SimpleDateFormat("dd_MM_yyyy_HH:mm:ss").format(System.currentTimeMillis());
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String computationSession = this.getAlgorithmClass().getSimpleName() + "_ID_" + UUID.randomUUID().toString();
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if (wpsExternalID != null) {
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LOGGER.info("Using wps External ID " + wpsExternalID);
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@ -332,16 +340,19 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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} else
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LOGGER.info("Wps External ID not set");
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InputsManager inputsManager = null;
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ConfigurationManager configManager = new ConfigurationManager(this.env); // initializes parameters from web.xml
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ConfigurationManager configManager = new ConfigurationManager(this.env); // initializes
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// parameters
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// from
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// web.xml
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manageUserToken();
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boolean canWriteOnShub = checkWriteAuthorization(tokenm.getUserName());
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Path dir = Paths.get(System.getProperty("java.io.tmpdir"), "dmlocks");
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if (!Files.exists(dir))
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dir = Files.createDirectory(dir);
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Path lockFile = Files.createTempFile(dir, "dm", ".lck");
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LOGGER.info("lock file created {}",lockFile.toUri().toURL());
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LOGGER.info("lock file created {}", lockFile.toUri().toURL());
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try {
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// wait for server resources to be available
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@ -364,8 +375,10 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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String scope = configManager.getScope();
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String username = configManager.getUsername();
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LOGGER.info("1 - Algorithm environment initialized in scope " + scope + " with user name " + username + " and session " + computationSession);
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LOGGER.info("Max allowed computations " + ConfigurationManager.getMaxComputations() + " using storage " + ConfigurationManager.useStorage());
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LOGGER.info("1 - Algorithm environment initialized in scope " + scope + " with user name " + username
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+ " and session " + computationSession);
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LOGGER.info("Max allowed computations " + ConfigurationManager.getMaxComputations() + " using storage "
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+ ConfigurationManager.useStorage());
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// init the infrastructure dialoguer
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LOGGER.info("2 - Initializing connection to the e-Infrastructure");
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infrastructureDialoguer = new InfrastructureDialoguer(scope);
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@ -392,7 +405,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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// adding service parameters to the configuration
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LOGGER.info("5 - Adding Service parameters to the configuration");
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List<StatisticalType> dataminerInputParameters = getInputParameters(algorithm);
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LOGGER.debug("Dataminer Algo Default InputParameters: "+dataminerInputParameters);
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LOGGER.debug("Dataminer Algo Default InputParameters: " + dataminerInputParameters);
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inputsManager.addInputServiceParameters(dataminerInputParameters, infrastructureDialoguer);
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time("Service parameters added to the algorithm");
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// merging wps with ecological engine parameters - modifies the
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@ -400,7 +413,9 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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LOGGER.info("6 - Translating WPS Inputs into Ecological Engine Inputs");
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LOGGER.debug("Operator class is " + this.getClass().getCanonicalName());
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// build computation Data
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currentComputation = new ComputationData(config.getTaskID(), config.getAgent(), "", "", startTime, "-", "0", config.getTaskID(), configManager.getUsername(), config.getGcubeScope(), this.getClass().getCanonicalName());
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currentComputation = new ComputationData(config.getTaskID(), config.getAgent(), "", "", startTime, "-", "0",
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config.getTaskID(), configManager.getUsername(), config.getGcubeScope(),
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this.getClass().getCanonicalName());
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inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo, dataminerInputParameters);
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generatedInputTables = inputsManager.getGeneratedTables();
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generatedFiles = inputsManager.getGeneratedInputFiles();
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@ -452,14 +467,16 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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time("Output preparation for WPS document (no storage manager)");
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outputmanager.shutdown();
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LOGGER.debug("12 - Final Computation Output");
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LOGGER.debug("Outputs: "+ outputs);
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LOGGER.debug("Outputs: " + outputs);
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endTime = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
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if (!isCancelled()) {
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LOGGER.debug("Save Computation Data");
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if (canWriteOnShub) saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent, generatedFiles);
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if (canWriteOnShub)
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saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent,
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generatedFiles);
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} else {
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LOGGER.debug("Computation interrupted - no update");
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throw new Exception("Computation cancelled");
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@ -468,21 +485,26 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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operationResult = OperationResult.SUCCESS;
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} catch (Exception e) {
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operationResult = OperationResult.FAILED;
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LOGGER.error("Error execution Algorithm {}",algorithm,e);
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LOGGER.error("Error execution Algorithm {}", algorithm, e);
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int exitstatus = -2;
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if (isCancelled())
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exitstatus = -1;
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if (inputsManager != null)
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if (canWriteOnShub) updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(), generatedFiles);
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else
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if (canWriteOnShub) updateComputationOnWS(exitstatus, e.getMessage());
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if (canWriteOnShub)
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updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(),
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generatedFiles);
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else if (canWriteOnShub)
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updateComputationOnWS(exitstatus, e.getMessage());
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if (isCancelled())
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throw new Exception("Computation cancelled");
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else
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throw e;
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} finally {
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LOGGER.debug("accounting algorithm");
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if(operationResult==null){
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operationResult=OperationResult.FAILED;
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}
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accountAlgorithmExecution(startTimeLong, System.currentTimeMillis(), operationResult);
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LOGGER.debug("Deleting Input Tables");
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deleteTemporaryTables(generatedInputTables);
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@ -496,7 +518,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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time("Cleaning of resources");
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displayTimes();
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cleanResources();
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if (observer!=null) observer.isFinished(this);
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if (observer != null)
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observer.isFinished(this);
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LOGGER.debug("All done - Computation Finished");
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Files.deleteIfExists(lockFile);
