Path	Lines of Code
modules/agent-framework/agent-service/src/main/assembly/agent-service-bin-assembly.xml	67
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/AgentServiceApplication.java	11
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/UserContext.java	25
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/config/AuthzTokenFilter.java	38
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/config/ClusterApplicationConfig.java	18
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/AgentController.java	73
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/ExperimentController.java	41
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/controllers/PlanController.java	73
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/entity/AgentDeploymentInfo.java	44
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/entity/AgentExecution.java	36
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/entity/AgentExecutionStatus.java	57
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/entity/Plan.java	40
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/repo/AgentDeploymentInfoRepo.java	7
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/repo/AgentExecutionRepo.java	7
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/repo/AgentExecutionStatusRepo.java	7
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/db/repo/PlanRepo.java	9
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/handlers/AgentConnectionHandler.java	254
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/handlers/AgentManagementHandler.java	151
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/handlers/FuseFSHandler.java	95
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/handlers/PlanHandler.java	26
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandAck.java	17
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandRequest.java	26
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentCommandResponse.java	24
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentInfoResponse.java	21
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonRunAck.java	3
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonRunRequest.java	47
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentPythonRunResponse.java	31
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTunnelAck.java	17
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/AgentTunnelCreationRequest.java	52
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/DirectoryInfo.java	17
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/ExperimentStorageResponse.java	32
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/FileInfo.java	67
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/JupyterExecutionAck.java	3
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/JupyterExecutionRequest.java	31
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/JupyterExecutionResponse.java	31
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/LaunchAgentRequest.java	63
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/LaunchAgentResponse.java	28
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/models/TerminateAgentResponse.java	21
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/services/AiravataFileService.java	130
modules/agent-framework/agent-service/src/main/java/org/apache/airavata/agent/connection/service/services/AiravataService.java	89
modules/agent-framework/agent-service/src/main/proto/agent-communication.proto	123
modules/agent-framework/agent-service/src/main/proto/airavata-fuse.proto	166
modules/agent-framework/agent-service/src/main/resources/distribution/conf/log4j2.xml	31
modules/agent-framework/airavata-agent/agent-communication.proto	106
modules/agent-framework/airavata-agent/agent.go	371
modules/agent-framework/airavata-agent/kernel.py	100
modules/agent-framework/airavata-agent/protos/agent-communication.pb.go	1567
modules/agent-framework/airavata-agent/protos/agent-communication_grpc.pb.go	99
modules/agent-framework/airavata-fuse/src/grpcfs/adapters.go	48
modules/agent-framework/airavata-fuse/src/grpcfs/fs.go	203
modules/agent-framework/airavata-fuse/src/grpcfs/grpc.go	101
modules/agent-framework/airavata-fuse/src/grpcfs/inode.go	121
modules/agent-framework/airavata-fuse/src/grpcfs/pb/grpcfs.pb.go	2004
modules/agent-framework/airavata-fuse/src/grpcfs/pb/grpcfs_grpc.pb.go	326
modules/agent-framework/airavata-fuse/src/grpcfs_client/main.go	50
modules/agent-framework/airavata-fuse/src/grpcfs_server/main.go	195
modules/agent-framework/airavata-fuse/src/proto/grpcfs.proto	121
modules/agent-framework/airavata-jupyter-magic/__init__.py	1
modules/agent-framework/airavata-jupyter-magic/airavata_jupyter_magic.py	472
modules/agent-framework/airavata-jupyter-magic/device_auth.py	45
modules/agent-framework/airavata-jupyter-magic/pyproject.toml	26
modules/agent-framework/deployments/jupyterhub/data/experiment_sdk/1_experiment_sdk.ipynb	401
modules/agent-framework/deployments/jupyterhub/data/gkeyll/plotE_z.ipynb	164
modules/agent-framework/deployments/jupyterhub/data/iguide/cyberfaces.ipynb	868
modules/agent-framework/deployments/jupyterhub/data/md_demo/data/amber/md.in	9
modules/agent-framework/deployments/jupyterhub/data/md_demo/molecular_dynamics.ipynb	1706
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_cpu.ipynb	401
modules/agent-framework/deployments/jupyterhub/data/namd_workshop/smd_gpu.ipynb	401
modules/agent-framework/deployments/jupyterhub/jupyterhub_config.py	53
modules/agent-framework/proto/agent-communication.proto	123
modules/agent-framework/proto/airavata-fuse.proto	166
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/AdaptorParams.java	14
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/Agent.java	3
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/AgentAdaptor.java	22
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/AgentException.java	18
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/AgentUtils.java	30
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/CommandOutput.java	7
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/FileMetadata.java	24
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/JobSubmissionOutput.java	66
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/api/StorageResourceAdaptor.java	18
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/streaming/TransferResult.java	34
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/streaming/VirtualInputStream.java	53
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/streaming/VirtualOutputStream.java	29
modules/airavata-helix/agent-api/src/main/java/org/apache/airavata/agents/streaming/VirtualStreamProducer.java	28
modules/airavata-helix/agent-impl/ssh-agent/src/main/java/org/apache/airavata/helix/agent/ssh/SshAdaptorParams.java	84
modules/airavata-helix/agent-impl/ssh-agent/src/main/java/org/apache/airavata/helix/agent/ssh/SshAgentAdaptor.java	493
modules/airavata-helix/agent-impl/ssh-agent/src/main/java/org/apache/airavata/helix/agent/ssh/StandardOutReader.java	35
modules/airavata-helix/agent-impl/ssh-agent/src/main/java/org/apache/airavata/helix/agent/storage/StorageResourceAdaptorImpl.java	51
modules/airavata-helix/agent-impl/sshj-agent/src/main/java/org/apache/airavata/helix/adaptor/PoolingSSHJClient.java	319
modules/airavata-helix/agent-impl/sshj-agent/src/main/java/org/apache/airavata/helix/adaptor/SSHJAgentAdaptor.java	444
modules/airavata-helix/agent-impl/sshj-agent/src/main/java/org/apache/airavata/helix/adaptor/SSHJStorageAdaptor.java	57
modules/airavata-helix/agent-impl/sshj-agent/src/main/java/org/apache/airavata/helix/adaptor/wrapper/SCPFileTransferWrapper.java	69
modules/airavata-helix/agent-impl/sshj-agent/src/main/java/org/apache/airavata/helix/adaptor/wrapper/SFTPClientWrapper.java	24
modules/airavata-helix/agent-impl/sshj-agent/src/main/java/org/apache/airavata/helix/adaptor/wrapper/SSHClientWrapper.java	18
modules/airavata-helix/agent-impl/sshj-agent/src/main/java/org/apache/airavata/helix/adaptor/wrapper/SessionWrapper.java	140
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/controller/HelixController.java	81
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/controller/WorkflowCleanupAgent.java	62
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/participant/GlobalParticipant.java	61
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/AiravataTask.java	514
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/TaskContext.java	775
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/TaskOnFailException.java	21
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/cancel/CancelCompletingTask.java	36
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/cancel/RemoteJobCancellationTask.java	119
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/cancel/WorkflowCancellationTask.java	112
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/completing/CompletingTask.java	26
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/env/EnvSetupTask.java	39
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/mock/MockTask.java	15
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/DataParsingTask.java	360
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/ParsingTriggeringTask.java	58
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/ProcessCompletionMessage.java	24
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/kafka/ProcessCompletionMessageDeserializer.java	22
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/kafka/ProcessCompletionMessageSerializer.java	17
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/models/ParsingTaskInput.java	38
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/models/ParsingTaskInputs.java	26
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/models/ParsingTaskOutput.java	31
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/parsing/models/ParsingTaskOutputs.java	26
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/ArchiveTask.java	125
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/DataStagingTask.java	327
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/InputDataStagingTask.java	77
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/JobVerificationTask.java	87
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/staging/OutputDataStagingTask.java	154
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/DefaultJobSubmissionTask.java	215
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/ForkJobSubmissionTask.java	67
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/JobSubmissionTask.java	181
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/LocalJobSubmissionTask.java	39
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapBuilder.java	398
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/GroovyMapData.java	420
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobFactory.java	102
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/JobManagerConfiguration.java	16
