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From: Jon A. <jon...@du...> - 2010-03-29 20:29:42
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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... ------------------------------------------------------ |
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From: Hilmar L. <hl...@ne...> - 2010-03-29 20:31:16
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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 : =========================================================== |
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From: William P. <wil...@ya...> - 2010-03-29 20:34:08
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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 |
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From: Jon A. <jon...@du...> - 2010-03-29 20:34:36
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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... ------------------------------------------------------ |
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From: Hilmar L. <hl...@ne...> - 2010-03-29 20:39:48
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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 : =========================================================== |
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From: Vladimir G. <vla...@du...> - 2010-03-29 21:01:27
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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 |
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From: Rutger V. <rut...@gm...> - 2010-03-29 22:00:56
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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
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From: Hilmar L. <hl...@ne...> - 2010-03-29 22:06:34
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Rutger - we really need a release identifier that is displayed, so
users and everyone else can report it. A hidden svn revision will not
solve this.
-hilmar
On Mar 29, 2010, at 6:00 PM, Rutger Vos wrote:
> 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
>
> ------------------------------------------------------------------------------
> 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 :
===========================================================
|
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From: Rutger V. <rut...@gm...> - 2010-03-30 13:39:45
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Sure, but maybe it's a starting point. Are we talking about the same
sort of principle where there is some point in the output produced by
the webapp where we (and other users) can see "release XXX, revision
YYY"?
By the way, this would be nice to have both in html and in other
produced files, potentially. E.g. to diagnose the provenance of
inconsistencies in produced nexus/nexml/rdf.
On Mon, Mar 29, 2010 at 11:06 PM, Hilmar Lapp <hl...@ne...> wrote:
> Rutger - we really need a release identifier that is displayed, so users and
> everyone else can report it. A hidden svn revision will not solve this.
>
> -hilmar
>
> On Mar 29, 2010, at 6:00 PM, Rutger Vos wrote:
>
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> 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 :
> ===========================================================
>
>
>
>
--
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: Hilmar L. <hl...@ne...> - 2010-03-30 15:51:06
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You can look at http://demo.plhdb.org for an example. So yes, some kind of indicator of release, and an unequivocal identifier of the build that it was deployed from. -hilmar On Mar 30, 2010, at 9:39 AM, Rutger Vos wrote: > Sure, but maybe it's a starting point. Are we talking about the same > sort of principle where there is some point in the output produced by > the webapp where we (and other users) can see "release XXX, revision > YYY"? > > By the way, this would be nice to have both in html and in other > produced files, potentially. E.g. to diagnose the provenance of > inconsistencies in produced nexus/nexml/rdf. > > On Mon, Mar 29, 2010 at 11:06 PM, Hilmar Lapp <hl...@ne...> > wrote: >> Rutger - we really need a release identifier that is displayed, so >> users and >> everyone else can report it. A hidden svn revision will not solve >> this. >> >> -hilmar >> >> On Mar 29, 2010, at 6:00 PM, Rutger Vos wrote: >> >>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 : >> =========================================================== >> >> >> >> > > > > -- > 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2010-04-02 13:03:33
|
Let's rebuild to reflect the latest fixes regarding phylowidget. Also, I need the dev rebuilt because there is a serious bug in either the delete trees or delete matrices features that seems to corrupt the system -- to figure out exactly what's going on, I need to be able to test against dev. bp |
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From: Vladimir G. <vla...@du...> - 2010-04-02 14:49:39
|
On Apr 2, 2010, at 9:03 AM, William Piel wrote: > > Let's rebuild to reflect the latest fixes regarding phylowidget. I have asked Jon to redeploy with a build for svn#667 to treebase-dev --- looking at what URL it generates for Phylowidget on mu local server, I doubt it would work: http://www.phylowidget.org/full/?tree='http://localhost:8080TB2:Tr31' > Also, I need the dev rebuilt because there is a serious bug in > either the delete trees or delete matrices features that seems to > corrupt the system -- to figure out exactly what's going on, I need > to be able to test against dev. I think yesterday's redeploy includes the matrix delete fix. --Vg |
