https://wiki.geneontology.org/index.php?title=OEWG_20120221&feed=atom&action=historyOEWG 20120221 - Revision history2024-03-29T13:14:03ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=52704&oldid=prevGail at 22:00, 30 June 20142014-06-30T22:00:54Z<p></p>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">[[Category:OBO-Edit working group]]</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== OBO-Edit Working Group Meeting: Tuesday, February 21, 2012, 8:30am PST ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== OBO-Edit Working Group Meeting: Tuesday, February 21, 2012, 8:30am PST ==</div></td></tr>
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</table>Gailhttps://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=39383&oldid=prevNomi: /* Discussion */2012-02-21T19:43:19Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:43, 21 February 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** Reworded warning. Added a popup message that appears if you say Yes to the move that tells you where the directory was moved to.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** Reworded warning. Added a popup message that appears if you say Yes to the move that tells you where the directory was moved to.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** The consequences of not renaming/resetting your oboedit_config/perspectives can be serious enough that I'm considering just having it just move the perspectives directory automatically when you upgrade OE, tell you where it's moved to, and let power users restore it themselves if they want to. Opinions?</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** The consequences of not renaming/resetting your oboedit_config/perspectives can be serious enough that I'm considering just having it just move the perspectives directory automatically when you upgrade OE, tell you where it's moved to, and let power users restore it themselves if they want to. Opinions?</div></td></tr>
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<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**** Midori and Ramona confirmed that they have frequently (and recently) observed OE "bugs" that are cured by removing their perspectives directory, so it's clearly still important.</ins></div></td></tr>
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</table>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=39381&oldid=prevNomi: /* OBO-Edit Working Group Meeting: Tuesday, February 21, 2012, 8:30am PST */2012-02-21T17:03:44Z<p><span dir="auto"><span class="autocomment">OBO-Edit Working Group Meeting: Tuesday, February 21, 2012, 8:30am PST</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:03, 21 February 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Minutes: Nomi<br /></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Minutes: Nomi<br /></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Attendees: Nomi, Heiko, Ramona, Midori<br /></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Attendees: Nomi, Heiko, Ramona, Midori<ins style="font-weight: bold; text-decoration: none;">, Laurel</ins><br /></div></td></tr>
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</table>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=39380&oldid=prevNomi: /* Fixed or newly added since last meeting */2012-02-21T16:47:59Z<p><span dir="auto"><span class="autocomment">Fixed or newly added since last meeting</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:47, 21 February 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3487349&group_id=36855&atid=418260 Quick save lets you save the first time when it shouldn't]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3487349&group_id=36855&atid=418260 Quick save lets you save the first time when it shouldn't]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** If you loaded via Advanced interface, you could then do a Quick Save the first time you saved (but it didn't actually know yet what file to save to, so it tried to save to null).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** If you loaded via Advanced interface, you could then do a Quick Save the first time you saved (but it didn't actually know yet what file to save to, so it tried to save to null).</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">** Ramona reported a bug in quick save--will submit bug report</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/index.php?func=detail&aid=3486945&group_id=36855&atid=418257 64bit JRE can not be used on windows 7]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/index.php?func=detail&aid=3486945&group_id=36855&atid=418257 64bit JRE can not be used on windows 7]</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>** Windows apparently doesn't let you designate a preferred Java version, so the installer can do no better than using the first Java it comes across. The fix is <del style="font-weight: bold; text-decoration: none;">to istribute </del>two Windows installers: 32-bit and 64-bit, and let Windows users choose the appropriate one.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>** Windows apparently doesn't let you designate a preferred Java version, so the installer can do no better than using the first Java it comes across. The fix is <ins style="font-weight: bold; text-decoration: none;">that we will distribute </ins>two Windows installers: 32-bit and 64-bit, and let Windows users choose the appropriate one.</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Currently working on==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Currently working on==</div></td></tr>
</table>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=39379&oldid=prevNomi: /* OBO-Edit Working Group Meeting: Tuesday, February 21, 2012, 8:30am PST */2012-02-21T16:33:02Z<p><span dir="auto"><span class="autocomment">OBO-Edit Working Group Meeting: Tuesday, February 21, 2012, 8:30am PST</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:33, 21 February 2012</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Minutes: Nomi<br /></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Minutes: Nomi<br /></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Attendees: <br /></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Attendees: <ins style="font-weight: bold; text-decoration: none;">Nomi, Heiko, Ramona, Midori</ins><br /></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Bug and Feature Trackers ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Bug and Feature Trackers ==</div></td></tr>
