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You are here: Home Community Minutes Conference Calls 2010 2010-08-26 Thursday Meeting

2010-08-26 Thursday Meeting

Attending: Brian, Andrew, Chris, Jean-Marie, Josh, Melissa, Colin, Carlos, Brian Jones, Jason, Ola, Will, Donald


Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)

  1. Accepting minutes from last meeting

  2. Matters Arising (5 mins)

    • @Jason will get the presentation for the website

    • @Jason still needs to talk to Curtis about ImageJ

    • Virtualization

      • Running from hudson?
    • Delete status

    • N-Dim and SPIM

  3. Christoph, Ingvar visit. Future work...

  4. Email and Forum Review - checked at (5 mins)

    • Email -

      • [ome-devel] Patch for ticket #2648: Image and plate names population issues
      • [ome-users] Best practise OMERO.server configuartion
      • Re: [ome-users] need help with the OMERO upgrade to OMERO 4.2.0 on a Mac server
      • Re: [ome-users] OMERO 4.2 release and python version
    • Forums -

      • Re: Moving binary repository by ahar » Wed Aug 25, 2010 11:42 am link
      • Editing the OMERO.insight java code to add feature by pkat » Mon Aug 23, 2010 9:02 pm link
    • QA -


ID  Status  User/email  Type    Created Selected file   Comment Error
2660    new erdem.karate... Insight 4.1.1   2010 08 25  -   I've just set up omero.web and...   java.lang.Exception: Abno...
2659    new avgise@ender... Insight 4.2.0   2010 08 25  -   -   java.lang.Exception: org....
2658    new unknown Importer 4.2.0  2010 08 24  tubhiswt_C1.ome.tif -   java.lang.RuntimeExceptio...
2650    new peter.lipp@u... Importer 4.2.0  2010 08 18  20100818D.tif   TIFF files from TillPhotonics ...   java.lang.RuntimeExceptio...
2645    new peter.lipp@u... Importer 4.2.0  2010 08 18  20100817-A.lif  -   Ice.ObjectNotExistExcepti...
2636    new raymond.lau@... Importer 4.2.0  2010 08 17  feb02-2009.lei  tell me which files you would ...   loci.formats.FormatExcept...
2610    new raymond.lau@... Importer 4.2.0  2010 08 17  8 bit.jp2   tell me which files you would ...   java.lang.NumberFormatExc...
2605    new raymond.lau@... Importer 4.2.0  2010 08 17  38.tif  tell me which files you would ...   java.lang.RuntimeExceptio...
2603    new raymond.lau@... Importer 4.2.0  2010 08 17  ...0333_DG8L0828_2old wallbig.tif   1hr and 13 minutes to import 4...   Ice.UnknownLocalException...
2601    new Raymond.Lau@... Insight 4.2.0   2010 08 16  -   viewing an image. This image ...    java.lang.Exception: java...
2600    new Raymond.Lau@... Insight 4.2.0   2010 08 16  -   viewing images  java.lang.Exception: java...
2599    new m.porter@dun... Insight 4.1.1   2010 08 13  -   I was deleting a dataset, and ...   java.lang.Exception: org....
2598    new stevendflyga... QA  2010 08 12  -   I converted these files to ome...   -
2597    new noc@ifom-ieo... Insight 4.2.0   2010 08 11  -   From Insight I was under the s...   java.lang.Exception: Abno...
2591    new unknown Insight 4.2.0   2010 08 05  -   -   java.lang.Exception: org....
2588    new unknown Insight 4.2.0   2010 07 30  -   -   java.lang.Exception: org....
2584    new mirella.kole... Insight 4.2.0   2010 07 30  -   Changing the colours of the ch...   java.lang.Exception: Abno...
2582    new mirella.kole... Insight 4.2.0   2010 07 28  -   trying to delete some old Leic...   java.lang.Exception: org....
  1. AOCB (<5 mins)
    • full email included in agilo ticket, trac truncate it to user_id@...

In Attendance:

Brian, Andrew, Chris, Jean-Marie, Josh, Melissa, Colin, Carlos, Brian Jones, Jason, Ola, Will, Donald

  1. Last Meetings Minutes: Approved

  2. Matters Arising:

    • still some issues to clarify about ImageJ conference
  3. Virtualization review

    • scripts working
    • web running
    • script to create new VM, and then install OMERO for reboot
    • Few things outstanding:
      • SSH without password on mac (can it be done?)
      • Seeing if it runs on Hudson
      • Person still needs to manually select the 'snapshot' data directory (can't be fixed)
    • Jean-Marie: Do you think the group idea is working?
      • Donald did a lot of work, one ticket (is Donald's)
      • Ola did documentation
      • Everyone needs to record their tickets for what they are doing on these group projects
      • Nothing is recorded; need better discipline
      • Jason: need more granularity on the work
        • E.g.: concept of "rollbacks" is interesting
        • But not clear that it's something we have to have
        • Let's make that decision together
        • Anything can go on forever
        • Verbal reports may miss something
        • (Despite the fact that this is all great)
    • Donald: need to get it on hudson and then it's time to test
      • Ola: before Hudson is the start
      • Jean-Marie: need to figure out the blockers
      • Even investigation needs to be recorded
      • Jason: a day and half of work HAS to be a ticket.
        • Even something silly like SSH
      • Jason: the value of being disciplined has been demonstrated for 4.2
        • toward the end, we stopped being careful and things went sproing
    • Summary
      • What's left: at the point "install VM" gets everything running
      • Next step is to get it on hudson and make it manual
      • Need to have revision configurable
      • Not yet bothering to build Insight (Josh: webstart??)
      • Requires Virtual Box running close to Hudson
      • Chris: does it have to be on necromancer? No.
      • Jason: A ticket for VirtualBox installed would be appropriate.
      • Timescale: by end of tomorrow?
  4. Delete service

