OBO-Edit 2.0 Testing Tasks

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Please study the list of testing tasks below, and make a note after the ones that you would like to be responsible for in the OBO-Edit 2.0 release. When testing, if a feature is broken in the latest release, please highlight it in red and add a link to the sourceforge bug report. If a feature works, please highlight it in blue. For a particular component/task please update the corresponding documentation or make a note if content and figures are not up to date. Please feel free to add testing tasks, sub-tasks or notes as necessary.

Things to be tested:



  • Graph Editor (non-animated) Jen (Windows and Mac)
    • Expanding/collapsing nodes
    • Editing operations
    • Add term icon
    • Delete term or link icon
    • Different relationship types
    • All editing commands
    • Mutual selection works properly between graph editor and obo editor panel

I have tested this component thoroughly, and there are a few small bugs left, but I don't think they are show stoppers. I would be happy for the tool to be released. (Jen)

Note: this tool does not work well at all on a computer with 1.7GHz single core processor, but with 2.53GHz dual core it works fine. With longer edits I have had problems with running out of memory on a 3Gb machine.

SF 1878279 (rather old) - icon size
SF2540160 - cannot delete terms
SF2540177 - make children disjoint broken

  • Graph Editor (animated) Karen (Mac)
    • Expanding/collapsing nodes
    • Editing operations
    • Mutual selection works properly between graph editor and obo editor panel

SF 2541014 mouseover bubbles for the editing icons don't stay up long enough
SF 2541023 icons in editing toolbar shift positions annoyingly depending on size of optional info to right
SF 2541038 no way to change a relationship in the Graph Editor & when 2 relationships btw 2 terms, can't see the first one

  • Ontology Tree Editor
    • also see 'standard editing operations' below

SF2187636 - rogue menus
SF2023388 - multiple house icons
SF1944186 - wrong menus popping up
SF2065087 - flag if we are obsoleting a term referenced in a consider or replaced_by tag
SF 2315190 - unexpected OTE autoscroll
SF 2093230 - display oddities; may be fixed now
SF 2271697 - no refresh of global selection after clicking a relation

  • Parent Editor - Midori (Mac), Melissa (windows) - Documentation done (Midori)
    • All seems to be working fine (except one bit about cardinality that I don't really understand, but that won't delay release - ticket here) -midori
    • all working fine for me too (windows) -melissa
    • Definition Tab
    • Comment Tab
    • Cross Products Tab
      • Check for correct appearance of relations - see 'loading' below
    • Dbxrefs Tab
    • Synonyms Tab
    • Subsets Tab

Commit is fairly slow if we have all the verification checks enabled on edit and commit, but I do not think this needs to be fixed before release, as we can just turn these features off. What do others think?

  • Standard editing operations (All "Edit" Menu Options) - remember to test all different ways of accessing each operation (e.g. drag-and-drop, right-click, hotkey) - Tanya (Mac) - I've never used a hotkey before
    • Move - works for me (Jane, Jan 21 2009)
    • Add parent
    • Add child - works for me (Jane, Jan 21 2009)
    • Merge
    • Delete relationship - works for me (Jane, Jan 21 2009)
    • Obsolete term
    • Add new term - works for me (Jane, Jan 21 2009)
    • Add multiple new terms - works for me (Jane, Jan 21 2009)
    • Clone - works for me (Jane, Jan 21 2009)
    • Add new relationship type - Problem naming new relations SF:2593281 (Jane, Feb 12 2009)
    • Add/Remove replaced-by reference
    • Add/Remove consider reference
    • Text editing

SF 1863271 - merge hotkey problems


Harold (Mac)

  • Tree Viewer Jen (Mac and Windows)

This component is now ready to be released. (Jen)

  • Graph Viewer

SF2020610 - Shows incomplete graph even with reasoner
SF1812252 - Initial zoom should be set to reasonable value
SF 1919828 (rather old) - graph viewer flaky response

I have sent my recommendations for documentation updates for this component and the GraphViz component. hjd 3/17/09
  • Graphviz Viewer Jen (Mac and Windows)

This is ready for release now. I have updated the help guide. (Jen

SF 2277324 - unrecognized relation

SF2465040-Links display in graphviz but not in graphviewer [1]

Mac OSX when undocked, graphviz and graphview windows will not go to back, which obscures main application.

  • Term Image Display Panel


Amina (linux)

  • Term Search

SF2561035 - problem with searching Ancestors (Jane, 3 Feb 2009)
SF2561087 - problem with searching Aspect via specific relationship type (Jane, 3 Feb 2009)
SF2269624 - config settings are not retained over restart
SF 2023673 - missing search attributes
Also, auto-complete selection does not work for some fields: SF:2314626

  • Link Search

SF2269493 - easy - results column sizes set wrong
SF:2276989 - problem with implied link search (Jane, 13 Feb 2009)


Amina (linux), Jane (Mac)

  • Local Filters - all fine except this very minor bug SF 2053394 - renderer OTE redraw oddity
    • Term Filters - working (Jane, 16 Jan 2009)
    • Link Filters - working (Jane, 16 Jan 2009)
    • Term Renderers - working (Jane, 16 Jan 2009)
    • Link Renderers - working (Jane, 16 Jan 2009)
    • Quick filtering - working (Jane, 16 Jan 2009)

not checked since about betas 40-42:
SF 2034117 - heat map
SF 2031660 - render blending
- closed SF item; no demand for feature
Note: I don't think either of these relate to current features, so can probably ignore. (jane)
Response to note: Render blending can be ignored, because it simply isn't working and doesn't have to be available. The heat map coloring is working, though, and just needs a couple of small interface fixes (they're not a big deal, but on the surface they don't seem hard to fix). (midori 2009-01-19)


