2010-09-16 Thursday Meeting
Attending: Brian, Chris, Colin, Jean-Marie, Will, Ola, Melissa, Brian Jones
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)
Accepting minutes from last meeting
Matters Arising (<10 mins)
- Put in outstanding action points from last Thursday or Tuesday meeting
Status update (15 mins)
webemdb quick test (less than 5 mins) webemdb webemdb-data
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 -
-
Email -
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...
-
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
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).
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)
-
Won't have this for 4.2.1 (will need to be noted in release notes)
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
-
Some folks away, do we want to add another 7 days to this iteration?
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
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
-
Email:
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
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