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From: Rutger V. <rut...@gm...> - 2010-03-29 22:00:56
|
If you look in the html source of any page and you scroll all the way
down to 'p class="footerLogo"' it will show the SVN revision of that
deployment. At least, this used to work back when MJD and I were using
the 'publish' script, which used
${TREEBASE_HOME}/treebase-core/src/main/java/org/cipres/treebase/Version.java
as a little servlet to embed the SVN revision in the footer.jsp (this
is done by deleting and then updating this version file). Perhaps this
can be re-instated?
On Mon, Mar 29, 2010 at 10:01 PM, Vladimir Gapeyev
<vla...@du...> wrote:
>
> On Mar 29, 2010, at 4:39 PM, Hilmar Lapp wrote:
>
> This should be in the tracker as a feature request already. Is it not?
> -hilmar
> On Mar 29, 2010, at 4:34 PM, Jon Auman wrote:
>
> I suggested to Vladimir last week that we should put a version and timestamp
> on the builds, like we do with nead.nescent.org. (ex. Version:
> 2.2.1 Built: 03/26/2010 12:43 PM )
> Otherwise, how can we keep track of which version we are on?
> -Jon
> On Mar 29, 2010, at 4:31 PM, Hilmar Lapp wrote:
>
> I'll check and, if it is not there, will put a ticket for the suggestion,
> alongside tickets for a few other things we need to do here on the
> deployment side (restore the dev server; set up automatic builds, etc.).
> The 659 version will be deployed to production soon.
> --VG
>
>
> ------------------------------------------------------------------------------
> 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
|
|
From: Jon A. <jon...@du...> - 2010-03-29 21:15:34
|
------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
|
From: Vladimir G. <vla...@du...> - 2010-03-29 21:01:27
|
On Mar 29, 2010, at 4:39 PM, Hilmar Lapp wrote: > This should be in the tracker as a feature request already. Is it not? > > -hilmar > > On Mar 29, 2010, at 4:34 PM, Jon Auman wrote: > >> I suggested to Vladimir last week that we should put a version and >> timestamp on the builds, like we do with nead.nescent.org. (ex. >> Version: 2.2.1 Built: 03/26/2010 12:43 PM ) >> >> Otherwise, how can we keep track of which version we are on? >> >> -Jon >> >> On Mar 29, 2010, at 4:31 PM, Hilmar Lapp wrote: I'll check and, if it is not there, will put a ticket for the suggestion, alongside tickets for a few other things we need to do here on the deployment side (restore the dev server; set up automatic builds, etc.). The 659 version will be deployed to production soon. --VG |
|
From: Hilmar L. <hl...@ne...> - 2010-03-29 20:39:48
|
This should be in the tracker as a feature request already. Is it not? -hilmar On Mar 29, 2010, at 4:34 PM, Jon Auman wrote: > I suggested to Vladimir last week that we should put a version and > timestamp on the builds, like we do with nead.nescent.org. (ex. > Version: 2.2.1 Built: 03/26/2010 12:43 PM ) > > Otherwise, how can we keep track of which version we are on? > > -Jon > > On Mar 29, 2010, at 4:31 PM, Hilmar Lapp wrote: > >> There's a fix for this - has this not yet been committed and/or >> deployed? >> >> -hilmar >> >> On Mar 29, 2010, at 4:29 PM, Jon Auman wrote: >> >>> It appears to be an issue with tomcat. It started over the >>> weekend, so I'm assuming there is an issue with the last build. >>> This query runs for hours: >>> >>> delete from matrixelement where matrixelement_id IN (select >>> m.matrixelement_id from matrixelement m, MATRIXCOLUMN c where >>> m.MATRIXCOLUMN_ID = c >>> .MATRIXCOLUMN_ID and c.MATRIX_ID = $1) >>> >>> And I'mn seeing this in the tomcat logs during the hang: >>> >>> [http-8080-Processor8] DEBUG >>> org.cipres.treebase.domain.search.StudySearchResults - >>> discardUnpublished: before: 7; after: 7 >>> >>> >>> I'll >>> >>> -Jon >>> >>> >>> >>> On Mar 29, 2010, at 4:19 PM, William Piel wrote: >>> >>>> times-out with proxy error for simple searches. >>>> >>>> bp >>>> >>>> >>> >>> ------------------------------------------------------- >>> Jon Auman >>> Systems Administrator >>> National Evolutionary Synthesis Center >>> Duke University >>> http:www.nescent.org >>> jon...@ne... >>> ------------------------------------------------------ >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: Jon A. <jon...@du...> - 2010-03-29 20:34:36
