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You are here: Home Community Minutes Conference Calls 2013 2013-07-16 Tuesday Team Meeting

2013-07-16 Tuesday Team Meeting


Dundee: Chris, Kenny, Ola, Błażej, Roger, Simon, Petr, Andrew, Helen, Jason Remote: Ian Munro, Colin, Curtis, Mark Hiner, Melissa, Sebastien Besson, Sebastien Simard

Agenda - 2:30pm Start

  1. Accepting minutes from last meeting

  2. Ice 3.5 Testing Plan

    • Roger: Petr has sorted out testing.
    • Petr: After main bugs, real crashes / problems. We are checking for connection between client and server mainly.
    • Roger: Not following scenario absolutely: just, does is fundamentally work.
    • Roger: Server is an Ice 3.5 server running on Gretzky, testing different client versions.
  3. 4.4.9 Release 14:39

    • Java 1.7 issues. Melissa created a fix, testing done at Dundee. Chris/Roger think situation will be as good as 4.4.5.
    • Chris: Couple more things to be done, probably ready for tomorrow. Can do testing without running Insight.
    • Chris: Client smoke test to be run. Doesn’t make sense to release whole consortium at 4.4.9 - 4.4.8p1?
    • Timeframe
      • Chris: As soon as possible, can’t wait for JM and Josh.
      • Sebastien: Most of the release process has been tuned. Sebastien will check open PRs.
      • Sebastien: Can’t commit to testing Ice 3.5 tomorrow as will need to do this testing pre-release.
      • Sebastien: Need a tag to start working, and we’ll need to clarify naming.
      • Chris: All work stops till this release is out.
      • Sebastien: Chris has rights for ome-release repo to include release PRs and release?
      • Sebastien: Could have RC Thurs AM, potentially release Thursday.
      • Chris: Confirms admin privileges on ome-release repo.
    • What is included
      • Chris: Client release only?
      • Chris: Perhaps add additional logging, allowing better debugging for Logan at NREL’s issue, #11277
  4. Summer testing updates 14:52

    • CI/Partner Projects (Sebastien) 14:52

      • Code integration. Tracking - code in a private repo we’ll need to mirror, possibly with submodules
      • Need to work on tools to sync this. Need for each project:
      • 1st version of OMERO against which we have a working tool
      • Mapping between tool and OMERO versions - explicit release coupling
      • ome-analysis-02 being replaced for Tracking / Ian Munro
      • In contact with Sardinia, will deploy OMERO.biobank on a CI node, play with graph
      • Simon: getting merge builds with OMERO.searcher - difficulty with SCC / private repo
      • Simon: running SCC by hand, pushing to a branch.
      • Chris: Glencoe had same issue. Andreas/Chris maintain a series of private forks of openmicroscopy for customer specific builds. Forking inherits permissions, but parent permissions don’t cascade down. So you can remove permissions for child forks. Parent maintainer needs to manage child forks privileges.
      • Chris: can show Simon this approach.
      • Sebastien: Github permissions also a problem.
      • Chris: managing the keys correctly can solve this.
      • Chris: SCC creating SSH based remotes, issues if keys and users aren’t in the right places.
    • OMERO.server (Blazej) 14:59

      • Moving slowly forward. Petr/Colin in the loop. Colin has ownership of a ticket.
      • Trying to resolve Moztrap showstopper (ldap auth users can’t perform create operations on DB)
      • Writing an auth backend for Moztrap - should be done today / post 4.4.8 issues.
    • OMERO.web (Will on leave) 15:00

      • Ola: Will set up Selenium. Deciding what will be covered by the Selenium tests with Will / Carlos.
      • Simon: Test anything that could be used by third party apps, e.g. OMERO.searcher?
      • Ola: Existing tests - viewer tests, how are they handled by Selenium 2 / Migrated?
    • OMERO.insight (Mark on leave) (progress tracked on ticket)

    • Docs & website (Helen) 15:04

      • General tidying, at the being cleared for merging
      • Formats documentation plan coming together
      • Andrew/Helen have updated Paris Meeting logo on front page
      • To sort out Plone pages (removing/updating), draft version of Script Sharing page
      • Stuff from Sardinia re: OMERO.biobank - discussions with Sebastien and Josh re: where it should go
      • Sebastien: Sardinia folks have a wiki on Github for installation
      • Jason: changes and reorganisation of pages on OME-TIFF, will be a proposal
    • Scenario writing (Petr) 15:07

      • Move scenario is in last stages of writing. Rounds up backlog from Paris.
      • Next one FLIMfit, not sure how far Ian is re: bugfix, can Petr download a new version?
      • Other issues we discussed earlier
      • OMERO.insight - testing packages Petr will look at
    • Bio-Formats (Melissa) 15:08

      • Kenny / Melissa made good progress speeding up test jobs (multiple threads)
      • Still investigating best place for jobs to run
      • Finished PR rebasing, on track for a 4.4.9 release
      • Going through bugs and doc changes which have been in testing
      • New hardware in progress
    • Workflows for tagging/UI scoping (Gus on leave) 15:12

      • Petr: will be looking at ‘Create’ workflow
      • Chris: Andreas has made great progress getting the workflow UI on the tagging front
      • Chris: Test version currently up, happy to show to interested parties shortly
      • Chris: Sam Hart has been getting as much of the CLI tools to work with tagging as much as possible.
      • Chris: Brand new omero CLI plugin and OMERO.web plugin add/subtracting new tags - moving along at good pace
    • Roger: long standing issue: can’t adjust levels of values in an image. Min/Max set to the pixel values in the image. Can’t set this to normalise across a series of images.

      • Chris: Can do this with entry dialogues, but not with the sliders.
      • Roger: Full range button not useful
      • Chris: workflow could do with work
      • Roger: some tickets with Carlos CC’d exist - we could do a bit more
      • Andrew: storing the settings in the metadata? It’s not stored at the moment.
      • Roger: Rendering settings which were manually set before upload to JCB, hours of work were lost after uploading.
      • Roger: Would be nice to be able to save the rendering settings e.g. LSM, Leica
      • Roger: Would be good to link rendering settings across a batch of images.
      • Chris: Can only be done via scripts.
  5. Future Exhibitions (e.g ASCB, EMBO,...) 15:20

    • Jason: ASCB time. Definitely send people with posters / attend workshops etc.
    • Andrew: Early on, did a great job of raising OME profile.
    • Jason: Possibly a group booth - something different to grab attention?
  6. Glencoe Update 15:34

    • Tagging mentioned earlier in meeting.
  7. Consortium update 15:35

    • OMERO.searcher
      • Simon: Merge builds created pyslid and searcher.
      • Chris: Have to be careful about publishing everything including sample files via Hudson.
      • Curtis: Private jobs & cron jobs - permissions matrix needs managed.
      • Chris: We have some similar, but FYI entire workspace and logging exposed to world.
  8. Any other business (<5 mins) 15:38

    • GRE BBQ, anyone coming?
      • Jason: If you’re going, email Angie Blake

Over: 15:59

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