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From: William P. <wil...@ya...> - 2009-12-16 17:36:04
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On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > I just got an email from Wayne suggesting a programmatic way to tell > mesquite its location at runtime, I still have to try this. Has Jin Ruan responded? I'd imagine that he might be very useful, seeing as he modified Mesquite in the first place. If you think it would help, Val or I can write to him separately. On Dec 16, 2009, at 12:07 PM, Hilmar Lapp wrote: > I get the sense that no one has one local to their lap/desktop either. Youjun has one at the Peabody: http://130.132.27.212:8080/treebase-web/home.html (the code runs on his machine but it pulls data from postgresql at NESCent) ... but he's having some problems getting it to update with the latest code. He's working on that.. bp |
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From: Rutger V. <rut...@gm...> - 2009-12-16 17:18:25
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http://treebasedb-dev.nescent.org:6666/treebase-web is up and running again, though the mesquite runtime issue is still not resolved. I fixed the compile time issue by putting the dependency on treebase-2.01.tb.jar back in the pom.xml (and committed this). I just got an email from Wayne suggesting a programmatic way to tell mesquite its location at runtime, I still have to try this. I am quite happy to "reconfigure" my account by sharing my login credentials with Youjun and Vladimir off-list (or is there a better way to do this)? I thought Youjun was capable locally of building and deploying the war (while talking to the remote db). I certainly can so I don't *have* to use the rv...@tr... account to get any work done. Vladimir, if you do an update on your end, will the source now build on your system? The complaints about mesquite.lib.* missing should go away. Rutger On Wed, Dec 16, 2009 at 5:07 PM, Hilmar Lapp <hl...@ne...> wrote: > Rutger - > > it looks like at this point we do not have a second deployment-capable > installation on treebase-dev, and I get the sense that no one has one local > to their lap/desktop either. > > Since Jon is on parental leave, can you reconfigure your account so that it > can function as the shared developer account for now until Jon gets a minute > to create that? > > Also, given that we want to do development work on the web-application in > parallel, I'd consider it high priority that we work out local deployments > of the web-application on the developers' own machines. Vladimir seems to be > almost there - what is missing right now? > > -hilmar > > On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: > >> Didn't we talk about this already, that we wanted to create a shared >> developer account or group so that we're all talking about the same >> environment with the same configuration? I'm not sure what the best >> way would be to set this up. >> >> On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> wrote: >>> >>> Except that that person can't remain Rutger. -hilmar >>> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >>> >>> Now I kind of understand, once other developers finish a task and pass >>> the >>> testing on their own environment, just submit the code to sourceforg, >>> Rutger >>> will be the person who redeploy the new code. >>> >>> Thanks >>> >>> Youjun >>> >>> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne...> >>> wrote: >>>> >>>> http://treebase-dev.nescent.org:6666/treebase-web is the only common >>>> TreeBase instance I am aware of. I presumed everyone had their own >>>> local >>>> tomcats for development purposes -- that's what I have been trying to >>>> set up >>>> for myself for the past two days... >>>> --Vladimir >>>> >>>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>>> >>>> Do you know which Tomcat server is assigned for all the TreeBASE >>>> developers? >>>> >>>> Youjun >>>> >>>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev >>>> <vga...@ne...> >>>> wrote: >>>>> >>>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>>> >>>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>>> >>>>> Vladimir, >>>>> >>>>> Do you know why I cannot access the treebase-web @ >>>>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>>>> >>>>> Youjun >>>>> >>>>> The server itself is up: http://treebase-dev.nescent.org/. My first >>>>> guess that 6666 is down due to Rutger's ongoing experimentation with >>>>> Mesquite. (The same reasons I could not set up my deployment >>>>> yesterday?) >>>>> I'll try to find and check the logs. >>>>> >>>>> Il'' take the last one back: according to the notes Jon gave me, 6666 >>>>> starts from Rutger's homedir, to which only he has access. >>>>> --Vladimir >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.Net email is sponsored by the Verizon Developer Community >>> Take advantage of Verizon's best-in-class app development support >>> A streamlined, 14 day to market process makes app distribution fast and >>> easy >>> Join now and get one step closer to millions of Verizon customers >>> http://p.sf.net/sfu/verizon-dev2dev >>> _______________________________________________ >>> Treebase-devel mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>> =========================================================== >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.Net email is sponsored by the Verizon Developer Community >>> Take advantage of Verizon's best-in-class app development support >>> A streamlined, 14 day to market process makes app distribution fast and >>> easy >>> Join now and get one step closer to millions of Verizon customers >>> http://p.sf.net/sfu/verizon-dev2dev >>> _______________________________________________ >>> 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 > > -- > =========================================================== > : 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...> - 2009-12-16 17:07:46
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Rutger - it looks like at this point we do not have a second deployment-capable installation on treebase-dev, and I get the sense that no one has one local to their lap/desktop either. Since Jon is on parental leave, can you reconfigure your account so that it can function as the shared developer account for now until Jon gets a minute to create that? Also, given that we want to do development work on the web-application in parallel, I'd consider it high priority that we work out local deployments of the web-application on the developers' own machines. Vladimir seems to be almost there - what is missing right now? -hilmar On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: > Didn't we talk about this already, that we wanted to create a shared > developer account or group so that we're all talking about the same > environment with the same configuration? I'm not sure what the best > way would be to set this up. > > On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> > wrote: >> Except that that person can't remain Rutger. -hilmar >> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >> >> Now I kind of understand, once other developers finish a task and >> pass the >> testing on their own environment, just submit the code to >> sourceforg, Rutger >> will be the person who redeploy the new code. >> >> Thanks >> >> Youjun >> >> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... >> > >> wrote: >>> >>> http://treebase-dev.nescent.org:6666/treebase-web is the only >>> common >>> TreeBase instance I am aware of. I presumed everyone had their >>> own local >>> tomcats for development purposes -- that's what I have been trying >>> to set up >>> for myself for the past two days... >>> --Vladimir >>> >>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>> >>> Do you know which Tomcat server is assigned for all the TreeBASE >>> developers? >>> >>> Youjun >>> >>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne... >>> > >>> wrote: >>>> >>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>> >>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>> >>>> Vladimir, >>>> >>>> Do you know why I cannot access the treebase-web @ >>>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>>> >>>> Youjun >>>> >>>> The server itself is up: http://treebase-dev.nescent.org/. My >>>> first >>>> guess that 6666 is down due to Rutger's ongoing experimentation >>>> with >>>> Mesquite. (The same reasons I could not set up my deployment >>>> yesterday?) >>>> I'll try to find and check the logs. >>>> >>>> Il'' take the last one back: according to the notes Jon gave me, >>>> 6666 >>>> starts from Rutger's homedir, to which only he has access. >>>> --Vladimir >>> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2009-12-16 16:23:44
