Ecoinformatics Redmine

05/05/2010

04:37 PM Morpho Bug #4366: morpho should display common mime types (e.g., images)

I'm using the MIME type from
javax.activation.MimetypesFileTypeMap
which may or may not include all mime types we'd ... ben leinfelder

04:12 PM Morpho Bug #4366: morpho should display common mime types (e.g., images)

Images and text are now being displayed correctly.
PDFs and other binary files will still show as text with crazy cha... ben leinfelder

04:22 PM Morpho Bug #4364: Convert otherEntity from registry to dataTable

you can now delete _any_ entity, not just data tables ben leinfelder

12:09 PM Morpho Bug #4364: Convert otherEntity from registry to dataTable

First section of "Data" menu now has these options:
--------------------------
Create/Import New Data Table...
Replac... ben leinfelder

04:14 PM Morpho Bug #4365: New feature for creating otherEntity

"Import Other Data..." is now an option ben leinfelder

12:09 PM Morpho Bug #3473: allow user to attach, replace, or delete data table on existing entity description

First section of "Data" menu now has these options:
--------------------------
Create/Import New Data Table...
Replac... ben leinfelder

05/04/2010

02:02 PM Semtools Bug #4675: EML:DataTable:Annotation cardinality

This notion of multiple annotations per data table came up again recently (due to a bug, actually).
I'm wondering if... ben leinfelder

10:41 AM Morpho Bug #4975: Morpho can't handle docid prefix containing a period

periods not allowed anymore.
help/error text indicates such. ben leinfelder

09:57 AM Morpho Bug #4975: Morpho can't handle docid prefix containing a period

I'm pretty sure this has come up before. We're already preventing the use of "temporary" as a prefix. I believe Metac... ben leinfelder

05/03/2010

10:59 AM Morpho Bug #4364: Convert otherEntity from registry to dataTable

I tracked down the "stylesheet error" that was preventing mixed entities from being displayed. Turns out the styleshe... ben leinfelder

07:14 AM Morpho Bug #3473: allow user to attach, replace, or delete data table on existing entity description

I double checked that the data docid conflict was caught and that you are prompted for action (locally). Still works! ben leinfelder

04/30/2010

10:24 AM Morpho Bug #3473: allow user to attach, replace, or delete data table on existing entity description

for #1:
I've incremented the data file id now.
I have reservations about doing this - especially in a networked envi... ben leinfelder

09:21 AM Morpho Bug #4364: Convert otherEntity from registry to dataTable

conversion now works, which is to say the entity wizard can be launched and pre-populated with the otherEntity data f... ben leinfelder

04/29/2010

05:02 PM Morpho Bug #4364: Convert otherEntity from registry to dataTable

I'm wading through the various wizard screens to get the workflow to make sense. Almost there.
The basic gist is thi... ben leinfelder

01:38 PM Morpho Bug #3473: allow user to attach, replace, or delete data table on existing entity description

"Data->Replace Current Data Table..." presents a dialog where you can select a different local data file.
The file is... ben leinfelder

04/27/2010

02:15 PM Semtools Bug #4856: Ontology Browser as a non-modal palette

there's now a blue border around the "active" field that will disappear when a different field is selected or if the ... ben leinfelder

11:59 AM Semtools Bug #4856: Ontology Browser as a non-modal palette

I've noticed it's quite easy to "forget" which field is driving the onotology palette - perhaps I'll had some clear v... ben leinfelder

11:55 AM Semtools Bug #4853: Save as Duplicate... should copy the Annotation too

Now responding to the "save duplicate event". You will be prompted as to whether or not you want to copy the annotati... ben leinfelder

04/26/2010

04:13 PM Semtools Bug #4946: Look-ahead search freezes

with the new[er] ontology palette, the look ahead searching might become less important. It's nearly impossible to ge... ben leinfelder

04:09 PM Semtools Bug #4922: DB-driven Annotation Manager

the bulk of this is complete - i'll add individual tasks to refine its use as they are identified. ben leinfelder

04:05 PM Semtools Bug #4844: Dynamically resize Ontology selection fields

the fields now have helping prompts underneath them. and the tool tip is great.
Dynamically resizing the fields was u... ben leinfelder

