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)

   • Andrew: Evaluate 'basic image' reverse stylesheets (newer to older versions)
     • Will is going to reply to the email about this problem with customer
   • Jason: contact vendors about exporting previous versions.
   • Donald: Update outstanding FLIM tickets with status, move to future of sprint
     • meeting with David? Wiki page? Any work on annotations?
   • Jean-Marie: #3581 move to Scott, move foward to new sprint
   • Handling Upgrades with users:
     • Need to write up more for technical requirements (#814) & new user story by Scott (#3670)
     • Scott & Josh (& other interested): go over #814 for Thursday
   • Brian: share spreadsheet for comments before he leaves
   • Brian: Create ticket, change the importCandidates in include the LSMs and retest

3. Multiple repositories now enabled on trac (10 minutes)

   • Example of multiple commits on ticket 3698
   • Browser's new look
   • How to handle specification?

4. OME-XML/TIFF discussion (15 minutes)

   • Reviewing examples (http://users.openmicroscopy.org.uk/~jmoore/external_xml.zip)
   • Need to take implementation in steps
   • Various possible more advanced scenarious: log, xinclude, etc.

5. Glencoe Update (Include this section every other week)

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

   • Email - none

   • Forums -

     • Invalid application host - configuring apache
     • Re: Ice 3.4 vs. 3.3?
     • Re: import tif files
     • OMERO Imports fail on Windows
     • Not a Valid Image
     • Re: Ordering and OMERO
     • Re: Importing colors
     • Re: OMERO Importer

   • QA -
     link

     ID  Status  User/email  Type    Created Selected file   Comment Error
     3079    new n.y.patel@du... Insight 4.2.2   2010 12 16  -   I tried to access the ROI atta...   java.lang.Exception: org....
     3078    new n.y.patel@du... Insight 4.2.2   2010 12 16  -   -   java.lang.Exception: org....
     3077    new n.y.patel@du... Insight 4.2.2   2010 12 16  -   -   java.lang.Exception: org....
     3076    new n.y.patel@du... Insight 4.2.2   2010 12 16  -   Trying to save some ROIs.   java.lang.Exception: org....
     3075    new unknown Insight 4.2.0   2010 12 14  -   -   java.lang.Exception: Abno...
     3074    new n.hattersley... Insight 4.2.1   2010 12 13  -   projecting files - was doing m...   java.lang.Exception: org....
     3073    new glyn.nelson@... Importer 4.2.2-r871 2010 12 13  ...i_composite_flatrainbowRGB.jpg   was a largish jpg that failed   java.lang.RuntimeExceptio...
     3072    new glyn.nelson@... Importer 4.2.2-r871 2010 12 13  ...i_composite_flatrainbowRGB.jpg   was a largish jpg that failed   java.lang.RuntimeExceptio...
     3071    new glyn.nelson@... Insight 4.2.2   2010 12 13  -   trying to change the colour on...   java.lang.Exception: org....
     3070    new unknown Importer 4.2.2-r871 2010 12 10  101007_EGFR_Ab_test_E07.pnl -   java.io.FileNotFoundExcep...
     3068    new glyn.nelson@... Importer 4.2.2-r871 2010 12 10  ...s_senSODcat_3h_L1_L9_tiled.tif   first time user, so may be my ...   omero.InternalException ...
     3067    new unknown Insight 4.2.1   2010 12 09  -   -   java.lang.Exception: org....
     3064    new ziegler@zmb.... Insight 4.2.1   2010 12 07  -   aaaa    java.lang.Exception: org....
     3060    new andres.kaech... Insight 4.2.0   2010 12 03  -   -   java.lang.Exception: org....
     

