Difference between revisions of "OBO-Edit 2.0 Testing Tasks"

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[[Category:OBO-Edit]]
 
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 <font color=red>in red</font> and add [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418257 a link to the sourceforge bug report]. If a feature works, please highlight it <font color=blue>in blue</font>.
 
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 <font color=red>in red</font> and add [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418257 a link to the sourceforge bug report]. If a feature works, please highlight it <font color=blue>in blue</font>.
 
For a particular component/task please update the corresponding documentation or make a note if content and figures are not up to date.
 
For a particular component/task please update the corresponding documentation or make a note if content and figures are not up to date.
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=== Editors ===
 
=== Editors ===
  
* Graph Editor (non-animated)
+
* Graph Editor (non-animated) '''Jen (Windows and Mac)'''
 
** Expanding/collapsing nodes
 
** Expanding/collapsing nodes
 
** Editing operations
 
** Editing operations
Line 19: Line 20:
 
** Mutual selection works properly between graph editor and obo editor panel
 
** Mutual selection works properly between graph editor and obo editor panel
  
* Graph Editor (animated)
+
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.
 +
 
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=1878279&group_id=36855&atid=418257 SF 1878279 (rather old) - icon size]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2540160&group_id=36855&atid=418257 SF2540160 - cannot delete terms]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2540177&group_id=36855&atid=418257 SF2540177 - make children disjoint broken]
 +
 
 +
* Graph Editor (animated) '''Karen (Mac)'''
 
** Expanding/collapsing nodes
 
** Expanding/collapsing nodes
 
** Editing operations
 
** Editing operations
 
** Mutual selection works properly between graph editor and obo editor panel
 
** Mutual selection works properly between graph editor and obo editor panel
+
 
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2541014&group_id=36855&atid=418260 SF 2541014 mouseover bubbles for the editing icons don't stay up long enough]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2541023&group_id=36855&atid=418260 SF 2541023 icons in editing toolbar shift positions annoyingly depending on size of optional info to right]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2541038&group_id=36855&atid=418260 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
 
* Ontology Tree Editor
 
**also see 'standard editing operations' below
 
**also see 'standard editing operations' below
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2187636&group_id=36855&atid=418257 SF2187636 - rogue menus]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2023388&group_id=36855&atid=418257 SF2023388 - multiple house icons]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=1944186&group_id=36855&atid=418257 SF1944186 - wrong menus popping up]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2065087&group_id=36855&atid=418260 SF2065087 - flag if we are obsoleting a term referenced in a consider or replaced_by tag]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2315190&group_id=36855&atid=418257 SF 2315190 - unexpected OTE autoscroll]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2093230&group_id=36855&atid=418257 SF 2093230 - display oddities]; may be fixed now<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2271697&group_id=36855&atid=418257 SF 2271697 - no refresh of global selection after clicking a relation]<br>
  
* Parent Editor
 
  
* Text Editor
+
 
 +
* Parent Editor - '''Midori (Mac), Melissa (windows)''' - Documentation done (Midori)
 +
**<font color=blue>All seems to be working fine</font> (except one bit about cardinality that I don't really understand, but that won't delay release - [https://sourceforge.net/tracker/?func=detail&atid=418257&aid=2433920&group_id=36855 ticket here]) -midori
 +
** <font color=blue>all working fine for me too (windows)</font> -melissa<br>
 +
 
 +
* Text Editor '''Melissa (windows), Amina (linux), Tanya (Mac)'''
 +
** General<br>
 +
** General<br>
 +
***[https://sourceforge.net/tracker/index.php?func=detail&aid=2338226&group_id=36855&atid=418257 SF2338226 - extra space in text editor]
 +
***[https://sourceforge.net/tracker/index.php?func=detail&aid=2355661&group_id=36855&atid=418257 SF 2355661 - dbxref redraw problem]
 +
***[https://sourceforge.net/tracker/index.php?func=detail&aid=2142711&group_id=36855&atid=418257 SF 2142711 - 'pending edits' and 'fatal error' messages]
 +
***[https://sourceforge.net/tracker/index.php?func=detail&aid=2010579&group_id=36855&atid=418257 SF 2010579 - clearing domain & range]
 +
 