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/OutputParser.java	10
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/RawCommandInfo.java	16
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/ScriptTag.java	11
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/ForkJobConfiguration.java	82
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/HTCondorJobConfiguration.java	83
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/JobUtil.java	32
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/LSFJobConfiguration.java	87
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/PBSJobConfiguration.java	86
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/SlurmJobConfiguration.java	86
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/UGEJobConfiguration.java	82
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/AiravataCustomCommandOutputParser.java	29
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/ForkOutputParser.java	29
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/HTCondorOutputParser.java	112
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/LSFOutputParser.java	98
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/PBSOutputParser.java	106
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/SlurmOutputParser.java	101
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/task/submission/config/app/parser/UGEOutputParser.java	77
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/ParserWorkflowManager.java	323
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PostWorkflowManager.java	307
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/PreWorkflowManager.java	259
modules/airavata-helix/helix-spectator/src/main/java/org/apache/airavata/helix/impl/workflow/WorkflowManager.java	153
modules/airavata-helix/helix-spectator/src/main/resources/log4j2.xml	31
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/TaskHelper.java	5
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/TaskParamType.java	5
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/annotation/TaskDef.java	10
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/annotation/TaskOutPort.java	10
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/annotation/TaskParam.java	12
modules/airavata-helix/task-api/src/main/java/org/apache/airavata/helix/task/api/support/AdaptorSupport.java	10
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/AbstractTask.java	174
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/OutPort.java	29
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/participant/HelixParticipant.java	172
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/support/TaskHelperImpl.java	8
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/support/adaptor/AdaptorSupportImpl.java	85
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/support/adaptor/AgentStore.java	61
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/util/MonitoringUtil.java	36
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/util/PropertyResolver.java	32
modules/airavata-helix/task-core/src/main/java/org/apache/airavata/helix/core/util/TaskUtil.java	106
modules/airavata-helix/workflow-impl/src/main/java/org/apache/airavata/helix/workflow/QueueOperator.java	88
modules/airavata-helix/workflow-impl/src/main/java/org/apache/airavata/helix/workflow/WorkflowOperator.java	92
modules/airavata-metascheduler/metadata-analyzer/src/main/java/org/apache/airavata/metascheduler/metadata/analyzer/DataInterpreterService.java	79
modules/airavata-metascheduler/metadata-analyzer/src/main/java/org/apache/airavata/metascheduler/metadata/analyzer/impl/DataAnalyzerImpl.java	56
modules/airavata-metascheduler/metadata-analyzer/src/main/java/org/apache/airavata/metascheduler/metadata/analyzer/utils/Constants.java	6
modules/airavata-metascheduler/metascheduler-core/src/main/java/org/apache/airavata/metascheduler/core/api/ProcessScheduler.java	7
modules/airavata-metascheduler/metascheduler-core/src/main/java/org/apache/airavata/metascheduler/core/engine/ComputeResourceSelectionPolicy.java	6
modules/airavata-metascheduler/metascheduler-core/src/main/java/org/apache/airavata/metascheduler/core/engine/DataAnalyzer.java	4
modules/airavata-metascheduler/metascheduler-core/src/main/java/org/apache/airavata/metascheduler/core/engine/ProcessScanner.java	4
modules/airavata-metascheduler/metascheduler-core/src/main/java/org/apache/airavata/metascheduler/core/engine/ReScheduler.java	6
modules/airavata-metascheduler/metascheduler-core/src/main/java/org/apache/airavata/metascheduler/core/utils/Utils.java	107
modules/airavata-metascheduler/process-scheduler/src/main/java/org/apache/airavata/metascheduler/process/scheduling/api/ProcessSchedulerImpl.java	95
modules/airavata-metascheduler/process-scheduler/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/cr/selection/ComputeResourceSelectionPolicyImpl.java	27
modules/airavata-metascheduler/process-scheduler/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/cr/selection/DefaultComputeResourceSelectionPolicy.java	50
modules/airavata-metascheduler/process-scheduler/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/cr/selection/MultipleComputeResourcePolicy.java	59
modules/airavata-metascheduler/process-scheduler/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/rescheduler/ExponentialBackOffReScheduler.java	138
modules/airavata-metascheduler/process-scheduler/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/rescheduler/ProcessReschedulingService.java	78
modules/airavata-metascheduler/process-scheduler/src/main/java/org/apache/airavata/metascheduler/process/scheduling/engine/rescheduler/ProcessScannerImpl.java	51
modules/airavata-metascheduler/process-scheduler/src/main/java/org/apache/airavata/metascheduler/process/scheduling/utils/Constants.java	6
modules/cluster-monitoring/src/main/java/org/apache/airavata/cluster/monitoring/ClusterStatusMonitorJob.java	229
modules/cluster-monitoring/src/main/java/org/apache/airavata/cluster/monitoring/ClusterStatusMonitorJobScheduler.java	37
modules/commons/src/main/java-templates/org/apache/airavata/common/utils/BuildConstant.java	4
modules/commons/src/main/java/org/apache/airavata/common/context/RequestContext.java	17
modules/commons/src/main/java/org/apache/airavata/common/context/WorkflowContext.java	27
modules/commons/src/main/java/org/apache/airavata/common/exception/AiravataConfigurationException.java	12
modules/commons/src/main/java/org/apache/airavata/common/exception/AiravataException.java	12
modules/commons/src/main/java/org/apache/airavata/common/exception/AiravataStartupException.java	19
modules/commons/src/main/java/org/apache/airavata/common/exception/ApplicationSettingsException.java	10
modules/commons/src/main/java/org/apache/airavata/common/logging/Exception.java	33
modules/commons/src/main/java/org/apache/airavata/common/logging/MDCConstants.java	8
modules/commons/src/main/java/org/apache/airavata/common/logging/MDCUtil.java	25
modules/commons/src/main/java/org/apache/airavata/common/utils/AiravataJobState.java	87
modules/commons/src/main/java/org/apache/airavata/common/utils/AiravataUtils.java	20
modules/commons/src/main/java/org/apache/airavata/common/utils/ApplicationSettings.java	396
modules/commons/src/main/java/org/apache/airavata/common/utils/Constants.java	33
modules/commons/src/main/java/org/apache/airavata/common/utils/DBEventManagerConstants.java	27
modules/commons/src/main/java/org/apache/airavata/common/utils/DBEventService.java	16
modules/commons/src/main/java/org/apache/airavata/common/utils/DBInitConfig.java	8
modules/commons/src/main/java/org/apache/airavata/common/utils/DBInitializer.java	42
modules/commons/src/main/java/org/apache/airavata/common/utils/DBUtil.java	163
modules/commons/src/main/java/org/apache/airavata/common/utils/DatabaseCreator.java	244
modules/commons/src/main/java/org/apache/airavata/common/utils/DatabaseTestCases.java	72
modules/commons/src/main/java/org/apache/airavata/common/utils/DefaultKeyStorePasswordCallback.java	22
modules/commons/src/main/java/org/apache/airavata/common/utils/DerbyTestUtil.java	306
modules/commons/src/main/java/org/apache/airavata/common/utils/DerbyUtil.java	48
modules/commons/src/main/java/org/apache/airavata/common/utils/ExecutionMode.java	6
modules/commons/src/main/java/org/apache/airavata/common/utils/IOUtil.java	93
modules/commons/src/main/java/org/apache/airavata/common/utils/IServer.java	26
modules/commons/src/main/java/org/apache/airavata/common/utils/JDBCConfig.java	8
modules/commons/src/main/java/org/apache/airavata/common/utils/JPAUtils.java	43
modules/commons/src/main/java/org/apache/airavata/common/utils/JSONUtil.java	120
modules/commons/src/main/java/org/apache/airavata/common/utils/KeyStorePasswordCallback.java	5
modules/commons/src/main/java/org/apache/airavata/common/utils/LocalEventPublisher.java	20
modules/commons/src/main/java/org/apache/airavata/common/utils/NameValidator.java	22
modules/commons/src/main/java/org/apache/airavata/common/utils/Pair.java	21
modules/commons/src/main/java/org/apache/airavata/common/utils/SecurityUtil.java	109
modules/commons/src/main/java/org/apache/airavata/common/utils/ServerSettings.java	431
modules/commons/src/main/java/org/apache/airavata/common/utils/ServiceUtils.java	1
modules/commons/src/main/java/org/apache/airavata/common/utils/StringUtil.java	332
modules/commons/src/main/java/org/apache/airavata/common/utils/SwingUtil.java	193
modules/commons/src/main/java/org/apache/airavata/common/utils/ThriftClientPool.java	176
modules/commons/src/main/java/org/apache/airavata/common/utils/ThriftUtils.java	43
modules/commons/src/main/java/org/apache/airavata/common/utils/Version.java	82
modules/commons/src/main/java/org/apache/airavata/common/utils/WSConstants.java	36
modules/commons/src/main/java/org/apache/airavata/common/utils/WSDLUtil.java	95
modules/commons/src/main/java/org/apache/airavata/common/utils/ZkConstants.java	10
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/ConfigParam.java	53
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/InvalidSetupException.java	14
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/InvalidUsernameException.java	14
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountManager.java	221
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountProvisioner.java	10
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountProvisionerFactory.java	31
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHAccountProvisionerProvider.java	12
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/SSHUtil.java	113
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/provisioner/IULdapSSHAccountProvisioner.java	203
modules/compute-account-provisioning/src/main/java/org/apache/airavata/accountprovisioning/provisioner/IULdapSSHAccountProvisionerProvider.java	56
modules/computer-resource-monitoring-service/src/main/java/org/apache/airavata/compute/resource/monitoring/ComputationalResourceMonitoringService.java	90