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We did - does anyone know where that currently stands? -hilmar On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: > Didn't we talk about this already, that we wanted to create a shared > developer account or group so that we're all talking about the same > environment with the same configuration? I'm not sure what the best > way would be to set this up. > > On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> > wrote: >> Except that that person can't remain Rutger. -hilmar >> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >> >> Now I kind of understand, once other developers finish a task and >> pass the >> testing on their own environment, just submit the code to >> sourceforg, Rutger >> will be the person who redeploy the new code. >> >> Thanks >> >> Youjun >> >> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... >> > >> wrote: >>> >>> http://treebase-dev.nescent.org:6666/treebase-web is the only >>> common >>> TreeBase instance I am aware of. I presumed everyone had their >>> own local >>> tomcats for development purposes -- that's what I have been trying >>> to set up >>> for myself for the past two days... >>> --Vladimir >>> >>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>> >>> Do you know which Tomcat server is assigned for all the TreeBASE >>> developers? >>> >>> Youjun >>> >>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne... >>> > >>> wrote: >>>> >>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>> >>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>> >>>> Vladimir, >>>> >>>> Do you know why I cannot access the treebase-web @ >>>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>>> >>>> Youjun >>>> >>>> The server itself is up: http://treebase-dev.nescent.org/. My >>>> first >>>> guess that 6666 is down due to Rutger's ongoing experimentation >>>> with >>>> Mesquite. (The same reasons I could not set up my deployment >>>> yesterday?) >>>> I'll try to find and check the logs. >>>> >>>> Il'' take the last one back: according to the notes Jon gave me, >>>> 6666 >>>> starts from Rutger's homedir, to which only he has access. >>>> --Vladimir >>> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2009-12-16 16:22:21
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Didn't we talk about this already, that we wanted to create a shared developer account or group so that we're all talking about the same environment with the same configuration? I'm not sure what the best way would be to set this up. On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> wrote: > Except that that person can't remain Rutger. -hilmar > On Dec 16, 2009, at 11:01 AM, youjun guo wrote: > > Now I kind of understand, once other developers finish a task and pass the > testing on their own environment, just submit the code to sourceforg, Rutger > will be the person who redeploy the new code. > > Thanks > > Youjun > > On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne...> > wrote: >> >> http://treebase-dev.nescent.org:6666/treebase-web is the only common >> TreeBase instance I am aware of. I presumed everyone had their own local >> tomcats for development purposes -- that's what I have been trying to set up >> for myself for the past two days... >> --Vladimir >> >> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >> >> Do you know which Tomcat server is assigned for all the TreeBASE >> developers? >> >> Youjun >> >> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne...> >> wrote: >>> >>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>> >>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>> >>> Vladimir, >>> >>> Do you know why I cannot access the treebase-web @ >>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>> >>> Youjun >>> >>> The server itself is up: http://treebase-dev.nescent.org/. My first >>> guess that 6666 is down due to Rutger's ongoing experimentation with >>> Mesquite. (The same reasons I could not set up my deployment yesterday?) >>> I'll try to find and check the logs. >>> >>> Il'' take the last one back: according to the notes Jon gave me, 6666 >>> starts from Rutger's homedir, to which only he has access. >>> --Vladimir >> > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > 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...> - 2009-12-16 16:16:57
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Except that that person can't remain Rutger. -hilmar On Dec 16, 2009, at 11:01 AM, youjun guo wrote: > Now I kind of understand, once other developers finish a task and > pass the testing on their own environment, just submit the code to > sourceforg, Rutger will be the person who redeploy the new code. > > Thanks > > Youjun > > On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... > > wrote: > > http://treebase-dev.nescent.org:6666/treebase-web is the only > common TreeBase instance I am aware of. I presumed everyone had > their own local tomcats for development purposes -- that's what I > have been trying to set up for myself for the past two days... > --Vladimir > > > On Dec 16, 2009, at 10:40 AM, youjun guo wrote: > >> Do you know which Tomcat server is assigned for all the TreeBASE >> developers? >> >> Youjun >> >> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne... >> > wrote: >> >> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >> >>> >>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>> >>>> Vladimir, >>>> >>>> Do you know why I cannot access the treebase-web @ treebase- >>>> dev.nescent.org:6666? I saw the home page flash and gone. >>>> >>>> Youjun >>> >>> The server itself is up: http://treebase-dev.nescent.org/. My >>> first guess that 6666 is down due to Rutger's ongoing >>> experimentation with Mesquite. (The same reasons I could not set >>> up my deployment yesterday?) >>> >>> I'll try to find and check the logs. >> >> Il'' take the last one back: according to the notes Jon gave me, >> 6666 starts from Rutger's homedir, to which only he has access. >> >> --Vladimir >> > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > 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: youjun g. <you...@ya...> - 2009-12-16 16:01:40
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Now I kind of understand, once other developers finish a task and pass the testing on their own environment, just submit the code to sourceforg, Rutger will be the person who redeploy the new code. Thanks Youjun On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne...>wrote: > > http://treebase-dev.nescent.org:6666/treebase-web is the only common > TreeBase instance I am aware of. I presumed everyone had their own local > tomcats for development purposes -- that's what I have been trying to set up > for myself for the past two days... > --Vladimir > > > On Dec 16, 2009, at 10:40 AM, youjun guo wrote: > > Do you know which Tomcat server is assigned for all the TreeBASE > developers? > > Youjun > > On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne...>wrote: > >> >> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >> >> >> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >> >> Vladimir, >> >> Do you know why I cannot access the treebase-web @ >> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >> >> Youjun >> >> >> The server itself is up: http://treebase-dev.nescent.org/. My first >> guess that 6666 is down due to Rutger's ongoing experimentation with >> Mesquite. (The same reasons I could not set up my deployment yesterday?) >> >> I'll try to find and check the logs. >> >> >> Il'' take the last one back: according to the notes Jon gave me, 6666 >> starts from Rutger's homedir, to which only he has access. >> >> --Vladimir >> > > > |
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From: Vladimir G. <vga...@ne...> - 2009-12-16 15:48:05
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http://treebase-dev.nescent.org:6666/treebase-web is the only common TreeBase instance I am aware of. I presumed everyone had their own local tomcats for development purposes -- that's what I have been trying to set up for myself for the past two days... --Vladimir On Dec 16, 2009, at 10:40 AM, youjun guo wrote: > Do you know which Tomcat server is assigned for all the TreeBASE > developers? > > Youjun > > On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne... > > wrote: > > On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: > >> >> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >> >>> Vladimir, >>> >>> Do you know why I cannot access the treebase-web @ treebase- >>> dev.nescent.org:6666? I saw the home page flash and gone. >>> >>> Youjun >> >> The server itself is up: http://treebase-dev.nescent.org/. My >> first guess that 6666 is down due to Rutger's ongoing >> experimentation with Mesquite. (The same reasons I could not set >> up my deployment yesterday?) >> >> I'll try to find and check the logs. > > Il'' take the last one back: according to the notes Jon gave me, > 6666 starts from Rutger's homedir, to which only he has access. > > --Vladimir > |
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From: youjun g. <you...@ya...> - 2009-12-16 15:40:26
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Do you know which Tomcat server is assigned for all the TreeBASE developers? Youjun On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne...>wrote: > > On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: > > > On Dec 15, 2009, at 6:23 PM, youjun guo wrote: > > Vladimir, > > Do you know why I cannot access the treebase-web @ > treebase-dev.nescent.org:6666? I saw the home page flash and gone. > > Youjun > > > The server itself is up: http://treebase-dev.nescent.org/. My first guess > that 6666 is down due to Rutger's ongoing experimentation with Mesquite. > (The same reasons I could not set up my deployment yesterday?) > > I'll try to find and check the logs. > > > Il'' take the last one back: according to the notes Jon gave me, 6666 > starts from Rutger's homedir, to which only he has access. > > --Vladimir > |
