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Goal

The main goal for the hackathon is to have a Taverna Workbench running on an OSGi framework (no Raven!) that can create/edit/run workflows. It will use SCUFL2 and the Platform.

Current status

Jenkins has automated builds for all Taverna 3 modules. They are all "trunk" in Subversion, and Jenkins deploys x-SNAPSHOT versions to the Maven repository.

We currently have a Taverna Workbench running on an OSGi framework with a Design Perspective and most menus that can edit workflows containing beanshells and string constants. It is not using SCUFL2 or the Platform, but David has started porting this.

There is a version of Taverna Command Line that runs SCUFL2 workflows using the Platform and running on an OSGi framework.

25%

TODO

  1. handler

    Loop in Scufl2

    MEDIUM
    stain
    2012-10-08
    2012-10-09
  2. handler

    Move edits from edits-api to new module.. workflow-edits?

    MEDIUM
    stain
    2012-10-08
  3. handler

    Scufl2Tools - refactor from existing edits

    HIGH
    stain
    2012-10-08
  4. handler

    ReceiverPort merge port Details view

    LOW
    stain
    2012-10-08
  5. handler

    Update SVN checking frequency in Jenkins

    MEDIUM
    stain
    2012-10-08
    2012-10-09
  6. handler

    Nightly build in Jenkins

    MEDIUM
    stain
    2012-10-08
    2012-10-09
  7. handler

    Update upstream/downStream from Tools -> Scufl2Tools

    HIGH
    stain
    2012-10-08
  8. handler

    scufl2 annotations loading from wfbundle

    MEDIUM
    stain
    2012-10-08
  9. handler

    Use scufl2 annotations in Details

    MEDIUM
    stain
    2012-10-08
  10. handler

    Check SCUFL2 has "safe overwrite"

    MEDIUM
    stain
    2012-10-08
    2012-10-09
  11. handler

    Check wiki permissions - why not public?

    MEDIUM
    stain
    2012-10-08
    2012-10-09
  12. handler

    Write taverna workbench product build instructions

    MEDIUM
    witherd5
    2012-10-08
    2012-10-08
  13. handler

    Workbench version number are hardcoded in config/shell script

    MEDIUM
    stain
    2012-10-09
  14. handler

    David: Wiki page about decission on Activity versions / definitions

    MEDIUM
    witherd5
    2012-10-09
  15. handler

    re-enable ignored FileManager tests

    MEDIUM
    stain
    2012-10-09
    2012-10-09
  16. handler

    Make zip from workbench-product – nightly/release profile?

    MEDIUM
    stain
    2012-10-09
  17. handler

    Include dot.exe for Windows? Avoid NullPointerException

    MEDIUM
    stain
    2012-10-09
  18. handler

    OS-specific builds

    MEDIUM
    stain
    2012-10-09
  19. handler

    Broken layout on startup (Windows) - even after resize!

    HIGH
    stain
    2012-10-09
  20. handler

    Add isBoundToNestedWorkflow for Processor in Profile within Scufl2Tools

    MEDIUM
    awilliams
    2012-10-09
  21. handler

    Add profile selection to the command line

    MEDIUM
    awilliams
    2012-10-10
  22. handler

    Add profile selection to the server

    MEDIUM
    awilliams
    2012-10-10
  23. handler

    Put identification chain on WorkflowBundle, Workflow and Profile - not as annotation

    MEDIUM
    awilliams
    2012-10-10
  24. handler

    Add getWorkflowBundle, getWorkflow and getProfile to the selection manager

    MEDIUM
    awilliams
    2012-10-10
  25. handler

    Add check that main workflow/profile is set

    MEDIUM
    witherd5
    2012-10-10
  26. handler

    Decide what it means for an activity to be "disabled" or "unrecognized"

    MEDIUM
    awilliams
    2012-10-10
  27. handler

    Move ReportManager into Scufl2 and do UI event listening elsewhere

    MEDIUM
    awilliams
    2012-10-10
  28. handler

    Move RemoteHealthChecker

    MEDIUM
    awilliams
    2012-10-10
  29. handler

    Put DataNature on Data

    MEDIUM
    awilliams
    2012-10-16
    2012-10-25
  30. handler

    Put getStream onto Data

    MEDIUM
    awilliams
    2012-10-16
  31. handler

    Check version numbers e.g. commons.codec is old

    MEDIUM
    awilliams
    2012-10-16
  32. handler

    Does getValue of an error Data return the message?

