2010-05-13 Thursday Meeting
Attending|: Brian, Jean-Marie, Colin, Andrew, Ola, Will, Josh, Melissa, Curtis
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)
- Andrew: Writing to Ilya / responding to FindSpots
- Everyone: think about annotations for Thursday discussion (see nitpick thread)
Annotations in OMERO and OME-XML
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
-
Unstarted tickets or those with significant dev time? Push or start?
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...
AOCB (<5 mins)
- Hudson emails - how do I stop them
- Hudson specific channel to not flood devteam
Notes
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
- http://trac.openmicroscopy.org.uk/omero/browser/trunk/etc/grid/default.xml#L56
-
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
-
Jean-Marie: behind because we cannot import with the new bf
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