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From: Vladimir G. <vga...@ne...> - 2009-12-16 15:20:16
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On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: > > On Dec 15, 2009, at 6:23 PM, youjun guo wrote: > >> Vladimir, >> >> Do you know why I cannot access the treebase-web @ treebase- >> dev.nescent.org:6666? I saw the home page flash and gone. >> >> Youjun > > The server itself is up: http://treebase-dev.nescent.org/. My first > guess that 6666 is down due to Rutger's ongoing experimentation with > Mesquite. (The same reasons I could not set up my deployment > yesterday?) > > I'll try to find and check the logs. Il'' take the last one back: according to the notes Jon gave me, 6666 starts from Rutger's homedir, to which only he has access. --Vladimir |
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From: Vladimir G. <vga...@ne...> - 2009-12-16 15:02:23
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On Dec 15, 2009, at 6:23 PM, youjun guo wrote: > Vladimir, > > Do you know why I cannot access the treebase-web @ treebase- > dev.nescent.org:6666? I saw the home page flash and gone. > > Youjun The server itself is up: http://treebase-dev.nescent.org/. My first guess that 6666 is down due to Rutger's ongoing experimentation with Mesquite. (The same reasons I could not set up my deployment yesterday?) I'll try to find and check the logs. I'll also drop a message to Jon, but he is mostly out of reach since yesterday. --Vladimir |
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From: youjun g. <you...@ya...> - 2009-12-16 14:02:49
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Never mind, I was confused about what Vladimir want to do. Accurately eclipse offer so many ways to integrity a testing purpose Tomcat. As long as one can build the war file, the deployment and testing is just one button away. Youjun On Wed, Dec 16, 2009 at 5:07 AM, Rutger Vos <rut...@gm...> wrote: > I agree that it's useful to have a local web application inside a > local tomcat, and it shouldn't be too hard to get that up and running > beyond the point where you are now. I am aware of the mesquite.lib.* > issues and have just sent out an email discussing this on the > "Mesquite troubles" thread. > > On Wed, Dec 16, 2009 at 4:23 AM, Hilmar Lapp <hl...@ne...> wrote: > > Youjun - I don't know whether by TreeBASE installation you mean the > database > > or the web-application or both. I think it's pretty critical that every > > developer can bring up a local version of the web-application. They may > all > > be accessing the same database, but if everyone is updating and > redeploying > > on the same application server for every change or debugging run then > chaos > > of the unproductive kind will ensue quickly. > > -hilmar > > On Dec 15, 2009, at 11:17 PM, youjun guo wrote: > > > > Vladimir, > > > > Why do you want to deploy a new TreeBASE installation? If you just want > to > > add a java encrypt implementation like MD5 to TreeBASE code, I my be able > to > > help with it. Then you can focus on some other task. > > > > Youjun > > > > On Tue, Dec 15, 2009 at 5:50 PM, Vladimir Gapeyev <vga...@ne...> > > wrote: > >> > >> On Dec 15, 2009, at 4:41 PM, youjun guo wrote: > >> > >>> Vladimir, > >>> > >>> jdbc.properties should be add to main/resource of treebase-core before > >>> bilud, and it will be built into treebase-core jar file. > >>> > >> > >> Thanks, this has moved me forward. The deployment still fails, > apparently > >> due to mesquite again. See the excerpt from logs/catalina.out below. > >> > >> I do see numerous Eclipse complaints about failing 'import > >> mesquite.lib.*'., which I did not see earlier in the day! I did update > from > >> SVN, as well as all Maven-related update commands I could see in the UI. > >> > >> --Vladimir > >> > >> > >> > >> [main] ERROR org.springframework.web.context.ContextLoader - Context > >> initialization failed > >> org.springframework.beans.factory.BeanCreationException: Error creating > >> bean with name 'sessionFactory' defined in URL > >> > [jar:file:/Users/vgapeyev/Work/TreeBase/devel/applications/apache-tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar!/applicationContext-dao.xml]: > >> Invocation of init method failed; nested exception is > >> org.hibernate.InstantiationException: could not instantiate test > >> objectorg.cipres.treebase.domain.taxon.TaxonLabelSet > >> Caused by: > >> org.hibernate.InstantiationException: could not instantiate test > >> objectorg.cipres.treebase.domain.taxon.TaxonLabelSet > >> at > >> > org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:25) > >> at > >> > org.hibernate.engine.UnsavedValueFactory.getUnsavedIdentifierValue(UnsavedValueFactory.java:44) > >> at > >> > org.hibernate.tuple.PropertyFactory.buildIdentifierProperty(PropertyFactory.java:44) > >> at > >> > org.hibernate.tuple.entity.EntityMetamodel.<init>(EntityMetamodel.java:124) > >> at > >> > org.hibernate.persister.entity.AbstractEntityPersister.<init>(AbstractEntityPersister.java:434) > >> at > >> > org.hibernate.persister.entity.SingleTableEntityPersister.<init>(SingleTableEntityPersister.java:109) > >> at > >> > org.hibernate.persister.PersisterFactory.createClassPersister(PersisterFactory.java:55) > >> at > >> > org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:226) > >> at > >> > org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1300) > >> at > >> > org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:859) > >> at > >> > org.springframework.orm.hibernate3.LocalSessionFactoryBean.newSessionFactory(LocalSessionFactoryBean.java:805) > >> at > >> > org.springframework.orm.hibernate3.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:745) > >> at > >> > org.springframework.orm.hibernate3.AbstractSessionFactoryBean.afterPropertiesSet(AbstractSessionFactoryBean.java:134) > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1198) > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1167) > >> at > >> > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:427) > >> at > >> > org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:249) > >> at > >> > org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:155) > >> at > >> > org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:246) > >> at > >> > org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160) > >> at > >> > org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:285) > >> at > >> > org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352) > >> at > >> > org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:245) > >> at > >> > org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:188) > >> at > >> > org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:49) > >> at > >> > org.cipres.treebase.web.listeners.StartupListener.contextInitialized(StartupListener.java:45) > >> at > >> > org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3795) > >> at > >> > org.apache.catalina.core.StandardContext.start(StandardContext.java:4252) > >> at > >> > org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) > >> at > >> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) > >> at > >> org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) > >> at > >> org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831) > >> at > >> org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720) > >> at > >> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) > >> at > >> org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150) > >> at > >> > org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) > >> at > >> > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) > >> at > >> org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) > >> at > >> org.apache.catalina.core.StandardHost.start(StandardHost.java:736) > >> at > >> org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) > >> at > >> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443) > >> at > >> org.apache.catalina.core.StandardService.start(StandardService.java:448) > >> at > >> org.apache.catalina.core.StandardServer.start(StandardServer.java:700) > >> at org.apache.catalina.startup.Catalina.start(Catalina.java:552) > >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > >> at > >> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > >> at > >> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > >> at java.lang.reflect.Method.invoke(Method.java:592) > >> at > org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) > >> at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) > >> Caused by: java.lang.reflect.InvocationTargetException > >> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native > >> Method) > >> at > >> > sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) > >> at > >> > sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > >> at > java.lang.reflect.Constructor.newInstance(Constructor.java:501) > >> at > >> > org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:22) > >> ... 49 more > >> Caused by: java.lang.Error: Unresolved compilation problems: > >> The import mesquite.lib cannot be resolved > >> StringUtil cannot be resolved > >> StringUtil cannot be resolved > >> StringUtil cannot be resolved > >> StringUtil cannot be resolved > >> > >> at > >> > org.cipres.treebase.domain.taxon.TaxonLabelSet.<init>(TaxonLabelSet.java:18) > >> ... 54 more > >> > >> > >> > >> > >> > > > > > ------------------------------------------------------------------------------ > > This SF.Net email is sponsored by the Verizon Developer Community > > Take advantage of Verizon's best-in-class app development support > > A streamlined, 14 day to market process makes app distribution fast and > easy > > Join now and get one step closer to millions of Verizon customers > > http://p.sf.net/sfu/verizon-dev2dev > > _______________________________________________ > > Treebase-devel mailing list > > Tre...@li... > > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > -- > > =========================================================== > > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > > =========================================================== > > > > > > > > > ------------------------------------------------------------------------------ > > This SF.Net email is sponsored by the Verizon Developer Community > > Take advantage of Verizon's best-in-class app development support > > A streamlined, 14 day to market process makes app distribution fast and > easy > > Join now and get one step closer to millions of Verizon customers > > http://p.sf.net/sfu/verizon-dev2dev > > _______________________________________________ > > 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: Rutger V. <rut...@gm...> - 2009-12-16 10:07:59
