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Reflection of work in progress for the upcoming VIVO 1.8 release

Projected Release Timing

One outcome of the meeting of VIVO sponsors at the March, 2014 DuraSpace Summit even in Washington was a request to move to a regular release schedule where timing would be predictable and new features included only if ready.  Any feature not on target to be finished by the code freeze data would have to be deferred until the next release.

A schedule of two releases per year targets a May code freeze for a June release (VIVO 1.7), and a November code freeze for December release.

The VIVO 1.8 release is being was originally delayed to allow completion of a task that has been deemed essential for moving the VIVO project from incubator to full project status – replacement of the Pellet reasoner (VIVO-778)..

With that work complete before the holiday break, additional performance-related improvements were prioritized for early January:

Release Mechanics

The VIVO project uses the DuraSpace JIRA issue tracking system to manage issues and time tracking leading up to any given release.  Issues are categorized as bug fixes, tasks, code tasks, or improvements, grouped into components such as ontology or testing or technical debt, and assigned a status based on criticality to the release.

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• recently made improvements to startup time after the first-time startup (saving approximately 20 seconds)
• modularity improvements
  search indexing (VIVO-869 being the parent issue)
  • reasoner (VIVO-778)
  • triple store (RDFService) (VIVO-225)
• VIVO-909 and VIVO-907 – if change one of the ontology files, the entire reasoning has to be re-done – the TBox reasoning that takes 20 seconds triggers a full ABox re-inferencing
  • pointed out by Eliza in testing with Virtuoso
  • a maxCardinality property was being specified as a non-negative integer but was stored as an integer, so on startup the TBox reasoner interpreted an ontology change
    • saw the same thing in Virtuoso and TDB, but doesn't show the problem with SDB
      • got around it with a kluge to the Virtuoso driver – would like to distribute with that patch if can't get around it
    • worth a couple more hours to pursue – may be an issue in the general RDFService code, that is not used for SDB
  • steps to address this may also shave more time off the startup time
• We will also need to distribute a patch for a SPARQL query syntax that Virtuoso doesn't accept
• Reasoner improvements
  • Open questions – is LGPL an acceptable license to DuraSpace? – the Lesser release removes the copyleft provision provided you don't modify the code itself
  • Can now try alternate reasoners in a matter of a couple of hours – given the refactoring
  • So far is comparing output to what Pellet did, without full confidence in which of those types of reasoning actually influence VIVO behavior and hence are required for a reasoner used by VIVO
  • We still have to determine the best alternative reasoner to Pellet to use
  • All of the SimpleReasoner unit tests still make reference to a Pellet class
• Updating the VCard ontologyWe will swap in the updated 5/14 W3C VCard ontology and test in

VIVO

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VIVO application code

For the complete list of issues under consideration for VIVO v1.8, view the full, version-specific report in Jira.

Other general goals

• Modularization
  • Major pieces of the application are selected at startup, based on a configuration file.
• Improvements in display
• Model handling
  • Technical debt: all access of triples goes through two parallel sets of channels (content and configuration)

Ontology

Documentation

• Wiki restructuring
• Customization guide

Testing

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Ontology

Ontology issues for VIVO v1.8 have been managed in 3 places as the community workflow process evolves.

1. Within the primary DuraSpace VIVO Project JIRA space
2. In a older, now-deprecated DuraSpace VIVO Ontology JIRA space (a decision was made in 2014 to stop segregating ontology issues specific to VIVO from the main VIVO project JIRA space 
3. In a tracker on GitHub

Documentation

Documentation issues for VIVO v1.8 are managed using the community/documentation component within the primary DuraSpace VIVO Project JIRA space.

Testing

Acceptance tests for VIVO v1.8 are managed using the testing component within the primary DuraSpace VIVO Project JIRA space. Additional issues related to testing be found by searching for "test" among the issues assigned to version 1.8 that may be listed under components such as technical debt or bug fixes.

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