modules/computer-resource-monitoring-service/src/main/java/org/apache/airavata/compute/resource/monitoring/job/ComputeResourceMonitor.java	102
modules/computer-resource-monitoring-service/src/main/java/org/apache/airavata/compute/resource/monitoring/job/MonitoringJob.java	146
modules/computer-resource-monitoring-service/src/main/java/org/apache/airavata/compute/resource/monitoring/job/output/OutputParser.java	6
modules/computer-resource-monitoring-service/src/main/java/org/apache/airavata/compute/resource/monitoring/job/output/OutputParserImpl.java	36
modules/computer-resource-monitoring-service/src/main/java/org/apache/airavata/compute/resource/monitoring/utils/Constants.java	14
modules/configuration/server/src/main/resources/log4j2.xml	31
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/credential/AuditInfo.java	8
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/credential/CommunityUser.java	35
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/credential/Credential.java	38
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/credential/CredentialOwnerType.java	21
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/credential/impl/certificate/CertificateAuditInfo.java	58
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/credential/impl/certificate/CertificateCredential.java	52
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/credential/impl/password/PasswordCredential.java	25
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/credential/impl/ssh/SSHCredential.java	45
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/notifier/CredentialStoreNotifier.java	5
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/notifier/NotificationMessage.java	10
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/notifier/NotifierBootstrap.java	79
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/notifier/impl/EmailNotificationMessage.java	23
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/notifier/impl/EmailNotifier.java	33
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/notifier/impl/EmailNotifierConfiguration.java	46
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServer.java	111
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServerHandler.java	426
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/servlet/CredentialBootstrapper.java	15
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/servlet/CredentialStoreCallbackServlet.java	181
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/servlet/CredentialStoreStartServlet.java	117
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/CredentialReader.java	17
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/CredentialReaderFactory.java	13
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/CredentialStoreException.java	12
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/CredentialWriter.java	5
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/CertificateCredentialWriter.java	59
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/CredentialReaderImpl.java	121
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/SSHCredentialWriter.java	47
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/db/CommunityUserDAO.java	154
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/db/CredentialsDAO.java	308
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/db/ParentDAO.java	9
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/CredentialStoreDBInitConfig.java	17
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/CredentialStoreJDBCConfig.java	46
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/util/ConfigurationReader.java	64
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/util/CredentialStoreConstants.java	8
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/util/PrivateKeyStore.java	27
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/util/TokenGenerator.java	16
modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/util/Utility.java	66
modules/credential-store/credential-store-service/src/main/resources/credstore-derby.sql	23
modules/credential-store/credential-store-service/src/main/resources/credstore-mysql.sql	23
modules/credential-store/credential-store-stubs/src/main/java/org/apache/airavata/credential/store/client/CredentialStoreClientFactory.java	22
modules/credential-store/credential-store-stubs/src/main/java/org/apache/airavata/credential/store/client/TestSSLClient.java	103
modules/credential-store/credential-store-stubs/src/main/java/org/apache/airavata/credential/store/cpi/credential_store_cpiConstants.java	5
modules/credential-store/credential-store-stubs/src/main/java/org/apache/airavata/credential/store/exception/CredentialStoreException.java	293
modules/db-event-manager/src/main/java/org/apache/airavata/db/event/manager/DBEventManagerRunner.java	84
modules/db-event-manager/src/main/java/org/apache/airavata/db/event/manager/messaging/DBEventManagerException.java	13
modules/db-event-manager/src/main/java/org/apache/airavata/db/event/manager/messaging/DBEventManagerMessagingFactory.java	39
modules/db-event-manager/src/main/java/org/apache/airavata/db/event/manager/messaging/impl/DBEventMessageHandler.java	73
modules/db-event-manager/src/main/java/org/apache/airavata/db/event/manager/utils/Constants.java	7
modules/db-event-manager/src/main/java/org/apache/airavata/db/event/manager/utils/DbEventManagerZkUtils.java	43
modules/distribution/src/main/assembly/api-server-bin-assembly.xml	145
modules/distribution/src/main/assembly/api-server-src-assembly.xml	50
modules/distribution/src/main/assembly/controller-bin-assembly.xml	156
modules/distribution/src/main/assembly/email-monitor-bin-assembly.xml	101
modules/distribution/src/main/assembly/parser-wm-bin-assembly.xml	155
modules/distribution/src/main/assembly/participant-bin-assembly.xml	202
modules/distribution/src/main/assembly/post-wm-bin-assembly.xml	161
modules/distribution/src/main/assembly/pre-wm-bin-assembly.xml	161
modules/distribution/src/main/assembly/realtime-monitor-bin-assembly.xml	94
modules/distribution/src/main/resources/controller/conf/log4j2.xml	31
modules/distribution/src/main/resources/email-monitor/conf/email-config.yaml	49
modules/distribution/src/main/resources/email-monitor/conf/log4j2.xml	31
modules/distribution/src/main/resources/parser-wm/conf/log4j2.xml	31
modules/distribution/src/main/resources/participant/conf/log4j2.xml	31
modules/distribution/src/main/resources/post-wm/conf/log4j2.xml	31
modules/distribution/src/main/resources/pre-wm/conf/log4j2.xml	31
modules/distribution/src/main/resources/realtime-monitor/conf/log4j2.xml	31
modules/file-server/src/main/assembly/file-service-bin-assembly.xml	66
modules/file-server/src/main/java/org/apache/airavata/file/server/FileServerApplication.java	14
modules/file-server/src/main/java/org/apache/airavata/file/server/FileServerConfiguration.java	37
modules/file-server/src/main/java/org/apache/airavata/file/server/controller/FileController.java	79
modules/file-server/src/main/java/org/apache/airavata/file/server/model/AiravataDirectory.java	37
modules/file-server/src/main/java/org/apache/airavata/file/server/model/AiravataFile.java	37
modules/file-server/src/main/java/org/apache/airavata/file/server/model/FileUploadResponse.java	37
modules/file-server/src/main/java/org/apache/airavata/file/server/service/AirvataFileService.java	92
modules/file-server/src/main/java/org/apache/airavata/file/server/service/ProcessDataManager.java	45
modules/file-server/src/main/resources/distribution/conf/log4j2.xml	31
modules/ide-integration/src/main/containers/database_scripts/init/02-sharing-registry-migrations.sql	3
modules/ide-integration/src/main/containers/database_scripts/init/03-appcatalog-migrations.sql	10
modules/ide-integration/src/main/containers/database_scripts/init/04-expcatalog-migrations.sql	28
modules/ide-integration/src/main/containers/database_scripts/init/05-replica-catalog-migrations.sql	21
modules/ide-integration/src/main/containers/keycloak/standalone.xml	520
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/app.php	90
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/auth.php	11
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/cache.php	11
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/compile.php	3
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/database.php	49
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/local/app.php	4
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/local/database.php	25
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/mail.php	12
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/packages/markdown/config.php	4
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/packages/teepluss/theme/config.php	30
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/packages/teepluss/theme/twig.php	22
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/pga_config.php	73
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/queue.php	37
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/remote.php	17
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/services.php	14
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/session.php	14
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/testing/cache.php	4
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/testing/session.php	4
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/view.php	5
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/config/workbench.php	5
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/AccountController.php	436
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/AdminController.php	517
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/ApplicationController.php	143
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/BaseController.php	14
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/ComputeResourceController.php	252
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/DataCatController.php	17
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/ExperimentController.php	536
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/FilemanagerController.php	35
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/GatewayRequestUpdateController.php	44
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/GatewayprofileController.php	103
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/GroupController.php	37
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/HomeController.php	17
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/ProjectController.php	199
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/StorageResourceController.php	112
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/controllers/UserSettingsController.php	259
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/database/seeds/DatabaseSeeder.php	7
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/filters.php	84
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/lang/en/pagination.php	5
