ref 20971: ShortLink - Check for obsolete short urls

https://support.d4science.org/issues/20971

Fixed ShortLink urls.
feature/22700
Giancarlo Panichi 3 years ago
parent 2d982938ce
commit dbb87e55f7

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

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