|
I agree that it's useful to have a local web application inside a local tomcat, and it shouldn't be too hard to get that up and running beyond the point where you are now. I am aware of the mesquite.lib.* issues and have just sent out an email discussing this on the "Mesquite troubles" thread. On Wed, Dec 16, 2009 at 4:23 AM, Hilmar Lapp <hl...@ne...> wrote: > Youjun - I don't know whether by TreeBASE installation you mean the database > or the web-application or both. I think it's pretty critical that every > developer can bring up a local version of the web-application. They may all > be accessing the same database, but if everyone is updating and redeploying > on the same application server for every change or debugging run then chaos > of the unproductive kind will ensue quickly. > -hilmar > On Dec 15, 2009, at 11:17 PM, youjun guo wrote: > > Vladimir, > > Why do you want to deploy a new TreeBASE installation? If you just want to > add a java encrypt implementation like MD5 to TreeBASE code, I my be able to > help with it. Then you can focus on some other task. > > Youjun > > On Tue, Dec 15, 2009 at 5:50 PM, Vladimir Gapeyev <vga...@ne...> > wrote: >> >> On Dec 15, 2009, at 4:41 PM, youjun guo wrote: >> >>> Vladimir, >>> >>> jdbc.properties should be add to main/resource of treebase-core before >>> bilud, and it will be built into treebase-core jar file. >>> >> >> Thanks, this has moved me forward. The deployment still fails, apparently >> due to mesquite again. See the excerpt from logs/catalina.out below. >> >> I do see numerous Eclipse complaints about failing 'import >> mesquite.lib.*'., which I did not see earlier in the day! I did update from >> SVN, as well as all Maven-related update commands I could see in the UI. >> >> --Vladimir >> >> >> >> [main] ERROR org.springframework.web.context.ContextLoader - Context >> initialization failed >> org.springframework.beans.factory.BeanCreationException: Error creating >> bean with name 'sessionFactory' defined in URL >> [jar:file:/Users/vgapeyev/Work/TreeBase/devel/applications/apache-tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar!/applicationContext-dao.xml]: >> Invocation of init method failed; nested exception is >> org.hibernate.InstantiationException: could not instantiate test >> objectorg.cipres.treebase.domain.taxon.TaxonLabelSet >> Caused by: >> org.hibernate.InstantiationException: could not instantiate test >> objectorg.cipres.treebase.domain.taxon.TaxonLabelSet >> at >> org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:25) >> at >> org.hibernate.engine.UnsavedValueFactory.getUnsavedIdentifierValue(UnsavedValueFactory.java:44) >> at >> org.hibernate.tuple.PropertyFactory.buildIdentifierProperty(PropertyFactory.java:44) >> at >> org.hibernate.tuple.entity.EntityMetamodel.<init>(EntityMetamodel.java:124) >> at >> org.hibernate.persister.entity.AbstractEntityPersister.<init>(AbstractEntityPersister.java:434) >> at >> org.hibernate.persister.entity.SingleTableEntityPersister.<init>(SingleTableEntityPersister.java:109) >> at >> org.hibernate.persister.PersisterFactory.createClassPersister(PersisterFactory.java:55) >> at >> org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:226) >> at >> org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1300) >> at >> org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:859) >> at >> org.springframework.orm.hibernate3.LocalSessionFactoryBean.newSessionFactory(LocalSessionFactoryBean.java:805) >> at >> org.springframework.orm.hibernate3.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:745) >> at >> org.springframework.orm.hibernate3.AbstractSessionFactoryBean.afterPropertiesSet(AbstractSessionFactoryBean.java:134) >> at >> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1198) >> at >> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1167) >> at >> org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:427) >> at >> org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:249) >> at >> org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:155) >> at >> org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:246) >> at >> org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160) >> at >> org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:285) >> at >> org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352) >> at >> org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:245) >> at >> org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:188) >> at >> org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:49) >> at >> org.cipres.treebase.web.listeners.StartupListener.contextInitialized(StartupListener.java:45) >> at >> org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3795) >> at >> org.apache.catalina.core.StandardContext.start(StandardContext.java:4252) >> at >> org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) >> at >> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) >> at >> org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) >> at >> org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831) >> at >> org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720) >> at >> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) >> at >> org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150) >> at >> org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) >> at >> org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) >> at >> org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) >> at >> org.apache.catalina.core.StandardHost.start(StandardHost.java:736) >> at >> org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) >> at >> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443) >> at >> org.apache.catalina.core.StandardService.start(StandardService.java:448) >> at >> org.apache.catalina.core.StandardServer.start(StandardServer.java:700) >> at org.apache.catalina.startup.Catalina.start(Catalina.java:552) >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> at >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> at java.lang.reflect.Method.invoke(Method.java:592) >> at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) >> at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) >> Caused by: java.lang.reflect.InvocationTargetException >> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >> Method) >> at >> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) >> at >> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) >> at java.lang.reflect.Constructor.newInstance(Constructor.java:501) >> at >> org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:22) >> ... 49 more >> Caused by: java.lang.Error: Unresolved compilation problems: >> The import mesquite.lib cannot be resolved >> StringUtil cannot be resolved >> StringUtil cannot be resolved >> StringUtil cannot be resolved >> StringUtil cannot be resolved >> >> at >> org.cipres.treebase.domain.taxon.TaxonLabelSet.<init>(TaxonLabelSet.java:18) >> ... 54 more >> >> >> >> >> > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > 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: Rutger V. <rut...@gm...> - 2009-12-16 10:02:34
|