 
** Definition Tab
 
** Definition Tab
 +
***[https://sourceforge.net/tracker/index.php?func=detail&aid=2009926&group_id=36855&atid=418257 SF 2009926 - undo takes a few tries] term definitions get merged, but don't unmerge with undo
 
** Comment Tab
 
** Comment Tab
 
** Cross Products Tab
 
** Cross Products Tab
Line 37: Line 69:
 
** Synonyms Tab
 
** Synonyms Tab
 
** Subsets 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)
+
* 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
+
** Move - <font color=blue>works for me</font> (Jane, Jan 21 2009)
 
** Add parent
 
** Add parent
** Add child
+
** Add child - <font color=blue>works for me</font> (Jane, Jan 21 2009)
 
** Merge
 
** Merge
** Delete relationship
+
** Delete relationship - <font color=blue>works for me</font> (Jane, Jan 21 2009)
 
** Obsolete term
 
** Obsolete term
** Add new term
+
** Add new term - <font color=blue>works for me</font> (Jane, Jan 21 2009)
** Add multiple new terms
+
** Add multiple new terms - <font color=blue>works for me</font> (Jane, Jan 21 2009)
** Add new relationship type
+
** Clone - <font color=blue>works for me</font> (Jane, Jan 21 2009)
 +
** Add new relationship type - [https://sourceforge.net/tracker2/?func=detail&aid=2593281&group_id=36855&atid=418257 Problem naming new relations SF:2593281]  (Jane, Feb 12 2009)
 
** Add/Remove replaced-by reference
 
** Add/Remove replaced-by reference
 
** Add/Remove consider reference
 
** Add/Remove consider reference
 
** Text editing
 
** Text editing
  
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=1863271&group_id=36855&atid=418257 SF 1863271 - merge hotkey problems]
 +
 +
=== Viewers ===
 +
'''Harold (Mac)'''
 +
* Tree Viewer '''Jen (Mac and Windows)'''
  
=== Viewers: Harold (Mac) ===
+
This component is now ready to be released. (Jen)
  
* Tree Viewer
 
 
* Graph Viewer
 
* Graph Viewer
* Graphviz Viewer
+
[https://sourceforge.net/tracker/index.php?func=detail&aid=2020610&group_id=36855&atid=418257 SF2020610 - Shows incomplete graph even with reasoner]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=1812252&group_id=36855&atid=418260 SF1812252 - Initial zoom should be set to reasonable value]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=1919828&group_id=36855&atid=418257 SF 1919828 (rather old) - graph viewer flaky response]<br>
 +
 
 +
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
 +
 
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2277324&group_id=36855&atid=418257 SF 2277324 - unrecognized relation]
 +
 
 +
SF2465040-Links display in graphviz but not in graphviewer [http://sourceforge.net/tracker/index.php?func=detail&aid=2465040&group_id=36855&atid=418257]
 +
 
 +
Mac OSX when undocked, graphviz and graphview windows will not go to back, which obscures main application.
 +
 
 +
 
 
* Term Image Display Panel
 
* Term Image Display Panel
  
 
=== Search ===
 
=== Search ===
 +
''' Amina (linux)'''
 +
* Term Search
 +
[https://sourceforge.net/tracker2/?func=detail&aid=2561035&group_id=36855&atid=418257 SF2561035 - problem with searching Ancestors] (Jane, 3 Feb 2009) <br>
 +
[https://sourceforge.net/tracker2/?func=detail&aid=2561087&group_id=36855&atid=418257 SF2561087 - problem with searching Aspect via specific relationship type] (Jane, 3 Feb 2009) <br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2269624&group_id=36855&atid=418257 SF2269624 - config settings are not retained over restart]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2023673&group_id=36855&atid=418257 SF 2023673 - missing search attributes]
 +
<br>
 +
Also, auto-complete selection does not work for some fields: [https://sourceforge.net/tracker2/?func=detail&aid=2314626&group_id=36855&atid=418257 SF:2314626]
 +
<br>
 +
* Link Search
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2269493&group_id=36855&atid=418257 SF2269493 - easy - results column sizes set wrong]<br>
 +
[https://sourceforge.net/tracker2/index.php?func=detail&aid=2276989&group_id=36855&atid=418257 SF:2276989 - problem with implied link search] (Jane, 13 Feb 2009) <br>
  
