OBO-Edit: v2.1 Release Notes

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OBO-Edit v2.1 Consolidated Release Notes

OBO-Edit v2.1beta1-4Release Notes

  • [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-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

OBO-Edit v2.1beta1 Release Notes

FEATURES:

  • 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
  • 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
  • IMPORTANT* ANNOUNCEMENT FOR 2.1beta1 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.

Bug Fixes

  • - Fixed bug that stopped the box at the bottom of the history browser from appearing unless another component was clicked on.
  • (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


Frequently Asked Questions

1. Why is there a beta release for OBO-Edit after the 2.0 official release? This version includes bug fixes and some new features while additional significant features are in the pipeline. The 2.1 official release is pending completion of those features and fixing of bugs posted for 2.0.

2. Why has the location of the configuration folder changed? In the previous versions the location of the config folder was a characteristic of the operating system used. This led to a lot of confusion and most users could not locate their config folder hence I decided to change it to a standard location in the file system.

3. What can I do to help? The success of any software tool is dependent on feedback from the user community. Ways in which you can help:
Participate in OBO-Edit Working Group Weekly Meetings held on alternate Tuesdays over webex and conference call.

  • You can subscribe to the OEWG meeting calendar here:

https://www.google.com/calendar/render?cid=cDN1bXNkOG45bDMyYW5kbGR1M2xqcjNuazhAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ&invEmailKey=geneontology-oboedit-working-group%40lists.sourceforge.net%3Af41cf4fbc1e0ab381b88e541f31307dd73d92ab1

  • Email aabdulla[at]berkeleybop[dot]org if you experience issues subscribing to the OEWG meeting calendar.
  • Join the OBO-Edit Working Group sourceforge mailing list:

https://sourceforge.net/mailarchive/forum.php?forum_name=geneontology-oboedit-working-group

  • Program or Report New Features - Let us know your ideas for new features or how we can improve existing features.
  • Report Bugs
  • Add Documentation
  • Write Tutorials and put them up on the OBO-Edit wiki page
  • Help others learn to use OBO-Edit, etc.

4. Where can I find the source code? http://wiki.geneontology.org/index.php/OBO-Edit:_Getting_the_Source_Code

5. Why haven't you responded to the mail I sent you? The probability of your question getting answered quickly is the highest when you write to the OBO-Edit Working Group Sourceforge Mailing list: https://sourceforge.net/mailarchive/forum.php?forum_name=geneontology-oboedit-working-group

6. Who develops OBO-Edit?
Amina Abdulla at Berkeley Bioinformatics and Open Source Projects Group (BBOP),LBL,Berkeley,California is the lead OBO-Edit developer. You can email her at: aabdulla[at]berkeleybop[dot]org or attend a working group meeting to discuss any questions/comments about the tool.


To Do's

Documentation:
- user.dict usage and backup info
- Assert Implied Links Component
- Update Advanced Save interface options

Troubleshooting- add note about:
https://sourceforge.net/tracker2/index.php?func=detail&aid=2683791&group_id=36855&atid=418257

Notes

Effective bug reports are the most likely to be fixed. These guidelines explain how to write such reports.

  • Reproduce your bug using the most recent release, to see weather it has already been fixed.
  • Be precise and clear - explain the behavior so others can reproduce the bug
  • Limit bugs to one per report
  • No bug is too trivial to report - small bugs may hide big bugs
  • Clearly separate fact from speculation
  • Search the Bugs Tracker to check weather your bug has already been reported


  • Reporting a New Bug *

- If you have reproduced a bug in the most recent release and no-one else appears to have reported it, then report it on our sourceforge bug tracker: https://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse


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