|
I suggested to Vladimir last week that we should put a version and timestamp on the builds, like we do with nead.nescent.org. (ex. Version: 2.2.1 Built: 03/26/2010 12:43 PM ) Otherwise, how can we keep track of which version we are on? -Jon On Mar 29, 2010, at 4:31 PM, Hilmar Lapp wrote: > There's a fix for this - has this not yet been committed and/or deployed? > > -hilmar > > On Mar 29, 2010, at 4:29 PM, Jon Auman wrote: > >> It appears to be an issue with tomcat. It started over the weekend, so I'm assuming there is an issue with the last build. This query runs for hours: >> >> delete from matrixelement where matrixelement_id IN (select m.matrixelement_id from matrixelement m, MATRIXCOLUMN c where m.MATRIXCOLUMN_ID = c >> .MATRIXCOLUMN_ID and c.MATRIX_ID = $1) >> >> And I'mn seeing this in the tomcat logs during the hang: >> >> [http-8080-Processor8] DEBUG org.cipres.treebase.domain.search.StudySearchResults - discardUnpublished: before: 7; after: 7 >> >> >> I'll >> >> -Jon >> >> >> >> On Mar 29, 2010, at 4:19 PM, William Piel wrote: >> >>> times-out with proxy error for simple searches. >>> >>> bp >>> >>> >> >> ------------------------------------------------------- >> Jon Auman >> Systems Administrator >> National Evolutionary Synthesis Center >> Duke University >> http:www.nescent.org >> jon...@ne... >> ------------------------------------------------------ >> >> >> >> ------------------------------------------------------------------------------ >> 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 > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
|
From: William P. <wil...@ya...> - 2010-03-29 20:34:08
|
On Mar 29, 2010, at 4:31 PM, Hilmar Lapp wrote: > There's a fix for this - has this not yet been committed and/or deployed? yeah, Youjun fixed this. Please rebuild at the first opportunity. bp |
|
From: Jon A. <jon...@du...> - 2010-03-29 20:32:01
|
Tomcat also hard crashed twice last week. I suspect there are memory leaks in the application. Maybe I should restart it once a day? Anybody object? -Jon On Mar 29, 2010, at 4:29 PM, Jon Auman wrote: > It appears to be an issue with tomcat. It started over the weekend, so I'm assuming there is an issue with the last build. This query runs for hours: > > delete from matrixelement where matrixelement_id IN (select m.matrixelement_id from matrixelement m, MATRIXCOLUMN c where m.MATRIXCOLUMN_ID = c > .MATRIXCOLUMN_ID and c.MATRIX_ID = $1) > > And I'mn seeing this in the tomcat logs during the hang: > > [http-8080-Processor8] DEBUG org.cipres.treebase.domain.search.StudySearchResults - discardUnpublished: before: 7; after: 7 > > > I'll > > -Jon > > > > On Mar 29, 2010, at 4:19 PM, William Piel wrote: > >> times-out with proxy error for simple searches. >> >> bp >> >> > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
|
From: Hilmar L. <hl...@ne...> - 2010-03-29 20:31:16
|
There's a fix for this - has this not yet been committed and/or deployed? -hilmar On Mar 29, 2010, at 4:29 PM, Jon Auman wrote: > It appears to be an issue with tomcat. It started over the weekend, > so I'm assuming there is an issue with the last build. This query > runs for hours: > > delete from matrixelement where matrixelement_id IN (select > m.matrixelement_id from matrixelement m, MATRIXCOLUMN c where > m.MATRIXCOLUMN_ID = c > .MATRIXCOLUMN_ID and c.MATRIX_ID = $1) > > And I'mn seeing this in the tomcat logs during the hang: > > [http-8080-Processor8] DEBUG > org.cipres.treebase.domain.search.StudySearchResults - > discardUnpublished: before: 7; after: 7 > > > I'll > > -Jon > > > > On Mar 29, 2010, at 4:19 PM, William Piel wrote: > >> times-out with proxy error for simple searches. >> >> bp >> >> > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: Jon A. <jon...@du...> - 2010-03-29 20:29:42
|
