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You are here: Home Community Minutes Conference Calls 2007 2007-12-27 Project-wide 3:45 GMT

2007-12-27 Project-wide 3:45 GMT

Attending: Jason, Ilya, Josh, Curtis, Cat

Agenda


  • OME-XML
    • Bio-Formats 2007 XML schema support status
    • Issues with the online OME-XML / OME-TIFF validator
      • Internal error if xsi:schemaLocation not defined? (e.g., erroneous use of "schemaLocation" attribute without namespace) — see data/ome-tiff/prairie/SingleImage-12062007-1400-019/ SingleImage-12062007-1400-019_Cycle001_CurrentSettings_Ch1_000001.tif
      • Online validator does not display all error messages compared to Bio-Formats command line validator — see data/ome-tiff/volocity/FromVolocity-2007-12-11.ome.tif
    • Kevin's proposed changes to Objective
    • Should we relax restrictions around Objective parameters (Type, Manufacturer, Correction, Immersion, etc.)? Comment from a developer: "We currently do not store the model or serial number of the objective, nor the Microscope information (which it appears is also required), so I guess we will just have to remove that element for now and put it on the list of things to include in the next version."
    • OME-HDF proposal
  • OMERO server
    • Beta2.3 Released!
    • Sha1 checking during import
    • Beta2.2 incompatibilities
      • Printing out nicer messages than:
      • java.io.InvalidClassException: org.jboss.ejb3.session.BaseSessionRemoteProxy ; local class incompatible: stream classdesc serialVersionUID = 2609262789016232311, local class serialVersionUID = 8310915813626447181]
  • Website
    • Comment from a developer: "I didn't realize there was a newer OME schema. I had been looking at what I thought was the latest version, which is linked from this page: http://www.openmicroscopy.org/api/xml/"


Notes


  • OME-XML
    • schema support
      • Warning (flashing lights, etc.)
        • Commit something big to head.
        • Week from Monday (7th of January).
        • After a bio-formats release.
        • Latest version.
        • Will break everything.
        • Lots of post-commit testing needed.
        • Ilya available for testing
        • @Curtis emails Brian
      • Close to having new schema working in bio-formats
        • Fields suported in bio-formats are a small number of fields
        • Can flip a switch later to read OME-XML files
    • validator(s)
      • Can Andrew also test with these files? Might be nice to add more information on missing "xsi" in "xsi:schemaLocation"
      • Would also be good to cross-reference with the bio-formats command-line tool
      • cf. w3c generic validator's "keep going" option. Might be nice to have that. Seems that only first problem is being listed.
      • "What's the vision?"
        • Who are the customers for the online validator v. commandline validator.
        • Java was easy and does a good job
        • But a lot of people are going to want to use the web one (haters of CLI)
        • Also good to compare the Java and Python facilities for different bugs
        • online validator checks OME-TIFF, Java doesn't.
        • @Jason writes to Andrews
    • Next task
      • OME-TIFF and validation type things with companies
    • Objective: tabled
      • e.g. Correction-color on the lense probably needs an ObjectiveRef
    • Relaxing restrictions on Objective
      • "Always required? Oh, then I won't do any of it"
      • Need to have a better way of determining user needs (more than developer or single opinion)
      • "ObjectiveCharacteristic?"
      • Whose needs? Users? But we talk to developers.
        • Is the statement "we don't care about that" a developer or company/customer opinion?
        • Cat: perhaps something that will change over the coming months as the user base changes
      • Should support partial information.
      • Shouldn't make the perfect enemy of the good
      • Possibilities
        • 1. New type
        • 2. An AbstractObjective super type, which is looser
        • 3. Storing incomplete information as quasi-valid OME-XML block
      • Whole web2.0 debate ("There's a war goin' on, man")
      • Curtis fundamentally wants to get as much information from 3rd party formats into the db.
      • Why can't we store wishy-washy information in the db?
        • DB reflection of philosophy
        • Only way to store it is to remove all nullable information
        • Why not?
        • > But it doesn't help Curtis solve his problem!
          • Curtis is happy with using CustomAttributes
          • Just: (1) Unambiguous, (2) No new things/i.e. not too much to learn
          • "Incomplete: no LSID for you"
          • But also provide disincentive to doing things this way.
            • Different name. "ObjectiveFragment"
            • Loss of queryability
            • Also the Gold star certification is lost with the use of fragments
  • OME-HDF
    • bioformats: seen as a different model
    • but using HDF data types?
    • Yeah, that's good.
    • Have to find a middle ground.
    • What's the purpose?
      • What of all the abilities do we want to support?
      • Who's ready to use it?
      • What would we use it for? (Other than just another format)
      • Define what we want to do

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