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/lang/en/reminders.php	7
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/lang/en/validation.php	66
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/AdminUtilities.php	337
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/API/Error/Types.php	921
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/API/Sharing/Types.php	10
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/API/Types.php	17
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/AiravataServiceProvider.php	47
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Facades/Airavata.php	6
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Facades/IamAdminServices.php	6
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Facades/TenantProfileServices.php	6
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Facades/UserProfileServices.php	6
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/IamAdminServiceProvider.php	50
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/AccountProvisioning/Types.php	296
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/AppDeployment/Types.php	878
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/AppInterface/Types.php	297
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/ComputeResource/Types.php	2057
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/GatewayGroups/Types.php	135
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/GatewayProfile/Types.php	775
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/GroupResourceProfile/Types.php	1193
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/Parallelism/Types.php	26
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/StorageResource/Types.php	223
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/AppCatalog/UserResourceProfile/Types.php	641
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Application/Io/Types.php	598
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Commons/Types.php	405
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Credential/Store/Types.php	916
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Data/Movement/Types.php	639
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Data/Replica/Types.php	704
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Dbevent/Types.php	495
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Experiment/Types.php	1657
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Group/Types.php	209
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Job/Types.php	323
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Messaging/Event/Types.php	1642
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Model/Process/Types.php	726
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modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/Airavata/Service/Profile/Groupmanager/CPI/Error/Types.php	75
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modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/libraries/IamAdminServicesUtilities.php	38
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modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/module-block.blade.php	14
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/queue-block.blade.php	77
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/resource-job-manager.blade.php	45
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/sharing-display-body.blade.php	18
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/sharing-form-body.blade.php	12
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/sharing-form-modal.blade.php	19
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/storage-resource-preferences.blade.php	45
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/streaming-data.blade.php	4
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/user-compute-resource-preferences.blade.php	122
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/partials/user-storage-resource-preferences.blade.php	45
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/project/browse.blade.php	114
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/project/create.blade.php	42
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/project/edit.blade.php	58
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/project/no-sharing-create.blade.php	23
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/project/no-sharing-edit.blade.php	36
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/project/no-sharing-summary.blade.php	91
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/project/summary.blade.php	106
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/resource/browse.blade.php	181
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/resource/create.blade.php	46
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/resource/edit.blade.php	719
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/resource/view.blade.php	365
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/scigap-admin/manage-gateway.blade.php	149
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/server-down.blade.php	12
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/storage-resource/browse.blade.php	173
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/storage-resource/create.blade.php	36
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/storage-resource/edit.blade.php	329
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/app/views/storage-resource/view.blade.php	345
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/bootstrap/autoload.php	13
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/bootstrap/paths.php	7
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/bootstrap/start.php	10
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/phpunit.xml	18
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/css/admin.css	253
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/css/bootstrap-toggle.css	21
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/css/filemanager.css	37
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/css/morris.css	2
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/css/sharing.css	95
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/css/style.css	1
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/css/user-settings.css	13
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/index.php	4
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/bootstrap-toggle.js	133
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/datacat/GLmol.js	594
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/deployment.js	113
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/filemanager.js	101
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/flot/flot-data.js	1046
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/gateway.js	69
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/interface.js	108
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/moment.js	2345
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/morris/morris-data.js	207
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/script.js	280
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/sharing/groups.js	121
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/sharing/share.js	370
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/sharing/sharing_utils.js	174
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/simstream.js	127
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/time-conversion.js	43
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/js/util.js	11
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/themes/base/layouts/default.blade.php	1
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/themes/base/partials/about.blade.php	1
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/themes/base/partials/documentation.blade.php	1
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/themes/base/partials/footer.blade.php	1
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/themes/base/partials/header.blade.php	33
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/themes/base/partials/template.blade.php	1
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/public/themes/base/views/index.blade.php	1
modules/ide-integration/src/main/containers/pga/airavata-php-gateway/server.php	10
modules/ide-integration/src/main/java/org/apache/airavata/ide/integration/APIServerStarter.java	26
modules/ide-integration/src/main/java/org/apache/airavata/ide/integration/JobEngineStarter.java	37
modules/ide-integration/src/main/java/org/apache/airavata/ide/integration/JobMonitorStarter.java	8
modules/ide-integration/src/main/resources/email-config.yaml	49
modules/ide-integration/src/main/resources/log4j2.xml	31
modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/EmailBasedMonitor.java	261
modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/AiravataCustomMailParser.java	48
modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/EmailParser.java	13
modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/HTCondorEmailParser.java	73
modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/LSFEmailParser.java	54
modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/PBSEmailParser.java	76
modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/ResourceConfig.java	26
modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/SLURMEmailParser.java	59
modules/job-monitor/email-monitor/src/main/java/org/apache/airavata/monitor/email/parser/UGEEmailParser.java	78
modules/job-monitor/email-monitor/src/main/resources/email-config.yaml	19
modules/job-monitor/email-monitor/src/main/resources/log4j2.xml	31
modules/job-monitor/job-monitor-api/src/main/java/org/apache/airavata/monitor/AbstractMonitor.java	91
modules/job-monitor/job-monitor-api/src/main/java/org/apache/airavata/monitor/JobStateValidator.java	62
modules/job-monitor/job-monitor-api/src/main/java/org/apache/airavata/monitor/JobStatusResult.java	39
modules/job-monitor/job-monitor-api/src/main/java/org/apache/airavata/monitor/MonitoringException.java	17
modules/job-monitor/job-monitor-api/src/main/java/org/apache/airavata/monitor/kafka/JobStatusResultDeserializer.java	24
modules/job-monitor/job-monitor-api/src/main/java/org/apache/airavata/monitor/kafka/JobStatusResultSerializer.java	20
modules/job-monitor/job-monitor-api/src/main/java/org/apache/airavata/monitor/kafka/MessageProducer.java	33
modules/job-monitor/real-time-monitor/src/main/java/org/apache/airavata/monitor/realtime/RealtimeMonitor.java	64
modules/job-monitor/real-time-monitor/src/main/java/org/apache/airavata/monitor/realtime/parser/RealtimeJobStatusParser.java	105
modules/job-monitor/real-time-monitor/src/main/resources/log4j2.xml	31
modules/messaging/client/src/main/java/org/apache/airavata/messaging/client/RabbitMQListener.java	198
modules/messaging/client/src/main/java/org/apache/airavata/messaging/client/TestReader.java	6
