Ecoinformatics Redmine

04/02/2010

02:25 PM Semtools 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 Semtools 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 Semtools 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 Semtools 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

11:21 AM Semtools 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 Semtools Bug #4922 (Resolved): DB-driven Annotation Manager

The current AnnotationManager implementation reads XML serializations into Annotation objects in memory. Any operatio... ben leinfelder

02:53 PM Semtools 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

02:04 PM Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4889: Compound Search UI

Consensus was to abandon this UI in favor of the iTunes-esque UI ben leinfelder

07:45 AM Semtools 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

07:41 AM Kepler Bug #4161: Develop kepler workflow execution engine

I know in early february I was able to use the commandline to execute a KAR (after some tweaks) and then Josep was un... ben leinfelder

03/30/2010

11:20 PM FIRST Bug #4901: Web interface does not display assessments!

You could try having Arthur restart Tomcat. You're correct in thinking the stylesheets are to blame. I'm not sure wha... ben leinfelder

03/29/2010

11:33 AM Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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

03/23/2010

01:28 PM Metacat Bug #4900: LDAP referral connection timeout

added code to skip the referral and continue to the next one if there was a problem with the first referral. This all... ben leinfelder

11:22 AM Metacat Bug #4900: LDAP referral connection timeout

matt's suggestions
2) modify metacat to gracefully deal with referral failures and timeouts
3) modify metacat to quer... ben leinfelder

11:12 AM Metacat Bug #4900: LDAP referral connection timeout

This came to light when Judith and Victoria were trying to authenticate with the saeonocean metacat node (that points... ben leinfelder

11:09 AM Metacat Bug #4900 (Resolved): LDAP referral connection timeout

When trying to authenticate with a SANParks username from Metacat hosts that point to ldap.ecoinformatics.org, the au... ben leinfelder

03/18/2010

11:25 AM Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4891 (Resolved): Rank annotation search results

"just like google" ben leinfelder

04:48 PM Semtools 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 Semtools Bug #4889: Compound Search UI

Include Context relationship searching. This needs to be added to the SMS AnnotationManager ben leinfelder

04:00 PM Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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

03/11/2010

06:03 PM Semtools Bug #4878: Ontology Browser - popup closes when clicked anywhere (Win XP)

Now checking that the focus shift is from one field to another (rather than to a popup). This prevents the popup from... ben leinfelder

05:31 PM Semtools Bug #4878 (Resolved): Ontology Browser - popup closes when clicked anywhere (Win XP)

From the madlib (column) view:
-click a class selection field
-pop up shows
-try to expand the root node
-popup c... ben leinfelder

03:25 PM Kepler Bug #4876 (New): RExpression - recursively handle arrays

Currently you can only have a list of lists - it would be nice to handle the Token->R->Token conversion recursively s... ben leinfelder

10:22 AM Kepler Bug #4869: changes made to workflows during dialogs before committing (Edit Parameters/Cancel)

Christopher,
The _handleClosing() method in ptolemy.actor.gui.EditParametersDialog
does not restore the values of ... ben leinfelder

03/10/2010

06:16 PM Kepler Bug #4869: changes made to workflows during dialogs before committing (Edit Parameters/Cancel)

This happens when you just run Vergil:
-drag a StringConst actor to the stage
-edit the actor params
-type some value... ben leinfelder

04:16 PM Kepler Bug #4869: changes made to workflows during dialogs before committing (Edit Parameters/Cancel)

You can get into trouble if you Edit the actor parameters then press other buttons (other than Cancel and Commit):
-H... ben leinfelder

02:41 PM Kepler Bug #4869: changes made to workflows during dialogs before committing (Edit Parameters/Cancel)

from conf. call:
-verify that "cancel" does work for all normal cases
-isolate the sequence that caused the changes t... ben leinfelder

09:59 AM Kepler Bug #4869: changes made to workflows during dialogs before committing (Edit Parameters/Cancel)

It's that attributeChanged() method - I know the EML actor does a lot of things in that method, and I remember it bei... ben leinfelder

01:04 PM Kepler Bug #4868: Update R paths in documentation and demos

Just noticed that the GSG also uses workflows with RExpression actors (00-StatisticalSummary and 05-LinearRegression)... ben leinfelder