04:03 PM Semtools Bug #4769: Save annotations to network

now responding to the save event (on a data package) and saving to the same location as the eml package.
The "Save An... ben leinfelder

11:34 AM Semtools Bug #4856: Ontology Browser as a non-modal palette

Now the palette remains open. When a different field is clicked, the contents change to match (filter class and selec... ben leinfelder

08:10 AM Semtools Bug #4856: Ontology Browser as a non-modal palette

from shawn:
-do not close/reopen palette, just refresh the contents
-include search field in palette window
-include ... ben leinfelder

08:36 AM Semtools Bug #4950: Toggle "edit mode" on Annotation tabs

much better as a checkbox ben leinfelder

08:26 AM Semtools Bug #4950: Toggle "edit mode" on Annotation tabs

change to checkbox ben leinfelder

04/23/2010

03:28 PM Semtools Bug #4855: Reorder the Full Annotation rows to match madlib order

I think this makes the table even more confusing than it already is.
The current order matches the examples laid out... ben leinfelder

02:42 PM Kepler Bug #4524: no prompt to save a changed report

i don't think that's a "fix" for this issue.
If I've been making report layout changes and then i close Kepler, I am ... ben leinfelder

04/22/2010

05:49 PM Semtools Bug #4950: Toggle "edit mode" on Annotation tabs

the toggle button is now in charge of issuing the save. not a full save-to-disk, but a save-for-when-you-navigate-awa... ben leinfelder

01:34 PM Kepler Bug #4893: WRP Kepler Frame vertically fills entire screen

doesn't the Report Designed have a HUGE canvas in a scrollpane. is it possible that is affecting vertical window sizing? ben leinfelder

04/21/2010

04:14 PM Semtools Bug #4950: Toggle "edit mode" on Annotation tabs

i've got the pages set up so that they can be enabled/disabled.
Now for the toggling and saving. ben leinfelder

11:51 AM Semtools Bug #4951: Add "?" help buttons/info on the annotation tabs

Made the help dialog accessible from buttons/links on:
-Full Annotation tab
-Column Annotation tab
-Context Annotatio... ben leinfelder

04/20/2010

03:35 PM Semtools Bug #4949: Add class label under madlib fields

Wrapping the text field in a jpanel with a titled border. The title is the name of the class that field is filtering ... ben leinfelder

11:22 AM Semtools Bug #4856: Ontology Browser as a non-modal palette

The only other thing I can think to add to this is that it not close unless you hit the close button on the window. C... ben leinfelder

11:15 AM Semtools Bug #4856: Ontology Browser as a non-modal palette

1. modal issue resolved: made those modal dialogs non-modal so that the palette is not inactivated.
2. window closing... ben leinfelder

04/19/2010

05:18 PM Semtools 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

01:46 PM Semtools 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

03:24 PM Semtools Bug #4945: Add scrollbars to search UI

was not expecting it to take only 1 line of code...done! ben leinfelder

01:16 PM Semtools 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 Semtools 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 Semtools 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

02:05 PM Semtools 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 Semtools 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 Semtools Bug #4947: Search ontology tree only using class name

not searching labels/descriptions now. ben leinfelder

01:20 PM Semtools 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

01:37 PM Semtools 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 Semtools 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 Semtools 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

04:39 PM Kepler Bug #4942: KarXmlGenerator generated a invalid kar xml if KarEntry has dependsOnModule element

Also - for WRP we are going to be adding more children to <karEntryAttributes> - ideally we'd like to add any element... ben leinfelder

04:34 PM Kepler Bug #4942: KarXmlGenerator generated a invalid kar xml if KarEntry has dependsOnModule element

whichever is less of a headache to change. we are in charge of both of them, so you might as well make it easy for yo... ben leinfelder

11:05 AM Semtools Bug #4922: DB-driven Annotation Manager

this is now the implementation in the packaged installer. ben leinfelder

09:59 AM Kepler Bug #4874: Modify existing KARFile schema for use with KAR File Parser

I believe this is done in that it largely duplicates this bug:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4798 ben leinfelder

09:53 AM Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4905: iTunes-inspired search UI

Hey, this is all done now! ben leinfelder