V2.1 fixes and updates

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OBO-Edit v2.1 RELEASE NOTES

What's New in OBO-Edit v2.1-beta7

Bug Fixes: [ geneontology-Bugs-3076730 ] Filter on save problems OE b4

[ geneontology-Bugs-2948445 ] Loss of intersection status on merge

[ geneontology-Bugs-3029689 ] Subset manager - subset name change not saved

[ geneontology-Bugs-2745699 ] 2.0 graph viewer now shows only one parent

[ geneontology-Bugs-3049416 ] Selection from auto-complete search menu flaky

[ geneontology-Bugs-2815514 ] overzealous autosave

[ geneontology-Bugs-2722517 ] autocomplete term selection in search panel

[ geneontology-Bugs-2685810 ] Graph Editor - Move option not working for multiple terms

[ geneontology-Bugs-2840516 ] no way to get to genus term while defining xps
fuzzy purple ball == cotton ball icon == Go To term button. Correct tooltip message added for both genus and differentia terms. Spanning to the term in OTE works well now, provided the OTE is in global mode.

Fixes in progress:
[ geneontology-Bugs-2971364 ] b4 - still having problems committing text edits


What's New in OBO-Edit v2.1-beta6

Bug Fixes: Fixed comments being eliminated from load cycle.


What's New in OBO-Edit v2.1-beta5

Bug Fixes:
[ geneontology-Bugs-3011139 ] delete term not deleting
[ geneontology-Bugs-3017846 ] Ubuntu 10.04 crashes
[ geneontology-Bugs-3007375 ] spontaneous cross products
[ geneontology-Bugs-2996789 ] Search Panel look-ahead keyboard selection problem
[ geneontology-Bugs-2997272 ] not all typedefs are shown in relationship branch
[ geneontology-Bugs-3000534 ] Search function (arrow key select)
[ geneontology-Bugs-3000571 ] problem with config manager display- 2.1 b4
[ geneontology-Bugs-2996688 ] Comments section being duplicated with is_a closure p
[ geneontology-Bugs-2996593 ] Weird search results OE beta 4
[ geneontology-Bugs-2990477 ] spontaneous replication of upper level terms
[ geneontology-Bugs-3035323 ] OE 2.1 beta 2 - clone problems
[ geneontology-Bugs-3035322 ] 2.1 betas - GraphViz problem

obo2obo: allowdangling true by default for input and output files.
v2.1b5 onwards the comments are overwritten. The order in which the files are loaded dictates precedence. In the OBOEdit Advanced file load menu, if file1 and file2 both have different comments for a particular term - and file2 is below file1 in the load list - the definition from file2 will hold.


  • IMPORTANT* ANNOUNCEMENT FOR v2.1x on Importing Settings From Previous Versions

Config directory located in the users home directory and called "oboedit_config". Settings from the previous releases (OBO-Edit 1. 2.0 or 2.0 beta versions) are located in the configuration folder found at the default application installation location of your operating system. You can import the perspective and layout settings from previous versions to the folder called "oboedit_config".

  • Please note the config folder naming convention is not consistent with previous version.*

Config files can also be reset when required through the Configuration Manager.