* Term Search
+
=== Filters/Renders ===
* Link Search
+
''' Amina (linux), Jane (Mac)'''
  
 +
* Local Filters - all fine except this very minor bug [https://sourceforge.net/tracker/index.php?func=detail&aid=2053394&group_id=36855&atid=418257 SF 2053394 - renderer OTE redraw oddity]
 +
** Term Filters - <font color=blue>working</font> (Jane, 16 Jan 2009)
 +
** Link Filters - <font color=blue>working</font> (Jane, 16 Jan 2009)
 +
** Term Renderers - <font color=blue>working</font> (Jane, 16 Jan 2009)
 +
** Link Renderers - <font color=blue>working</font> (Jane, 16 Jan 2009)
 +
** Quick filtering - <font color=blue>working</font> (Jane, 16 Jan 2009)
  
 +
* Global Filters
 +
** Term Filters - <font color=blue>working</font> (Jane, 28 Jan 2009) [https://sourceforge.net/tracker/index.php?func=detail&aid=2513366&group_id=36855&atid=418257 SF2513366 - removal of default filters cases redraw instability] (Jen)
 +
** Link Filters - <font color=red>can't delete new filters</font> [https://sourceforge.net/tracker2/?func=detail&aid=2513346&group_id=36855&atid=418257 SF:2513346] (Jane, 16 Jan 2009)
 +
** Term Renderers - <font color=blue>working</font> (Jane, 16 Jan 2009)
 +
** Link Renderers - <font color=blue>working</font> (Jane, 16 Jan 2009)
 +
<br>
 +
not checked since about betas 40-42:<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2034117&group_id=36855&atid=418257 SF 2034117 - heat map]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2031660&group_id=36855&atid=418257 SF 2031660] - <strike>render blending</strike><br> - closed SF item; no demand for feature<br>
 +
Note: I don't think either of these relate to current features, so can probably ignore. (jane)<br>
 +
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)
  
=== Filters ===
+
=== Tools ===
* Local Filters
+
'''Jane (Mac)'''
** Term Filters
+
* Verification Manager
** Link Filters
+
** Checking correctness of results - <font color=blue>working</font> (Jane: 13 Jan 2009)
** Term Renderers
+
** Making sure quick-fixes work:
** Link Renderers
+
*** Adding to dictionaries - <font color=blue>working</font>, but see below for problem with adding to user-defined dictionary (Jane: 13 Jan 2009)
 +
*** Replacing misspelled words - <font color=red>not working</font> [https://sourceforge.net/tracker2/?func=detail&aid=2504879&group_id=36855&atid=418257 SF:2504879] (Jane: 13 Jan 2009)
 +
*** Adding legal always lowercase words - <font color=red>not working</font> [https://sourceforge.net/tracker2/?func=detail&aid=2504879&group_id=36855&atid=418257 SF:2504879] (Jane: 13 Jan 2009)
 +
*** Adding period, explanation mark or question mark to end of sentence - <font color=red>not working</font> [https://sourceforge.net/tracker2/?func=detail&aid=2504879&group_id=36855&atid=418257 SF:2504879] (Jane: 13 Jan 2009)
 +
*** Replace multiple whitespeaces with a single space - <font color=red>not working</font> [https://sourceforge.net/tracker2/?func=detail&aid=2504879&group_id=36855&atid=418257 SF:2504879] (Jane: 13 Jan 2009)
 +
** Checking runtime verification behaviour in text editor - <font color=blue>working</font> (Jane: 13 Jan 2009)
 +
** User-defined verification checks - <font color=red>working</font> (Jane: 13 Jan 2009)
 +
** Dictionaries:
 +
*** saving to user-defined dictionary - <font color=red>not working:</font> [https://sourceforge.net/tracker2/?func=detail&aid=2504817&group_id=36855&atid=418257 SF:2504817] (Jane: 13 Jan 2009)
 +
*** saving to standard system dictionary - <font color=blue>working</font> (Jane: 13 Jan 2009)
 +
** Warnings during text edit [https://sourceforge.net/tracker/index.php?func=detail&aid=2263749&group_id=36855&atid=418257 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.
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=1871096&group_id=36855&atid=418257 SF1871096 - consider tags]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=1871092&group_id=36855&atid=418257 SF1871092 - consider tags]<br>
 +
also [https://sourceforge.net/tracker/index.php?func=detail&aid=2051721&group_id=36855&atid=418257 SF 2051721 - obomerge loses replaced_by tags]
  
