git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner@131699 82a268e6-3cf1-43bd-a215-b396298e98cf
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@ -238,7 +238,10 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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for (File file : generatedFiles) {
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if (file.exists()) {
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AnalysisLogger.getLogger().debug("Deleting File " + file.getAbsolutePath());
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try{AnalysisLogger.getLogger().debug("Deleting File Check " + file.delete());}catch(Exception e){}
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try {
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AnalysisLogger.getLogger().debug("Deleting File Check " + file.delete());
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} catch (Exception e) {
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}
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} else
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AnalysisLogger.getLogger().debug("Deleting File - File does not exist " + file.getAbsolutePath());
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}
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@ -249,58 +252,72 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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public void manageUserToken() {
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String scope = null;
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String username = null;
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String token = null;
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// DONE get scope and username from SmartGears
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// get scope from SmartGears
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TokenManager tokenm = new TokenManager();
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tokenm.getCredentials();
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scope = tokenm.getScope();
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username = tokenm.getUserName();
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token = tokenm.getToken();
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// set parameters
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inputs.put(ConfigurationManager.scopeParameter, scope);
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inputs.put(ConfigurationManager.usernameParameter, username);
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inputs.put(ConfigurationManager.tokenParameter, token);
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}
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long statusInterrupt = 0;
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float previousStatus = -3;
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public void updateStatus(float status) {
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if (agent != null) {
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long stream =0;
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try{
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long stream = 0;
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try {
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stream = org.n52.wps.server.database.DatabaseFactory.getDatabase().getContentLengthForStoreResponse(wpsExternalID);
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//AnalysisLogger.getLogger().debug("STATUS bytes " + stream + " interrupt bytes " + statusInterrupt);
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if (statusInterrupt == 0 || statusInterrupt > stream - 3 && stream != 468) {
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statusInterrupt = stream;
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} else {
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AnalysisLogger.getLogger().debug("STATUS INTERRUPTED!");
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agent.shutdown();
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statusInterrupt = -1;
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agent = null;
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status = -1f;
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super.update(new Integer((int) status));
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updateComputationOnWS(status, null);
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System.gc();
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// AnalysisLogger.getLogger().debug("STATUS bytes " + stream + " interrupt bytes " + statusInterrupt);
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if (statusInterrupt == 0 || statusInterrupt > stream - 3 && stream != 468) {
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statusInterrupt = stream;
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} else {
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AnalysisLogger.getLogger().debug("STATUS INTERRUPTED!");
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agent.shutdown();
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statusInterrupt = -1;
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agent = null;
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status = -1f;
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super.update(new Integer((int) status));
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try {
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updateComputationOnWS(status, null);
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} catch (Exception e) {
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}
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System.gc();
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}
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if (status != previousStatus) {
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AnalysisLogger.getLogger().debug("STATUS update to:" + status + " - status interrupt " + statusInterrupt);
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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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updateComputationOnWS(status, null);
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} catch (Exception e) {
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}
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}
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("WARNING - STATUS RETRIEVAL EXCEPTION " + e.getLocalizedMessage());
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AnalysisLogger.getLogger().debug(e);
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// stream = statusInterrupt;
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}
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if (status!=previousStatus){
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AnalysisLogger.getLogger().debug("STATUS update to:" + status+" - status interrupt "+statusInterrupt);
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previousStatus=status;
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super.update(new Integer((int) status));
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updateComputationOnWS(status, null);
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}
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}catch(Exception e){
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AnalysisLogger.getLogger().debug("WARNING: STATUS RETRIEVAL EXCEPTION "+e.getLocalizedMessage());
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//stream = statusInterrupt;
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}
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}
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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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public void updateComputationOnWS(float status, String exception, List<StoredData> inputData, 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.setStatus("" + status);
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if (exception != null && exception.length() > 0)
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currentComputation.setException(exception);
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DataspaceManager manager = new DataspaceManager(config, currentComputation, inputData, null, generatedData);
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try {
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@ -311,7 +328,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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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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String algorithm = "";
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@ -383,9 +400,9 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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// merging wps with ecological engine parameters - modifies the
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// config
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AnalysisLogger.getLogger().info("6 - Translating WPS Inputs into Ecological Engine Inputs");
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AnalysisLogger.getLogger().debug("Operator class is "+this.getClass().getCanonicalName());
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AnalysisLogger.getLogger().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", config.getTaskID(), configManager.getUsername(), config.getGcubeScope(), this.getClass().getCanonicalName());
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inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo);
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generatedInputTables = inputsManager.getGeneratedTables();
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generatedFiles = inputsManager.getGeneratedInputFiles();
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@ -408,9 +425,10 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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time("A priori output retrieval");
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// run the computation
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AnalysisLogger.getLogger().info("9 - Running the computation and updater");
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AnalysisLogger.getLogger().info("Initializing the computation");
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AnalysisLogger.getLogger().info("Initializing the WPS status of the computation");
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updateStatus(0);
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AnalysisLogger.getLogger().info("Initializing the computation");
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agent.init();
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AnalysisLogger.getLogger().info("Updating status");
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runStatusUpdater();
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@ -440,13 +458,13 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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// delete all temporary tables
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AnalysisLogger.getLogger().info("12 - Deleting possible generated temporary tables");
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AnalysisLogger.getLogger().debug("Final Computation Output: " + outputs);
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endTime = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
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if (statusInterrupt!=-1){
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if (statusInterrupt != -1) {