It appears to be an issue with tomcat. It started over the weekend, so I'm assuming there is an issue with the last build. This query runs for hours: delete from matrixelement where matrixelement_id IN (select m.matrixelement_id from matrixelement m, MATRIXCOLUMN c where m.MATRIXCOLUMN_ID = c .MATRIXCOLUMN_ID and c.MATRIX_ID = $1) And I'mn seeing this in the tomcat logs during the hang: [http-8080-Processor8] DEBUG org.cipres.treebase.domain.search.StudySearchResults - discardUnpublished: before: 7; after: 7 I'll -Jon On Mar 29, 2010, at 4:19 PM, William Piel wrote: > times-out with proxy error for simple searches. > > bp > > ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
|
From: Vladimir G. <vla...@du...> - 2010-03-28 19:38:35
|
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 |
|
From: youjun g. <you...@ya...> - 2010-03-27 23:06:19
|
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 > > |
|
From: youjun g. <you...@ya...> - 2010-03-27 22:46:08
|
> > 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 |
|
From: Vladimir G. <vla...@du...> - 2010-03-27 21:18:55
|
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 |
|
From: William P. <wil...@ya...> - 2010-03-27 14:03:38
|
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 |
|
From: Rutger V. <rut...@gm...> - 2010-03-27 12:50:38
|
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 |
|
From: youjun g. <you...@ya...> - 2010-03-27 12:31:01
|
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 > |
|
From: Rutger V. <rut...@gm...> - 2010-03-27 11:27:34
|
Sorry about the late reply, I'm not going to either ISMB or BOSC, so it'd be great if Hilmar presents there. We should probably all sit down and look at the poster, make sure it is up to date and think about what should go in which iEvoBio talks (for which the application deadline looming in the back of my head). On Fri, Mar 26, 2010 at 2:08 PM, Hilmar Lapp <hl...@ne...> wrote: > > On Mar 25, 2010, at 10:56 PM, William Piel wrote: > >> I have a poster that, with a few edits, could be used there. Would >> you be willing to host it? > > I would, though I also think we should all try to make sure it is up- > to-date and complete in terms of presenting the salient features of TB2. > > Do you have an abstract? The deadline for regular posters has already > passed, but late poster submission will open in April. > > And we still haven't heard from Rutger - if he's going to be there, it > would be most natural for him to present it. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > 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 |
|
From: Rutger V. <rut...@gm...> - 2010-03-27 11:15:27
|
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 |
|
From: Hilmar L. <hl...@ne...> - 2010-03-26 14:08:21
|
On Mar 25, 2010, at 10:56 PM, William Piel wrote: > I have a poster that, with a few edits, could be used there. Would > you be willing to host it? I would, though I also think we should all try to make sure it is up- to-date and complete in terms of presenting the salient features of TB2. Do you have an abstract? The deadline for regular posters has already passed, but late poster submission will open in April. And we still haven't heard from Rutger - if he's going to be there, it would be most natural for him to present it. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: William P. <wil...@ya...> - 2010-03-26 02:56:15
|
On Mar 25, 2010, at 1:17 PM, Hilmar Lapp wrote: > Do any of you have plans to attend ISMB and/or BOSC in Boston this > summer? If yes, have you submitted a poster on TB2? > > I will be attending both, and if nobody else does could present a TB > poster as I think it's pretty relevant to the computational biology > crowd, though there isn't much awareness. I was not planning to attend. I have a poster that, with a few edits, could be used there. Would you be willing to host it? bp |
|
From: youjun g. <you...@ya...> - 2010-03-25 23:29:16
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Bill traversed all TB tables and finally found out to delete a matrix record, we will need to cascade delete related data from more than 50 other tables. Surprisingly the bottle neck that halt the deletion actually come from a piece of sql. So we may not need to bring in any new sql query, instead I will do some test and see if we can solve the problem with Hibernate only. Youjun On Wed, Mar 24, 2010 at 10:27 AM, youjun guo <you...@ya...> wrote: > In theory making it 100% Hibernate should solve the problem, and should >> also make it consistent with the Hibernate ORM tier for data access. The >> more straight SQL we have in there, the more maintenance problems or risks >> we have down the road. Why does a pure Hibernate solution not work here? >> Hibernate is perfectly capable of orchestrating cascading deletes. > > >> >> -hilmar >> >> >> > |
