Package org.apache.airavata.gfac.core.handler

Examples of org.apache.airavata.gfac.core.handler.GFacHandlerException

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  }
  private void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
        try{
        Cluster cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
        if (cluster == null) {
            throw new GFacHandlerException("Security context is not set properly");
        } else {
            log.info("Successfully retrieved the Security Context");
        }
        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
            String workingDirectory = app.getScratchWorkingDirectory();
            cluster.makeDirectory(workingDirectory);
            cluster.makeDirectory(app.getScratchWorkingDirectory());
            cluster.makeDirectory(app.getInputDataDirectory());
            cluster.makeDirectory(app.getOutputDataDirectory());
            DataTransferDetails detail = new DataTransferDetails();
            TransferStatus status = new TransferStatus();
            status.setTransferState(TransferState.DIRECTORY_SETUP);
            detail.setTransferStatus(status);
            detail.setTransferDescription("Working directory = " + workingDirectory);

            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());

        } catch (SSHApiException e) {
            throw new GFacHandlerException("Error executing the Handler: " + SSHDirectorySetupHandler.class, e);
        } catch (Exception e) {
            DataTransferDetails detail = new DataTransferDetails();
            TransferStatus status = new TransferStatus();
            status.setTransferState(TransferState.FAILED);
            detail.setTransferStatus(status);
            try {
                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
                GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
            } catch (Exception e1) {
                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
            }
            throw new GFacHandlerException("Error executing the Handler: " + SSHDirectorySetupHandler.class, e);
        }
  }
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            if(jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null){
            try {
                GFACSSHUtils.addSecurityContext(jobExecutionContext);
            } catch (ApplicationSettingsException e) {
                log.error(e.getMessage());
                throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
            }
        }
            ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
                .getApplicationDeploymentDescription().getType();

            AuthenticationInfo authenticationInfo = null;
            if (password != null) {
            authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
        } else {
            authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
                    this.passPhrase);
        }
            // Server info
            ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
            Cluster pbsCluster = null;
            // here doesn't matter what the job manager is because we are only doing some file handling
            // not really dealing with monitoring or job submission, so we pa
            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
            String parentPath = inputPath + File.separator + jobExecutionContext.getExperimentID() + File.separator + jobExecutionContext.getTaskData().getTaskID();
            (new File(parentPath)).mkdirs();
            MessageContext input = jobExecutionContext.getInMessageContext();
            Set<String> parameters = input.getParameters().keySet();
            for (String paramName : parameters) {
                ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
                String paramValue = MappingFactory.toString(actualParameter);
                //TODO: Review this with type
                if ("URI".equals(actualParameter.getType().getType().toString())) {
                    ((URIParameterType) actualParameter.getType()).setValue(stageInputFiles(pbsCluster, paramValue, parentPath));
                } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
                    List<String> newFiles = new ArrayList<String>();
                    for (String paramValueEach : split) {
                        String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
                        newFiles.add(stageInputFiles);
                    }
                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
                }
                inputNew.getParameters().put(paramName, actualParameter);
            }
        } catch (Exception e) {
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
        }
        jobExecutionContext.setInMessageContext(inputNew);
    }
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            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
            }
        } catch (ApplicationSettingsException e) {
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
        } catch (GFacException e) {
          throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
        }

        log.info("Setup SSH job directorties");
        super.invoke(jobExecutionContext);
        makeDirectory(jobExecutionContext);
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  }
  private void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
                try {
        Cluster cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
        if (cluster == null) {
            throw new GFacHandlerException("Security context is not set properly");
        } else {
            log.info("Successfully retrieved the Security Context");
        }
        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();

            String workingDirectory = app.getScratchWorkingDirectory();
            cluster.makeDirectory(workingDirectory);
            cluster.makeDirectory(app.getScratchWorkingDirectory());
            cluster.makeDirectory(app.getInputDataDirectory());
            cluster.makeDirectory(app.getOutputDataDirectory());
            DataTransferDetails detail = new DataTransferDetails();
            TransferStatus status = new TransferStatus();
            status.setTransferState(TransferState.DIRECTORY_SETUP);
            detail.setTransferStatus(status);
            detail.setTransferDescription("Working directory = " + workingDirectory);

