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You are here: Home Community Minutes Conference Calls 2010 2010-05-13 Thursday Meeting

2010-05-13 Thursday Meeting

Attending|: Brian, Jean-Marie, Colin, Andrew, Ola, Will, Josh, Melissa, Curtis


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 (<10 mins)

    • Andrew: Writing to Ilya / responding to FindSpots
    • Everyone: think about annotations for Thursday discussion (see nitpick thread)
  3. Annotations in OMERO and OME-XML

  4. Generating sprint # (45 mins)

    • Unstarted tickets or those with significant dev time? Push or start?
      • Trac query
      • Shoola Trac query
      • ticket:1708 IDelete.deletePlate() of large plate with many rois fails with OOM
      • ticket:2243 Upgrade CellProfiler for 4.2
      • Various tables work
      • Database upgrade
      • ...
    • What New Tasks were added to old sprint
    • What Tasks are left in old sprint
    • Make new sprint
    • Estimates
    • Close old sprint and move other tasks into new sprint
  5. Email and Forum Review - checked at (5 mins)

    • Email - [ome-users] Another newbie question - why won't Omero web come up?
    • Forums - New file type into omero
    • QA -
      ID  Status  User/email  Type    Created Selected file   Comment Error
      2441    new bhcho@cmu.ed... Importer 4.1.1-r592 2010 05 11  img_1_p.ome.tif As I noted in the forum http:/...   java.lang.IllegalArgument...
      2440    new bhcho@cmu.ed... Importer 4.1.1-r592 2010 05 11  img_1_d.ome.tif As I noted in the forum http:/...   java.lang.IllegalArgument...
      2435    new alessandro.d... Insight 4.1.1   2010 05 05  -   I was just trying to login on ...   java.lang.Exception: Abno...
  6. AOCB (<5 mins)

    • Hudson emails - how do I stop them
    • Hudson specific channel to not flood devteam


  • Annotations:

    • Problem is that we have no way of accurately importing String annotations
    • Andrew's recommendation was to use a custom namespace for tags
      • This would mean everyone would have to use our namespace
    • Josh suggests we just turn it a type
  • Handling Ontologies:

    • Josh: use a Unique Identifier in OMERO and create a service to interact with external ontologies
    • Carlos: use a separate ontology database and store the term as a tag
    • Jean-Marie: create a copy of the ontology internally (keep flag on the term indicating if the ontology is internal/external).
    • Will: ontology version in the SA
    • Josh: putting the ontology terms in the common user space (partial UNIQUE)
    • Jean-Marie: so we should add a tag for ontologies in the model?
    • Jason: will need to support the same granularity that we have in the applications
    • Josh: do we want to store tags differently?? don't know yet.
    • Andrew: existing annotations, all split on type
      • current annotation types are primatives not function-based (which is at the namespace level). Adding a new functional tag would break this concept.
      • Jean-Marie: practically we might have to break that concept
      • Josh: the current string types are differentiated based on the parsing of the string not the function
        • xml, cvs, etc.
        • NB: might want to remove QueryAnnotation
  • Sprint

    • Jean-Marie: behind because we cannot import with the new bf
      • Problem: bf has dropped LogicalChannel but OMERO has not.
      • Assumption: the entire stack would keep LC (miscommunication?)
      • Brian: all now working. still an issue of primitives/enums (adjusting server code)
      • Jason: specific - done by end of today? Yes.
      • Otherwise clients are ready to start digesting
    • "Bigger pieces of development left" and/or "is query complete and fair list of what to be done"
      • Web: nothing new
      • Client: add "Open With" for Paris (possibly just demo size)
      • FS: can now do multi-images files.
        • waiting on metadata on import from Chris
        • for Paris need real file-system not /tmp
      • Importer: holding off on tables, no critical tickets, doable?
        • Depends on bf fixes
      • Scripting:
        • Finally have what we wanted. Now using grouping
        • Extremely slow (retrieving parameters)
      • Server:
        • configuration changes
      • CellProfiler: Have to ask Donald
  • schema

    • Discussion tomorrow about Annotations
    • @Then contact lists about when we will release (major version)
    • @Asking at Paris
  • forums / web

    • @Ola responds about web server start
    • @Brian looks at QA since 2 days ago
  • hudson

    • ending emails? fix the build!
    • devteam:
      • another channel is dangerous if everyone is not in
      • perhaps we could store full history somewhere.

Action Items

  • Tagging Group: Meeting on Friday morning (10:15ish)
  • Andrew: Contact list about when we release the next major schema (and Paris)
  • Ola: respond to web start question
  • Brian: 2 QA tickets need loking at
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