    MEDIUM
    awilliams
    2012-10-16
  33. handler

    Server: pull files and workflows from (public) URLs

    MEDIUM
    donal
    2012-10-17
    2012-10-17
  34. handler

    Do something about SshReference

    MEDIUM
    awilliams
    2012-10-29
  35. handler

    Remove singleton DataService assumption in e.g. uk.org.taverna.platform.RunIT

    MEDIUM
    awilliams
    2012-10-29
  36. handler

    put getValue onto Data

    MEDIUM
    awilliams
    2012-10-31

Use this list for small outstanding work items, such as "Check Graphviz on Windows installation" or "Move functionA to moduleB".

Scope

This is what I think need to be in scope for the hackathon to achieve the main goal.

Replace Raven with OSGi

This has mostly been done but there are some workbench modules that have yet to be converted to OSGi bundles, the run perspective, activity-uis and myexperiment/biocatalogue perspectives.

This work involves:

  • Changing the pom packaging type to 'bundle'
  • Ensuring that all dependencies are also OSGi bundles
  • Removing implementation dependencies (may involve refactoring to introduce api/impl split)
  • Converting SPI resources to Spring DM
  • Changing code to use OSGi service model instead of SPI instance registries

Note: biomoby is ruled out of scope for this hackathon, Taverna 1 SCUFL import is out of scope, t2flow output is out of scope, some local services may be out of scope, biocatalogue perspective is optional (time constraint)

Integrate the Platform

This involves fairly major changes to the Run Perspective to:

  • Integrate the run manager
  • Change workflow run monitoring to use platform report interface

Do we attempt a redesign / rewrite or adapt the current code?

Same look. Need to start with "blank canvas" for underlying code.

Will use command line tool as a second run executor (along with inbuilt platform)

Use SCUFL2 as workbench model

This affects most workbench modules and involves removing all dependencies on workflowmodel-api (and impl!). This is mostly just refactoring but more work is required for:

  • Edits - we could either use existing edit system or move functionality to SCUFL2 and use standard Swing undo.
    • Alan says standard Swing unless there is a very good reason - the only reason is that the current implementation exists and works.

Leave as is for the initial version

  • Diagram - generate graph model

Initial version will be without merge (subject to review)

  • File Actions - use SCUFL2 tools
  • Validation report - use SCUFL2 validation

We need to decide on whether to replace Dataflow with SCUFL2 Workflow or WorkflowBundle.

Neither

Alan needs to know the implications

Should we attempt to support multiple profiles?

Yes. Code for filling in the profile may not be there in initial version.

You mean workflow bundle profiles that control the running? - Yes

We need annotation support for SCUFL2

For initial version keep few possibilities but use DC predicates

Data Format

This is Baclava 2 / Data Bundle and will be used for workflow inputs/ouputs/intermediates. We need:

  • API definition
  • Basic storage implementation

We should also consider structured data support.

Rob to do based on ORE/OAI gunk. Stian says need to specialize. Desperately needs user input. Stian to write up current state and send to BioVeL and SCAPE.

Update procedure

One reason for moving to OSGi is to make updates easier and support a shorter release cycle. It would be great to implement this early and use to integrate hackathon results.

Ask Protege people?

Plugin mechanism

This is essentially just adding OSGi bundles to the framework but we need to handle dependency version conflicts.

We've talked about having a Taverna AppStore/Marketplace/ToolBox - should this be in scope for the hackathon?

Revisit once initial version done

Additional work

Things not required to achieve the main goal.

myExperiment support for SCUFL2

New workbench will save workflows as workflow bundles so myExperiment support will be required

Reference Service

Provenance

We need to improve provenance performance - I think we need to change provenance capture mechanism and internal storage format.

Server

  • Need to integrate Scufl2 tooling libs and content handling.
  • Capabilities descriptors (per user, but pre-workflow submission)
  • No change to execution model as there are forces that drive it to be what it is now (isolation critical for stability)
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