</table>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=39377&oldid=prevNomi at 16:24, 21 February 20122012-02-21T16:24:59Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Currently working on==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Currently working on==</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3487892&group_id=36855&atid=418257 Query bug makes choosing relation impossible]</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3487892&group_id=36855&atid=418257 Query bug makes choosing relation impossible<ins style="font-weight: bold; text-decoration: none;">] [[Image:compound-query.png|right|Compound query]</ins>]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** David O-S wrote, "Try any query of the form "find terms that ... the [value] <blah> in Ancestor that can be reached via []"--the pick list constantly resets itself to 'Any type', so that is is impossible to scroll down to choose a relation further down the list."</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** David O-S wrote, "Try any query of the form "find terms that ... the [value] <blah> in Ancestor that can be reached via []"--the pick list constantly resets itself to 'Any type', so that is is impossible to scroll down to choose a relation further down the list."</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** It turns out that this happens only when you have a compound query--with just one query panel, it doesn't happen.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** It turns out that this happens only when you have a compound query--with just one query panel, it doesn't happen.</div></td></tr>
</table>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=39376&oldid=prevNomi: /* Currently working on */2012-02-21T16:21:32Z<p><span dir="auto"><span class="autocomment">Currently working on</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:21, 21 February 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l33">Line 33:</td>
<td colspan="2" class="diff-lineno">Line 33:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** David O-S wrote, "Try any query of the form "find terms that ... the [value] <blah> in Ancestor that can be reached via []"--the pick list constantly resets itself to 'Any type', so that is is impossible to scroll down to choose a relation further down the list."</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** David O-S wrote, "Try any query of the form "find terms that ... the [value] <blah> in Ancestor that can be reached via []"--the pick list constantly resets itself to 'Any type', so that is is impossible to scroll down to choose a relation further down the list."</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** It turns out that this happens only when you have a compound query--with just one query panel, it doesn't happen.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** It turns out that this happens only when you have a compound query--with just one query panel, it doesn't happen.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>** The problem started in 2.1-b16 (released in July 2011). Before that, the <del style="font-weight: bold; text-decoration: none;">interested </del>relations didn't even appear in the pulldown list. After that, they do appear in the pulldown lists, but when you have compound queries, the pulldown list acts weird and makes it hard to choose the relation you want.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>** The problem started in 2.1-b16 (released in July 2011). Before that, the <ins style="font-weight: bold; text-decoration: none;">ontology-specific </ins>relations didn't even appear in the pulldown list. After that, they do appear in the pulldown lists, but when you have compound queries, the pulldown list acts weird and makes it hard to choose the relation you want.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3487351&group_id=36855&atid=418257 Deleted differentia (in XP editor) sometimes reappear]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3487351&group_id=36855&atid=418257 Deleted differentia (in XP editor) sometimes reappear]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** Non-deterministic--you can load the same ontology file and delete the same differentium, and sometimes it will reappear whereas other times it will stay gone.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** Non-deterministic--you can load the same ontology file and delete the same differentium, and sometimes it will reappear whereas other times it will stay gone.</div></td></tr>
</table>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=39358&oldid=prevNomi: /* Discussion */2012-02-21T02:19:48Z<p><span dir="auto"><span class="autocomment">Discussion</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
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<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 22:19, 20 February 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l19">Line 19:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3476913&group_id=36855&atid=418260 Warn about possible stale config files when launching new version] [[Image:warn-on-upgrade.png|right|Warning about perspectives]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3476913&group_id=36855&atid=418260 Warn about possible stale config files when launching new version] [[Image:warn-on-upgrade.png|right|Warning about perspectives]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** Whenever you upgrade to a new version of OBO-Edit, there is the risk that out-of-date binary files in your ~/oboedit_config (mostly in oboedit_config/perspectives) will cause bad behavior of various unexpected sorts (perhaps even the relation-choosing issue above). Now a warning message pops up the first time you run a new OBO-Edit release (and it offers to rename oboedit_config/perspectives for you.)</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** Whenever you upgrade to a new version of OBO-Edit, there is the risk that out-of-date binary files in your ~/oboedit_config (mostly in oboedit_config/perspectives) will cause bad behavior of various unexpected sorts (perhaps even the relation-choosing issue above). Now a warning message pops up the first time you run a new OBO-Edit release (and it offers to rename oboedit_config/perspectives for you.)</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*** Added a popup message that tells you where the directory was moved</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*** <ins style="font-weight: bold; text-decoration: none;">Reworded warning. </ins>Added a popup message <ins style="font-weight: bold; text-decoration: none;">that appears if you say Yes to the move </ins>that tells you where the directory was moved <ins style="font-weight: bold; text-decoration: none;">to.</ins></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*** The consequences of not renaming/resetting your oboedit_config/perspectives <del style="font-weight: bold; text-decoration: none;">are annoying </del>enough that I'm considering just having it just move the perspectives directory automatically when you upgrade OE, tell you where it's moved to, and let power users restore it themselves if they want to. Opinions?</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*** The consequences of not renaming/resetting your oboedit_config/perspectives <ins style="font-weight: bold; text-decoration: none;">can be serious </ins>enough that I'm considering just having it just move the perspectives directory automatically when you upgrade OE, tell you where it's moved to, and let power users restore it themselves if they want to. Opinions?</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Fixed or newly added since last meeting==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Fixed or newly added since last meeting==</div></td></tr>
