Taverna Components: The Basics
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The document discusses Taverna components, which are reusable pieces of workflows that are well-described, curated, and produce and consume data and provenance in standard ways. Components are implemented through workflows, collected into families that share profiles defining what it means to be a member, and stored in registries like myExperiment. The document provides instructions for finding, making, using, updating, and sharing components and their families.
Taverna Components: The Basics
- 1. Taverna Components The Basics Donal Fellows School of Computer Science, The University of Manchester SCAPE Developer Workshop Brno, 1921 November 2013
- 2. Taverna Components Are Something that can be put into a workflow Well described What the component does Where to find it Behaves well Conforms to agreed good practice policy Curated Someone looks after it Produces and consumes data in agreed formats Fails in described ways Meaningful error messages Produces agreed type of provenance This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 2
- 3. Components Model Implemented by Workflows Collect Components in Families Groups similar components together Families share common Profile Defines what it means to be a family member Profiles inherit from Base Profile Defines semantics of workflows and standard annotations Store in a Registry We use myExperiment as the shared Registry Use a local registry on your filesystem when developing new components This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 3
- 4. Component Architecture This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 4
- 5. Finding Components Within Taverna Online on myExperiment This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 5
- 6. Supported Versions Make sure you have the right version of the tools! Out Now: Taverna Workbench 2.4 with Plugin Component Plugin 1.1.2 Out Very Soon: Taverna Workbench 2.5 Incorporated as core functionality Out Very Soon: Taverna Server 2.5.1 or later 2.5.2 will have provenance support This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 6
- 7. Making a Component 1. Decide what you want to do Combine measures documents 2. Create a workflow to do it Dont forget to annotate! 3. Turn it into a component 1. Components Menu 2. Create component 3. Choose registry, family and name You may need to create a family (see next slide) 4. Any final adjustments before publication? Do now 5. Save component, providing a description 4. If it is public, share component with SCAPE via myExperiment website This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 7
- 8. Creating a Component Family 1. Components Create family 2. Select registry and profile TIP: You can create profiles from the Components menu by importing them from myExperiment 3. Provide a name and description 4. If it is a family on a public repository, set the sharing policy and license 5. If you want to share your family with SCAPE, you do that via the myExperiment web interface TIP: Try to avoid creating families unless theres a functional reason This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 8
- 9. Using a Component Import the Family into service panel Import new services Component service Pick registry and family See that family members are now available Drag the component across (or right-click and add from menu) to add to your workflow TIP: Private components will not be usable by others or by the execution platform (got to read the component definition to run it!) This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 9
- 10. Updating a Component Open the component Components Open component Edit the component Save (either normally or via Components menu) Provide description of version Tell workflows to use new version Right-click Configure component Pick the version to use TIP: They do not update automatically This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 10
- 11. Open Issues SPARQL searches not exposed in plugin Theyre there in myExperiment, but too hard to use for most users so that UI is switched off Full semantic annotation not exposed Gets very problematic when dealing with FOAF annotations for creators Profile validation not complete No true interface for creating profiles Just importing already existing profile documents Many features wanted by other projects are missing This work was partially supported by the SCAPE Project. The SCAPE project is cofunded by the European Union under FP7 ICT2009.4.1 (Grant Agreement number 270137). 11