7. Any other business (<5 mins)

Attending

• Carlos, Donald, Jason, Josh, Melissa, Brian, Chris, Andrew

Notes

1. Matters Arising (<10 mins)

   • Andrew: Evaluate 'basic image' reverse stylesheets (newer to older versions) SOME PROGRESS
     • Will is going to reply to the email about this problem with customer UNDONE
     • 2008 reverse xslt: Works for the given data
       • Need tests of the attributes explicitly
       • If downgrading to 8, can use upgrade script to go to any version
         • this is a lossy process though
         • (We do not 2003 to 2007, for example)
         • No doubt other things that need to be transformed, removed, etc. Needs testing
         • Could write a compatability mode schema with just objects for cogen
         • Chris: What should we do in the meantime, give users a little app to change versions?
           • Andrew: or a commandline version (or both?)
           • Step one is style sheets first though
           • Andrew will make a list of style sheets required.
     • Imaris seems to use 2003-FC
     • Couldn't get volocity working
   • Jason: contact vendors about exporting previous versions. TABLED FOR NEW YEAR.
     • Chris: name & shame policy?
     • Melissa: add column to bf table page
     • Andrew: 10 year rule. so in 2013,...
     • Chris: will the vendors simply point to no library being available
     • Jason: target perhaps roughly update once per year
     • Chris: Lots to decide. In 4.3? What code goes where? etc.
   • Donald: Update outstanding FLIM tickets with status, move to future of sprint MOVED/UPDATED/CLOSED TICKETS
     • Topics: meeting with David? Wiki page? Any work on annotations?
     • Tickets updated or moved
     • Wiki page was not done
     • Jos on holiday; so server just fixed last night.
     • David will hopefully test today.
     • Annotations are changed.
     • Keywords/NS are not done. Holding off for more concrete discussion.
     • Summary:
       • Pretty much done but needs wiki page for Pieta
         • setting up cluster, etc.
         • ETA: before 25th
       • Waiting for user feedback from David (that has
     • Gone from 27th to the 3rd.
   • Handling Upgrades with users TABLED UNTIL NEW YEAR
     • Need to write up more for technical requirements (#814) & new user story by Scott (#3670)
     • Scott & Josh (& other interested): go over #814 for Thursday
     • For the team need to move forward on two fronts:
       • Finding out what the users want / are willing to deal with
       • What we are committed to do? Webstart? Something more? What caveats exist?
         • What other solutions are possible? OSGI (lots of work)
         • Needs more discussion
   • Brian: share spreadsheet for comments before he leaves SHARED
     • Blank fields for page owners to fill out
     • spreadsheet includes about 2/3: remaining, 50 pages on plone, 20 pages on xml, insight?
     • Perhaps we can encapsulate the metadata on the pages themselves.
     • Reviewers?
       • Outgoing in the next few days. Start in January.
       • Not worried about the orphan pages.
       • 3-4 weeks to deal with anything egregious.
       • Hopefully at least get a 'table of contents' page out of this thats 'clean' with relevant pages
       • Looks at future changes to better support documentation after that
   • Brian: Create ticket, change the importCandidates in include the LSMs and retest TOMORROW

2. Multiple repositories now enabled on trac (10 minutes)

   • Example of multiple commits on ticket 3698
   • Browser's new look
   • How to handle specification?
   • Tested Git, seems to work well
   • Most of the move done and working, some tickets still need moving
   • Getting BF into here would require a git clone or hosting subversion in Dundee
   • What are we going to do wit the specification repo? Link it or move it in?
     • In the new year, decide what other changes need to be made
   • Andrew: Moved some of the OME-XML tickets (~1/3); working through the rest
     • The big negative of moving the code first / trac second makes things break
     • Moving the wiki pages will break all the links
       • Andrew: probably not that many
       • Chris: best if we move it in one stage to keep links, etc.
       • Andrew: The end result is that ome-xml site becomes just a documentation site
       • Josh: If all wiki pages become some sort of ome-xml/wikiPage can then just link from old website to new
       • Brian: Probably need to decide on "where documentation sits" to make a final decision
       • Josh: Some scripts (like validator) might break - looking for specific directories
       • See https://trac.openmicroscopy.org.uk/agilo/browser/josh-merged for fully merged example
       • new spec repo will be 'ome-xml'

3. OME-XML/TIFF discussion (15 minutes)

   • Reviewing examples (http://users.openmicroscopy.org.uk/~jmoore/external_xml.zip) * Josh & Chris discussed the examples. * Go from very simple to very detailed * Going to deliver simple case right away (tiffs with references) * Some challenges with the EMBL data (they want distributed metadata in the future) * Complicated to implement, complicated specification * Andrew will take a look at the example data * Chris suggests we start with 'Example 1'. Hopefully have proposal out by Chrismas time * Chris & Josh discussed a log based ome-xml format (history based mvcc xml like format) * This would solve some of the problems with 'using ome-xml in a database like way' * Do we want to go this way is the question? * Also talked about x-includes, but this is a ton of work and not well defined * currently the best thing seems to be support the base requirements and wait for user feedback
   • Need to take implementation in steps
   • Various possible more advanced scenarious: log, xinclude, etc.

