Activity
From 02/02/2010 to 03/03/2010
03/01/2010
- 02:36 PM Bug #4856: Ontology Browser as a non-modal palette
- Use Proposals:
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1. Drag and Drop
-class can be selected from the tree and dragged to a:
-madlib field ... - 09:42 AM Bug #4856 (New): Ontology Browser as a non-modal palette
- From Shawn:
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5. I still think we should display the current drop-down term
selection as a panel in the right-ha... - 09:39 AM Bug #4855 (New): Reorder the Full Annotation rows to match madlib order
- From Shawn:
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2. The full annotation should be more closely aligned to the terms
used in the madlib. So, e.g., I... - 09:37 AM Bug #4854 (New): Integrate Context Annotation tab with Column Annotation tab
- Make one compete madlib for the column annotation.
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1. I'd like to see the context annotation tab be folded int... - 09:11 AM Bug #4853 (Resolved): Save as Duplicate... should copy the Annotation too
- If you duplicate an EML package, the Annotation should be duplicated as well
02/25/2010
- 01:32 PM Bug #4844 (Resolved): Dynamically resize Ontology selection fields
- This used to work when I was using a label to render the ontology selection widget, but the text field does not resiz...
- 12:03 PM Bug #4824: Ontology Browser - double click does not always select and close the popup
- while working on this, I noticed that if you tab between windows (cmd+tab on Mac) you'd trigger the pop up to be show...
- 11:34 AM Bug #4824: Ontology Browser - double click does not always select and close the popup
- ...because the tree is recreated during the search (typing in the text field), the double click listener was lost.
It... - 11:13 AM Bug #4824: Ontology Browser - double click does not always select and close the popup
- This seems to be happening when I type in the text field to initiate a search
- 11:09 AM Bug #4819: "Column Annotation" view duplicates mappings
- I should have been editing this bug instead of the bug about overwriting annotations. They were caused by the same is...
- 10:51 AM Bug #4836: Column Annotation page overwrites changes made in Full Annotation
- -added logging
-use member variable for annotation page reference (used in event handling methods)
-reset the annotat... - 09:57 AM Bug #4836: Column Annotation page overwrites changes made in Full Annotation
- and it's back
- 09:42 AM Bug #4836: Column Annotation page overwrites changes made in Full Annotation
- this is working now. I've restricted how you can use the AnnotationPage's methods so as to avoid duplicating mappings...
02/24/2010
- 03:16 PM Bug #4836: Column Annotation page overwrites changes made in Full Annotation
- here's my thinking:
-there should be a [rather lightweight] class that holds the tabbed pane
-this AnnotationTabPane ... - 02:08 PM Bug #4836: Column Annotation page overwrites changes made in Full Annotation
- Alternatively, create StateChangeEvents that reflect the change regardless of where it happens, so that updates to th...
- 02:02 PM Bug #4836 (Resolved): Column Annotation page overwrites changes made in Full Annotation
- Because of how I've set up the listener on the madlib tab, if you make a change directly to the annotation table, the...
- 01:38 PM Bug #4833: Direct Annotation (table) is adding incomplete mappings
- I introduced this bug when consolidation the code that looks up the current annotation and attribute. simple as omitt...
- 01:27 PM Bug #4833 (Resolved): Direct Annotation (table) is adding incomplete mappings
- When I double click a cell in the annotation table to select a class I end up completely hosing the annotation and th...
- 01:16 PM Bug #4823: Save Annotations... menu option improvements
- these are committed. 'course we have to figure out a better "whole package" save eventually.
- 11:15 AM Bug #4822: Include "Annotation Context" tab for editing the contexts
- done
- 10:54 AM Bug #4822: Include "Annotation Context" tab for editing the contexts
- Now using the Context tab to add/edit/remove the entries.
Now I just need to remove the Add/Remove Context... menu it...
02/23/2010
- 03:28 PM Bug #4822: Include "Annotation Context" tab for editing the contexts
- the sizing issue has been dealt with.
- 02:23 PM Bug #4822: Include "Annotation Context" tab for editing the contexts
- added a new page that uses one of Morpho's CustomList widgets to make the modifications.
so far:
-the page is a third... - 08:21 AM Bug #4822 (Resolved): Include "Annotation Context" tab for editing the contexts
- Currently you can only add a new context relationship or remove an existing one. There is no dedicated UI for display...
- 10:30 AM Bug #4825: Add Context is not saving the Relationship
- now getting the class from the widget, whereas previously the whole class URI was in the text field
- 09:51 AM Bug #4825 (Resolved): Add Context is not saving the Relationship
- When you add a Context to the currently selected Observation, the context is saved in the XML, but the Relationship i...
