Agenda

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)

   • Put in outstanding action points from last Thursday or Tuesday meeting

3. Status update (15 mins)

4. webemdb quick test (less than 5 mins) webemdb webemdb-data

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

   • Email -
     • 17 August 2010 [ome-users] Best practise OMERO.server configuration
     • 30 August 2010 [ome-users] omero 4.2: database busy exception during import
     • 15 September 2010 [ome-devel] OMERO 4.2-installation problems..... Too many images open ?!
     • Couple today from Rubén about Scanr & SP5
   • Forums -
     • Also cannot login to webadmin by oscshall » Thu Sep 09, 2010 7:07 pm link
     • Re: Moving binary repository by ahar » Tue Sep 07, 2010 4:43 pm link
     • Re: OMERO.web using mod_python on Mac OS X 10.6.4 by stephenogg@gmail.com » Mon Sep 06, 2010 11:40 pm link
     • Advice on Software development PROJECT COORDINATION by strambc » Fri Sep 10, 2010 5:24 pm link
     • Re: db.sqlite3 Missing by brandon.scott » Mon Sep 13, 2010 6:35 pm link
     • Two versions of python (2.4 and 2.6) installed by carandraug » Wed Sep 15, 2010 1:59 am link
   • QA -

link

ID  Status  User/email  Type    Created Selected file   Comment Error
2742    brian.lorang... Importer 5.0.0-DEV  2010 09 15  max-sample-2008-02.ome  latest 2008-08.ome error    loci.formats.FormatExcept...
2725 - 2741 a.ferrand@du... Importer 4.2.0-DEV  2010 09 15  ...00914-siCTL_HP1b_01_R3D_D3D.dv   Over 50% failed imports :( It ...   java.lang.ArrayIndexOutOf...
2724    m.porter@dun... Insight 4.2.0   2010 09 15  -   I tried to 'publish' a movie f...   java.lang.Exception: java...
2722    p.schregle@i... Importer 4.2.0-DEV  2010 09 15  LA_31.08.2010_15_26_50.tif  In response to Brian W. Lorang...   java.lang.RuntimeExceptio...
2721    unknown Importer 4.2.0-DEV  2010 09 14  bru3handgal4_06_1wk.cxd -   java.lang.ArrayIndexOutOf...
2714 - 2720 unknown Importer 5.0.0-DEV  2010 09 14  ...NEOlog2008-08-08-18h07m58s.txt   Sent from CLI   loci.formats.FormatExcept...
2710    brandon.scot... Importer 4.1.1-r592 2010 09 13  Cell01_1.ome.tif    -   java.lang.RuntimeExceptio...
2709    jay_copeland... Importer 4.2.1-DEV  2010 09 13  HCC1187_A01.pnl This is my first attempt at im...   loci.formats.FormatExcept...
2708    i.porter@lif... Insight 4.2.0   2010 09 13  -   If you only have a dataset sel...   -
2706    i.porter@lif... Insight 4.2.0   2010 09 13  -   Tried opening the FLIM script ...   -
2701    i.porter@lif... Insight 4.2.0   2010 09 13  -   When enlarging thumbnails the ...   -
2699    anlkae@uks.e... Insight 4.2.0   2010 09 11  -   tried data retrieval    java.lang.Exception: org....
2698    unknown Insight 4.2.0   2010 09 10  -   -   java.lang.Exception: org....
2694 - 2697 columbus.hel... Insight 4.1.1   2010 09 09  -   -   java.lang.Exception: Abno...
2693    unknown Insight 4.2.0   2010 09 09  -   -   java.lang.Exception: org....
2692    m.porter@dun... Insight 4.2.0   2010 09 09  -   I had Insight open for a while...   java.lang.Exception: org....
2690 & 2691 unknown Importer 4.2.0-DEV  2010 09 07  A8_fish2_headareazoom2.lsm  Data import error   java.lang.ArrayIndexOutOf...
2687 & 2689 N.Hegarat@su... Insight 4.1.1   2010 09 06  -   I was fitting to the window java.lang.Exception: Abno...
2686    mirella.kole... Insight 4.2.0   2010 09 03  -   refreshing the application  java.lang.Exception: org....
2685    team-sysadmi... Insight 4.2.0   2010 09 02  -   I was opening a dataset consis...   java.lang.Exception: org....
2680    andrea.gohlk... Insight 4.2.0   2010 08 31  -   -   java.lang.Exception: org....
2661    ealexand@cs.... Web 4.2.0-r757  2010 08 26  -   I was attempting to change a u...   Traceback (most recent ca...
2659    avgise@ender... Insight 4.2.0   2010 08 25  -   -   java.lang.Exception: org....
2658    unknown Importer 4.2.0  2010 08 24  tubhiswt_C1.ome.tif -   java.lang.RuntimeExceptio...
2645 & 2650 peter.lipp@u... Importer 4.2.0  2010 08 18  20100817-A.lif  -   Ice.ObjectNotExistExcepti...
2603, 2605, 2610, 2636  raymond.lau@... Importer 4.2.0  2010 08 17  ...0333_DG8L0828_2old wallbig.tif   1hr and 13 minutes to import 4...   Ice.UnknownLocalException...