Jane (Mac)

  • Verification Manager
    • Checking correctness of results - working (Jane: 13 Jan 2009)
    • Making sure quick-fixes work:
      • Adding to dictionaries - working, but see below for problem with adding to user-defined dictionary (Jane: 13 Jan 2009)
      • Replacing misspelled words - not working SF:2504879 (Jane: 13 Jan 2009)
      • Adding legal always lowercase words - not working SF:2504879 (Jane: 13 Jan 2009)
      • Adding period, explanation mark or question mark to end of sentence - not working SF:2504879 (Jane: 13 Jan 2009)
      • Replace multiple whitespeaces with a single space - not working SF:2504879 (Jane: 13 Jan 2009)
    • Checking runtime verification behaviour in text editor - working (Jane: 13 Jan 2009)
    • User-defined verification checks - working (Jane: 13 Jan 2009)
    • Dictionaries:
      • saving to user-defined dictionary - not working: SF:2504817 (Jane: 13 Jan 2009)
      • saving to standard system dictionary - working (Jane: 13 Jan 2009)
    • Warnings during text edit SF2263749 - easy - cannot turn off pop-up warnings in def text box (Jen)
  • Ontology Change Tracker (Currently being tested by David OS)
  • OBO Merge (Jen)
    • Two serious bugs: In both cases consider or replaced_by tags are essentially ignored.

SF1871096 - consider tags
SF1871092 - consider tags
also SF 2051721 - obomerge loses replaced_by tags

These are being addressed together and the progress notes are at:

  • History
    • History Browser
      • records history events correctly - working (Jane, 14 Jan 2009)
      • copy/paste box - minor bugs: SF:2507044 (Jane, 14 Jan 2009)
      • saving (from within history browser) - not working SF:2507049 (Jane, 14 Jan 2009)
    • History Save in File menu - working (Jane, 21 Jan 2009)
    • History Load in File menu - not working SF:2526247 (Jane, 21 Jan 2009)
  • Configurable message - working but pointless! No idea what this is supposed to be for, suggest we remove from release (Jane 14 Jan 2009)
  • ID Fixer - Remove from this release (Jane 14 Jan 2009)


Midori (Mac), Amina (linux)
Documentation done (Midori)

  • Dbxref Library
    • SF ticket submitted, with what is either a bug or a feature request about the 'apply to all' option. Otherwise, working fine. (midori 2009-01-06)
  • Subset Manager
    • Working. Note: must update documentation text and screenshots to reflect name change (used to be 'category manager'). (midori 2009-01-06)
  • Synonym Type Manager
    • Working. Note: must update documentation text and screenshots to reflect name change (used to be 'synonym category manager'). (midori 2009-01-16)
  • ID Manager
    • Working. (midori 2009-01-16)
  • Namespace Manager
    • Working. (midori 2009-01-16)


Currently being being tested by: David OS

  • Reasoner starts/stops correctly

BUG: Cancelling the reasoner stops it being run again for a whole session.--Dosumis 09:17, 9 December 2008 (PST) ticket here

  • GUI components that need to be updated when the reasoner is enabled/disabled update properly
  • Reasoner incorporates live edits quickly/accurately

BUG: Reasoner does not incorporate all edits correctly. Incremental reasoning often gets confused. --Dosumis 09:17, 9 December 2008 (PST) (Working on some examples before making ticket).

  • Can everybody's hardware run OBO-Edit at a decent speed with the reasoner on? This is needed for the Graph Viewer to fill in all of the paths. Please add data to OE2_Benchmarking_by_Users
  • Reasoner Benchmarks (includes non-OE packaged reasoners)

Explanations Component

  • Remember to switch Reasoner ON as explanations are interesting only when the reasoner

creates links. In all other cases it just shows "This link was explicitly added to the ontology by a human being." which is assumed by default.

XP files

  • XP files with or without reasoner: BP-Self XP file quickly gives 'out of memory' error on machines with 2GB RAM SF2262464

SF2509493 - name conflicts not flagged on load


SF2520105 - relationship list in OTE not scrollable
SF2520099 - intersections and relationships not distinguished
SF2520061 - part_of v. OBO_REL:part_of
SF2519883 - confusing propagation of graph editor changes to other viewers


  • Annotation Summary
  • Cross Product Info
  • Extended Info
  • Table of Contents


Amina (linux)

  • Configuration Manager

SF2269539 - easy - font size changes do not take in tab top
SF2111929 - OE2 does not work on computers with a lot of RAM

User Guide

  • Check for correctness of text and diagrams. (Done simultaneously while testing individual components).
  • Update/ Delete old pages.

Loading/ Saving

Loading (all file formats)

  • Unrecognized relationship types handled correctly (see bug report for one thing that should NOT happen)
  • File paths added to profiles not remembered in some cases SF2262439
  • When a syntax error is encountered in the file, loading silently fails: SF:2513220

Saving (all file formats)

  • Advanced save
    • Filters in advanced save

SF 2032911 - duplicate transitive_over tags


  • All components in Show menu appear/disappear correctly
  • All GUI components that have a configurable state load/save the state correctly
  • Adding/Deleting/Selecting/Configuring Perspectives
  • Dock/undock panels works
  • Config files
  • undo/redo

SF2137969 - undo does not currently specify what will be undone
win v. mac os x config files