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From: William P. <wil...@ya...> - 2010-04-02 15:04:50
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On Apr 2, 2010, at 9:49 AM, Vladimir Gapeyev wrote: > I have asked Jon to redeploy with a build for svn#667 to treebase-dev > --- looking at what URL it generates for Phylowidget on mu local > server, I doubt it would work: > http://www.phylowidget.org/full/?tree='http://localhost:8080TB2:Tr31' > Do you not have this javascript ? <script type="text/javascript"> function openPhylowidget(tree_id) { var realURL = "http://www.phylowidget.org/full/?tree='http://"+location.host+"/treebase-web/tree_for_phylowidget/"+"TB2:Tr"+tree_id+"'"; window.open(realURL,'myplwidget') } </script> (As in here) Or you do have that, but it still creates a "localhost" link? bp |
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From: youjun g. <you...@ya...> - 2010-04-02 15:15:40
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Based on Rutger's discription: 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. the current version number on treebase.org is 245. Youjun On Fri, Apr 2, 2010 at 11:04 AM, William Piel <wil...@ya...> wrote: > > On Apr 2, 2010, at 9:49 AM, Vladimir Gapeyev wrote: > > I have asked Jon to redeploy with a build for svn#667 to treebase-dev > --- looking at what URL it generates for Phylowidget on mu local > server, I doubt it would work: > http://www.phylowidget.org/full/?tree='http://localhost:8080TB2:Tr31'<http://www.phylowidget.org/full/?tree=%27http://localhost:8080TB2:Tr31%27> > > > Do you not have this javascript ? > > <script type="text/javascript"> > function openPhylowidget(tree_id) > { > var realURL = "http://www.phylowidget.org/full/?tree='http://<http://www.phylowidget.org/full/?tree=%27http://> > "+location.host+"/treebase-web/tree_for_phylowidget/"+"TB2:Tr"+tree_id+"'"; > window.open(realURL,'myplwidget') > } > </script> > > (As in here<http://130.132.27.212:8080/treebase-web/search/treeSearch.html> > ) > > Or you do have that, but it still creates a "localhost" link? > > 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: William P. <wil...@ya...> - 2010-04-02 15:30:12
|
On Apr 2, 2010, at 10:15 AM, youjun guo wrote: > the current version number on treebase.org is 245. Yeah, I just don't know exactly what version Vladimir has on his laptop: On Apr 2, 2010, at 9:49 AM, Vladimir Gapeyev wrote: > looking at what URL it generates for Phylowidget on my local > server, I doubt it would work: |
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From: Rutger V. <rut...@gm...> - 2010-04-02 16:09:25
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That number is no longer being incremented because it requires a step in the deployment process that was implemented in the publish script, but no longer in the current procedure, I don't think. On Friday, April 2, 2010, youjun guo <you...@ya...> wrote: > Based on Rutger's discription: > > 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. > the current version number on treebase.org is 245. > > Youjun > > On Fri, Apr 2, 2010 at 11:04 AM, William Piel <wil...@ya...> wrote: > > On Apr 2, 2010, at 9:49 AM, Vladimir Gapeyev wrote: > > I have asked Jon to redeploy with a build for svn#667 to treebase-dev > --- looking at what URL it generates for Phylowidget on mu local > server, I doubt it would work: > http://www.phylowidget.org/full/?tree='http://localhost:8080TB2:Tr31' > > > Do you not have this javascript ? > <script type="text/javascript"> function openPhylowidget(tree_id) > { var realURL = "http://www.phylowidget.org/full/?tree='http://"+location.host+"/treebase-web/tree_for_phylowidget/"+"TB2:Tr"+tree_id+"'"; > window.open(realURL,'myplwidget') }</script> > > (As in here <http://130.132.27.212:8080/treebase-web/search/treeSearch.html>) > > Or you do have that, but it still creates a "localhost" link? > 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 > > > -- 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: Vladimir G. <vla...@du...> - 2010-04-02 18:19:13
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On Apr 2, 2010, at 11:04 AM, William Piel wrote: > > On Apr 2, 2010, at 9:49 AM, Vladimir Gapeyev wrote: > >> I have asked Jon to redeploy with a build for svn#667 to treebase-dev >> --- looking at what URL it generates for Phylowidget on mu local >> server, I doubt it would work: >> http://www.phylowidget.org/full/?tree='http://localhost:8080TB2:Tr31' >> > > Do you not have this javascript ? > > <script type="text/javascript"> > function openPhylowidget(tree_id) > { > var realURL = "http://www.phylowidget.org/full/? > tree='http://"+location.host+"/treebase-web/ > tree_for_phylowidget/"+"TB2:Tr"+tree_id+"'"; > window.open(realURL,'myplwidget') > } > </script> > > (As in here) > > Or you do have that, but it still creates a "localhost" link? The "localhost" part is ok, since that's where I run the app from. I meant there were missing slashes or even URL fragments. Jon has now deployed #667 to treebase-dev, and this is how it looks there: http://www.phylowidget.org/full/?tree='http://treebase-dev.nescent.orgTB2:Tr4207' Most likely, Youjun did not yet commit the most recent version of the JavaScript. As for the versions that I mention, they are the ones SVN reports when I update. You can compare them to the ones in the commit emails. --VG |
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From: youjun g. <you...@ya...> - 2010-04-02 18:49:02
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That javascript exist since 665. Bill fixed a open bracket on 666, and I
moved the script out of a loop structure (a table tag) to avoid repeat on
667, this cause ${url}
lost the correct value.
