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Comment: Migrated to Confluence 4.0

Date: 2013-02-25
Participants: Sean (absent), Alan, Stian, Don, Finn, Piotr


  • Discussion about semantic annotations:
    • Alan is modifying component plugin to provide semi-generic semantic annotations
    • Requesting which terms to support - Wf4Ever requirements suggestions a bit vague or too comprehensive.
    • Annotations to be displayed and queriable on myExperiment
    • BioVel annotation more on the level of 'input type: PNG' rather than 'dcterms:title'
    • Unclear which annotations should be made in Taverna and which in myExperiment
      • .. leading to potential difficulties in merge conflicts
      • Taverna should load annotations live from myXP on display
      • Potential update and identifier issue - when uploading new version of workflow to myXP; what happens to descriptions of a processor in the old workflow?
  • Finn has worked on REST API; permission policy support
  • Pique reported that some workflows don't show in Taverna's myXP perspective - unclear if fault is in picky plugin or if REST data has changed
  • Piotr to work on RODL indexing and search; might be useful for myXP
  • Don has done work to prepare for upgrade to Ruby 1.9.2 (enabling later move to Rails 3) and upgrade to SOLR Sunspot. 40% speed increase in integration tests, SOLR indexes in 2 minutes rather than 2 hours. To be deployed on sandbox first.
  • ACTION Don: proposing a Wf4Ever sprint to expose ROSRS API from myExperiment ; part of the grand plan to move mainline myExperiment to Wf4Ever. Would mean including support for say arbitrary annotations.
  • Stian: To work on a RO Bundle specification - ZIPed RO. To be used by Taverna 3's data bundle (also to be speced and implemented in the next weeks). Piotr also volunteered for this.

Skype chat log

Monday, 25 February 2013
[13:16:26] * Sean Bechhofer has changed the chat topic to ""
[13:16:40] * Sean Bechhofer has changed the chat topic to "myExperiment 130225"
[13:16:55] Sean Bechhofer: Apologies from me this afternoon – I will be in transit to a meeting.
[13:17:27] Sean Bechhofer: There is a sprint planning meeting for w4fever tomorrow.
[13:17:31] Sean Bechhofer: backlog:
[13:19:37] Sean Bechhofer: Would be good to understand myexp issues here.
[13:19:46] Don Cruickshank: i'm at home today due to illness and will have to at least duck out at 2.50 to go and get alex from school (next door)
[13:20:16] Don Cruickshank: i must read that document (sad)
[13:43:38] Alan R Williams: I am working on the annotation of workflows in Taverna (for the components plugin). It would be extremely useful to know what predicates wf4ever would like us to use.
[13:44:28] Alan R Williams: I have talked with Stian and also looked at but we need stronger recommendations.
[13:47:02] Alan R Williams: To recap what I've just told Finn - yes the components plugin lets you annotate for predicates specific to a domain, but there is also a more general wish for predicates that could apply to most workflows e.g. license.
[13:47:33] Sean Bechhofer: The RO template work should help here.
[13:47:53] Alan R Williams: Is there an RO template for workflows?
[14:31:04] Don Cruickshank: hi
[14:31:20] Piotr Holubowicz: Hi
[14:31:30] Finn Bacall: hi
[14:33:03] Don Cruickshank: OK - on my list of things to talk about are:

1. Next steps for wf4ever as sprint planning meeting is tomorrow
2. wf4ever recommended predicates
3. quick updates
[14:33:30] Don Cruickshank: i need to at least step out to pick alex up in about quarter of an hour
[14:33:42] Don Cruickshank: but that doesn't take long as it's next door
[14:34:26] Don Cruickshank: (placing call)
[14:34:59] Stian Soiland-Reyes: Hi. I have started looking at the RO Bundle spec as a requirement from Taverna 3, and have added a sprint description of this on the Wf4Ever showcase wiki. I am finishing up something for the PAV paper right now; it's currently gone for internal review with Carole and Tim.
[14:59:15] Stian Soiland-Reyes: Finn: Been working on REST API; show revision comments. Allowing people to specify a preset policy when they upload a workflow through the API rather than adding all the permissions; just pick a policy that exists.
[15:00:04] Stian Soiland-Reyes: Alan: Pique has reported that something is wrong with showing preview dialogue in the myExperiment plugin for some of his workflows
[15:00:21] Stian Soiland-Reyes: Alan: Preeviously caused by REST interface failing..
[15:00:46] Stian Soiland-Reyes: Alan: But noone has time to look at it
[15:01:13] Stian Soiland-Reyes: Alan: The Taverna myXP plugin fails badly on anything 'unusual'. We're not sure who's 'fault' it is for those workflows.
[15:02:45] Stian Soiland-Reyes: Piotr: Not much to add on myXP.. will be working soon on RODL features; search, indexing etc. which might be used by myXP, but not related to annotations
[15:10:27] Stian Soiland-Reyes: Don: been updating lots of stuff. Can work on Ruby 1.9.2 now. To be done before Rails 3.
[15:10:57] Stian Soiland-Reyes: Moving from acts_as_solr (question) to Sunspot ..(question) version of SOLR which is much quicker to update site; a few minutes vs. an hour
[15:11:10] Don Cruickshank: acts_as_solr
[15:12:02] Stian Soiland-Reyes: new ruby is 40% faster just on the functional tests
[15:12:34] Stian Soiland-Reyes: Don: Change the sandbox over first; do the general procedure
[15:12:48] Stian Soiland-Reyes: that update would include replacing the SOLR server
[15:12:54] Stian Soiland-Reyes: and fiddle with the runner passwords
[15:13:09] Stian Soiland-Reyes: (not quite used; but to move to Ruby 1.9,2)
[15:14:04] Stian Soiland-Reyes: Don: For next week; in on sprint; idea being to work on implementing ROSRS in myExperiment, making the bits of the demo real
[15:14:25] Stian Soiland-Reyes: Don: To expose myXP data according to RODL API
[15:15:36] Stian Soiland-Reyes: Don: should mean that myXP could work on its own; that the existing www.myXP setup would remain.
[15:15:49] Stian Soiland-Reyes: with federations moving data as now to the sandbox
[15:18:02] Stian Soiland-Reyes: Stian: So it would mean that the mainline myXP would move to implement all of the ROSRS APIs and would have to implement support for say arbitrary annotation bodies etc
[15:21:52] Stian Soiland-Reyes: Action Don: Add the above to the wf4ever showcase backlog page
[15:24:11] Conference call, duration 49:35.