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/MessageContext.java	56
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/MessageHandler.java	5
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/MessagingConstants.java	12
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/MessagingFactory.java	144
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/Publisher.java	6
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/PublisherFactory.java	1
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/RabbitMQProperties.java	83
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/Subscriber.java	14
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/TestClient.java	46
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/Type.java	6
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/ExperimentConsumer.java	92
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/MessageConsumer.java	57
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/ProcessConsumer.java	91
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQProcessLaunchConsumer.java	1
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQProcessLaunchPublisher.java	1
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQProducer.java	1
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQPublisher.java	119
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQStatusPublisher.java	1
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQStatusSubscriber.java	1
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/RabbitMQSubscriber.java	150
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/impl/StatusConsumer.java	113
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/stats/CountWriterTask.java	28
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/stats/LatencyWriterTask.java	30
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/stats/StatCounter.java	65
modules/messaging/core/src/main/java/org/apache/airavata/messaging/core/util/DBEventPublisherUtils.java	61
modules/orchestrator/orchestrator-client/src/main/java/org/apache/airavata/orchestrator/client/OrchestratorClientFactory.java	20
modules/orchestrator/orchestrator-client/src/main/java/org/apache/airavata/orchestrator/cpi/OrchestratorService.java	4448
modules/orchestrator/orchestrator-client/src/main/java/org/apache/airavata/orchestrator/cpi/orchestrator_cpiConstants.java	5
modules/orchestrator/orchestrator-client/src/main/java/org/apache/airavata/orchestrator/sample/OrchestratorClientSample.java	65
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/OrchestratorConfiguration.java	68
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/context/OrchestratorContext.java	26
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/exception/OrchestratorException.java	13
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACPassiveJobSubmitter.java	102
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/job/JobSubmitter.java	8
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/schedule/DefaultHostScheduler.java	13
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/schedule/HostScheduler.java	6
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/utils/OrchestratorConstants.java	14
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/utils/OrchestratorUtils.java	374
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/validator/JobMetadataValidator.java	8
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/validator/impl/BatchQueueValidator.java	185
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/validator/impl/ExperimentStatusValidator.java	32
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/validator/impl/GroupResourceProfileValidator.java	158
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/Orchestrator.java	13
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/AbstractOrchestrator.java	67
modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/cpi/impl/SimpleOrchestratorImpl.java	688
modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServer.java	177
modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java	831
modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/Constants.java	6
modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/OrchestratorServerThreadPoolExecutor.java	28
modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/util/OrchestratorUtils.java	73
modules/platform-monitoring/src/main/java/org/apache/airavata/patform/monitoring/CountMonitor.java	23
modules/platform-monitoring/src/main/java/org/apache/airavata/patform/monitoring/GaugeMonitor.java	20
modules/platform-monitoring/src/main/java/org/apache/airavata/patform/monitoring/MonitoringServer.java	29
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/RegistryException.java	6
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowEntity.java	93
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowErrorEntity.java	82
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowErrorPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowStatusEntity.java	65
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/AiravataWorkflowStatusPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/ApplicationErrorEntity.java	82
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/ApplicationErrorPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/ApplicationStatusEntity.java	65
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/ApplicationStatusPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerErrorEntity.java	85
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerErrorPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerInputEntity.java	140
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerInputPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerOutputEntity.java	124
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerOutputPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerStatusEntity.java	66
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/HandlerStatusPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowApplicationEntity.java	137
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowApplicationPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowConnectionEntity.java	123
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowConnectionPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowDataBlockEntity.java	78
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowHandlerEntity.java	98
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/airavataworkflowcatalog/WorkflowHandlerPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/AppEnvironmentEntity.java	57
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/AppEnvironmentPK.java	35
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/AppModuleMappingEntity.java	47
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/AppModuleMappingPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationDeploymentEntity.java	189
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInputEntity.java	141
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInputPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationInterfaceEntity.java	101
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationModuleEntity.java	71
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationOutputEntity.java	123
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ApplicationOutputPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/BatchQueueEntity.java	134
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/BatchQueuePK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/BatchQueueResourcePolicyEntity.java	84
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/CloudJobSubmissionEntity.java	61
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourceEntity.java	173
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourceFileSystemEntity.java	48
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourceFileSystemPK.java	41
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourcePolicyEntity.java	67
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourcePreferenceEntity.java	172
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourcePreferencePK.java	44
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ComputeResourceReservationEntity.java	80
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/DataMovementInterfaceEntity.java	73
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/DataMovementInterfacePK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GatewayGroupsEntity.java	60
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GatewayProfileEntity.java	79
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GlobusGkEndpointEntity.java	29
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GlobusGkEndpointPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GlobusSubmissionEntity.java	37
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GridftpDataMovementEntity.java	46
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GridftpEndpointEntity.java	55
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GridftpEndpointPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupComputeResourcePrefEntity.java	172
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupComputeResourcePrefPK.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupResourceProfileEntity.java	93
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupSSHAccountProvisionerConfig.java	69
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GroupSSHAccountProvisionerConfigPK.java	50
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshExportEntity.java	29
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshExportPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshPostjobcommandEntity.java	29
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshPostjobcommandPK.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshPrejobcommandEntity.java	29
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshPrejobcommandPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/GsisshSubmissionEntity.java	54
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/JobManagerCommandEntity.java	48
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/JobManagerCommandPK.java	41
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/JobSubmissionInterfaceEntity.java	73
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/JobSubmissionInterfacePK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LibraryApendPathEntity.java	49
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LibraryAppendPathPK.java	33
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LibraryPrependPathEntity.java	49
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LibraryPrependPathPK.java	33
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LocalDataMovementEntity.java	22
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/LocalSubmissionEntity.java	63
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ModuleLoadCmdEntity.java	49