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From: Hilmar L. <hl...@ne...> - 2010-03-25 17:18:08
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Do any of you have plans to attend ISMB and/or BOSC in Boston this summer? If yes, have you submitted a poster on TB2? I will be attending both, and if nobody else does could present a TB poster as I think it's pretty relevant to the computational biology crowd, though there isn't much awareness. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: youjun g. <you...@ya...> - 2010-03-24 14:28:00
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> > In theory making it 100% Hibernate should solve the problem, and should > also make it consistent with the Hibernate ORM tier for data access. The > more straight SQL we have in there, the more maintenance problems or risks > we have down the road. Why does a pure Hibernate solution not work here? > Hibernate is perfectly capable of orchestrating cascading deletes. > > -hilmar > > > Based on the information I get from Bill, the historic reason why Jin Ruan bring in SQL here is because the performance issue of hibernate. I think the sql created by hibernate is not as efficient when a task involved too many tables and too many cascade deletions. To delete a matrix we need to delete all related record from study, submission, matrix, sub_matrix matrixrow, rowsegment matrixcolumn, MATRIXCOLUMN_ITEMDEFINITION matrixelemnt, STATEMODIFIER ITEMVALUE Compound_element taxonlabelset taxonlabelset_taxonlabel taxonlabel and also need to check a group of tables to see make sure a taxonlabel is not refered by some other matrices or trees. While listing of the steps above I think our database schema may need a optimizing some how. Youjun |
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From: Hilmar L. <hl...@ne...> - 2010-03-24 13:20:59
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On Mar 24, 2010, at 9:16 AM, youjun guo wrote: > The current code for deleting a matrix is a hybrid of hibernate > operations and sql queries, I am going to make it 100% of sql > queries. See if it will solve the problem. In theory making it 100% Hibernate should solve the problem, and should also make it consistent with the Hibernate ORM tier for data access. The more straight SQL we have in there, the more maintenance problems or risks we have down the road. Why does a pure Hibernate solution not work here? Hibernate is perfectly capable of orchestrating cascading deletes. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: youjun g. <you...@ya...> - 2010-03-24 13:16:39
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The current code for deleting a matrix is a hybrid of hibernate operations and sql queries, I am going to make it 100% of sql queries. See if it will solve the problem. YOujun On Tue, Mar 23, 2010 at 10:43 PM, William Piel <wil...@ya...>wrote: > > On Mar 23, 2010, at 9:41 PM, Rutger Vos wrote: > > > In theory it should be possible to delete a matrix from the matrixList > > page, but in practice clearing out all the matrix elements takes so > > long it hampers userfriendliness, no? > > Currently deleting even small matrices cause a proxy time-out. We're > working of fixing this. > > The other thing that was never implemented in the original code is that > taxon labels belonging to a deleted matrix or tree do not get deleted > themselves, even if they are not used by anything else. Hence garbage builds > up -- and it's confusing to the submitter to still find taxon labels there > after deleting all matrices and trees. So we're also working to fix this. > > Youjun will try to implement this in the usual java-hibernate way, but if > that proves too slow, other solutions like a Postgresql stored procedure > might need to be used. > > 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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