1. AOCB (<5 mins)
   • Type is a XSD:List Attribute in Experiment and MicrobeamManipulation
   • Draft but usable SPIM solution asap.

Notes

Attending: Brian, Chris, Colin, Jean-Marie, Will, Ola, Melissa, Brian Jones

1. Last Meeting's Status Update

   • FS: Some new tickets are in based on conversations last week.
   • Python Integration Tests Fixes: Will fixed a few things here.
   • We have been disabling failing tests not being worked on which breaks TDD methodology.
     • Need to think making this work with 'hudson green'.
   • Chris as removed the omero build and redirected to omero trunk (as discussed last meeting).

2. Delete Front:

   • First run works, Jean-Marie submitting insight changes today.
   • Will is going to write some edge cases for the delete workflow.
   • Ola has support for queue.
     • Needs to modify webclient after a delete.
     • Added support for annotations, need to add other options.
   • Icontainer needs to updated to ignore delete queue items.
     
     • Won't have this for 4.2.1 (will need to be noted in release notes)
       

3. Iteration:

   • Some folks away, do we want to add another 7 days to this iteration?
     • Vote is yes.
   • 4.2 internal release is out.
     • Some of those bugs are already fixed.
   • Export fixes are in today (new version of server and importer coming out)
     • Export not 100%. Need to schedule more work soon on this.
     • Its not a 100% round trip (some imported data no exported).
       • Custom attribues not imported
       • subset of model supported currently
   • FLIM scripting is fixed

4. EMDB

   • Will has a bug with login which needs debugging.
   • Needs to have a few folks login at the same moment for testing
   • After fixing the connection issue, need to send out for feedback

5. Email/Forum/QA

   • Email:
     • Best Practice email needs reply.
     • Image Open email is probably related to bug Chris just fixed (he will reply).
     • Melissa will talk to Ruben about his email.
   • Forum
     • Bogus Error: Fixed, Ola will reply
     • Web Error with file path: Seems his path is broken (Ola will reply).
     • Project Process: Chris will reply to Katarina.
     • 4.1 setup: Chris will reply.
   • QA
     • Lots already closed from morning's fixes
     • Brian/Chris/Jean-Marie will go through it

6. Type is a XSD:List Attribute in Experiment and MicrobeamManipulation

   • Currently supported in the model, not supported in OMERO
   • XML model also doesn't support this
   • This needs solving!
   • Jean-Marie suggests as a short term solution to increase the cardinality of these items (multiple experiments)
   • Also other solutions

7. SPIM

   • Jason would like a solution that people can start to use right away (in 2 weeks?) for later upgrade
   • Proposal was sent to gunther, but its not a general solution
     • Could start with this, but its going to need to be migrated to a better system later
   • Needs a discussion tomorrow afternoon about this.
   • Need to be careful not to make model changes a few weeks before a release
     • Huge task (testing needed accross the board)
   • For modelling tasks, need to choose a top priority (too much on the existing story)

Action Items

* Jean-Marie Ticket: Icontainer needs to updated to ignore delete queue items.
* Chris: Deal with open file email replies (see other emails above as well).
* Chris: https://www.openmicroscopy.org/site/support/omero4/server/installation (wrong version of Python)
* Jean-Marie/Chris/Andrew: SPIM meeting on Friday 2:00
* Andrew: look over your modelling story, pick top item for us to complete before ASCB