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ModuleLoadCmdPK.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParallelismCommandEntity.java	48
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParallelismCommandPK.java	41
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserConnectorEntity.java	78
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserConnectorInputEntity.java	76
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserEntity.java	76
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserInputEntity.java	58
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParserOutputEntity.java	58
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParsingTemplateEntity.java	52
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ParsingTemplateInputEntity.java	67
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/PostjobCommandEntity.java	45
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/PostjobCommandPK.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/PrejobCommandEntity.java	45
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/PrejobCommandPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ResourceJobManagerEntity.java	63
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/SSHAccountProvisionerConfiguration.java	62
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/SSHAccountProvisionerConfigurationPK.java	30
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/ScpDataMovementEntity.java	70
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/SshJobSubmissionEntity.java	80
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StorageInterfaceEntity.java	73
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StorageInterfacePK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StoragePreferenceEntity.java	62
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StoragePreferencePK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/StorageResourceEntity.java	70
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UnicoreDatamovementEntity.java	42
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UnicoreSubmissionEntity.java	37
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserComputeResourcePreferenceEntity.java	130
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserComputeResourcePreferencePK.java	49
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserResourceProfileEntity.java	88
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserResourceProfilePK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserStoragePreferenceEntity.java	73
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/appcatalog/UserStoragePreferencePK.java	49
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ComputationalResourceSchedulingEntity.java	121
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ComputationalResourceSchedulingPK.java	49
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentEntity.java	175
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentErrorEntity.java	83
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentErrorPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentInputEntity.java	144
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentInputPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentOutputEntity.java	129
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentOutputPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentStatusEntity.java	66
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentStatusPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ExperimentSummaryEntity.java	100
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayEntity.java	166
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayUsageReportingCommandEntity.java	36
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayUsageReportingPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayWorkerEntity.java	29
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/GatewayWorkerPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/JobEntity.java	125
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/JobPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/JobStatusEntity.java	78
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/JobStatusPK.java	49
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/NotificationEntity.java	78
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessEntity.java	242
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessErrorEntity.java	83
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessErrorPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessInputEntity.java	146
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessInputPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessOutputEntity.java	129
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessOutputPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessResourceScheduleEntity.java	116
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessStatusEntity.java	66
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessStatusPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessWorkflowEntity.java	51
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProcessWorkflowPK.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProjectEntity.java	61
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProjectUserEntity.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/ProjectUserPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/QueueStatusEntity.java	64
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/QueueStatusPK.java	51
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskEntity.java	110
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskErrorEntity.java	83
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskErrorPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskStatusEntity.java	66
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/TaskStatusPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/UserConfigurationDataEntity.java	207
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/UserEntity.java	50
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/expcatalog/UserPK.java	37
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/ConfigurationEntity.java	27
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/ConfigurationPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataProductEntity.java	111
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataProductMetadataEntity.java	35
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataProductMetadataPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataReplicaLocationEntity.java	124
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataReplicaMetadataEntity.java	35
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/replicacatalog/DataReplicaMetadataPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/ComponentStatusEntity.java	55
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/EdgeEntity.java	63
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/EdgePK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/NodeEntity.java	79
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/NodePK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/PortEntity.java	63
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/PortPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowEntity.java	98
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowInputEntity.java	118
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowInputPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowOutputEntity.java	110
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowOutputPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowStatusEntity.java	54
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/entities/workflowcatalog/WorkflowStatusPK.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/AbstractRepository.java	167
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/AppCatAbstractRepository.java	13
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationDeploymentRepository.java	190
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInputRepository.java	9
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationInterfaceRepository.java	232
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationModuleRepository.java	8
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ApplicationOutputRepository.java	9
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/BatchQueuePolicyRepository.java	8
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/BatchQueueRepository.java	9
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ComputeResourcePolicyRepository.java	8
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ComputeResourcePrefRepository.java	27
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ComputeResourceRepository.java	483
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/DataMovementRepository.java	18
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/GatewayGroupsRepository.java	8
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/GroupResourceProfileRepository.java	149
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/GrpComputePrefRepository.java	9
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/GwyResourceProfileRepository.java	156
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/JobSubmissionInterfaceRepository.java	18
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ParserInputRepository.java	20
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ParserOutputRepository.java	20
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ParserRepository.java	47
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ParsingTemplateRepository.java	23
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/ResourceJobManagerRepository.java	74
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/StoragePrefRepository.java	9
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/StorageResourceRepository.java	169
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserComputeResourcePreferenceRepository.java	11
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserResourceProfileRepository.java	171
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/appcatalog/UserStoragePreferenceRepository.java	11
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExpCatAbstractRepository.java	13
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentErrorRepository.java	43
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentInputRepository.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentOutputRepository.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentRepository.java	136
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentStatusRepository.java	72
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ExperimentSummaryRepository.java	343
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/GatewayRepository.java	67
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/GatewayUsageReportingCommandRepository.java	42