    • Big pushes that are finished:
      • Writing the tests
      • Asynchronous processing
      • Generic graph parsing (IN PROGRESS)
    • Won't be finish today, hopefully will have the initial graph deleting tomorrow
    • Some features still missing, may leave them till after 4.2
    • Should be able to test soon!
    • Currently only working with Java (will port after we get things settled)
    • Will need to setup a location for BIG TESTS
      • will only run nightly, not on every commit
    • Chris: another effort is to produce a massive SPW dataset
      • some problems with import (bf bugs in OmeXmlReader)
      • allows for creating any content we want
      • next few days, should be able to generate very large data in a compact/controlled way
    • Timescales: Still look at 2 more interations to finish (on schedule)
    • Discussing what gets tested where on Friday
  5. NDIM & SPIM

    • Jason: had a meeting with Andrew. Correspondence gathered.
      • Reasonable documentation around "Will's proposal" (#112)
      • Capsulation of all we discussed (re: Paris, etc.)
      • Should provide a way to solv
      • Haven't found a way to break it yet
    • Andrew has gotten real data from Günther
      • data stored as collection of tiff files (possibly OME-TIFFs)
      • but they save an extra xml file with the OME-XML (not quite valid)
      • using 2008 schema and writing into a couple of dropped objects
      • 3 other (non-tiff) files
        • the OME-XML data (encapsulated)
        • xml log file with the extra metadata (instrument metadata)
        • txt of the same data
      • Will try to put together an annotation with an XML block of the information
        • schema changes
          • need NDIM
          • also need Instrument/LightSource annotation
    • Jean-Marie: Can we attach samples to the ticket? @Yes.
      • Jason: nice thing about the ticket is the examples for other data types (lifetime)
      • tie to write to our community. "advice? strong feelings?"
    • Note: previously instruments were well-defined
      • but now we're getting very hand-made things
      • Jason: now it's getting more common (new modalities w/o turnkey solutions)
      • "here are a bunch of statements about my scope" (cF. RDF discussion)
      • how big is that community? (it's certainly growing)
      • InstrumentAnnotation is a transition to something more flexible
      • Do we want to do these transitions at the same time?
      • Jean-Marie: We should go to the community with our proposals
      • Jason: We should try to get this released in bio-formats and see what the response is
    • Chris: need to be careful
      • We didn't want to release a schema without full support
      • Should possibly be a pre-release
      • Jason: right. we need to get something out there. huge change.
      • "BF/SPIM" branch?
  6. EMDB meeting

    • Current demo target is the september EM meeting in Rutgers,New Jersey
    • Show demo of Web Client to see if the community wants to keep working in this direction
    • Another target: use of EMDB in labs
    • Ingvar liked flexible way of adding annotations
      • Relatively straight-forward to write own views on annotations
      • Probably a good package for a labs data management tool
    • Started adding some of the features that have been on the plate
    • Bit unclear what the future work looks like (OA viewer, etc.)
      • a lot of OA work to manage memory as an applet
      • code access and licensing issues arise
    • Jason: Should again go to the community and show what we can do
    • Need some community based labs to work along side us on this
    • Q's:
      • Josh: How do we want to encourage/setup additional code committers?
      • Josh: What are the priorities/requirements gathering needed (needs tickets?)
        • Needs a meeting here?
  7. Sprint

    • Moving all tickets forward
    • Several people aren't represented in the discussion above
    • Colin wanted to contact Jean-Marie about work on FS (users managing own dirs)
      • Need a presentation about where we want to go
      • Skeleton ticket with no stories
      • Need more discussion to no how we're moving forward
      • Next Tuesday meeting? Off next week. or 2 weeks for an in-person.
      • 7th September for FS discussion
      • NB: Jason - difficult being remote
        • need a way to give demos and presentations
        • Motion: use webex facility for sharing desktop
        • Chris had also discussed streaming video. Can also try it.
    • Next week Tues - a short intro on the test scaffolding?
      • Alternatively, linkage discussion.
      • @Everyone send suggestions by email
  8. Emails/Forums:

    • @Chris will respond to #2648 patch
    • Best practice email
      • Andrew: we keep getting requests, and the answers are "well it depends..."
      • @Andrew will send a reply with a pointer to the FAQ
    • 4.2.0 mac server upgrade: fixed.
    • 4.2 relase and python: sorted out.
    • Forums
      • Chris will respond to "Moving binary repo"
      • Jean-Marie will respond to insight question
    • QA
      • Follow up on 2659 with ticket, 2650 & 2636 with emails
  • Donald: Ticket for VirtualBox setup to Chris
  • Donald: Talk to the guys downstairs (ticket, maye hand off to someone else?)
  • Josh: Need to add big memory test
  • Jean-Marie, et al: Meeting early next week to discuss client unification.
  • Andrew: Please attach some sample data to the tickets for SPIM/NDIM
  • Jason: Write the director of the EBI about EMDB support
  • Eveyrone: Vital we maintain ticketing! Please remember!
  • Jean-Marie: Move current tickets to new iteration
  • FS Team: Meeting on September 7th
  • Need to fix emails in agilo
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