I will do a new submission.
Youjun
On Fri, Apr 2, 2010 at 2:19 PM, Vladimir Gapeyev
<vla...@du...>wrote:
>
> On Apr 2, 2010, at 11:04 AM, William Piel wrote:
>
>
> On Apr 2, 2010, at 9:49 AM, Vladimir Gapeyev wrote:
>
> I have asked Jon to redeploy with a build for svn#667 to treebase-dev
> --- looking at what URL it generates for Phylowidget on mu local
> server, I doubt it would work:
> http://www.phylowidget.org/full/?tree='http://localhost:8080TB2:Tr31'<http://www.phylowidget.org/full/?tree=%27http://localhost:8080TB2:Tr31%27>
>
>
> Do you not have this javascript ?
>
> <script type="text/javascript">
> function openPhylowidget(tree_id)
> {
> var realURL = "http://www.phylowidget.org/full/?tree='http://<http://www.phylowidget.org/full/?tree=%27http://>
> "+location.host+"/treebase-web/tree_for_phylowidget/"+"TB2:Tr"+tree_id+"'";
> window.open(realURL,'myplwidget')
> }
> </script>
>
> (As in here<http://130.132.27.212:8080/treebase-web/search/treeSearch.html>
> )
>
> Or you do have that, but it still creates a "localhost" link?
>
>
> The "localhost" part is ok, since that's where I run the app from. I meant
> there were missing slashes or even URL fragments. Jon has now deployed #667
> to treebase-dev, and this is how it looks there:
>
> http://www.phylowidget.org/full/?tree='http://treebase-dev.nescent.orgTB2:Tr4207'<http://www.phylowidget.org/full/?tree=%27http://treebase-dev.nescent.orgTB2:Tr4207%27>
>
> Most likely, Youjun did not yet commit the most recent version of the
> JavaScript.
>
> As for the versions that I mention, they are the ones SVN reports when I
> update. You can compare them to the ones in the commit emails.
>
> --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
>
>
|
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From: youjun g. <you...@ya...> - 2010-04-02 19:13:13
|
Vladimir, I just did a new submission to modify the script, since today is yale holiday I don't have the access to my personal server until next Mon., Can you try it on your testing server see if the phylowidget link works? It looks to me the current version of treebase.org is 664 or earlier. Thanks Youjun On Fri, Apr 2, 2010 at 2:19 PM, Vladimir Gapeyev <vla...@du...>wrote: > > On Apr 2, 2010, at 11:04 AM, William Piel wrote: > > > On Apr 2, 2010, at 9:49 AM, Vladimir Gapeyev wrote: > > I have asked Jon to redeploy with a build for svn#667 to treebase-dev > --- looking at what URL it generates for Phylowidget on mu local > server, I doubt it would work: > http://www.phylowidget.org/full/?tree='http://localhost:8080TB2:Tr31'<http://www.phylowidget.org/full/?tree=%27http://localhost:8080TB2:Tr31%27> > > > Do you not have this javascript ? > > <script type="text/javascript"> > function openPhylowidget(tree_id) > { > var realURL = "http://www.phylowidget.org/full/?tree='http://<http://www.phylowidget.org/full/?tree=%27http://> > "+location.host+"/treebase-web/tree_for_phylowidget/"+"TB2:Tr"+tree_id+"'"; > window.open(realURL,'myplwidget') > } > </script> > > (As in here<http://130.132.27.212:8080/treebase-web/search/treeSearch.html> > ) > > Or you do have that, but it still creates a "localhost" link? > > > The "localhost" part is ok, since that's where I run the app from. I meant > there were missing slashes or even URL fragments. Jon has now deployed #667 > to treebase-dev, and this is how it looks there: > > http://www.phylowidget.org/full/?tree='http://treebase-dev.nescent.orgTB2:Tr4207'<http://www.phylowidget.org/full/?tree=%27http://treebase-dev.nescent.orgTB2:Tr4207%27> > > Most likely, Youjun did not yet commit the most recent version of the > JavaScript. > > As for the versions that I mention, they are the ones SVN reports when I > update. You can compare them to the ones in the commit emails. > > --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 > > |
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From: Vladimir G. <vla...@du...> - 2010-04-02 20:02:57
|
