ben leinfelder's activity
From 02/05/2010 to 03/06/2010
03/04/2010
- 04:44 PM Kepler Bug #4802: KARs in KeplerData/workflows are being parsed on startup
- commented out that bit of code - i believe it is redundant since it is also called in the open() method.
we should ke... - 03:26 PM Semtools Bug #4856: Ontology Browser as a non-modal palette
- IRC conversation:
----
bowers: what if instead of or in addition to drag and drop, it worked more palette like
[12:27... - 10:39 AM Semtools Bug #4854: Integrate Context Annotation tab with Column Annotation tab
- Started by making the CustomList have a madlib string representation of the context entry. The template is such:
"The... - 10:00 AM Semtools Bug #4853: Save as Duplicate... should copy the Annotation too
- Or should it?
It could also be an option since I can see wanting to get rid of the annotation (starting fresh) like i...
03/03/2010
- 04:29 PM Kepler Bug #4802: KARs in KeplerData/workflows are being parsed on startup
- is that a "yes"?
- 04:27 PM FIRST Bug #4861: NBII Connectivity Issues
- In the code, I only see an error message like the one you have phrased as:
"Could not load vocabulary: nbii"
This sho... - 04:06 PM Kepler Bug #4077: Rework Section 8
- only a couple minor things.
we do need to be aware of the act that the R examples are located in a the r module, not ... - 03:16 PM Kepler Bug #4081: Rework Appendix B
- Reviewed the R appendix - some minor typos corrected, but no glaring omissions re: functionality. I was concerned abo...
- 11:06 AM FIRST Bug #4863: Assessments saved on the server and opened on a non-local machine do not display images
- changed the download method to use InputStream for the binary image data.
verified that it works with this doc on the... - 10:39 AM FIRST Bug #4863: Assessments saved on the server and opened on a non-local machine do not display images
- i've added code to look up image ids and also download them when performing the synchronize.
03/02/2010
- 06:13 PM FIRST Bug #4861: NBII Connectivity Issues
- 1. At what point in the process is the error box popping up? I am assuming it is when you enter a search term and sea...
- 03:30 PM FIRST Bug #4861: NBII Connectivity Issues
- are you asking to add a loop that will retry the search if there is a failure?
I've actually never experienced a hicc... - 06:08 PM FIRST Bug #4863: Assessments saved on the server and opened on a non-local machine do not display images
- actually i don't see any code that would download the images for the QTI packages...so this may have never worked
- 03:40 PM FIRST Bug #4863: Assessments saved on the server and opened on a non-local machine do not display images
- do you see those image files in the local store like:
~/.first/profiles/<profile>/data/<profile>/1.1
you may have t... - 09:54 AM Kepler Bug #4860 (Resolved): GUI-free class for Workflow Run Export
- I'm trying to get the command-line execution working where I run a KAR and it produces a run KAR with the workflow/la...
03/01/2010
- 02:36 PM Semtools Bug #4856: Ontology Browser as a non-modal palette
- Use Proposals:
------------
1. Drag and Drop
-class can be selected from the tree and dragged to a:
-madlib field ... - 09:42 AM Semtools Bug #4856 (New): Ontology Browser as a non-modal palette
- From Shawn:
---
5. I still think we should display the current drop-down term
selection as a panel in the right-ha... - 09:39 AM Semtools Bug #4855 (New): Reorder the Full Annotation rows to match madlib order
- From Shawn:
---
2. The full annotation should be more closely aligned to the terms
used in the madlib. So, e.g., I... - 09:37 AM Semtools Bug #4854 (New): Integrate Context Annotation tab with Column Annotation tab
- Make one compete madlib for the column annotation.
---
1. I'd like to see the context annotation tab be folded int... - 09:11 AM Semtools Bug #4853 (Resolved): Save as Duplicate... should copy the Annotation too
- If you duplicate an EML package, the Annotation should be duplicated as well
02/26/2010
- 03:26 PM Kepler Bug #4802: KARs in KeplerData/workflows are being parsed on startup
- I can see the cache() method will eventually call the ObjectManager. is this the culprit that forces parsing of the m...