2.1 beta1 through beta4 Bug Fixes

[geneontology-Bugs-2899760] Too easy to make link to self in graph editor
[geneontology-Bugs-2971221] eliminate possibility to create is_a relationships to self
Text Editor and Parent Editor are now in sync
[ geneontology-Bugs-2971364 ] b3 - problems committing text edits
[ geneontology-Bugs-2987680 ] spontaneous intersection_of terms when cloning
[ geneontology-Bugs-2922369 ] Is_a closure not working as expected
[ geneontology-Bugs-2908106 ] OBO-merge fail
[ geneontology-Bugs-2915594] Not saving
[ geneontology-Bugs-2968827 ] saving implied links
[ geneontology-Bugs-2952892 ] Reasoning with union_of terms
[ geneontology-Bugs-2949754 ] Verification plugin dictionary - problem with quickfixes
[ geneontology-Bugs-2922331 ] No log file for OE2.1beta2
[ geneontology-Bugs-2874878 ] Missing log files in Mac
[ geneontology-Bugs-2610787] disjointness violations not detected
[ geneontology-Bugs-2821857] disjoint violations not being checked by RBR
[ geneontology-Bugs-2941032] Functionality - application does not run on windows 7
[ geneontology-Bugs-2915594 ] Not saving
[ geneontology-Bugs-2914257 ] When a term is cloned, intersections become relationships
[ geneontology-Bugs-2828905 ] verification config in 2.1 test release
[ geneontology-Bugs-2869195 ] text editor is not working
[ geneontology-Bugs-2864861 ] replaced_by statement causing problems in SO
[ geneontology-Bugs-2840516 ] no way to get to genus term while defing xps
[ geneontology-Bugs-2840500 ] relation name vanishes
[ geneontology-Bugs-2908106 ] OBO-merge fail
[ geneontology-Bugs-2610787] disjointness violations not detected
[ geneontology-Bugs-2821857] disjoint violations not being checked by RBR
[ geneontology-Bugs-2749049] disjoinedness check working?
[ geneontology-Bugs-2750699 ] config manager memory settings option out of sync
[ geneontology-Bugs-2785074 ] OBO-Edit2-rc still present
[ geneontology-Bugs-2787869 ] very minor bug with saving filters
[ geneontology-Bugs-2812189 ] GAZ.obo not displayed correctly in OBOEdit2.0
[ geneontology-Bugs-2824732 ] obodiff is broken!
[ geneontology-Bugs-2818616] stop panel changes if click on top
[ geneontology-Bugs-2814791] OBO merge doesn't work!
[ geneontology-Bugs-2805373] Assert implied links - color table rows
[ geneontology-Bugs-2818549] parent search ignores relationship type
[ geneontology-Bugs-2815689] change tracker save
[ geneontology-Bugs-2805371] Assert implied links - resize
[ geneontology-Bugs-2801684] OBO-Merge generates null-pointer exception
[ geneontology-Bugs-2790372] Mac version 2 does not generate log files
[ geneontology-Bugs-2749070] reasoner active even in OFF mode
[ geneontology-Bugs-2722323] assert implied links pop-up hogs focus and halts editing
[ geneontology-Bugs-2787869] very minor bug with saving filters
[ geneontology-Bugs-2815829] Simplify 'save implied links'
[ geneontology-Bugs-2722318] OTE local mode indication not intuitive
- Fixed bug that stopped the box at the bottom of the history browser from appearing unless another component was clicked on.
- flaky xp commit
- graph viewer issue
- filtering union_of cycles in OTE
- lock view selection behavior
- fixed root detection algorithm to detect inverse relations and display root
(Part of OE2.0 - history browser minor bugs - ID: 2507044)
- Fixed the history browser html message so it shows 'name (id)' rather then 'id (id)'. (Part of OE2.0 - history browser minor bugs - ID: 2507044) - Graphviz uses a lot of memory when you assign dbxrefs: ID: 2057452 The Graphviz interface redraws have been removed for the bulk addition of dbxrefs.
Now there is only one redraw at the end of the bulk process.
- Added new feature to OBOMerge so that it reports if any term has been edited in both the live and branch files.
- Added new feature to TermMergeHistoryItem, so it can update substitution tags that mention any term that
is in the process of being subsumed in a merge. Fixes bug: ID: 2790775


Features

- Parent Editor and Cross Product Text Editor component are now in synch and warn regarding changes made in either component

- Graph Viewer Improvements -- Renamed "Succinct" configuration option to "Trim reasoner-generated (implied) links from display".
--> Removed reasoner dependency from displaying all-types panels and showing ancestors upto root

- New Default Global Term Renderer for highlighting terms with cross product definitions

- Cross Product Editor -> Go to Genus term button

- J. Deegan committed new Tag Filter code. This feature enables
users to choose which tags are saved out into OBO files. The GUI is in the 'save as' dialog. There is still some work to do to make the GUI look less intimidating. Also, though the feature has been carefully tested, further testing will be required in case an obscure bug is causing parts of the data not to be saved out at all. I have not yet run the JUnit tests. When this code is released we should warn in-house users to watch diffs carefully for lost tags.

- Assert Implied Links Component
-- Displays impled links table and asserts selected links.
-- Row sorting enabled (ascending and descending) for Child and Parent name columns
-- Clicking the more info icon brings up the explanation for the reasoner made link in the Explanation Component and highlights the link in the Graph Editor

- New Reasoner Modes (IN PROGRESS - WILL BE AVAILABLE in the next release)
-- Two new options that represent step-wise and continuous incremental reasoning
-- Activate incremental reasoning by selecting the "Avtivate Incremental Reasoning" checkbox through the Reasoner Manager
-- Users have a choice between activating continuous incremental reasoning or partial/step reasoning modes. If neither of these options are selected incremental reasoning is off by default.

- New option in Advanced Save - Perform is_a closure (behaviour under testing for various use cases)
-- Performs is_a closure for all cross-referenced terms while saving

- Changed naming coventions for Advanced Save - Save implied links:
-- "Realize links" changed to "Assert Implied Links"
-- "Save for presentation" changed to "Save trimmed links"

- Lock/Unlock Layout option
-- Locking the layout freezes current application layout and prevents addition/removal of components.

- Scroll Lock for the Ontology Tree Editor
-- Select any term in the OTE; right-click for Lock View option which enforces a scroll lock on the path currently displayed.

- NEW Configuration directory location: users home directory/oboedit_config
- Cloning behavior corrected - clones now persist on the same branch as the original term.