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/JobRepository.java	115
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/JobStatusRepository.java	74
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/NotificationRepository.java	66
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessErrorRepository.java	42
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessInputRepository.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessOutputRepository.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessRepository.java	164
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessStatusRepository.java	87
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProcessWorkflowRepository.java	41
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/ProjectRepository.java	143
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/QueueStatusRepository.java	42
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskErrorRepository.java	41
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskRepository.java	118
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/TaskStatusRepository.java	60
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/expcatalog/UserRepository.java	37
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/replicacatalog/DataProductRepository.java	105
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/replicacatalog/DataReplicaLocationRepository.java	60
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/replicacatalog/RepCatAbstractRepository.java	13
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/workflowcatalog/WorkflowCatAbstractRepository.java	13
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/repositories/workflowcatalog/WorkflowRepository.java	120
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/AppCatalogDBInitConfig.java	40
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/AppCatalogJDBCConfig.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/AppCatalogUtils.java	8
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/Committer.java	5
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/CustomBeanFactory.java	52
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/DBConstants.java	149
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/DozerConverter/CsvStringConverter.java	25
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/DozerConverter/StorageDateConverter.java	23
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/ExpCatalogDBInitConfig.java	53
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/ExpCatalogJDBCConfig.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/ExpCatalogUtils.java	8
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/JPAUtil/AppCatalogJPAUtils.java	15
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/JPAUtil/ExpCatalogJPAUtils.java	14
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/JPAUtil/RepCatalogJPAUtils.java	14
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/JPAUtil/WorkflowCatalogJPAUtils.java	14
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/ObjectMapperSingleton.java	53
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/QueryConstants.java	166
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/ReplicaCatalogDBInitConfig.java	23
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/ReplicaCatalogJDBCConfig.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/WorkflowCatalogDBInitConfig.java	22
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/WorkflowCatalogJDBCConfig.java	38
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/WorkflowCatalogUtils.java	8
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/migration/MappingToolRunner.java	34
modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/utils/migration/MigrationSchemaGenerator.java	86
modules/registry/registry-core/src/main/resources/META-INF/persistence.xml	120
modules/registry/registry-core/src/main/resources/airavataworkflowcatalog-derby.sql	177
modules/registry/registry-core/src/main/resources/appcatalog-derby.sql	631
modules/registry/registry-core/src/main/resources/appcatalog-mysql.sql	636
modules/registry/registry-core/src/main/resources/dozer_mapping.xml	45
modules/registry/registry-core/src/main/resources/expcatalog-derby.sql	387
modules/registry/registry-core/src/main/resources/expcatalog-mysql.sql	387
modules/registry/registry-core/src/main/resources/migrations-util/mysql/docker-entrypoint-initdb.d/create_databases.sql	6
modules/registry/registry-core/src/main/resources/replicacatalog-derby.sql	54
modules/registry/registry-core/src/main/resources/replicacatalog-mysql.sql	52
modules/registry/registry-core/src/main/resources/workflowcatalog-derby.sql	100
modules/registry/registry-core/src/main/resources/workflowcatalog-mysql.sql	100
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/AppCatalog.java	10
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/AppCatalogException.java	13
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ApplicationDeployment.java	16
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ApplicationInterface.java	28
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/CompositeIdentifier.java	33
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ComputeResource.java	43
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/DataProductInterface.java	15
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/DataReplicaLocationInterface.java	10
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ExpCatChildDataType.java	20
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ExpCatParentDataType.java	11
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ExperimentCatalog.java	24
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ExperimentCatalogException.java	13
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ExperimentCatalogModelType.java	29
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/GwyClientCredential.java	8
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/GwyResourceProfile.java	20
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/Registry.java	7
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/RegistryException.java	13
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ReplicaCatalog.java	3
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ReplicaCatalogException.java	12
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/ResultOrderType.java	5
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/StorageResource.java	16
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/UsrResourceProfile.java	22
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/WorkflowCatalog.java	11
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/WorkflowCatalogException.java	13
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/utils/Constants.java	64
modules/registry/registry-cpi/src/main/java/org/apache/airavata/registry/cpi/utils/StatusType.java	9
modules/registry/registry-server/registry-api-service/src/main/java/org/apache/airavata/registry/api/service/RegistryAPIServer.java	145
modules/registry/registry-server/registry-api-service/src/main/java/org/apache/airavata/registry/api/service/handler/RegistryServerHandler.java	3811
modules/registry/registry-server/registry-api-service/src/main/java/org/apache/airavata/registry/api/service/messaging/RegistryServiceDBEventHandler.java	152
modules/registry/registry-server/registry-api-service/src/main/java/org/apache/airavata/registry/api/service/messaging/RegistryServiceDBEventMessagingFactory.java	58
modules/registry/registry-server/registry-api-service/src/main/java/org/apache/airavata/registry/api/service/util/Constants.java	15
modules/registry/registry-server/registry-api-stubs/src/main/java/org/apache/airavata/registry/api/client/RegistryServiceClientFactory.java	20
modules/registry/registry-server/registry-api-stubs/src/main/java/org/apache/airavata/registry/api/exception/RegistryServiceException.java	293
modules/registry/registry-server/registry-api-stubs/src/main/java/org/apache/airavata/registry/api/registry_apiConstants.java	5
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/BatchQueueGenerator.java	59
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/ComputeResourceDescriptionGenerator.java	53
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/DataMovementInterfaceGenerator.java	56
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/FileSystemsGenerator.java	55
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/GridFTPDataMovementGenerator.java	52
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/GridFTPEndpointsGenerator.java	54
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/JobManagerCommandGenerator.java	55
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/JobSubmissionInterfaceGenerator.java	56
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/LocalDataMovementGenerator.java	51
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/LocalSubmissionGenerator.java	53
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/ModuleCMDGenerator.java	54
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/ResourceJobManagerGenerator.java	54
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/SCPDataMovementGenerator.java	54
modules/registry/registry-tools/jpa-gen/src/main/java/appcatalog/computeresource/SSHJobSubmissionGenerator.java	56
modules/registry/registry-tools/jpa-gen/src/main/java/generators/AbstractGenerator.java	84
modules/registry/registry-tools/jpa-gen/src/main/java/generators/JPAClassGenerator.java	160
modules/registry/registry-tools/jpa-gen/src/main/java/generators/JPAResourceClassGenerator.java	430
modules/registry/registry-tools/jpa-gen/src/main/java/generators/SQLGenerator.java	49
modules/registry/registry-tools/jpa-gen/src/main/java/model/JPAClassField.java	23
modules/registry/registry-tools/jpa-gen/src/main/java/model/JPAClassModel.java	11
modules/registry/registry-tools/jpa-gen/src/main/java/model/JPAPKClassModel.java	7
modules/registry/registry-tools/jpa-gen/src/main/java/model/JPAResourceClassModel.java	6
modules/registry/registry-tools/jpa-gen/src/main/java/model/SQLData.java	54
modules/registry/registry-tools/registry-tool/src/main/java/org/apache/airavata/registry/tool/DBMigrator.java	312
modules/registry/registry-tools/registry-tool/src/main/resources/db-scripts/0.6/migrate_derby.sql	7
modules/registry/registry-tools/registry-tool/src/main/resources/db-scripts/0.6/migrate_mysql.sql	7
modules/registry/registry-tools/registry-tool/src/main/resources/db-scripts/0.7/migrate_derby.sql	17
modules/registry/registry-tools/registry-tool/src/main/resources/db-scripts/0.7/migrate_mysql.sql	17
modules/registry/registry-tools/registry-tool/src/main/resources/db-scripts/0.8/migrate_derby.sql	48
modules/registry/registry-tools/registry-tool/src/main/resources/db-scripts/0.8/migrate_mysql.sql	48
modules/registry/release-migration-scripts/0.16-0.17/DeltaScripts/appCatalog_schema_delta.sql	77