- 03:14 PM Metacat Bug #4850: Get the new TPC scheduler working with the new changes in Kepler from the KarXmlGenerator
- adding kepler bug dependency
- 02:59 PM Metacat Bug #4850: Get the new TPC scheduler working with the new changes in Kepler from the KarXmlGenerator
- I'm in the process of adding tpcStatus in the KarEntryAttributes such that it should look like this:
<karEntryAttrib... - 03:09 PM Kepler Bug #4851 (Resolved): KarEntryAttributes not saved in MANIFEST.MF/KarXML
- I'm trying to add some key metadata entries to the KAREntries I provide in the ReportInstanceKAREntryHandler. I can s...
- 01:31 PM Kepler Bug #4828: Uploading a top-level workflow to the repository fails
- targeting for 2.0
- 11:54 AM Kepler Bug #4799: "Login Anonymously" gave an error during the data search
- Refactored the anonymous login configuration to be at the Domain class rather than the Repository class.
-adds config... - 10:53 AM Kepler Bug #4799: "Login Anonymously" gave an error during the data search
- Ugh. We still have two different systems for managing our various "remote services":
-Repositories (components)
-Ecog... - 10:38 AM Kepler Bug #4799: "Login Anonymously" gave an error during the data search
- I figured it out!
when you try to use the "Login Anonymously" button, the authentication service will try to look of... - 09:10 AM Kepler Bug #4849: ant eclipse fails
- I should mention this is on trunk
- 09:10 AM Kepler Bug #4849 (Resolved): ant eclipse fails
- [eclipse] java.io.FileNotFoundException: /Users/leinfelder/workspace_kepler/kepler/build-area/resources/eclipse/Ptole...
02/25/2010
- 01:32 PM Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4836: Column Annotation page overwrites changes made in Full Annotation
- and it's back
- 09:42 AM Semtools 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 Semtools 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 ... - 02:02 PM Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4822: Include "Annotation Context" tab for editing the contexts
- done
- 10:54 AM Semtools 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 Semtools Bug #4822: Include "Annotation Context" tab for editing the contexts
- the sizing issue has been dealt with.
- 02:23 PM Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4813: Include class label/description when searching
- Now searching the labels that are included in the ontology.
- 09:25 AM Semtools 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 Semtools Bug #4780: "Mad lib" annotation screen
- closing for now - bound to be additional changes requested after review
- 10:01 AM Semtools Bug #4814: Highlight search result matches in ontology browser
- highlighting the first core match in the result tree
- 09:27 AM Semtools 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 Semtools 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
02/18/2010
- 03:48 PM Kepler Bug #4798: Create parser for KAR XML specification
- this is a 2.0 bug in that it is blocking the component search bug
- 03:46 PM Kepler Bug #4798: Create parser for KAR XML specification
- https://code.kepler-project.org/code/kepler/trunk/modules/core/src/org/kepler/kar/karxml/KARFile.xsd
is what exists ... - 12:47 PM Kepler Bug #4798: Create parser for KAR XML specification
- is there a complete XSD now?
- 12:45 PM Kepler Bug #4809: Kepler storing authenticated search results
- this has long been the case for datasets that have already been downloaded/cached - if you restart Kepler you don't n...
02/17/2010
- 02:13 PM Kepler Bug #4802 (Resolved): KARs in KeplerData/workflows are being parsed on startup
- When I launch Kepler with a clean cache but with a workflow sitting in my local workflow directory that uses protecte...
- 02:06 PM Kepler Bug #4578: tracking bug for changes to .kepler
- 'ant clean-cache' seems to not be deleting anything at the moment. shouldn't it?
- 01:55 PM Kepler Bug #4792: NPE from Eml200DataSource
- Now giving an actual message for the NPE and throwing it up the chain.