</table>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=39357&oldid=prevNomi: /* Currently working on */2012-02-21T02:18:53Z<p><span dir="auto"><span class="autocomment">Currently working on</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 22:18, 20 February 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l34">Line 34:</td>
<td colspan="2" class="diff-lineno">Line 34:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** It turns out that this happens only when you have a compound query--with just one query panel, it doesn't happen.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** It turns out that this happens only when you have a compound query--with just one query panel, it doesn't happen.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** The problem started in 2.1-b16 (released in July 2011). Before that, the interested relations didn't even appear in the pulldown list. After that, they do appear in the pulldown lists, but when you have compound queries, the pulldown list acts weird and makes it hard to choose the relation you want.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** The problem started in 2.1-b16 (released in July 2011). Before that, the interested relations didn't even appear in the pulldown list. After that, they do appear in the pulldown lists, but when you have compound queries, the pulldown list acts weird and makes it hard to choose the relation you want.</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">* [http://sourceforge.net/tracker/?func=detail&aid=3476915&group_id=36855&atid=418257 Graph Editor makes Text Editor show old version of term] [[Image:stale-term.png|right|Graph Editor makes Text Editor show stale version of term]]</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">** This is not a new issue (2.0 has it), but it's going to be more of a problem with a workflow that involves making changes to ontology files both inside OBO-Edit and outside in other applications (e.g., Protege) running at the same time.</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">** If you look at a term in the Text Editor, and then reload a changed-on-disk version of the current ontology file (with, for example, a changed term name) and look at the term again by reselecting it 'from the Graph Editor' you see, misleadingly, the OLD version of the term. (The Graph Editor itself correctly shows the new version of the term.) (See image at right.) If you instead select the term from the OTE, the new version shows up.</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">*** It looks as though the stale term is cached somewhere down in the Piccolo code that the Graph Editor uses. This is not going to be easy to fix.</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">** Most people present today said they don't tend to click on the Graph Editor to look at terms in the Text Editor, so this bug probably wouldn't affect them much.</del></div></td><td colspan="2" class="diff-side-added"></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3487351&group_id=36855&atid=418257 Deleted differentia (in XP editor) sometimes reappear]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3487351&group_id=36855&atid=418257 Deleted differentia (in XP editor) sometimes reappear]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** Non-deterministic--you can load the same ontology file and delete the same differentium, and sometimes it will reappear whereas other times it will stay gone.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** Non-deterministic--you can load the same ontology file and delete the same differentium, and sometimes it will reappear whereas other times it will stay gone.</div></td></tr>
</table>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120221&diff=39356&oldid=prevNomi: /* Currently working on */2012-02-21T02:13:38Z<p><span dir="auto"><span class="autocomment">Currently working on</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 22:13, 20 February 2012</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l29">Line 29:</td>
<td colspan="2" class="diff-lineno">Line 29:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Currently working on==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>==Currently working on==</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">* [http://sourceforge.net/tracker/?func=detail&aid=3487892&group_id=36855&atid=418257 Query bug makes choosing relation impossible]</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">** David O-S wrote, "Try any query of the form "find terms that ... the [value] <blah> in Ancestor that can be reached via []"--the pick list constantly resets itself to 'Any type', so that is is impossible to scroll down to choose a relation further down the list."</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">** It turns out that this happens only when you have a compound query--with just one query panel, it doesn't happen.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">** The problem started in 2.1-b16 (released in July 2011). Before that, the interested relations didn't even appear in the pulldown list. After that, they do appear in the pulldown lists, but when you have compound queries, the pulldown list acts weird and makes it hard to choose the relation you want.</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3476915&group_id=36855&atid=418257 Graph Editor makes Text Editor show old version of term] [[Image:stale-term.png|right|Graph Editor makes Text Editor show stale version of term]]</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* [http://sourceforge.net/tracker/?func=detail&aid=3476915&group_id=36855&atid=418257 Graph Editor makes Text Editor show old version of term] [[Image:stale-term.png|right|Graph Editor makes Text Editor show stale version of term]]</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** This is not a new issue (2.0 has it), but it's going to be more of a problem with a workflow that involves making changes to ontology files both inside OBO-Edit and outside in other applications (e.g., Protege) running at the same time.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>** This is not a new issue (2.0 has it), but it's going to be more of a problem with a workflow that involves making changes to ontology files both inside OBO-Edit and outside in other applications (e.g., Protege) running at the same time.</div></td></tr>
</table>Nomi