            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());

        } catch (SSHApiException e) {
            throw new GFacHandlerException("Error executing the Handler: " + GSISSHDirectorySetupHandler.class, e);
        } catch (Exception e) {
            DataTransferDetails detail = new DataTransferDetails();
            TransferStatus status = new TransferStatus();
            detail.setTransferDescription(e.getLocalizedMessage());
            status.setTransferState(TransferState.FAILED);
            detail.setTransferStatus(status);
            try {
                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
                GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
            } catch (Exception e1) {
                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
            }
            throw new GFacHandlerException("Error executing the Handler: " + GSISSHDirectorySetupHandler.class, e);
        }
  }
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                TaskDetails taskData = null;
                try {
                    taskData = (TaskDetails) registry.get(RegistryModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
                } catch (RegistryException e) {
                    log.error("Error retrieving job details from Registry");
                    throw new GFacHandlerException("Error retrieving job details from Registry", e);
                }
                JobDetails jobDetails = taskData.getJobDetailsList().get(0);
                String jobDescription = jobDetails.getJobDescription();
                if (jobDescription != null) {
                    JobDescriptor jobDescriptor = null;
                    try {
                        jobDescriptor = JobDescriptor.fromXML(jobDescription);
                    } catch (XmlException e1) {
                        e1.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                    }
                    applicationDeploymentDescription.getType().setScratchWorkingDirectory(
                            jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
                    applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
                    applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
                    applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
                    applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
                }
            }
        }

        try {
            if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {

                GFACSSHUtils.addSecurityContext(jobExecutionContext);
            }
        } catch (ApplicationSettingsException e) {
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
        } catch (GFacException e1) {
            log.error(e1.getMessage());
            throw new GFacHandlerException("Error while creating SSHSecurityContext", e1, e1.getLocalizedMessage());
        }

        super.invoke(jobExecutionContext);
        DataTransferDetails detail = new DataTransferDetails();
        TransferStatus status = new TransferStatus();

        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
                .getApplicationDeploymentDescription().getType();
        try {
            Cluster cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
            if (cluster == null) {
                throw new GFacProviderException("Security context is not set properly");
            } else {
                log.info("Successfully retrieved the Security Context");
            }

            // Get the Stdouts and StdErrs
            String timeStampedServiceName = GFacUtils.createUniqueNameForService(jobExecutionContext.getServiceName());

            TaskDetails taskData = jobExecutionContext.getTaskData();
            String outputDataDir = null;
            File localStdOutFile;
            File localStdErrFile;

            if (taskData.getAdvancedOutputDataHandling() != null) {
                outputDataDir = taskData.getAdvancedOutputDataHandling().getOutputDataDir();
            }
            if (outputDataDir == null) {
                outputDataDir = File.separator + "tmp";
            }
            outputDataDir = outputDataDir + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID();
            (new File(outputDataDir)).mkdirs();


            localStdOutFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stdout");
            localStdErrFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stderr");
//            cluster.makeDirectory(outputDataDir);
            cluster.scpFrom(app.getStandardOutput(), localStdOutFile.getAbsolutePath());
            Thread.sleep(1000);
            cluster.scpFrom(app.getStandardError(), localStdErrFile.getAbsolutePath());
            Thread.sleep(1000);

            String stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
            String stdErrStr = GFacUtils.readFileToString(localStdErrFile.getAbsolutePath());
            status.setTransferState(TransferState.COMPLETE);
            detail.setTransferStatus(status);
            detail.setTransferDescription("STDOUT:" + stdOutStr);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());

            status.setTransferState(TransferState.COMPLETE);
            detail.setTransferStatus(status);
            detail.setTransferDescription("STDERR:" + stdErrStr);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());