On Apr 2, 2010, at 3:13 PM, youjun guo wrote: > > I just did a new submission to modify the script, since today is > yale holiday I don't have the access to my personal server until > next Mon., Can you try it on your testing server see if the > phylowidget link works? Thanks, the URL it generates now is http://www.phylowidget.org/full/?tree='http://localhost:8080/treebase-web/tree_for_phylowidget/TB2:Tr4207' which looks ok. More surprisingly, it works with 'localhost' in it! How does phylowidget.org know to go to my server rather than to its own localhost??? Regardless, I am asking Jon to re-deploy both on dev and prod. Don't expect quick response, though - he is taking a day off today. --VG |
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From: Hilmar L. <hl...@ne...> - 2010-04-02 21:38:57
|
On Apr 2, 2010, at 4:02 PM, Vladimir Gapeyev wrote: > More surprisingly, it works with 'localhost' in it! How does > phylowidget.org know to go to my server rather than to its own > localhost??? > It's an applet running in your browser, so wherever that browser is is locahost. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Jon A. <jon...@du...> - 2010-04-02 21:31:35
|
I've updated dev and production to the latest war file. -Jon On Apr 2, 2010, at 4:02 PM, Vladimir Gapeyev wrote: > > On Apr 2, 2010, at 3:13 PM, youjun guo wrote: >> >> I just did a new submission to modify the script, since today is yale holiday I don't have the access to my personal server until next Mon., Can you try it on your testing server see if the phylowidget link works? > > Thanks, the URL it generates now is > http://www.phylowidget.org/full/?tree='http://localhost:8080/treebase-web/tree_for_phylowidget/TB2:Tr4207' > which looks ok. > > More surprisingly, it works with 'localhost' in it! How does phylowidget.org know to go to my server rather than to its own localhost??? > > Regardless, I am asking Jon to re-deploy both on dev and prod. Don't expect quick response, though - he is taking a day off today. > > --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 ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: youjun g. <you...@ya...> - 2010-04-02 21:47:04
|
Jon and Vladimir, Thank you very much! Youjun On Fri, Apr 2, 2010 at 5:31 PM, Jon Auman <jon...@du...> wrote: > I've updated dev and production to the latest war file. > -Jon > > On Apr 2, 2010, at 4:02 PM, Vladimir Gapeyev wrote: > > > On Apr 2, 2010, at 3:13 PM, youjun guo wrote: > > > I just did a new submission to modify the script, since today is yale > holiday I don't have the access to my personal server until next Mon., Can > you try it on your testing server see if the phylowidget link works? > > > Thanks, the URL it generates now is > > http://www.phylowidget.org/full/?tree='http://localhost:8080/treebase-web/tree_for_phylowidget/TB2:Tr4207'<http://www.phylowidget.org/full/?tree=%27http://localhost:8080/treebase-web/tree_for_phylowidget/TB2:Tr4207%27> > which looks ok. > > More surprisingly, it works with 'localhost' in it! How does > phylowidget.org know to go to my server rather than to its own > localhost??? > > Regardless, I am asking Jon to re-deploy both on dev and prod. Don't > expect quick response, though - he is taking a day off today. > > --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 > > > ------------------------------------------------------- > 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 > > |
|
From: William P. <wil...@ya...> - 2010-04-07 16:42:36
|
Any ideas when this will be up again? (now it's 12:34 PM) bp |
|
From: Jon A. <jon...@ne...> - 2010-04-07 16:48:32
|
Hi Bill, Sorry, I did get a page, but I was away from my computer. The application crashes at least once a week, sometimes more often. I've been thinking that maybe we should restart tomcat every night? If you like this idea, any preference in time? Thanks, Jon On Apr 7, 2010, at 12:33 PM, William Piel wrote: > > Any ideas when this will be up again? (now it's 12:34 PM) > > 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 ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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