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}
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@ -504,7 +527,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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}
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private boolean checkWriteAuthorization(String username) {
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if (env!=null && env.getShubUsersExcluded()!=null) {
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if (env != null && env.getShubUsersExcluded() != null) {
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if (env.getShubUsersExcluded().isEmpty()) {
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return false;
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}
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@ -516,41 +539,41 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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}
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private void accountAlgorithmExecution(long start, long end, OperationResult result) {
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try{
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try {
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JobUsageRecord jobUsageRecord = new JobUsageRecord();
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jobUsageRecord.setJobName(this.getAlgorithmClass().getSimpleName());
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jobUsageRecord.setConsumerId(tokenm.getUserName());
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jobUsageRecord.setDuration(end-start);
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jobUsageRecord.setDuration(end - start);
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jobUsageRecord.setOperationResult(result);
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jobUsageRecord.setServiceName("DataMiner");
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jobUsageRecord.setServiceClass("WPS");
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jobUsageRecord.setHost(WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
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jobUsageRecord.setCallerQualifier(tokenm.getTokenQualifier());
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AccountingPersistence accountingPersistence =
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AccountingPersistenceFactory.getPersistence();
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AccountingPersistence accountingPersistence = AccountingPersistenceFactory.getPersistence();
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accountingPersistence.account(jobUsageRecord);
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}catch(Throwable e){
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LOGGER.error("error accounting algorithm execution",e);
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} catch (Throwable e) {
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LOGGER.error("error accounting algorithm execution", e);
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}
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}
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public class StatusUpdater implements Runnable {
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private boolean canWrite = true;
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public StatusUpdater(boolean canWrite) {
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this.canWrite = canWrite;
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}
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@Override
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public void run() {
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while (agent != null && !isCancelled() && agent.getStatus() < 100) {
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try {
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updateStatus(agent.getStatus(), canWrite);
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Thread.sleep(10000);
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} catch (InterruptedException e) {}
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} catch (InterruptedException e) {
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}
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}
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LOGGER.info("Status updater terminated");
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}
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@ -564,15 +587,19 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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LOGGER.debug("Provenance manager running");
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}
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private void saveComputationOnWS(List<StoredData> inputData, List<StoredData> outputData, ComputationalAgent agent, List<File> generatedFiles) {
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private void saveComputationOnWS(List<StoredData> inputData, List<StoredData> outputData, ComputationalAgent agent,
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List<File> generatedFiles) {
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LOGGER.debug("Save Computation On WS");
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LOGGER.debug("InputData: "+inputData);
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LOGGER.debug("OutputData: "+outputData);
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LOGGER.debug("Agent: "+agent);
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LOGGER.debug("Generated files: "+generatedFiles);
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LOGGER.debug("InputData: " + inputData);
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LOGGER.debug("OutputData: " + outputData);
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LOGGER.debug("Agent: " + agent);
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LOGGER.debug("Generated files: " + generatedFiles);
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LOGGER.debug("Provenance manager started for operator " + this.getClass().getCanonicalName());
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ComputationData computation = new ComputationData(config.getTaskID(), config.getAgent(), agent.getDescription(), agent.getInfrastructure().name(), startTime, endTime, "100", config.getTaskID(), config.getParam(ConfigurationManager.serviceUserNameParameterVariable), config.getGcubeScope(), this.getClass().getCanonicalName());
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ComputationData computation = new ComputationData(config.getTaskID(), config.getAgent(), agent.getDescription(),
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agent.getInfrastructure().name(), startTime, endTime, "100", config.getTaskID(),
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config.getParam(ConfigurationManager.serviceUserNameParameterVariable), config.getGcubeScope(),
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this.getClass().getCanonicalName());
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// post on WS
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DataspaceManager manager = new DataspaceManager(config, computation, inputData, outputData, generatedFiles);
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@ -637,7 +664,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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public static List<String> command(final String cmdline, final String directory) {
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try {
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Process process = new ProcessBuilder(new String[] { "bash", "-c", cmdline }).redirectErrorStream(true).directory(new File(directory)).start();
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Process process = new ProcessBuilder(new String[] { "bash", "-c", cmdline }).redirectErrorStream(true)
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.directory(new File(directory)).start();
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List<String> output = new ArrayList<String>();
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BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));
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@ -658,16 +686,16 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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@Override
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public void setObserver(Observer o) {
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LOGGER.debug("setting observer in {} ",wpsExternalID);
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this.observer = o;
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LOGGER.debug("setting observer in {} ", wpsExternalID);
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this.observer = o;
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}
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@Override
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public synchronized boolean cancel() {
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if (!cancelled){
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LOGGER.debug("COMPUTATION INTERRUPTED! ({})",wpsExternalID);
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try{
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if (agent!=null){
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if (!cancelled) {
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LOGGER.debug("COMPUTATION INTERRUPTED! ({})", wpsExternalID);
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try {
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if (agent != null) {
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agent.shutdown();
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agent = null;
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}
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@ -680,12 +708,12 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
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}
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System.gc();
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cancelled = true;
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}catch(Exception e){
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LOGGER.warn("error cancelling computation with id {}",wpsExternalID);
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} catch (Exception e) {
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LOGGER.warn("error cancelling computation with id {}", wpsExternalID);
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return false;
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}
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} else {
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LOGGER.debug("COMPUTATION ALREADY INTERRUPT! ({})",wpsExternalID);
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LOGGER.debug("COMPUTATION ALREADY INTERRUPT! ({})", wpsExternalID);
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return false;
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}
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return true;
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