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From 03/14/2010 to 04/12/2010

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

03/18/2010

11:25 AM Bug #4890: findMatchingAnnotations(...) needs Context
Reopening but as a Morpho plugin bug.
Now that the annotation manager can search on context, we need to include it in...
ben leinfelder
11:22 AM Bug #4890: findMatchingAnnotations(...) needs Context
now you can provide a list of Triples (Entity, Relationship, Entity) as part of the search criteria. ben leinfelder

03/17/2010

04:51 PM Bug #4891: Rank annotation search results
[4:42pm] bowers: i'm not super big on using "or" and "and" in search
[4:42pm] bowers: i think it should all be "or" w...
ben leinfelder
04:51 PM Bug #4891 (Resolved): Rank annotation search results
"just like google" ben leinfelder
04:48 PM Bug #4889: Compound Search UI
Another recommendation: do away with AND/OR confusion and use the search results ranking to indicate how closely the ... ben leinfelder
04:25 PM Bug #4889: Compound Search UI
Include Context relationship searching. This needs to be added to the SMS AnnotationManager ben leinfelder
04:00 PM Bug #4889 (Resolved): Compound Search UI
Place-holding bug for work done on the search interface.
Initially there was a single screen for specifying Entity/C...
ben leinfelder
04:45 PM Bug #4890: findMatchingAnnotations(...) needs Context
[4:31pm] bowers: i think the madlib stuff could be reused for this ... although you might want a way to say that two ... ben leinfelder
04:28 PM Bug #4890 (Resolved): findMatchingAnnotations(...) needs Context
Likely the first of many enhancements to the AnnotationManager API.
We need to allow searching based on Context.
...
ben leinfelder
11:36 AM Bug #4882: Use OBOE Measurement class to auto-fill other fields
cutting installers for folks to check out this feature.
enter bugs as needed for tweaking
ben leinfelder

03/16/2010

03:50 PM Bug #4882: Use OBOE Measurement class to auto-fill other fields
I've added a method to the SMS OntologyManager that can be used to look up the restrictions that are defined on the M... ben leinfelder

03/15/2010

04:55 PM Bug #4882: Use OBOE Measurement class to auto-fill other fields
i've casually been calling this a "Measurement template" ben leinfelder
11:14 AM Bug #4882 (Resolved): Use OBOE Measurement class to auto-fill other fields
By defining subclasses of OBOE's Measurement class (of Characteristic, uses Protocol, etc...) we can just have one wi... ben leinfelder
 

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