Examples of GFacHandlerException

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

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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());
                }
            }
            delegateToMonitorHandlers(jobExecutionContext, (GsisshHostType) host, jobId);
        } catch (GFacHandlerException e) {
            throw new GFacProviderException("Error delegating already ran job to Monitoring", e);
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Examples of org.apache.airavata.gfac.core.handler.GFacHandlerException

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

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

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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");

            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())) {
                    if (index < oldIndex) {
                        log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                        ((URIParameterType) actualParameter.getType()).setValue(oldFiles.get(index));
                        data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
                    } else {
                        String s = stageInputFiles(jobExecutionContext, paramValue);
                        ((URIParameterType) actualParameter.getType()).setValue(s);
                        StringBuffer temp = new StringBuffer(data.append(s).append(",").toString());
                        GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                    }
                } 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) {
                        if (index < oldIndex) {
                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                            newFiles.add(oldFiles.get(index));
                            data.append(oldFiles.get(index++)).append(",");
                        } else {
                            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());
                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                            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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Examples of org.apache.airavata.gfac.core.handler.GFacHandlerException

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

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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();
            if (index < oldIndex) {
                parentPath = oldFiles.get(index);
                data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
            } else {
                (new File(parentPath)).mkdirs();
                StringBuffer temp = new StringBuffer(data.append(parentPath).append(",").toString());
                GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
            }
            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())) {
                    if (index < oldIndex) {
                        log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                        ((URIParameterType) actualParameter.getType()).setValue(oldFiles.get(index));
                        data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
                    } else {
                        String s = stageInputFiles(pbsCluster, paramValue, parentPath);
                        ((URIParameterType) actualParameter.getType()).setValue(s);
                        StringBuffer temp = new StringBuffer(data.append(s).append(",").toString());
                        GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                    }
                } 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) {
                        if (index < oldIndex) {
                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                            newFiles.add(oldFiles.get(index));
                            data.append(oldFiles.get(index++)).append(",");
                        } else {
                            String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                            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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Examples of org.apache.airavata.gfac.core.handler.GFacHandlerException

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                TaskDetails taskData = null;
                try {
                    taskData = (TaskDetails) jobExecutionContext.getRegistry().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(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) {
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
        }
        DataTransferDetails detail = new DataTransferDetails();
        TransferStatus status = new TransferStatus();

        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
                .getApplicationDeploymentDescription().getType();
        try {
            Cluster cluster = null;
            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
            } else {
                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_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 pluginData = GFacUtils.getPluginData(jobExecutionContext, this.getClass().getName());
            if (pluginData != null) {
                try {
                    oldIndex = Integer.parseInt(pluginData.split("\\|")[0].trim());
                    oldFiles = Arrays.asList(pluginData.split("\\|")[1].split(","));
                    if (oldIndex == oldFiles.size()) {
                        log.info("Old data looks good !!!!");
                    } else {
                        oldIndex = 0;
                        oldFiles.clear();
                    }
                } catch (NumberFormatException e) {
                    log.error("Previously stored data " + pluginData + " is wrong so we continue the operations");
                }
            }

            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();


            if (index < oldIndex) {
                localStdOutFile = new File(oldFiles.get(index));
                data.append(oldFiles.get(index++)).append(",");
            } else {
                localStdOutFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stdout");
                cluster.scpFrom(app.getStandardOutput(), localStdOutFile.getAbsolutePath());
                Thread.sleep(1000);
                StringBuffer temp = new StringBuffer(data.append(localStdOutFile.getAbsolutePath()).append(",").toString());
                GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
            }
            if (index < oldIndex) {
                localStdErrFile = new File(oldFiles.get(index));
                data.append(oldFiles.get(index++)).append(",");
            } else {
                localStdErrFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stderr");
                cluster.scpFrom(app.getStandardError(), localStdErrFile.getAbsolutePath());
                Thread.sleep(1000);
                StringBuffer temp = new StringBuffer(data.append(localStdErrFile.getAbsolutePath()).append(",").toString());
                GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
            }

            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());

            //todo this is a mess we have to fix this
            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);
                        Set<String> strings = output.keySet();
                        outputArray.clear();
                        for (String key : strings) {
                            ActualParameter actualParameter1 = (ActualParameter) output.get(key);
                            if ("URI".equals(actualParameter1.getType().getType().toString())) {
                                String downloadFile = MappingFactory.toString(actualParameter1);
                                String localFile;
                                if (index < oldIndex) {
                                    localFile = oldFiles.get(index);
                                    data.append(oldFiles.get(index++)).append(",");
                                } else {
                                    cluster.scpFrom(downloadFile, outputDataDir);
                                    String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar) + 1, downloadFile.length());
                                    localFile = outputDataDir + File.separator + fileName;
                                    StringBuffer temp = new StringBuffer(data.append(localFile).append(",").toString());
                                    GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                                }
                                jobExecutionContext.addOutputFile(localFile);
                                MappingFactory.fromString(actualParameter1, localFile);
                                DataObjectType dataObjectType = new DataObjectType();
                                dataObjectType.setValue(localFile);
                                dataObjectType.setKey(key);
                                dataObjectType.setType(DataType.URI);
                                outputArray.add(dataObjectType);
                            }
                        }
                        break;
                    } else {
                        String valueList = outputList.get(0);
                        String outputFile;
                        if (index < oldIndex) {
                            outputFile = oldFiles.get(index);
                            data.append(oldFiles.get(index++)).append(",");
                        } else {
                            cluster.scpFrom(app.getOutputDataDirectory() + File.separator + valueList, outputDataDir);
                            outputFile = outputDataDir + File.separator + valueList;
                            jobExecutionContext.addOutputFile(outputFile);
                            StringBuffer temp = new StringBuffer(data.append(outputFile).append(",").toString());
                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                        }
                        jobExecutionContext.addOutputFile(outputFile);
                        DataObjectType dataObjectType = new DataObjectType();
                        dataObjectType.setValue(valueList);
                        dataObjectType.setKey(paramName);
                        dataObjectType.setType(DataType.URI);
                        outputArray.add(dataObjectType);
                    }
                } else {
                    OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
                    break;
                }
            }
            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);
                detail.setTransferDescription(e.getLocalizedMessage());
                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);
        }

    }
View Full Code Here

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

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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);
                        Set<String> strings = output.keySet();
                        outputArray.clear();
                        for (String key : strings) {
                            ActualParameter actualParameter1 = (ActualParameter) output.get(key);
                            if ("URI".equals(actualParameter1.getType().getType().toString())) {
                                String downloadFile = MappingFactory.toString(actualParameter1);
                              cluster.scpFrom(downloadFile, outputDataDir);
                              String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar)+1, downloadFile.length());
                              String localFile = outputDataDir +  File.separator +fileName;
                jobExecutionContext.addOutputFile(localFile);
                MappingFactory.fromString(actualParameter1, localFile);
                DataObjectType dataObjectType = new DataObjectType();
                                dataObjectType.setValue(localFile);
                                dataObjectType.setKey(key);
                                dataObjectType.setType(DataType.URI);
                                outputArray.add(dataObjectType);
                            }
                        }
                   
                        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);
        }

    }
View Full Code Here

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

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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()) {
View Full Code Here

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

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        Stat exists = zk.exists(expZnodeHandlerPath, false);
        zk.setData(expZnodeHandlerPath, data.toString().getBytes(),
            exists.getVersion());
      }
    } catch (Exception e) {
      throw new GFacHandlerException(e);
    }
  }
View Full Code Here
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