Yes, you are both right: the mesquite jar is "needed", but unless you clean up your work environment (local repo) it will stick around and so you won't notice. Unfortunately, leaving it in won't help us because the issue is that the jar only works at compile time in that you can build against it, but at runtime mesquite won't work inside a jar (because of its own extension loading and bootstrapping implementation). What I'm doing instead is now committing the unpacked class folder for mesquite into /treebase-core/lib, and setting my eclipse .project to use that, which should amount to the same thing as having the jar file in your classpath. >From this point, we have to figure out how to correctly deploy this class folder into our web application. I've tried placing it in $CATALINA_HOME/shared/classes but it's not quite happy with that (same error as before). Next I'll try and see what happens if I place it directly inside the folder structure that is created when tomcat unpacks the treebase-web.war. Not an ideal solution of course, but at this point I just want to narrow down the variables. Rutger On Tue, Dec 15, 2009 at 10:57 PM, youjun guo <you...@ya...> wrote: > Rutger, > > I Just noticed the mesquite jar, which was commented by you in the pom.xml > of treebase-core, is actually needed for the project. Sometimes you can get > the system compiled without it is because it already got downloaded to the > classpath, > > But for a newly check out project, it will not compile without it. > > Youjun > > On Tue, Dec 15, 2009 at 11:34 AM, Rutger Vos <rut...@gm...> wrote: >> >> Hi all, >> >> I'm still having trouble getting mesquite to play nice, so this email >> is a cry for help! >> >> I'm hoping that Vladimir and/or Youjun can give this some thought as >> well, because maybe I'm just overlooking something obvious. What >> continues to happen is that mesquite can't figure out where it is >> located when I run it inside tomcat. It then tries to ask the user >> where the mesquite manual is located (so that it can compute the >> correct path relative to the manual file), but because in headless >> mode we default to "OK" on all user queries everything breaks down >> from then on. >> >> Here's what I've done recently: >> >> * I added anything that seems pertinent w.r.t. mesquite <=> treebase >> interaction to the wiki page: >> >> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=HeadlessMesquite >> >> * I committed the treebase class files to /treebase-core/lib >> >> * I removed all reference to mesquite from the pom.xml files >> (apologies for adding them in the first place, I was hoping we could >> integrate it in the maven system) >> >> * I emailed Jin Ruan, Peter Midford, Mark-Jason Dominus and Wayne >> Maddison. >> >> Is Peter at nescent right now? Could someone knock on his door and >> plead for his help? He knows a lot about mesquite! >> >> Thanks, >> >> 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 >> >> >> ------------------------------------------------------------------------------ >> Return on Information: >> Google Enterprise Search pays you back >> Get the facts. >> http://p.sf.net/sfu/google-dev2dev >> _______________________________________________ >> 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: Rutger V. <rut...@gm...> - 2009-12-16 09:54:12
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To be honest, I never even worried about checking or unchecking the "resolve workspace artifacts" option, so if this solution works for you I'm not in the least disturbed. On Tue, Dec 15, 2009 at 7:18 PM, Vladimir Gapeyev <vla...@du...> wrote: > Ok, I managed to build treebase-web.war > This required *unchecking* the 'Resolve Workspace artifacts' option in a > Maven build configuration. > Unless this resolution disturbs anyone, I suggest to close the current > thread. I'll post further trouble under new titles. > Thanks for all the help so far! > --Vladimir > > > On Dec 15, 2009, at 12:40 PM, Vladimir Gapeyev wrote: > > On Dec 14, 2009, at 8:16 PM, youjun guo wrote: > > I checked the newest version of TreeBASE code, the mesquite is not among our > dependencies anymore, it was commented, and Maven package running well. > > Check out the newest version and run, you may want to keep mesquite > commented. > > I have started all over in a new Eclipse workspace, with a new Maven project > built from SVN. The new failure log is below. > I have also tried putting treebase-core on the Java Build Path for > treebase-web, with no change to the outcome. > The log suggests "For more information, run with the -e flag". Is this a > Maven flag? How can I specify it in Eclipse? > --Vladimir > > > [INFO] Scanning for projects... > [INFO] Reactor build order: > [INFO] Treebase > [INFO] treebase-core > [INFO] treebase-web > [INFO] > ------------------------------------------------------------------------ > [INFO] Building Treebase > [INFO] > [INFO] Id: org.cipres.treebase:treebase:pom:1.0-SNAPSHOT > [INFO] task-segment: [package] > [INFO] > ------------------------------------------------------------------------ > [INFO] [site:attach-descriptor] > [INFO] > ------------------------------------------------------------------------ > [INFO] Building treebase-core > [INFO] > [INFO] Id: org.cipres.treebase:treebase-core:jar:1.0-SNAPSHOT > [INFO] task-segment: [package] > [INFO] > ------------------------------------------------------------------------ > [INFO] [resources:resources] > [INFO] Using default encoding to copy filtered resources. > [INFO] [compiler:compile] > [INFO] Nothing to compile - all classes are up to date > [INFO] [resources:testResources] > [INFO] Using default encoding to copy filtered resources. > [INFO] [compiler:testCompile] > [INFO] Not compiling test sources > [INFO] [surefire:test] > [INFO] Tests are skipped. > [INFO] [jar:jar] > [INFO] > ------------------------------------------------------------------------ > [INFO] Building treebase-web > [INFO] > [INFO] Id: org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT > [INFO] task-segment: [package] > [INFO] > ------------------------------------------------------------------------ > [INFO] [resources:resources] > [INFO] Using default encoding to copy filtered resources. > [INFO] [compiler:compile] > [INFO] Nothing to compile - all classes are up to date > [INFO] [resources:testResources] > [INFO] Using default encoding to copy filtered resources. > [INFO] [compiler:testCompile] > [INFO] Not compiling test sources > [INFO] [surefire:test] > [INFO] Tests are skipped. > [INFO] [war:war] > [INFO] Packaging webapp > [INFO] Assembling webapp[treebase-web] in > [/Users/vgapeyev/Work/TreeBase/EclipseMaven2/maven.1260896355245/trunk/treebase-web/target/treebase-web] > [INFO] Processing war project > [INFO] > [INFO] > [INFO] > ------------------------------------------------------------------------ > [INFO] Reactor Summary: > [INFO] > ------------------------------------------------------------------------ > [INFO] Treebase .............................................. SUCCESS > [0.830s] > [INFO] treebase-core ......................................... SUCCESS > [2.405s] > [INFO] treebase-web .......................................... FAILED > [2.600s] > [INFO] > ------------------------------------------------------------------------ > [ERROR] > The following mojo encountered an error while executing: > Group-Id: org.apache.maven.plugins > Artifact-Id: maven-war-plugin > Version: 2.1-alpha-1 > Mojo: war > brought in via: packaging: war > While building project: > Group-Id: org.cipres.treebase > Artifact-Id: treebase-web > Version: 1.0-SNAPSHOT > From file: > /Users/vgapeyev/Work/TreeBase/EclipseMaven2/maven.1260896355245/trunk/treebase-web/pom.xml > Reason: Failed to copy file for artifact[active project artifact: > artifact = org.cipres.treebase:treebase-core:jar:1.0-SNAPSHOT:compile; > project: MavenProject: org.cipres.treebase:treebase-core:1.0-SNAPSHOT @ > /Users/vgapeyev/Work/TreeBase/EclipseMaven2/maven.1260896355245/trunk/treebase-core/pom.xml] > > > [INFO] > ------------------------------------------------------------------------ > [INFO] For more information, run with the -e flag > [INFO] > ------------------------------------------------------------------------ > [INFO] BUILD FAILED > [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: 6 seconds > [INFO] Finished at: Tue Dec 15 12:26:47 EST 2009 > [INFO] Final Memory: 4M/27M > [INFO] > ------------------------------------------------------------------------ > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > 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...> - 2009-12-16 04:23:32
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Youjun - I don't know whether by TreeBASE installation you mean the database or the web-application or both. I think it's pretty critical that every developer can bring up a local version of the web- application. They may all be accessing the same database, but if everyone is updating and redeploying on the same application server for every change or debugging run then chaos of the unproductive kind will ensue quickly. -hilmar On Dec 15, 2009, at 11:17 PM, youjun guo wrote: > Vladimir, > > Why do you want to deploy a new TreeBASE installation? If you just > want to add a java encrypt implementation like MD5 to TreeBASE code, > I my be able to help with it. Then you can focus on some other task. > > Youjun > > On Tue, Dec 15, 2009 at 5:50 PM, Vladimir Gapeyev <vga...@ne... > > wrote: > > On Dec 15, 2009, at 4:41 PM, youjun guo wrote: > > Vladimir, > > jdbc.properties should be add to main/resource of treebase-core > before bilud, and it will be built into treebase-core jar file. > > > Thanks, this has moved me forward. The deployment still fails, > apparently due to mesquite again. See the excerpt from logs/ > catalina.out below. > > I do see numerous Eclipse complaints about failing 'import > mesquite.lib.*'., which I did not see earlier in the day! I did > update from SVN, as well as all Maven-related update commands I > could see in the UI. > > --Vladimir > > > > [main] ERROR org.springframework.web.context.ContextLoader - Context > initialization failed > org.springframework.beans.factory.BeanCreationException: Error > creating bean with name 'sessionFactory' defined in URL [jar:file:/ > Users/vgapeyev/Work/TreeBase/devel/applications/apache-tomcat-5.5.28/ > webapps/treebase-web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar!