Model-Driven Scientific Workflow Engineering

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1 A Framework for Model-Driven Scientific Workflow Engineering Dipl-Inform Guido Scherp Dissertation zur Erlangung des akademischen Grades Doktor der Ingenieurwissenschaften (Dr-Ing) der Technischen Fakultat der Christian-Albrechts-Universitat zu Kiel eingereicht im Jahr 2013

2 1 Introduction 1 11 The Fourth Research Paradigm and Scientific Workflows 1 12 Business Workflow Technologies for Scientific Workflows 3 13 Research Questions and Approach 5 14 Contribution 7 15 Structure of the Thesis 9 1 Foundations 13 2 Business Workflows Introduction and Basic Terminology Business Process Model and Notation (BPMN) Web Services Business Process Execution Language (BPEL) BPMN to BPEL Mapping Strategies 29 3 Scientific Workflows Introduction and Basic Terminology Business Workflows vs Scientific Workflows 39 4 Model-driven Software Development (MDSD) Introduction and Basic Terminology Model Transformations Domain-specific Languages (DSLs) Xtend Xtext 53 5 Grid Computing Introduction and Basic Terminology Grid Middleware 60 xiii

3 521 Globus Toolkit 4 (GT4) UNICORE Grid Security Infrastructure (GSI) BIS-Grid Workflow Engine 66 II Model-Driven Scientific Workflow Engineering with MoDFlow 71 6 Introduction to MoDFlow Basic Assumptions Concept and Components of MoDFlow 74 7 Scientific Workflow Requirements on MoDFlow Common Requirements on Scientific Workflows and SWfMS Definition of Requirements on MoDFlow 85 8 Scientific Workflow Model Representation with MoDFlowBPMN Basic Design Considerations Representation of Workflow Activities BPMN Metamodel Subset BPMN Metamodel Extensions Scientific Workflow Model Mapping with MoDFlowBPMN2BPEL Basic Design Considerations IWM2EWM Mapping Extensions Step 1: BPMN Process Expansion Step 2: BPMN Mapping Step 3: Workflow Engine Adaptation Utilization and Extension of MoDFlow Realization of a DWM and a DWM2IWM mapping Creation of DSLs Adoption of Existing Scientific Workflow Languages Mapping of Data Flow-centric to Control Flow-centric Workflow Languages 143 xiv

4 Extension of MoDFlowBPMN and MoDFlowBPMN2BPEL 1021 General Extension of MoDFlowBPMN General Extension of MoDFlowBPMN2BPEL Definition of Workflow Activities Integration of Third Party Software Adoption of other BPEL Process Engines Adoption of other Executable Workflow Languages Requirements on the MoDFlow Framework Classification of BPMN-to-BPEL mapping Classification Scheme for Model Transformation Prob lems Classification Scheme for Model Transformation Lan guages Requirements for a Transformation Framework Requirements for a BPMN-to-BPEL Transformation Chain Design of the MoDFlow Framework Transformation Framework BPMN-to-BPEL Transformation Chain 164 III Evaluation Implementation of the MoDFlow Framework Transformation Framework Implementation Decisions Implementation BPMN-to-BPEL Transformation Chain Implementation Decisions Implementation Application Scenarios Validation in Software Engineering Preparations for Scientific Workflow Execution in Grid Envi ronments 208 xv

5 1421 Workflow Interface for Scientific Workflows Support for BIS-Grid Workflow Engine Support of Globus Toolkit 4 Delegation Service Workflow Activity for GT4 Job Submissions Scientific Workflow Transformation Chain Scenario I: Optimization of 3D-Images Scenario II: Fishery Simulation Scenario III: Publication Workflows in PubFlow Discussion and Threats to Validity Related Work Utilization of Business Workflow Technologies for Grid and Scientific Workflows Mapping of BPMN to BPEL Transformation Chaining 243 IV Conclusion and Future Work Summary and Conclusion Future Work 255 V Appendix 261 A WSDL Definition for Scientific Workflows 263 B BPMN Workflow for Application Szenario I 267 C BPMN Workflow for Application Szenario II 273 D Xtext grammar PubFlowDSL for Application Szenario III 277 E PubFlowDSL Workflow for Application Szenario III 281 Bibliography 285 xvi

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