            List<DataObjectType> outputArray = new ArrayList<DataObjectType>();
            Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
            Set<String> keys = output.keySet();
            for (String paramName : keys) {
                ActualParameter actualParameter = (ActualParameter) output.get(paramName);
                if ("URI".equals(actualParameter.getType().getType().toString())) {

                    List<String> outputList = cluster.listDirectory(app.getOutputDataDirectory());
                    if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
                        OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr,outputArray);
                        break;
                    } else {
                        String valueList = outputList.get(0);
                        cluster.scpFrom(app.getOutputDataDirectory() + File.separator + valueList, outputDataDir);
                        jobExecutionContext.addOutputFile(outputDataDir + File.separator + valueList);
                        DataObjectType dataObjectType = new DataObjectType();
                        dataObjectType.setValue(valueList);
                        dataObjectType.setKey(paramName);
                        dataObjectType.setType(DataType.URI);
                        outputArray.add(dataObjectType);
                    }
                } else {
                    OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr,outputArray);
                }
            }
            if (outputArray == null || outputArray.isEmpty()) {
                throw new GFacHandlerException(
                        "Empty Output returned from the Application, Double check the application"
                                + "and ApplicationDescriptor output Parameter Names");
            }
            app.setStandardError(localStdErrFile.getAbsolutePath());
            app.setStandardOutput(localStdOutFile.getAbsolutePath());
            app.setOutputDataDirectory(outputDataDir);
            status.setTransferState(TransferState.DOWNLOAD);
            detail.setTransferStatus(status);
            detail.setTransferDescription(outputDataDir);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
            registry.add(ChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
           
        } catch (XmlException e) {
            throw new GFacHandlerException("Cannot read output:" + e.getMessage(), e);
        } catch (ConnectionException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (TransportException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (IOException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (Exception e) {
            try {
                status.setTransferState(TransferState.FAILED);
                detail.setTransferStatus(status);
                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
                GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
            } catch (Exception e1) {
                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
            }
            throw new GFacHandlerException("Error in retrieving results", e);
        }

    }
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            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
                try {
                    GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
                } catch (ApplicationSettingsException e) {
                    log.error(e.getMessage());
                    throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
                }
            }
            log.info("Invoking SCPInputHandler");
            super.invoke(jobExecutionContext);


            MessageContext input = jobExecutionContext.getInMessageContext();
            Set<String> parameters = input.getParameters().keySet();
            for (String paramName : parameters) {
                ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
                String paramValue = MappingFactory.toString(actualParameter);
                //TODO: Review this with type
                if ("URI".equals(actualParameter.getType().getType().toString())) {
                    ((URIParameterType) actualParameter.getType()).setValue(stageInputFiles(jobExecutionContext, paramValue));
                } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
                    List<String> newFiles = new ArrayList<String>();
                    for (String paramValueEach : split) {
                        String stageInputFiles = stageInputFiles(jobExecutionContext, paramValueEach);
                        status.setTransferState(TransferState.UPLOAD);
                        detail.setTransferStatus(status);
                        detail.setTransferDescription("Input Data Staged: " + stageInputFiles);
                        registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
                        newFiles.add(stageInputFiles);
                    }
                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
                }
                inputNew.getParameters().put(paramName, actualParameter);
            }
        } catch (Exception e) {
            log.error(e.getMessage());
            status.setTransferState(TransferState.FAILED);
            detail.setTransferDescription(e.getLocalizedMessage());
            detail.setTransferStatus(status);
            try {
                GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
            } catch (Exception e1) {
                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
            }
            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
        }
        jobExecutionContext.setInMessageContext(inputNew);
    }
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                paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
            }
            cluster.scpTo(targetFile, paramValue);
            return targetFile;
        } catch (SSHApiException e) {
            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
        }
    }
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       if(jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null){
            try {
                GFACSSHUtils.addSecurityContext(jobExecutionContext);
            } catch (ApplicationSettingsException e) {
                log.error(e.getMessage());
                throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
            }
        }
        taskID = jobExecutionContext.getTaskData().getTaskID();
    if (!((SSHHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType()).getHpcResource()) {
            jobID = "SSH_" + jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress() + "_" + Calendar.getInstance().getTimeInMillis();
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            if (gridFTPEndpointArray == null || gridFTPEndpointArray.length == 0) {
              gridFTPEndpointArray = new String[]{hostType.getHostAddress()};
            }
            boolean success = false;
            GFacHandlerException pe = null;// = new ProviderException("");
            for (String endpoint : gridFTPEndpointArray) {
                try {