- 01:41 PM Kepler Bug #4792: NPE from Eml200DataSource
- i'll take this.
- 10:15 AM Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4794: "Mad lib" as a "Column View" tab
- no more help text or scrollbars - fits nicely
02/16/2010
- 02:23 PM Semtools 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 Semtools 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 Semtools 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 Semtools 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
- 05:20 PM Kepler Bug #4795: RExpression & cache cleaning
- Dan H. already had some code in there for managing "too long of strings" for the script input - long numeric arrays c...
- 04:36 PM Kepler Bug #4795: RExpression & cache cleaning
- There are a few kinds of files generated by RExpression:
1. complex data transfer from one RExpression actor to anoth... - 05:14 PM Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4774: Make spyglass icon more button-like
- no more spyglass icon - replaced with a text field (for initiating searches)
- 03:50 PM Semtools 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... - 10:42 AM Kepler Bug #4792: NPE from Eml200DataSource
- The workflow shouldn't run w/o the data.
What should be happening that isn't currently? Cleaner error?
02/11/2010
- 01:06 PM Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4780: "Mad lib" annotation screen
- bowers: Here is the whole madlib (i think):
The <characteristic> of the <entity*> was recorded using the <standard>... - 03:41 PM Kepler Bug #4462: Component search in remote repositories not working
- then there's a sample of this "kar metadata" file that aaron uploaded here:
http://kepler-dev.nceas.ucsb.edu/kepler/m... - 03:36 PM Kepler Bug #4462: Component search in remote repositories not working
- if you go on Keper-dev's "dev skin" and search using this squery, you can see the "kar" metadata is returned.
(URL: h... - 03:34 PM Kepler Bug #4462: Component search in remote repositories not working
- Need to verify with Aaron, but I believe:
components are now being uploaded using a new XML metadata format (a wrappe... - 03:25 PM Kepler Bug #2493: actor repository tracking bug
- adding dependencies...
- 01:55 PM Semtools 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 Semtools 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 Semtools Bug #4776: Do not display ontology URI in any UI components
- removed from the comment field and from the ontology browser
- 01:51 PM Semtools 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 Semtools 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 Semtools 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... - 10:04 AM Morpho Bug #3314: Morpho abstract search comes up with 0
- closing - was included in 1.8.0 release
02/08/2010
- 04:46 PM Semtools Bug #4780 (Resolved): "Mad lib" annotation screen
- Discussed extensively on IRC, as well as a bit in email that kicked it off (bowers):
---
I think a "fill in the bla... - 04:44 PM Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4774 (Resolved): Make spyglass icon more button-like
- The icon for launching the ontology browser should encourage clicks
- 04:15 PM Semtools Bug #4768: UI for managing annotation ontologies
- now loading new ontologies and unloading ontologies that are removed from the configuration
- 03:10 PM Semtools 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... - 10:15 AM Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools 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 Semtools Bug #4768: UI for managing annotation ontologies
- Soe more background (from an email I sent a while ago):
-----
I went to use the ontology browser in Morpho and realiz... - 10:29 PM Semtools 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...
- 10:29 AM Kepler Bug #4462: Component search in remote repositories not working
- In regard to replicating problematic components on Kepler-dev, I sent this email to Sean:
----
If I was correct about... - 10:28 AM Kepler Bug #4462: Component search in remote repositories not working
- if synchronizing the local repositories is still running the moml parser, then that means you'll be prompted for auth...
02/05/2010
- 02:42 PM Semtools 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 Semtools 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 ... - 02:34 PM Semtools 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 Semtools 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... - 10:35 AM Semtools 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 Semtools 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 Semtools Bug #4732: Directly select/edit the Annotation classes from the table
- hey, look at that, this is done.
- 09:00 AM Kepler Bug #4462: Component search in remote repositories not working
- kepler-dev has been wiped clean.
This means we shouldn't be at risk of hosing up the KNB server when issuing searches...
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