4. Glencoe Update (Include this section every other week)

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

   • Email - none

   • Forums -

     • Invalid application host - configuring apache
     • Re: Ice 3.4 vs. 3.3?
       • We may need to update using multiple jars if we want to have both
       • Josh: Shares would be most dangerious, but we could have a compatibility layer
       • Chris: We could compile the server/client with both
       • Make 3.4 default, with 3.3 build as well - this could work (Josh will have to try)
     • Re: import tif files
     • OMERO Imports fail on Windows
     • Not a Valid Image
     • Re: Ordering and OMERO
     • Re: Importing colors
     • Re: OMERO Importer

   • QA -
     link

     ID  Status  User/email  Type    Created Selected file   Comment Error
     3079    new n.y.patel@du... Insight 4.2.2   2010 12 16  -   I tried to access the ROI atta...   java.lang.Exception: org....
     3078    new n.y.patel@du... Insight 4.2.2   2010 12 16  -   -   java.lang.Exception: org....
     3077    new n.y.patel@du... Insight 4.2.2   2010 12 16  -   -   java.lang.Exception: org....
     3076    new n.y.patel@du... Insight 4.2.2   2010 12 16  -   Trying to save some ROIs.   java.lang.Exception: org....
     3075    new unknown Insight 4.2.0   2010 12 14  -   -   java.lang.Exception: Abno...
     3074    new n.hattersley... Insight 4.2.1   2010 12 13  -   projecting files - was doing m...   java.lang.Exception: org....
     3073    new glyn.nelson@... Importer 4.2.2-r871 2010 12 13  ...i_composite_flatrainbowRGB.jpg   was a largish jpg that failed   java.lang.RuntimeExceptio...
     3072    new glyn.nelson@... Importer 4.2.2-r871 2010 12 13  ...i_composite_flatrainbowRGB.jpg   was a largish jpg that failed   java.lang.RuntimeExceptio...
     3071    new glyn.nelson@... Insight 4.2.2   2010 12 13  -   trying to change the colour on...   java.lang.Exception: org....
     3070    new unknown Importer 4.2.2-r871 2010 12 10  101007_EGFR_Ab_test_E07.pnl -   java.io.FileNotFoundExcep...
     3068    new glyn.nelson@... Importer 4.2.2-r871 2010 12 10  ...s_senSODcat_3h_L1_L9_tiled.tif   first time user, so may be my ...   omero.InternalException ...
     3067    new unknown Insight 4.2.1   2010 12 09  -   -   java.lang.Exception: org....
     3064    new ziegler@zmb.... Insight 4.2.1   2010 12 07  -   aaaa    java.lang.Exception: org....
     3060    new andres.kaech... Insight 4.2.0   2010 12 03  -   -   java.lang.Exception: org....
     

6. Other business (<5 mins)

   • ASCB was great! Very successful!
     • Interest in native OME-XML libraries.. going to have to think about that!
   • Meeting time changes suggested, everyone please respond!

Actions

1. Andrew: Create story, then tickets for backporting to 2003-FC, mapping enumerations, testing all attributes, CLI app, etc.
2. Andrew: Come up with a list of alll style sheets required for conversions. cF. softworx from OMX, etc.
3. Jason: See what can be done to update vendors?
4. Will is going to send out a message to the mailing list about the vendor ome-xml version problem
5. Chris & Josh: write to list about example 1 XML before Christmas
6. Chris add specification to multiple repositories
7. Everyone: in new year, discuss git
8. Everyone: in new year, discuss XSLTs, updaters, Ice 3.4 while looking at 4.3+ priorities
9. Andrew: See tabled items.
10. Meeting time changes suggested, everyone please respond!
11. ASCB Zapper: respond to the Zappee before Christmas