- 08:27 AM Bug #4824 (Resolved): Ontology Browser - double click does not always select and close the popup
- I've intermittently found that double clicking the tree does not actually close the popup - instead it behaves like t...
- 08:22 AM Bug #4823 (Resolved): Save Annotations... menu option improvements
- 1. There should be no ellipsis since there is not additional UI after invoking the option. (There should be when we s...
02/22/2010
- 05:23 PM Bug #4821: Changes in madlib view do not immediately show in table view
- When the tab is changed, a column selection event is fired which triggers the annotation to be saved as it currently ...
- 05:01 PM Bug #4821 (Resolved): Changes in madlib view do not immediately show in table view
- If you enter an annotation in the "Column Annotation" tab then switch to the "Full Annotation" view you will not see ...
- 04:45 PM Bug #4819: "Column Annotation" view duplicates mappings
- I encountered another case where the values from one annotation were populating and saving in another column's.
I cha... - 03:27 PM Bug #4819: "Column Annotation" view duplicates mappings
- Now "resetting" the madlib annotation tab so that the old values are not saved as a new mapping for the next selected...
- 11:57 AM Bug #4819 (Resolved): "Column Annotation" view duplicates mappings
- If you enter an Annotation using the Column Annotation madlib view, then switch to the table view and select another ...
02/19/2010
- 10:33 AM Bug #4813: Include class label/description when searching
- Now searching the labels that are included in the ontology.
- 09:25 AM Bug #4813 (Resolved): Include class label/description when searching
- Right now searches are fuzzy matching on the class name only. We should be looking into other text that is associated...
- 10:01 AM Bug #4780: "Mad lib" annotation screen
- closing for now - bound to be additional changes requested after review
- 10:01 AM Bug #4814: Highlight search result matches in ontology browser
- highlighting the first core match in the result tree
- 09:27 AM Bug #4814 (Resolved): Highlight search result matches in ontology browser
- Currently the tree expands and prunes to show only search matches, their ancestors, their children, and their sibling...
- 09:04 AM Bug #4788: Popup lightweight ontology browser
- closing this - i like how it's working at the moment. feels pretty natural to navigate and double click
02/17/2010
- 10:15 AM Bug #4788: Popup lightweight ontology browser
- would like to add:
-DOUBLE CLICK to select the class and close the popup
-text field should show currently selected c... - 10:13 AM Bug #4794: "Mad lib" as a "Column View" tab
- this is done - might be tweaked as others start to use it and provide feedback
- 10:04 AM Bug #4794: "Mad lib" as a "Column View" tab
- tweaked the padding of the data table so that the columns remain aligned with the annotation table that is now in a t...
- 09:15 AM Bug #4794: "Mad lib" as a "Column View" tab
- no more help text or scrollbars - fits nicely
02/16/2010
- 02:23 PM Bug #4794: "Mad lib" as a "Column View" tab
- I've parameterized the Annotation Page so that it omits the help text and the Observation/Measurement options and onl...
- 01:40 PM Bug #4794: "Mad lib" as a "Column View" tab
- oh, I also don't like that I have to save after each change in column selection (in case they have made a change in t...
- 01:34 PM Bug #4794: "Mad lib" as a "Column View" tab
- I've got the extra tab showing the contents of the same page that shows up when you "Annotate current column..."
This...
02/15/2010
- 08:01 AM Bug #4788: Popup lightweight ontology browser
- also, ENTER key is not being captured by the popup - the underlying frame hears it first as if you've clicked the Ok ...
02/12/2010
- 05:14 PM Bug #4788: Popup lightweight ontology browser
- Now:
-CLICK on the field and the popup is shown
-TAB will save current selection from the popup
-ESC exits without sa... - 03:46 PM Bug #4788: Popup lightweight ontology browser
- This is working with some more room for refinement:
-TAB and/or ENTER key should trigger the selection and close the ... - 03:54 PM Bug #4794 (Resolved): "Mad lib" as a "Column View" tab
- Include another tab where the Annotation Table resides. The "Column View" tab would show the madlib phrase for the cu...
- 03:51 PM Bug #4774: Make spyglass icon more button-like
- no more spyglass icon - replaced with a text field (for initiating searches)
- 03:50 PM Bug #4780: "Mad lib" annotation screen
- Reuse this madib UI in a tab where the Annotation Table is located.
When this "Column View" tab is selected:
-display...