/ > applicationContext-dao.xml]: Invocation of init method failed; > nested exception is org.hibernate.InstantiationException: could not > instantiate test objectorg.cipres.treebase.domain.taxon.TaxonLabelSet > Caused by: > org.hibernate.InstantiationException: could not instantiate test > objectorg.cipres.treebase.domain.taxon.TaxonLabelSet > at > org > .hibernate > .engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:25) > at > org > .hibernate > .engine > .UnsavedValueFactory > .getUnsavedIdentifierValue(UnsavedValueFactory.java:44) > at > org > .hibernate > .tuple.PropertyFactory.buildIdentifierProperty(PropertyFactory.java: > 44) > at > org > .hibernate.tuple.entity.EntityMetamodel.<init>(EntityMetamodel.java: > 124) > at > org > .hibernate > .persister > .entity.AbstractEntityPersister.<init>(AbstractEntityPersister.java: > 434) > at > org > .hibernate > .persister > .entity > .SingleTableEntityPersister.<init>(SingleTableEntityPersister.java: > 109) > at > org > .hibernate > .persister > .PersisterFactory.createClassPersister(PersisterFactory.java:55) > at > org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java: > 226) > at > org > .hibernate.cfg.Configuration.buildSessionFactory(Configuration.java: > 1300) > at > org > .hibernate > .cfg > .AnnotationConfiguration > .buildSessionFactory(AnnotationConfiguration.java:859) > at > org > .springframework > .orm > .hibernate3 > .LocalSessionFactoryBean > .newSessionFactory(LocalSessionFactoryBean.java:805) > at > org > .springframework > .orm > .hibernate3 > .LocalSessionFactoryBean > .buildSessionFactory(LocalSessionFactoryBean.java:745) > at > org > .springframework > .orm > .hibernate3 > .AbstractSessionFactoryBean > .afterPropertiesSet(AbstractSessionFactoryBean.java:134) > at > org > .springframework > .beans > .factory > .support > .AbstractAutowireCapableBeanFactory > .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1198) > at > org > .springframework > .beans > .factory > .support > .AbstractAutowireCapableBeanFactory > .initializeBean(AbstractAutowireCapableBeanFactory.java:1167) > at > org > .springframework > .beans > .factory > .support > .AbstractAutowireCapableBeanFactory > .createBean(AbstractAutowireCapableBeanFactory.java:427) > at > org.springframework.beans.factory.support.AbstractBeanFactory > $1.getObject(AbstractBeanFactory.java:249) > at > org > .springframework > .beans > .factory > .support > .DefaultSingletonBeanRegistry > .getSingleton(DefaultSingletonBeanRegistry.java:155) > at > org > .springframework > .beans > .factory > .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:246) > at > org > .springframework > .beans > .factory > .support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160) > at > org > .springframework > .beans > .factory > .support > .DefaultListableBeanFactory > .preInstantiateSingletons(DefaultListableBeanFactory.java:285) > at > org > .springframework > .context > .support > .AbstractApplicationContext.refresh(AbstractApplicationContext.java: > 352) > at org.springframework.web.context.ContextLoader.createWebApplicationContext > (ContextLoader.java:245) > at org.springframework.web.context.ContextLoader.initWebApplicationContext > (ContextLoader.java:188) > at org.springframework.web.context.ContextLoaderListener.contextInitialized > (ContextLoaderListener.java:49) > at org.cipres.treebase.web.listeners.StartupListener.contextInitialized > (StartupListener.java:45) > at > org > .apache > .catalina.core.StandardContext.listenerStart(StandardContext.java: > 3795) > at > org.apache.catalina.core.StandardContext.start(StandardContext.java: > 4252) > at > org > .apache > .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) > at > org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: > 740) > at > org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) > at > org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831) > at > org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720) > at > org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) > at > org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150) > at > org > .apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: > 311) > at > org > .apache > .catalina > .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) > at > org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) > at > org.apache.catalina.core.StandardHost.start(StandardHost.java:736) > at > org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) > at > org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443) > at > org.apache.catalina.core.StandardService.start(StandardService.java: > 448) > at > org.apache.catalina.core.StandardServer.start(StandardServer.java:700) > at org.apache.catalina.startup.Catalina.start(Catalina.java: > 552) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun > .reflect > .NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun > .reflect > .DelegatingMethodAccessorImpl > .invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:592) > at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java: > 295) > at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java: > 433) > Caused by: java.lang.reflect.InvocationTargetException > at > sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) > at > sun > .reflect > .NativeConstructorAccessorImpl > .newInstance(NativeConstructorAccessorImpl.java:39) > at > sun > .reflect > .DelegatingConstructorAccessorImpl > .newInstance(DelegatingConstructorAccessorImpl.java:27) > at java.lang.reflect.Constructor.newInstance(Constructor.java: > 501) > at > org > .hibernate > .engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:22) > ... 49 more > Caused by: java.lang.Error: Unresolved compilation problems: > The import mesquite.lib cannot be resolved > StringUtil cannot be resolved > StringUtil cannot be resolved > StringUtil cannot be resolved > StringUtil cannot be resolved > > at > org > .cipres > .treebase.domain.taxon.TaxonLabelSet.<init>(TaxonLabelSet.java:18) > ... 54 more > > > > > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > 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: youjun g. <you...@ya...> - 2009-12-16 04:17:58
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Vladimir, Why do you want to deploy a new TreeBASE installation? If you just want to add a java encrypt implementation like MD5 to TreeBASE code, I my be able to help with it. Then you can focus on some other task. Youjun On Tue, Dec 15, 2009 at 5:50 PM, Vladimir Gapeyev <vga...@ne...>wrote: > > On Dec 15, 2009, at 4:41 PM, youjun guo wrote: > > Vladimir, >> >> jdbc.properties should be add to main/resource of treebase-core before >> bilud, and it will be built into treebase-core jar file. >> >> > Thanks, this has moved me forward. The deployment still fails, apparently > due to mesquite again. See the excerpt from logs/catalina.out below. > > I do see numerous Eclipse complaints about failing 'import > mesquite.lib.*'., which I did not see earlier in the day! I did update from > SVN, as well as all Maven-related update commands I could see in the UI. > > --Vladimir > > > > [main] ERROR org.springframework.web.context.ContextLoader - Context > initialization failed > org.springframework.beans.factory.BeanCreationException: Error creating > bean with name 'sessionFactory' defined in URL > [jar:file:/Users/vgapeyev/Work/TreeBase/devel/applications/apache-tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar!/applicationContext-dao.xml]: > Invocation of init method failed; nested exception is > org.hibernate.InstantiationException: could not instantiate test > objectorg.cipres.treebase.domain.taxon.TaxonLabelSet > Caused by: > org.hibernate.InstantiationException: could not instantiate test > objectorg.cipres.treebase.domain.taxon.TaxonLabelSet > at > org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:25) > at > org.hibernate.engine.UnsavedValueFactory.getUnsavedIdentifierValue(UnsavedValueFactory.java:44) > at > org.hibernate.tuple.PropertyFactory.buildIdentifierProperty(PropertyFactory.java:44) > at > org.hibernate.tuple.entity.EntityMetamodel.<init>(EntityMetamodel.java:124) > at > org.hibernate.persister.entity.AbstractEntityPersister.<init>(AbstractEntityPersister.java:434) > at > org.hibernate.persister.entity.SingleTableEntityPersister.<init>(SingleTableEntityPersister.java:109) > at > org.hibernate.persister.PersisterFactory.createClassPersister(PersisterFactory.java:55) > at > org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:226) > at > org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1300) > at > org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:859) > at > org.springframework.orm.hibernate3.LocalSessionFactoryBean.newSessionFactory(LocalSessionFactoryBean.java:805) > at > org.springframework.orm.hibernate3.