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saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent, generatedFiles);
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}else{
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} else {
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AnalysisLogger.getLogger().debug("Computation interrupted - no update");
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throw new Exception ("Computation cancelled");
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throw new Exception("Computation cancelled");
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}
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AnalysisLogger.getLogger().debug("All done");
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} catch (Exception e) {
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@ -454,15 +472,15 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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AnalysisLogger.getLogger().debug(e);
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e.printStackTrace();
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int exitstatus = -2;
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if (statusInterrupt==-1)
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if (statusInterrupt == -1)
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exitstatus = -1;
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if (inputsManager!=null)
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updateComputationOnWS(exitstatus,e.getMessage(),inputsManager.getProvenanceData(),generatedFiles);
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else
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updateComputationOnWS(exitstatus,e.getMessage());
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if (statusInterrupt==-1)
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throw new Exception ("Computation cancelled");
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if (inputsManager != null)
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updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(), generatedFiles);
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else
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updateComputationOnWS(exitstatus, e.getMessage());
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if (statusInterrupt == -1)
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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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@ -479,7 +497,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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displayTimes();
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cleanResources();
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AnalysisLogger.getLogger().debug("All done - Computation Finished");
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}
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}
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@ -488,7 +506,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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@Override
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public void run() {
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while (agent != null && statusInterrupt!=-1 && agent.getStatus() < 100) {
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while (agent != null && statusInterrupt != -1 && agent.getStatus() < 100) {
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try {
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updateStatus(agent.getStatus());
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Thread.sleep(10000);
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@ -510,9 +528,9 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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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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AnalysisLogger.getLogger().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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AnalysisLogger.getLogger().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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// post on WS
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DataspaceManager manager = new DataspaceManager(config, computation, inputData, outputData, generatedFiles);
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Thread t = new Thread(manager);
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@ -542,66 +560,57 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm {
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}
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private void cleanResources() {
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times = null;
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agent = null;
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// manage open files and garbage
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AnalysisLogger.getLogger().debug("Managing open files");
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// String checkOpenFiles = "ls -l /proc/*/fd/* 2|grep \"wps/ecocfg\"";
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try{
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String checkOpenFiles = "for i in `ls -l /proc/*/fd/* 2>/dev/null | grep delete | grep tomcat | awk '{print $9}'`; do du -hL $i | awk '{print $1}' | tr '\n' ' '; ls -l $i | awk '{print $6\" \"$7\" \"$8\" \"$9\" \"$10\" \"$11\" \"$12}'; done";
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List<String> openFiles =command(checkOpenFiles,"./");
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AnalysisLogger.getLogger().debug("Open Files "+openFiles);
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if (openFiles!=null){
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for (String openFile:openFiles){
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if (!openFile.contains("cannot access") && openFile.contains("(deleted)")){
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String size = openFile.substring(0,openFile.indexOf(" ")).trim();
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String pid = openFile.substring(openFile.indexOf("/proc/"),openFile.indexOf("->"));
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pid = pid.trim();
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if (!size.equals("0")){
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AnalysisLogger.getLogger().debug("Killing "+pid + " with size "+size);
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command(":>"+pid,"./");
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// String checkOpenFiles = "ls -l /proc/*/fd/* 2|grep \"wps/ecocfg\"";
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try {
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String checkOpenFiles = "for i in `ls -l /proc/*/fd/* 2>/dev/null | grep delete | grep tomcat | awk '{print $9}'`; do du -hL $i | awk '{print $1}' | tr '\n' ' '; ls -l $i | awk '{print $6\" \"$7\" \"$8\" \"$9\" \"$10\" \"$11\" \"$12}'; done";
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List<String> openFiles = command(checkOpenFiles, "./");
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AnalysisLogger.getLogger().debug("Open Files " + openFiles);
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if (openFiles != null) {
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for (String openFile : openFiles) {
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if (!openFile.contains("cannot access") && openFile.contains("(deleted)")) {
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String size = openFile.substring(0, openFile.indexOf(" ")).trim();
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String pid = openFile.substring(openFile.indexOf("/proc/"), openFile.indexOf("->"));
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pid = pid.trim();
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if (!size.equals("0")) {
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AnalysisLogger.getLogger().debug("Killing " + pid + " with size " + size);
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command(":>" + pid, "./");
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}
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}
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}
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}
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("Could not kill files " + e.getLocalizedMessage());
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}
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}catch(Exception e){
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AnalysisLogger.getLogger().debug("Could not kill files "+e.getLocalizedMessage());
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}
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System.gc();
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}
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public static List<String> command(final String cmdline,
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final String directory) {
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try {
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Process process =
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new ProcessBuilder(new String[] {"bash", "-c", cmdline})
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.redirectErrorStream(true)
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.directory(new File(directory))
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.start();
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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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List<String> output = new ArrayList<String>();
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BufferedReader br = new BufferedReader(
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new InputStreamReader(process.getInputStream()));
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String line = null;
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while ( (line = br.readLine()) != null )
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output.add(line);
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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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String line = null;
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while ((line = br.readLine()) != null)
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output.add(line);
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//There should really be a timeout here.
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if (0 != process.waitFor())
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return null;
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// There should really be a timeout here.
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if (0 != process.waitFor())
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return null;
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return output;
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return output;
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} catch (Exception e) {
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return null;
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}
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}
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} catch (Exception e) {
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return null;
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}
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}
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}
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