02/11/2010
- 01:06 PM Bug #4779: Ontology Browser - use hybrid tree/table UI
- this now works - updated the JTreeTable code from the java tutorial
http://java.sun.com/products/jfc/tsc/articles/boo... - 10:39 AM Bug #4788 (Resolved): Popup lightweight ontology browser
- Instead of the modal dialog, the browser should just be a super-duper-combobox
02/10/2010
- 06:07 PM Bug #4777: Ontology Browser - show only search matches in the tree
- doing this in the "realtime ajaxy" style might be very resource intensive - especially as the number and size of the ...
- 05:53 PM Bug #4777: Ontology Browser - show only search matches in the tree
- I have the tree filtering for the searches now.
When no search term is entered, the tree resets itself (might want a ... - 09:57 AM Bug #4780: "Mad lib" annotation screen
- added mad lib phrasing to the "Add Context..." menu:
"The Observation was made where the <Entity> was <Relationship>...
02/09/2010
- 04:18 PM Bug #4780: "Mad lib" annotation screen
- There's now a version of the mad lib form when you use the "Annotate current column..." option.
- 02:40 PM Bug #4780: "Mad lib" annotation screen
- bowers: Here is the whole madlib (i think):
The <characteristic> of the <entity*> was recorded using the <standard>... - 01:55 PM Bug #4768: UI for managing annotation ontologies
- done for this round of plugin development - will revisit when loading remote (metacat) ontologies as well
- 01:54 PM Bug #4770: Load Annotations from Metacat in Annotation plugin
- adding dependency on the UI bug so I can close that but still have a link.
My hunch is that we'll want to manage loca... - 01:52 PM Bug #4776: Do not display ontology URI in any UI components
- removed from the comment field and from the ontology browser
- 01:51 PM Bug #4775: Ontology Browser - omit the ontology URI from top-level
- ontology is not the top level - only the appropriate superclass[es] for the widget are shown.
the Ontology name appea... - 01:27 PM Bug #4778: Ontology Browser - include more metadata about selected class
- now showing two columns:
-class name
-ontology name (not the URI)
when you select a class, the description shows in ... - 10:52 AM Bug #4779: Ontology Browser - use hybrid tree/table UI
- base classes were already in Morpho for the Access control page.
Made some modifications for use with Onology browsin...
02/08/2010
- 04:46 PM Bug #4780 (Resolved): "Mad lib" annotation screen
- Discussed extensively on IRC, as well as a bit in email that kicked it off (bowers):
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I think a "fill in the bla... - 04:44 PM Bug #4779 (Resolved): Ontology Browser - use hybrid tree/table UI
- Could augment the existing tree to include additional columns that will display additional information about the clas...
- 04:40 PM Bug #4778 (Resolved): Ontology Browser - include more metadata about selected class
- Descriptions and labels and other documentation (?) that can be pulled form the ontology should be accessible when th...
- 04:35 PM Bug #4777 (Resolved): Ontology Browser - show only search matches in the tree
- Searching for a match highlights and expands the tree to show the matches, but should also filter out non-matches.
... - 04:32 PM Bug #4776 (Resolved): Do not display ontology URI in any UI components
- We should be using a "friendlier" string to distinguish different ontologies instead of the formal URI.
versionInf... - 04:28 PM Bug #4775 (Resolved): Ontology Browser - omit the ontology URI from top-level
- The ontology browsing tree is confusing because the ontology URI for every active (and implicitly active) ontology is...
- 04:25 PM Bug #4774 (Resolved): Make spyglass icon more button-like
- The icon for launching the ontology browser should encourage clicks
- 04:15 PM Bug #4768: UI for managing annotation ontologies
- now loading new ontologies and unloading ontologies that are removed from the configuration
- 03:10 PM Bug #4768: UI for managing annotation ontologies
- created a very basic editor for the physical/logical mapping that is stored in Morpho's configuration.
It's just text... - 09:43 AM Bug #4768: UI for managing annotation ontologies
- You might see if the ontology manager/editor that Sean Riddle developed for Kepler could be reused in whole or part h...
- 10:15 AM Bug #4772 (New): Annotation cell selection also selects data table cell
- It seems that part of column model sharing between the annotation table and the data table results in the cell select...
02/06/2010
- 10:58 PM Bug #4738: Discard Annotation changes when datapackage window is closed
- this is done now. just need to figure out when and how to warn when discarding the changes
- 10:55 PM Bug #4771 (New): Decide permission policy for Annotations and Ontologies in Metacat
- My proposal:
-public read on all Ontologies
-same permissions as EML for Annotations that annotate that EML
This... - 10:48 PM Bug #4770 (New): Load Annotations from Metacat in Annotation plugin
- Currently only locally stored annotations are loaded (at startup when the Annotation Plugin is initialized).