* Global Filters
 
** Term Filters
 
** Link Filters
 
** Term Renderers
 
** Link Renderers
 
  
 +
These are being addressed together and the progress notes are at:<br>
 +
http://wiki.geneontology.org/index.php/Obomerge_on_consider_and_replaced_by_tags
  
=== Tools ===
+
* History
 +
** History Browser
 +
*** records history events correctly - <font color=blue>working</font> (Jane, 14 Jan 2009)
 +
*** copy/paste box - <font color=red>minor bugs:</font> [https://sourceforge.net/tracker2/?func=detail&aid=2507044&group_id=36855&atid=418257 SF:2507044] (Jane, 14 Jan 2009)
 +
*** saving (from within history browser) - <font color=red>not working</font> [https://sourceforge.net/tracker2/?func=detail&aid=2507049&group_id=36855&atid=418257 SF:2507049]  (Jane, 14 Jan 2009)
 +
** History Save in File menu - <font color=blue>working</font> (Jane, 21 Jan 2009)
 +
** History Load in File menu - <font color=red>not working</font> [https://sourceforge.net/tracker2/?func=detail&aid=2526247&group_id=36855&atid=418257 SF:2526247] (Jane, 21 Jan 2009)
  
* Verification Manager
+
* Configurable message - '''working but pointless!''' No idea what this is supposed to be for, suggest we remove from release  (Jane 14 Jan 2009)
** Checking correctness of results
+
* ID Fixer - '''Remove from this release'''  (Jane 14 Jan 2009)
** Making sure quick-fixes work
 
** Checking runtime verification behaviour in text editor
 
** User-defined verification checks
 
 
 
* Ontology Change Tracker (''Currently being tested by David OS'')
 
* OBO Merge
 
* History Browser
 
* Configurable message
 
* ID Fixer
 
  
 
=== Metadata ===
 
=== Metadata ===
 
+
'''Midori (Mac), Amina (linux)'''<br>
 +
'''Documentation done''' (Midori)
 
* Dbxref Library
 
* Dbxref Library
 +
** [https://sourceforge.net/tracker/index.php?func=detail&aid=2490376&group_id=36855&atid=418257 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
 
* Subset Manager
 +
** <font color=blue>Working.</font> Note: must update documentation text and screenshots to reflect name change (used to be 'category manager'). (midori 2009-01-06)
 
* Synonym Type Manager
 
* Synonym Type Manager
 +
** <font color=blue>Working.</font> Note: must update documentation text and screenshots to reflect name change (used to be 'synonym category manager'). (midori 2009-01-16)
 
* ID Manager
 
* ID Manager
 +
** <font color=blue>Working.</font> (midori 2009-01-16)
 
* Namespace Manager
 
* Namespace Manager
 
+
** <font color=blue>Working.</font> (midori 2009-01-16)
  
 
=== Reasoner ===
 
=== Reasoner ===
''Currently being being tested by: David OS''
+
'''Currently being being tested by: David OS'''
  
 
* Reasoner starts/stops correctly
 
* Reasoner starts/stops correctly
 +
BUG: Cancelling the reasoner stops it being run again for a whole session.--[[User:Dosumis|Dosumis]] 09:17, 9 December 2008 (PST) [https://sourceforge.net/tracker/index.php?func=detail&aid=2412159&group_id=36855&atid=418257 ticket here]
 