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:745) > at > org.springframework.orm.hibernate3.AbstractSessionFactoryBean.afterPropertiesSet(AbstractSessionFactoryBean.java:134) > at > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1198) > at > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1167) > at > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:427) > at > org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:249) > at > org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:155) > at > org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:246) > at > org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160) > at > org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:285) > at > org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352) > at > org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:245) > at > org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:188) > at > org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:49) > at > org.cipres.treebase.web.listeners.StartupListener.contextInitialized(StartupListener.java:45) > at > org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3795) > at > org.apache.catalina.core.StandardContext.start(StandardContext.java:4252) > at > org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) > at > org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) > at > org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) > at > org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831) > at > org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720) > at > org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) > at > org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150) > at > org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) > at > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) > at > org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) > at > org.apache.catalina.core.StandardHost.start(StandardHost.java:736) > at > org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) > at > org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443) > at > org.apache.catalina.core.StandardService.start(StandardService.java:448) > at > org.apache.catalina.core.StandardServer.start(StandardServer.java:700) > at org.apache.catalina.startup.Catalina.start(Catalina.java:552) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:592) > at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) > at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) > Caused by: java.lang.reflect.InvocationTargetException > at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native > Method) > at > sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) > at > sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > at java.lang.reflect.Constructor.newInstance(Constructor.java:501) > at > org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:22) > ... 49 more > Caused by: java.lang.Error: Unresolved compilation problems: > The import mesquite.lib cannot be resolved > StringUtil cannot be resolved > StringUtil cannot be resolved > StringUtil cannot be resolved > StringUtil cannot be resolved > > at > org.cipres.treebase.domain.taxon.TaxonLabelSet.<init>(TaxonLabelSet.java:18) > ... 54 more > > > > > > |
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From: youjun g. <you...@ya...> - 2009-12-15 23:23:46
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Vladimir, Do you know why I cannot access the treebase-web @ treebase-dev.nescent.org:6666? I saw the home page flash and gone. Youjun |
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From: youjun g. <you...@ya...> - 2009-12-15 23:10:13
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uncomment the mesquite dependency in treebase-core/pom.xml see if it works. Youjun On Tue, Dec 15, 2009 at 5:50 PM, Vladimir Gapeyev <vga...@ne...>wrote: > > On Dec 15, 2009, at 4:41 PM, youjun guo wrote: > > Vladimir, >> >> jdbc.properties should be add to main/resource of treebase-core before >> bilud, and it will be built into treebase-core jar file. >> >> > Thanks, this has moved me forward. The deployment still fails, apparently > due to mesquite again. See the excerpt from logs/catalina.out below. > > I do see numerous Eclipse complaints about failing 'import > mesquite.lib.*'., which I did not see earlier in the day! I did update from > SVN, as well as all Maven-related update commands I could see in the UI. > > --Vladimir > > > > [main] ERROR org.springframework.web.context.ContextLoader - Context > initialization failed > org.springframework.beans.factory.BeanCreationException: Error creating > bean with name 'sessionFactory' defined in URL > [jar:file:/Users/vgapeyev/Work/TreeBase/devel/applications/apache-tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar!/applicationContext-dao.xml]: > Invocation of init method failed; nested exception is > org.hibernate.InstantiationException: could not instantiate test > objectorg.cipres.treebase.domain.taxon.TaxonLabelSet > Caused by: > org.hibernate.InstantiationException: could not instantiate test > objectorg.cipres.treebase.domain.taxon.TaxonLabelSet > at > org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:25) > at > org.hibernate.engine.UnsavedValueFactory.getUnsavedIdentifierValue(UnsavedValueFactory.java:44) > at > org.hibernate.tuple.PropertyFactory.buildIdentifierProperty(PropertyFactory.java:44) > at > org.hibernate.tuple.entity.EntityMetamodel.<init>(EntityMetamodel.java:124) > at > org.hibernate.persister.entity.AbstractEntityPersister.<init>(AbstractEntityPersister.java:434) > at > org.hibernate.persister.entity.SingleTableEntityPersister.<init>(SingleTableEntityPersister.java:109) > at > org.hibernate.persister.PersisterFactory.createClassPersister(PersisterFactory.java:55) > at > org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java:226) > at > org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1300) > at > org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:859) > at > org.springframework.orm.hibernate3.LocalSessionFactoryBean.newSessionFactory(LocalSessionFactoryBean.java:805) > at > org.springframework.orm.hibernate3.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:745) > at > org.springframework.orm.hibernate3.AbstractSessionFactoryBean.afterPropertiesSet(AbstractSessionFactoryBean.java:134) > at > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1198) > at > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1167) > at > org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:427) > at > org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:249) > at > org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:155) > at > org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:246) > at > org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160) > at > org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:285) > at > org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352) > at > org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:245) > at > org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:188) > at > org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:49) > at > org.cipres.treebase.web.listeners.StartupListener.contextInitialized(StartupListener.java:45) > at > org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3795) > at > org.apache.catalina.core.StandardContext.start(StandardContext.java:4252) > at > org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) > at > org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) > at > org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) > at > org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:831) > at > org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720) > at > org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) > at > org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150) > at > org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) > at > org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) > at > org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) > at > org.apache.catalina.core.StandardHost.start(StandardHost.java:736) > at > org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) > at > org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443) > at > org.apache.catalina.core.StandardService.start(StandardService.java:448) > at > org.apache.catalina.core.StandardServer.start(StandardServer.java:700) > at org.apache.catalina.startup.Catalina.start(Catalina.java:552) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) > at java.lang.reflect.Method.invoke(Method.java:592) > at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) > at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) > Caused by: java.lang.reflect.InvocationTargetException > at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native > Method) > at > sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) > at > sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) > at java.lang.reflect.Constructor.newInstance(Constructor.java:501) > at > org.hibernate.engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:22) > ... 49 more > Caused by: java.lang.Error: Unresolved compilation problems: > The import mesquite.lib cannot be resolved > StringUtil cannot be resolved > StringUtil cannot be resolved > StringUtil cannot be resolved > StringUtil cannot be resolved > > at > org.cipres.treebase.domain.taxon.TaxonLabelSet.<init>(TaxonLabelSet.java:18) > ... 54 more > > > > > > |
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From: youjun g. <you...@ya...> - 2009-12-15 22:57:28
