2014-10-31 Taverna 3 architecture

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Presented 2014-10-30 at Taverna Open Development Workshop in Manchester http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Open+Development+Workshop Also available at http://slides.com/soilandreyes/2014-10-31-taverna-3-architecture#/

Technologie

Taverna 3 architecture andTaverna 3 architecture and
code basecode base
Stian Soiland-Reyes
myGrid team
University of Manchester
http://orcid.org/0000-0001-9842-9718
Taverna Open Development workshop, Manchester, 2014-10-31
This work is licensed under a
.
Creative Commons
Attribution 4.0 International License

Taverna PlatformTaverna Platform
Workﬂow language and API
Data Bundles (workﬂow runs)
OSGi services for XML handling
Plugins/services/conﬁguration
API wrapping execution engine
API for using platform outside OSGi
Creating Taverna plugins
Packaging Taverna 3 plugins
taverna-scuﬂ2
taverna-databundle
taverna3-osgi-services
taverna3-commons
taverna3-platform
taverna-starter
taverna-maven-archetypes
taverna3-maven-plugin

Taverna Platform inTaverna Platform in
IncubatorIncubator
Suggested:
(scuﬂ2, databundle)
/ (platform-api, engine-core,
core activities)
(wsdl, rest)
(use platform outside OSGi)
taverna-plugin-* (e.g. biomart)
taverna-language
taverna-engine-api -impl
taverna-engine-common-activities
taverna-engine-product

Taverna EngineTaverna Engine
Execution Engine core
Reference management
Security credentials
W3 Provenance export for Taverna
, Core
activities
taverna-engine-core
taverna-engine-referencetypes
taverna-engine-credential-manager
taverna-prov
taverna-stringconstant-activity, taverna-dataﬂow-activity,
taverna-beanshell-activity taverna-script-activity

Taverna activitiesTaverna activities
Wrap workﬂow as
reusable/updatable/shareable component
User interactions (web-based)
RESTful web services
WSDL SOAP 1/2 Web Services
Select parts of XML
Select parts of JSON
Load spreadsheet
data
Execute R script
Execute command line
tools (ssh+local)
taverna-component-activity
taverna-interaction-activity
taverna-rest-activity
taverna-wsdl-activity
taverna-xpath-activity
taverna-jsonpath-activity
taverna-spreadsheet-import-activity
taverna-rshell-activity
taverna-external-tool-activity

Taverna bioinformaticsTaverna bioinformatics
activitiesactivities
taverna-soaplab-activity
taverna-biomart-activity

Discontinued activitiesDiscontinued activities
.. or any volunteers?
taverna-biomoby-activity
taverna-apiconsumer-activity

Taverna WorkbenchTaverna Workbench
Workbench User Interface API (menus, ﬁle
opening, clipboard, perspectives)
Workbench User Interface
implementations, main window
Workbench components (diagram, explorer, results)
Workbench extensions (looping, renderers, shortcuts)
taverna-ui-api
taverna-ui-impl
taverna-ui-components
taverna-ui-exts

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2014-10-31 Taverna 3 architecture

1. Taverna 3 architecture andTaverna 3 architecture and code basecode base Stian Soiland-Reyes myGrid team University of Manchester http://orcid.org/0000-0001-9842-9718 Taverna Open Development workshop, Manchester, 2014-10-31 This work is licensed under a . Creative Commons Attribution 4.0 International License

2. ArchitectureArchitecture

3. Taverna PlatformTaverna Platform Workflow language and API Data Bundles (workflow runs) OSGi services for XML handling Plugins/services/configuration API wrapping execution engine API for using platform outside OSGi Creating Taverna plugins Packaging Taverna 3 plugins taverna-scufl2 taverna-databundle taverna3-osgi-services taverna3-commons taverna3-platform taverna-starter taverna-maven-archetypes taverna3-maven-plugin

4. Taverna Platform inTaverna Platform in IncubatorIncubator Suggested: (scuﬂ2, databundle) / (platform-api, engine-core, core activities) (wsdl, rest) (use platform outside OSGi) taverna-plugin-* (e.g. biomart) taverna-language taverna-engine-api -impl taverna-engine-common-activities taverna-engine-product

5. Taverna EngineTaverna Engine Execution Engine core Reference management Security credentials W3 Provenance export for Taverna , Core activities taverna-engine-core taverna-engine-referencetypes taverna-engine-credential-manager taverna-prov taverna-stringconstant-activity, taverna-dataﬂow-activity, taverna-beanshell-activity taverna-script-activity

6. Taverna activitiesTaverna activities Wrap workﬂow as reusable/updatable/shareable component User interactions (web-based) RESTful web services WSDL SOAP 1/2 Web Services Select parts of XML Select parts of JSON Load spreadsheet data Execute R script Execute command line tools (ssh+local) taverna-component-activity taverna-interaction-activity taverna-rest-activity taverna-wsdl-activity taverna-xpath-activity taverna-jsonpath-activity taverna-spreadsheet-import-activity taverna-rshell-activity taverna-external-tool-activity

7. Taverna bioinformaticsTaverna bioinformatics activitiesactivities taverna-soaplab-activity taverna-biomart-activity

8. Discontinued activitiesDiscontinued activities .. or any volunteers? taverna-biomoby-activity taverna-apiconsumer-activity

9. Taverna WorkbenchTaverna Workbench Workbench User Interface API (menus, ﬁle opening, clipboard, perspectives) Workbench User Interface implementations, main window Workbench components (diagram, explorer, results) Workbench extensions (looping, renderers, shortcuts) taverna-ui-api taverna-ui-impl taverna-ui-components taverna-ui-exts

2014-10-31 Taverna 3 architecture

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