modules/registry/release-migration-scripts/0.16-0.17/DeltaScripts/credentialStore_schema_delta.sql	8
modules/registry/release-migration-scripts/0.16-0.17/DeltaScripts/expCatalog_schema_delta.sql	25
modules/registry/release-migration-scripts/0.16-0.17/DeltaScripts/profile_service_schema_delta.sql	1
modules/registry/release-migration-scripts/0.16-0.17/DeltaScripts/replicaCatalog_schema_delta.sql	3
modules/registry/release-migration-scripts/0.16-0.17/DeltaScripts/sharingCatalog_schema_delta.sql	9
modules/registry/release-migration-scripts/0.16-0.17/DeltaScripts/workFlow_schema_delta.sql	2
modules/registry/release-migration-scripts/0.16-0.17/keycloak-migration-replica-catalog/replicaCatalog_lowercase_user_data_dir_example.sql	17
modules/registry/release-migration-scripts/0.16-0.17/keycloak-migration/credentialStore_keycloak_migration.sql	1
modules/registry/release-migration-scripts/0.16-0.17/keycloak-migration/expCatalog_keycloak_migration.sql	9
modules/registry/release-migration-scripts/0.16-0.17/keycloak-migration/profileService_keycloak_migration.sql	6
modules/registry/release-migration-scripts/0.16-0.17/keycloak-migration/sharingCatalog_keycloak_migration.sql	6
modules/registry/release-migration-scripts/0.17-0.18/DeltaScripts/expCatalog_schema_delta.sql	12
modules/registry/release-migration-scripts/0.17-0.18/DeltaScripts/profile_service_schema_delta.sql	31
modules/registry/release-migration-scripts/0.17-0.18/DeltaScripts/sharingCatalog_schema_delta.sql	7
modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/appCatalog_schema_delta.sql	370
modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/credential_store_schema_delta.sql	10
modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/experimentCatalog_schema_delta.sql	84
modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/profile_service_schema_delta.sql	42
modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/replicaCatalog_schema_delta.sql	19
modules/registry/release-migration-scripts/0.18-0.19/DeltaScripts/sharingCatalog_schema_delta.sql	17
modules/registry/release-migration-scripts/0.19-0.20/DeltaScripts/appCatalog_schema_delta.sql	5
modules/registry/release-migration-scripts/0.19-0.20/DeltaScripts/credential_store_schema_delta.sql	1
modules/registry/release-migration-scripts/0.19-0.20/DeltaScripts/experimentCatalog_schema_delta.sql	10
modules/registry/release-migration-scripts/0.19-0.20/DeltaScripts/profile_service_schema_delta.sql	1
modules/registry/release-migration-scripts/0.19-0.20/DeltaScripts/replicaCatalog_schema_delta.sql	1
modules/registry/release-migration-scripts/0.19-0.20/DeltaScripts/sharingCatalog_schema_delta.sql	1
modules/registry/release-migration-scripts/next/DeltaScripts/appCatalog_schema_delta.sql	1
modules/registry/release-migration-scripts/next/DeltaScripts/credential_store_schema_delta.sql	1
modules/registry/release-migration-scripts/next/DeltaScripts/experimentCatalog_schema_delta.sql	18
modules/registry/release-migration-scripts/next/DeltaScripts/profile_service_schema_delta.sql	1
modules/registry/release-migration-scripts/next/DeltaScripts/replicaCatalog_schema_delta.sql	21
modules/registry/release-migration-scripts/next/DeltaScripts/sharingCatalog_schema_delta.sql	1
modules/security/src/main/java/org/apache/airavata/security/AbstractAuthenticator.java	66
modules/security/src/main/java/org/apache/airavata/security/AbstractDatabaseAuthenticator.java	68
modules/security/src/main/java/org/apache/airavata/security/AiravataSecurityException.java	15
modules/security/src/main/java/org/apache/airavata/security/AuthenticationException.java	12
modules/security/src/main/java/org/apache/airavata/security/Authenticator.java	14
modules/security/src/main/java/org/apache/airavata/security/Authoriser.java	5
modules/security/src/main/java/org/apache/airavata/security/UserStore.java	7
modules/security/src/main/java/org/apache/airavata/security/UserStoreException.java	15
modules/security/src/main/java/org/apache/airavata/security/configurations/AbstractConfigurationReader.java	22
modules/security/src/main/java/org/apache/airavata/security/configurations/AuthenticatorConfigurationReader.java	149
modules/security/src/main/java/org/apache/airavata/security/userstore/AbstractJDBCUserStore.java	73
modules/security/src/main/java/org/apache/airavata/security/userstore/JDBCUserStore.java	99
modules/security/src/main/java/org/apache/airavata/security/userstore/LDAPUserStore.java	86
modules/security/src/main/java/org/apache/airavata/security/userstore/SessionDBUserStore.java	75
modules/security/src/main/java/org/apache/airavata/security/util/PasswordDigester.java	56
modules/security/src/main/java/org/apache/airavata/security/util/TrustStoreManager.java	66
modules/server/src/main/java/org/apache/airavata/server/ServerMain.java	319
modules/sharing-registry/sharing-data-migrator/src/main/java/org/apache/airavata/sharing/registry/migrator/airavata/AiravataDataMigrator.java	657
modules/sharing-registry/sharing-data-migrator/src/main/java/org/apache/airavata/sharing/registry/migrator/airavata/ConnectionFactory.java	37
modules/sharing-registry/sharing-registry-distribution/src/main/assembly/bin-assembly.xml	48
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/DomainEntity.java	88
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/EntityEntity.java	166
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/EntityPK.java	44
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/EntityTypeEntity.java	91
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/EntityTypePK.java	44
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/GroupAdminEntity.java	65
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/GroupAdminPK.java	52
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/GroupMembershipEntity.java	87
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/GroupMembershipPK.java	55
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/PermissionTypeEntity.java	88
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/PermissionTypePK.java	44
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/SharingEntity.java	105
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/SharingPK.java	79
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/UserEntity.java	116
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/UserGroupEntity.java	131
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/UserGroupPK.java	44
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/entities/UserPK.java	44
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/AbstractRepository.java	129
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/DomainRepository.java	11
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/EntityRepository.java	133
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/EntityTypeRepository.java	12
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/GroupAdminRepository.java	12
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/GroupMembershipRepository.java	77
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/PermissionTypeRepository.java	28
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/SharingRepository.java	85
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserGroupRepository.java	67
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/repositories/UserRepository.java	50
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/utils/Committer.java	5
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/utils/DBConstants.java	76
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/utils/JPAUtils.java	12
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/utils/ObjectMapperSingleton.java	14
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/utils/SharingRegistryDBInitConfig.java	21
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/db/utils/SharingRegistryJDBCConfig.java	38
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/messaging/SharingServiceDBEventHandler.java	240
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/messaging/SharingServiceDBEventMessagingFactory.java	58
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/server/ServerMain.java	60
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/server/SharingRegistryServer.java	149
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/server/SharingRegistryServerHandler.java	1057
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/utils/Constants.java	12
modules/sharing-registry/sharing-registry-server/src/main/java/org/apache/airavata/sharing/registry/utils/ThriftDataModelConversion.java	15
modules/sharing-registry/sharing-registry-server/src/main/resources/META-INF/persistence.xml	15
modules/sharing-registry/sharing-registry-server/src/main/resources/sharing-registry-derby.sql	115
modules/sharing-registry/sharing-registry-server/src/main/resources/sharing-registry-mysql.sql	116
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/client/SharingRegistryServiceClientFactory.java	22
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/Domain.java	772
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/DuplicateEntryException.java	293
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/Entity.java	1445
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/EntitySearchField.java	49
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/EntityType.java	771
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/GroupAdmin.java	493
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/GroupCardinality.java	25
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/GroupChildType.java	25
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/GroupMembership.java	771
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/GroupType.java	25
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/PermissionType.java	771
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/SearchCondition.java	37
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/SearchCriteria.java	493
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/Sharing.java	965
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/SharingRegistryException.java	293
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/SharingType.java	28
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/User.java	1073
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/UserGroup.java	1211
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/models/sharing_modelsConstants.java	5
modules/sharing-registry/sharing-registry-stubs/src/main/java/org/apache/airavata/sharing/registry/service/cpi/sharing_cpiConstants.java	5
modules/sharing-registry/sharing-service-docs/api-docs/index.html	104
modules/sharing-registry/sharing-service-docs/api-docs/sharing_cpi.html	389
modules/sharing-registry/sharing-service-docs/api-docs/sharing_models.html	292
modules/sharing-registry/sharing-service-docs/api-docs/style.css	174
modules/sharing-registry/sharing-service-docs/index.html	323
modules/sharing-registry/sharing-service-docs/style.css	174