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From 03/21/2010 to 04/19/2010

04/20/2010

05:18 PM Bug #4856: Ontology Browser as a non-modal palette
Almost there with the floating dialog palette...looking good with preliminary work at least.
A few issues/todos:
-nee...
ben leinfelder

04/19/2010

03:24 PM Bug #4945: Add scrollbars to search UI
was not expecting it to take only 1 line of code...done! ben leinfelder
01:16 PM Bug #4945 (Resolved): Add scrollbars to search UI
If you add enough criteria, you will exceed the size of the window. ben leinfelder
03:11 PM Bug #4948: Clarify importance of Measurement "template" field
added dividing lines with titles in them:
Attribute: DATE
-Measurement----------
The <blank> was recorded
-Or-------...
ben leinfelder
01:26 PM Bug #4948 (Resolved): Clarify importance of Measurement "template" field
In the Column Annotation (and also the search UI) you can select a single Measurement subclass and have the other 4 c... ben leinfelder
02:45 PM Bug #4946: Look-ahead search freezes
To make this fast, I think you'll want to use a specialized tree structure for the lookup index, rather than running ... Matt Jones
02:05 PM Bug #4946: Look-ahead search freezes
This still isn't the speediest feature. The implementation is naive in that it reconstructs the entire tree from the ... ben leinfelder
01:18 PM Bug #4946 (New): Look-ahead search freezes
In the ontology browser, quick typing will render the popup useless.
My hunch is that it will go away when we stop s...
ben leinfelder
01:57 PM Bug #4947: Search ontology tree only using class name
not searching labels/descriptions now. ben leinfelder
01:20 PM Bug #4947 (Resolved): Search ontology tree only using class name
We are currently searching classname and all descriptions/labels for contains (not starts-with). This should be limit... ben leinfelder
01:46 PM Bug #4856: Ontology Browser as a non-modal palette
We are newly-recommitted to this approach - it will replace the current "drop down" style ontology browser. The state... ben leinfelder
01:37 PM Bug #4951 (Resolved): Add "?" help buttons/info on the annotation tabs
Full, Column and Context tabs all need help buttons to walk future users through the UI/annotation process.
There is...
ben leinfelder
01:35 PM Bug #4950 (Resolved): Toggle "edit mode" on Annotation tabs
Currently the Column Annotation and Context Annotation tabs are always in edit mode, so to speak. Any changes made to... ben leinfelder
01:30 PM Bug #4949 (Resolved): Add class label under madlib fields
Easier said than done considering the limited vertical space: ever-present reminders of the appropriate class for a m... ben leinfelder

04/16/2010

11:05 AM Bug #4922: DB-driven Annotation Manager
this is now the implementation in the packaged installer. ben leinfelder
09:53 AM Bug #4854: Integrate Context Annotation tab with Column Annotation tab
Context can be edited in place, madlib-style. There are add/remove buttons for the context entries.
They are still in...
ben leinfelder

04/12/2010

03:12 PM Bug #4922: DB-driven Annotation Manager
implemented the "is not" operator for criteria. I'm not sure how useful it will be at this point given that searches ... ben leinfelder
02:28 PM Bug #4922: DB-driven Annotation Manager
Contexts are now processed recursively so that their transitive nature can be searched:
A rel B
B rel C
-----
A rel C...
ben leinfelder
02:14 PM Bug #4922: DB-driven Annotation Manager
Status:
The existing query methods have been re-implemented to use the db model.
If there's a "working" copy of the a...
ben leinfelder

04/09/2010

04:53 PM Bug #4922: DB-driven Annotation Manager
Making good progress on this implementation. Really it's more of a hybrid - extending the in-memory version to only h... ben leinfelder

04/07/2010

02:06 PM Bug #4935 (New): Lazily load semtools plugin
While Morpho has a good framework for developing and loading plugins for the application, it does not have a way to e... ben leinfelder

04/06/2010

04:19 PM Bug #4906: Annotation query implementation (SPARQL)
we are dropping this in favor of a relational-db approach:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4922
ben leinfelder
04:18 PM Bug #4905: iTunes-inspired search UI
Hey, this is all done now! ben leinfelder