                    URI tmpdirURI = GramProviderUtils.createGsiftpURI(endpoint, app.getScratchWorkingDirectory());
                    URI workingDirURI = GramProviderUtils.createGsiftpURI(endpoint, app.getStaticWorkingDirectory());
                    URI inputURI = GramProviderUtils.createGsiftpURI(endpoint, app.getInputDataDirectory());
                    URI outputURI = GramProviderUtils.createGsiftpURI(endpoint, app.getOutputDataDirectory());

                    log.info("Host FTP = " + gridFTPEndpointArray[0]);
                    log.info("temp directory = " + tmpdirURI);
                    log.info("Working directory = " + workingDirURI);
                    log.info("Input directory = " + inputURI);
                    log.info("Output directory = " + outputURI);
                    ftp.makeDir(tmpdirURI, gssCred);
                    ftp.makeDir(workingDirURI, gssCred);
                    ftp.makeDir(inputURI, gssCred);
                    ftp.makeDir(outputURI, gssCred);
                    success = true;
                    DataTransferDetails detail = new DataTransferDetails();
                    TransferStatus status = new TransferStatus();
                    status.setTransferState(TransferState.DIRECTORY_SETUP);
                    detail.setTransferStatus(status);
                    detail.setTransferDescription("Working directory = " + workingDirURI);
                    registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
                                 
                    break;
                } catch (URISyntaxException e) {
                    pe = new GFacHandlerException("URI is malformatted:" + e.getMessage(), e);

                } catch (Exception e) {
                pe = new GFacHandlerException(e.getMessage(), e);
                }
            }
            if (success == false) {
              GFacUtils.saveErrorDetails(jobExecutionContext, pe.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
            throw pe;
            }
        } catch (SecurityException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (ApplicationSettingsException e1) {
          throw new GFacHandlerException(e1.getMessage(), e1);
    } catch (GFacException e) {
            throw new GFacHandlerException(e);
        }
    }
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               status.setTransferState(TransferState.FAILED);
         detail.setTransferStatus(status);
         registry.add(ChildDataType.DATA_TRANSFER_DETAIL,detail, jobExecutionContext.getTaskData().getTaskID());
         GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
       } catch (Exception e1) {
            throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
         }
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
        }
        jobExecutionContext.setInMessageContext(inputNew);
    }
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Related Classes of org.apache.airavata.gfac.core.handler.GFacHandlerException

  • org.apache.airavata.gfac.core.utils.GFacUtils
  • org.apache.airavata.gfac.core.utils.OutputUtils
  • org.apache.airavata.gfac.gram.handler.GramDirectorySetupHandler
  • org.apache.airavata.gfac.gram.handler.GridFTPInputHandler
  • org.apache.airavata.gfac.gram.handler.GridFTPOutputHandler
  • org.apache.airavata.gfac.gsissh.handler.GSISSHDirectorySetupHandler
  • org.apache.airavata.gfac.gsissh.handler.GSISSHInputHandler
  • org.apache.airavata.gfac.gsissh.handler.GSISSHOutputHandler
  • org.apache.airavata.gfac.gsissh.provider.impl.GSISSHProvider
  • org.apache.airavata.gfac.hadoop.handler.HadoopDeploymentHandler
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