For a l... - 10:41 PM Bug #4769 (New): Save annotations to network
- Currently only supporting saving Annotations to local store
This has implications for loading Annotations as well si... - 10:30 PM Bug #4768: UI for managing annotation ontologies
- Soe more background (from an email I sent a while ago):
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I went to use the ontology browser in Morpho and realiz... - 10:29 PM Bug #4768 (Resolved): UI for managing annotation ontologies
- There is a section of the config.xml that contains ontology URI (and URL) mappings for ontologies we want to load whe...
02/05/2010
- 03:41 PM Bug #4737: Provide menu option for removing Observations and Measurements
- If a user wants to remove an observation that is context for other observations, I think the system could prompt the ...
- 02:34 PM Bug #4737: Provide menu option for removing Observations and Measurements
- Grouped the options, hopefully it's clear what they do and what the implications are.
Decided to require the Context... - 11:59 AM Bug #4737: Provide menu option for removing Observations and Measurements
- When we remove an Observation...
-do we want to remove the Context it might be providing for another Observation?
-d... - 02:42 PM Bug #4724: Mark data package as changed when Annotation is edited
- adding a dependency for the annotations being discarded when the window closes. I'm not sure what should rely on what...
- 02:37 PM Bug #4738: Discard Annotation changes when datapackage window is closed
- Now listening for the window to close.
If the window closes, then we throw away any unsaved changes and use whatever ... - 10:35 AM Bug #4739: Re-Reorder after editing Annotation
- now if you reorder the table once, it will remain "reordered" until you close the window.
- 09:14 AM Bug #4718: Include help text on the Annotation wizard page
- reopen if there are additional comments to make on the help text.
- 09:13 AM Bug #4732: Directly select/edit the Annotation classes from the table
- hey, look at that, this is done.
02/04/2010
- 04:48 PM Bug #4739 (Resolved): Re-Reorder after editing Annotation
- Whenever the annotation is edited, the annotation table gets updated and returned to it's original column order.
If ... - 04:40 PM Bug #4738 (Resolved): Discard Annotation changes when datapackage window is closed
- Because the SMS library keeps it's annotations in memory, you can actually close the data package after editing the a...
- 04:37 PM Bug #4737 (Resolved): Provide menu option for removing Observations and Measurements
- If you add an observation annotation there is no way to remove it - you can only edit it and remove all of the classe...
- 03:41 PM Bug #4732: Directly select/edit the Annotation classes from the table
- Now if you don't select a class in the ontology browser (actually it's not that easy to do since you have to cntrl+cl...
- 03:02 PM Bug #4732: Directly select/edit the Annotation classes from the table
- Double click on the cell you want to edit:
-if there's an existing value, the ontology browser opens to that selected... - 08:21 AM Bug #4732 (Resolved): Directly select/edit the Annotation classes from the table
- Instead of going through the motion of selecting a column, bringing up the annotation page, then bringing up the onto...
02/03/2010
- 05:20 PM Bug #4718: Include help text on the Annotation wizard page
- i've added a snippet of Shawn's explanation to the main UI page for annotations, and then put more text on a Help pop...
- 09:43 AM Bug #4718: Include help text on the Annotation wizard page
- The measurement "iskey" attribute in the annotation syntax is a constraint, much like (primary) key constraints in re...
- 08:21 AM Bug #4718: Include help text on the Annotation wizard page
- Added help for the class selection items (Entity, Char, Standard, Protocol).
I'd like some guidance on the Observati... - 11:56 AM Bug #4717: Grey-out Annotation menu options when not-applicable
- Here are the current scenarios:
1. When you first open Morpho (no data package is open)
-Only Search Annotations... i...
02/02/2010
- 03:51 PM Bug #4724: Mark data package as changed when Annotation is edited
- I've been thinking that the annotation will eventually supplement or supplant the current EML attribute description p...
- 03:42 PM Bug #4724: Mark data package as changed when Annotation is edited
- This is part of a bigger issue - how to balance the user's need to have all the underlying structure hidden with the ...
- 01:32 PM Bug #4724 (New): Mark data package as changed when Annotation is edited
- Currently you can make as many changes as you want to an Annotation without ever changing the EML data package that i...
- 12:33 PM Bug #4720: Automatically generate Measurement and Observation labels
- disabling the text field for the labels - now observations and measurements will be auto labeled
- 11:27 AM Bug #4719: Filter the Ontology Browser by superclass
- Now only the subclasses of the Annotation class being collected are shown in the tree.
Note: this involves regenerati...
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