04/02/2010

02:25 PM Bug #4905: iTunes-inspired search UI
Good news:
-there's now no dependency on Morpho for the AnnotationManager to query correctly.
-the row heights are ma...
ben leinfelder

04/01/2010

04:53 PM Bug #4844: Dynamically resize Ontology selection fields
the tooltip is now much more helpful when the classname runs off the text area. ben leinfelder
04:48 PM Bug #4844: Dynamically resize Ontology selection fields
at the very least, the tooltip for them could read the full text so there's someway of seeing what the full classname... ben leinfelder
03:53 PM Bug #4905: iTunes-inspired search UI
The criteria are now actually driving the query.
I'm not happy with how there's a slight dependency on the morpho co...
ben leinfelder
12:15 PM Bug #4922: DB-driven Annotation Manager
I'm not sure the cardinality is right on that ERD model. In particular, shouldn't the Measurement--Characteristic ca... Matt Jones
11:21 AM Bug #4922: DB-driven Annotation Manager
draft of the basic schema needed is here:
https://code.ecoinformatics.org/code/semtools/trunk/docs/design/AnnotationM...
ben leinfelder

03/31/2010

04:22 PM Bug #4922 (Resolved): DB-driven Annotation Manager
The current AnnotationManager implementation reads XML serializations into Annotation objects in memory. Any operatio... ben leinfelder
03:11 PM Bug #4906: Annotation query implementation (SPARQL)
(In reply to comment #5)
> Expressivity/simplicity?
> Something that would allow us to retrieve a list of annotation
...
Shawn Bowers
02:53 PM Bug #4906: Annotation query implementation (SPARQL)
Expressivity/simplicity?
Something that would allow us to retrieve a list of annotation [instances?/objects?] with a ...
ben leinfelder
02:14 PM Bug #4906: Annotation query implementation (SPARQL)
(In reply to comment #3)
> I think we were saying that an every annotation would be an Annotation Instance
> (in some...
Shawn Bowers
02:04 PM Bug #4906: Annotation query implementation (SPARQL)
I think we were saying that an every annotation would be an Annotation Instance (in some yet-undefined ontology that ... ben leinfelder
07:52 AM Bug #4906: Annotation query implementation (SPARQL)
the current search implementation is simple and generous. some features that are desired:
-compound grouping conditio...
ben leinfelder
07:58 AM Bug #4905: iTunes-inspired search UI
-The UI (first draft?) is completed.
-The underlying search capabilities are not hooked up (no query is actually per...
ben leinfelder
07:54 AM Bug #4889: Compound Search UI
Consensus was to abandon this UI in favor of the iTunes-esque UI ben leinfelder
07:45 AM Bug #4891: Rank annotation search results
closing this - they are ranked. I'll be sure to keep this feature as the search capabilities are augmented (grouping,... ben leinfelder

03/29/2010

01:24 PM Bug #4906: Annotation query implementation (SPARQL)
I am not sure what it means here to materialize an annotation, but if it implies storing an annotation per se as an i... Shawn Bowers
11:33 AM Bug #4906 (Resolved): Annotation query implementation (SPARQL)
Matt recommends materializing the Annotation and Ontology as instances in the OBOE model for running searches.
I nee...
ben leinfelder
11:30 AM Bug #4905 (Resolved): iTunes-inspired search UI
Compound search should be more flexible and allow 2-levels of any/all grouping.
Example query that should be express...
ben leinfelder

03/27/2010

07:58 AM Bug #4891: Rank annotation search results
current scheme for each annotation:
-5 possible search criteria (Entity, Characteristic, Standard, Protocol, Context)...
ben leinfelder

03/25/2010

02:11 PM Bug #4890: findMatchingAnnotations(...) needs Context
added to the UI.
One thing that could be improved is integration between the Observation Entity selection and the fir...
ben leinfelder

03/24/2010

02:33 PM Bug #4902: Annotations duplicated during editing
Stale listeners were hanging around and responding to events that they should not have responded to - hence duplicati... ben leinfelder
11:19 AM Bug #4902 (Resolved): Annotations duplicated during editing
Still trying to track down the scenario in which this occurs. I believe it might have something to do with re-reading... ben leinfelder
 

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