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From: Rutger V. <rut...@gm...> - 2010-03-27 11:15:27
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Hi all, a comment thread about treebase2 is developing on Rod Page's blog: http://iphylo.blogspot.com/2010/03/treebase-ii-has-been-released.html It seems that phylowidget and firefox is the issue that is bugging people the most. Is Youjun working on that? How is that going? Rutger -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: youjun g. <you...@ya...> - 2010-03-27 12:31:01
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I fixed it and the last ticket about the issue closed on 03/21, I am not sure if we re-deployed our server yet since then. The problem caused by the jar file signature issue User need to clean up their browser's "private data" to accept the new signature, if they accessed the page previously. Youjun On Sat, Mar 27, 2010 at 7:15 AM, Rutger Vos <rut...@gm...> wrote: > Hi all, > > a comment thread about treebase2 is developing on Rod Page's blog: > http://iphylo.blogspot.com/2010/03/treebase-ii-has-been-released.html > It seems that phylowidget and firefox is the issue that is bugging > people the most. Is Youjun working on that? How is that going? > > Rutger > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > |
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From: Rutger V. <rut...@gm...> - 2010-03-27 12:50:38
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Ah, terrific, thanks! On Sat, Mar 27, 2010 at 12:30 PM, youjun guo <you...@ya...> wrote: > I fixed it and the last ticket about the issue closed on 03/21, I am not > sure if we re-deployed our server yet since then. > > The problem caused by the jar file signature issue User need to clean up > their browser's "private data" to accept the new signature, if they accessed > the page previously. > > Youjun > > On Sat, Mar 27, 2010 at 7:15 AM, Rutger Vos <rut...@gm...> wrote: >> >> Hi all, >> >> a comment thread about treebase2 is developing on Rod Page's blog: >> http://iphylo.blogspot.com/2010/03/treebase-ii-has-been-released.html >> It seems that phylowidget and firefox is the issue that is bugging >> people the most. Is Youjun working on that? How is that going? >> >> Rutger >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2010-03-27 14:03:38
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On Mar 27, 2010, at 8:30 AM, youjun guo wrote: > I fixed it and the last ticket about the issue closed on 03/21, I am not sure if we re-deployed our server yet since then. > > The problem caused by the jar file signature issue User need to clean up their browser's "private data" to accept the new signature, if they accessed the page previously. > > Youjun In that case we should do a re-build. But I should point out that I added bug 2977247 yesterday -- the zoom, arrow, hand tools are missing from PhyloWidget. Presumably the parameter that tells it to turn off the "save to database" menu item went a little too far and got rid of these other tools. Phylowidget is not very useful without the zoom tool, because people can't view big trees. I know that you're in the midst of the matrix-delete issue, but perhaps it would be better to pause that and fix bug 2977247 before we rebuild? (I'm hoping that this is a fairly quick fix). Thanks. bp |
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From: youjun g. <you...@ya...> - 2010-03-27 23:06:19
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Yes, I saw the problem. The "limited-menu.xml" in PhyloWidget.jar configured the menu this way. We have to modify the menu configure file, re-build and re-sign the jar this time. Youjun On Sat, Mar 27, 2010 at 10:03 AM, William Piel <wil...@ya...>wrote: > > On Mar 27, 2010, at 8:30 AM, youjun guo wrote: > > I fixed it and the last ticket about the issue closed on 03/21, I am not > sure if we re-deployed our server yet since then. > > The problem caused by the jar file signature issue User need to clean up > their browser's "private data" to accept the new signature, if they accessed > the page previously. > > Youjun > > > In that case we should do a re-build. But I should point out that I added > bug 2977247<http://sourceforge.net/tracker/?func=detail&aid=2977247&group_id=248804&atid=1126676> yesterday > -- the zoom, arrow, hand tools are missing from PhyloWidget. > > Presumably the parameter that tells it to turn off the "save to database" > menu item went a little too far and got rid of these other tools. > Phylowidget is not very useful without the zoom tool, because people can't > view big trees. I know that you're in the midst of the matrix-delete issue, > but perhaps it would be better to pause that and fix bug 2977247<http://sourceforge.net/tracker/?func=detail&aid=2977247&group_id=248804&atid=1126676> before > we rebuild? (I'm hoping that this is a fairly quick fix). Thanks. > > bp > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: Vladimir G. <vla...@du...> - 2010-03-27 21:18:55
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On Mar 27, 2010, at 8:30 AM, youjun guo wrote: > I fixed it and the last ticket about the issue closed on 03/21, I am > not sure if we re-deployed our server yet since then. www.treebase.org was redeployed 2 or 3 times since 3/21 (last Sunday). > The problem caused by the jar file signature issue User need to > clean up their browser's "private data" to accept the new signature, > if they accessed the page previously. I could not find "clear private data" in my Firefox 3.6.2. (the current release) on MacOSX. I did Tools > clear recent history, selecting all the checkboxes, but Firefox still hangs forever while trying to open the phylowidget window. Rutger, did you have better luck making it work? --VG |
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From: youjun g. <you...@ya...> - 2010-03-27 22:46:08
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> > I did Tools > clear recent history, selecting all the checkboxes, > This should work. Please also make sure java is installed and enabled in you browser. Go to Tools>Option>content to check it. > but Firefox still hangs forever while trying to open the phylowidget window I am not sure, I don't have the test environment exactly like yours. I tested it on a mac desktop and Bill tested it on his mac laptop both worked. Can you also try it @ 130.132.27.212:8080/treebase-web and see if same problem happens. There are some security concerns about java applets, so different restriction may be applied on it depends on the OS and browser. Actually there are two kinds of the phylowiget in treebase know. One for authorized user the other for unauthorized user. When I worked on the bug I keep the first one untouched, and add the second one for unauthrized user. So the authorized user should always be able to use the phylowiget as previoursly. A good way to try it is access both and see if they act differently. Youjun |
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From: Vladimir G. <vla...@du...> - 2010-03-28 19:38:35
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There might indeed be something special in my setup, so maybe be there is no need to worry. I tried a couple more times and, regrettably, Firefox still hangs; details below. The browser probably still caches something, what I cannot find a way to erase. On my old pre-Intel Mac, Phylowidget started working, after just one or two initial hiccups. For some time now, I have been using exclusively Safari to work with TreeBase. --VG On Mar 27, 2010, at 6:46 PM, youjun guo wrote: > I did Tools > clear recent history, selecting all the checkboxes, > This should work. I have now been doing this prior to each attempt to test Phylowidget. > Please also make sure java is installed and enabled in you browser. > Go to Tools>Option>content to check it. I don't have this under the Tools menu, but this one is checked: Firefox menu > Preferences... > Content tab > Enable Javascript checkbox I have also clicked "advanced" in that item and enabled all the little things that scripts might want to do (like hiding status bar). > but Firefox still hangs forever while trying to open the phylowidget > window > I am not sure, I don't have the test environment exactly like yours. > I tested it on a mac desktop and Bill tested it on his mac laptop > both worked. Can you also try it @ 130.132.27.212:8080/treebase-web > and see if same problem happens. I tried on your server -- the same story. > > There are some security concerns about java applets, so different > restriction may be applied on it depends on the OS and browser. I answer "Bring it on!" on all security questions that pop up. > Actually there are two kinds of the phylowiget in treebase know. One > for authorized user the other for unauthorized user. When I worked > on the bug I keep the first one untouched, and add the second one > for unauthrized user. So the authorized user should always be able > to use the phylowiget as previoursly. A good way to try it is access > both and see if they act differently. As a logged-in user, I tried looking at a tree that I have submitted myself -- no luck. --VG |
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