From 03/21/2010 to 04/19/2010
- 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:
- 03:24 PM Bug #4945: Add scrollbars to search UI
- was not expecting it to take only 1 line of code...done!
- 01:16 PM Bug #4945 (Resolved): Add scrollbars to search UI
- If you add enough criteria, you will exceed the size of the window.
- 03:11 PM Bug #4948: Clarify importance of Measurement "template" field
- added dividing lines with titles in them:
The <blank> was recorded
- 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...
- 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 ...
- 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 ...
- 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...
- 01:57 PM Bug #4947: Search ontology tree only using class name
- not searching labels/descriptions now.
- 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...
- 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...
- 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.
- 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...
- 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...
- 11:05 AM Bug #4922: DB-driven Annotation Manager
- this is now the implementation in the packaged installer.
- 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...
- 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 ...
- 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...
- 02:14 PM Bug #4922: DB-driven Annotation Manager
The existing query methods have been re-implemented to use the db model.
If there's a "working" copy of the a...
- 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...
- 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...
- 04:19 PM Bug #4906: Annotation query implementation (SPARQL)
- we are dropping this in favor of a relational-db approach:
- 04:18 PM Bug #4905: iTunes-inspired search UI
- Hey, this is all done now!
- 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...
- 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.
- 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...
- 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...
- 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...
- 11:21 AM Bug #4922: DB-driven Annotation Manager
- draft of the basic schema needed is here:
- 04:22 PM Bug #4922 (Resolved): DB-driven Annotation Manager
- The current AnnotationManager implementation reads XML serializations into Annotation objects in memory. Any operatio...
- 03:11 PM Bug #4906: Annotation query implementation (SPARQL)
- (In reply to comment #5)
> Something that would allow us to retrieve a list of annotation
- 02:53 PM Bug #4906: Annotation query implementation (SPARQL)
Something that would allow us to retrieve a list of annotation [instances?/objects?] with a ...
- 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...
- 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 ...
- 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...
- 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...
- 07:54 AM Bug #4889: Compound Search UI
- Consensus was to abandon this UI in favor of the iTunes-esque UI
- 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,...
- 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...
- 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.
- 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...
- 07:58 AM Bug #4891: Rank annotation search results
- current scheme for each annotation:
-5 possible search criteria (Entity, Characteristic, Standard, Protocol, Context)...
- 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...
- 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...
- 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...
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