* GUI components that need to be updated when the reasoner is enabled/disabled update properly
 
* GUI components that need to be updated when the reasoner is enabled/disabled update properly
 
* Reasoner incorporates live edits quickly/accurately
 
* Reasoner incorporates live edits quickly/accurately
* 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.
+
BUG: Reasoner does not incorporate all edits correctly. Incremental reasoning often gets confused. --[[User:Dosumis|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]]
 +
* [[OBO-Edit:Reasoner_Benchmarks|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 [https://sourceforge.net/tracker/index.php?func=detail&aid=2262464&group_id=36855&atid=418257 SF2262464]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2509493&group_id=36855&atid=418257 SF2509493 - name conflicts not flagged on load]
 +
 
 +
Viewers/Editors
 +
 
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2520105&group_id=36855&atid=418257 SF2520105 - relationship list in OTE not scrollable]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2520099&group_id=36855&atid=418257 SF2520099 - intersections and relationships not distinguished]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2520061&group_id=36855&atid=418257 SF2520061 - part_of v. OBO_REL:part_of]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2519883&group_id=36855&atid=418257 SF2519883 - confusing propagation of graph editor changes to other viewers]
  
 
=== Summary ===
 
=== Summary ===
Line 123: Line 241:
  
 
=== Config ===
 
=== Config ===
 +
'''Amina (linux)'''
 +
* Configuration Manager<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2269539&group_id=36855&atid=418257 SF2269539 - easy - font size changes do not take in tab top]<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2111929&group_id=36855&atid=418257 SF2111929 - OE2 does not work on computers with a lot of RAM]
  
* Configuration Manager
+
===User Guide===
 
+
* Check for correctness of text and diagrams. (Done simultaneously while testing individual components).
 
+
* Update/ Delete old pages.
  
 
== Loading/ Saving ==
 
== Loading/ Saving ==
Line 133: Line 255:
 
=== Loading (all file formats) ===
 
=== Loading (all file formats) ===
 
*Unrecognized relationship types handled correctly (see [https://sourceforge.net/tracker/index.php?func=detail&aid=2309391&group_id=36855&atid=418257 bug report] for one thing that should NOT happen)
 
*Unrecognized relationship types handled correctly (see [https://sourceforge.net/tracker/index.php?func=detail&aid=2309391&group_id=36855&atid=418257 bug report] for one thing that should NOT happen)
 
+
*File paths added to profiles not remembered in some cases [https://sourceforge.net/tracker/index.php?func=detail&aid=2262439&group_id=36855&atid=418257 SF2262439]
 +
*When a syntax error is encountered in the file, loading silently fails: [https://sourceforge.net/tracker2/?func=detail&aid=2513220&group_id=36855&atid=418257 SF:2513220]
  
 
=== Saving (all file formats) ===
 
=== Saving (all file formats) ===
 
* Advanced save
 
* Advanced save
 
** Filters in advanced save
 
** Filters in advanced save
 +
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2032911&group_id=36855&atid=418257 SF 2032911 - duplicate transitive_over tags]
  
  
Line 146: Line 271:
 
* Dock/undock panels works
 
* Dock/undock panels works
 
* Config files
 
* Config files
 +
* undo/redo<br>
 +
[https://sourceforge.net/tracker/index.php?func=detail&aid=2137969&group_id=36855&atid=418260 SF2137969 - undo does not currently specify what will be undone]<br>
 
[[win v. mac os x config files]]
 
[[win v. mac os x config files]]
  
[[OBO-Edit2 speed tests]]
+
*[[OBO-Edit2 speed tests]]

Latest revision as of 11:34, 30 June 2014

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:

Components

Editors

  • 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

Viewers

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

Search

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)

Filters/Renders

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)

Tools

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:
http://wiki.geneontology.org/index.php/Obomerge_on_consider_and_replaced_by_tags

  • 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)

Metadata

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)

Reasoner

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

Viewers/Editors

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

Summary

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


Config

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


Misc

  • 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