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Rutger, I Just noticed the mesquite jar, which was commented by you in the pom.xml of treebase-core, is actually needed for the project. Sometimes you can get the system compiled without it is because it already got downloaded to the classpath, But for a newly check out project, it will not compile without it. Youjun On Tue, Dec 15, 2009 at 11:34 AM, Rutger Vos <rut...@gm...> wrote: > Hi all, > > I'm still having trouble getting mesquite to play nice, so this email > is a cry for help! > > I'm hoping that Vladimir and/or Youjun can give this some thought as > well, because maybe I'm just overlooking something obvious. What > continues to happen is that mesquite can't figure out where it is > located when I run it inside tomcat. It then tries to ask the user > where the mesquite manual is located (so that it can compute the > correct path relative to the manual file), but because in headless > mode we default to "OK" on all user queries everything breaks down > from then on. > > Here's what I've done recently: > > * I added anything that seems pertinent w.r.t. mesquite <=> treebase > interaction to the wiki page: > > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=HeadlessMesquite > > * I committed the treebase class files to /treebase-core/lib > > * I removed all reference to mesquite from the pom.xml files > (apologies for adding them in the first place, I was hoping we could > integrate it in the maven system) > > * I emailed Jin Ruan, Peter Midford, Mark-Jason Dominus and Wayne Maddison. > > Is Peter at nescent right now? Could someone knock on his door and > plead for his help? He knows a lot about mesquite! > > Thanks, > > 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 > > > ------------------------------------------------------------------------------ > Return on Information: > Google Enterprise Search pays you back > Get the facts. > http://p.sf.net/sfu/google-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > |
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From: Vladimir G. <vga...@ne...> - 2009-12-15 22:50:26
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On Dec 15, 2009, at 4:41 PM, youjun guo wrote: > Vladimir, > > jdbc.properties should be add to main/resource of treebase-core > before bilud, and it will be built into treebase-core jar file. > Thanks, this has moved me forward. The deployment still fails, apparently due to mesquite again. See the excerpt from logs/ catalina.out below. I do see numerous Eclipse complaints about failing 'import mesquite.lib.*'., which I did not see earlier in the day! I did update from SVN, as well as all Maven-related update commands I could see in the UI. --Vladimir [main] ERROR org.springframework.web.context.ContextLoader - Context initialization failed org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in URL [jar:file:/ Users/vgapeyev/Work/TreeBase/devel/applications/apache-tomcat-5.5.28/ webapps/treebase-web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar!/ applicationContext-dao.xml]: Invocation of init method failed; nested exception is org.hibernate.InstantiationException: could not instantiate test objectorg.cipres.treebase.domain.taxon.TaxonLabelSet Caused by: org.hibernate.InstantiationException: could not instantiate test objectorg.cipres.treebase.domain.taxon.TaxonLabelSet at org .hibernate .engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:25) at org .hibernate .engine .UnsavedValueFactory .getUnsavedIdentifierValue(UnsavedValueFactory.java:44) at org .hibernate .tuple.PropertyFactory.buildIdentifierProperty(PropertyFactory.java:44) at org.hibernate.tuple.entity.EntityMetamodel.<init>(EntityMetamodel.java: 124) at org .hibernate .persister .entity.AbstractEntityPersister.<init>(AbstractEntityPersister.java:434) at org .hibernate .persister .entity .SingleTableEntityPersister.<init>(SingleTableEntityPersister.java:109) at org .hibernate .persister.PersisterFactory.createClassPersister(PersisterFactory.java: 55) at org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java: 226) at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java: 1300) at org .hibernate .cfg .AnnotationConfiguration .buildSessionFactory(AnnotationConfiguration.java:859) at org .springframework .orm .hibernate3 .LocalSessionFactoryBean .newSessionFactory(LocalSessionFactoryBean.java:805) at org .springframework .orm .hibernate3 .LocalSessionFactoryBean .buildSessionFactory(LocalSessionFactoryBean.java:745) at org .springframework .orm .hibernate3 .AbstractSessionFactoryBean .afterPropertiesSet(AbstractSessionFactoryBean.java:134) at org .springframework .beans .factory .support .AbstractAutowireCapableBeanFactory .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1198) at org .springframework .beans .factory .support .AbstractAutowireCapableBeanFactory .initializeBean(AbstractAutowireCapableBeanFactory.java:1167) at org .springframework .beans .factory .support .AbstractAutowireCapableBeanFactory .createBean(AbstractAutowireCapableBeanFactory.java:427) at org.springframework.beans.factory.support.AbstractBeanFactory $1.getObject(AbstractBeanFactory.java:249) at org .springframework .beans .factory .support .DefaultSingletonBeanRegistry .getSingleton(DefaultSingletonBeanRegistry.java:155) at org .springframework .beans .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 246) at org .springframework .beans .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java: 160) at org .springframework .beans .factory .support .DefaultListableBeanFactory .preInstantiateSingletons(DefaultListableBeanFactory.java:285) at org .springframework .context .support .AbstractApplicationContext.refresh(AbstractApplicationContext.java:352) at org.springframework.web.context.ContextLoader.createWebApplicationContext (ContextLoader.java:245) at org.springframework.web.context.ContextLoader.initWebApplicationContext (ContextLoader.java:188) at org.springframework.web.context.ContextLoaderListener.contextInitialized (ContextLoaderListener.java:49) at org .cipres .treebase .web.listeners.StartupListener.contextInitialized(StartupListener.java: 45) at org .apache .catalina.core.StandardContext.listenerStart(StandardContext.java:3795) at org.apache.catalina.core.StandardContext.start(StandardContext.java: 4252) at org .apache .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: 740) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java: 544) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java: 831) at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java: 720) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java: 490) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: 311) at org .apache .catalina .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1022) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java: 700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 39) at sun .reflect .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 25) at java.lang.reflect.Method.invoke(Method.java:592) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun .reflect .NativeConstructorAccessorImpl .newInstance(NativeConstructorAccessorImpl.java:39) at sun .reflect .DelegatingConstructorAccessorImpl .newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:501) at org .hibernate .engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:22) ... 49 more Caused by: java.lang.Error: Unresolved compilation problems: The import mesquite.lib cannot be resolved StringUtil cannot be resolved StringUtil cannot be resolved StringUtil cannot be resolved StringUtil cannot be resolved at org .cipres.treebase.domain.taxon.TaxonLabelSet.<init>(TaxonLabelSet.java: 18) ... 54 more |
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From: Vladimir G. <vla...@du...> - 2009-12-15 22:45:13
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On Dec 15, 2009, at 11:34 AM, Rutger Vos wrote: > * I committed the treebase class files to /treebase-core/lib > > * I removed all reference to mesquite from the pom.xml files > (apologies for adding them in the first place, I was hoping we could > integrate it in the maven system) Is this in any way related to what I noticed last hour: Eclipse complaining about unresolved 'import mesquite.lib*' imports in many places in treebase-core? Whether related or not, I need advice how to show Eclipse the place to find these imports. Anyway, something mesquite-related is again at the core of my continuing quest to deploy treebase-war under Tomcat. --Vladimir |
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From: Vladimir G. <vga...@ne...> - 2009-12-15 20:27:28
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I am now trying to deploy treebase-web.war under Tomcat. Question: where should I place jdbc.properties so that Tomcat finds it when it starts treebase-web? I deploy by placing the war into my CATALINA-HOME/webapps, but it does not start correctly -- see below the relevant log fragment from logs/ catalina.out A looking-ahead question: should also install any dependency JARS in CATALINA/common/lib or something like that, or treebase-web.war comes with all dependencies included? --Vladimir [main] ERROR org.springframework.web.context.ContextLoader - Context initialization failed org.springframework.beans.factory.BeanInitializationException: Could not load properties; nested exception is java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist Caused by: java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist at org .springframework .core.io.ClassPathResource.getInputStream(ClassPathResource.java:135) at org .springframework .core .io .support .PropertiesLoaderSupport.loadProperties(PropertiesLoaderSupport.java: 179) at org .springframework .core .io .support .PropertiesLoaderSupport.mergeProperties(PropertiesLoaderSupport.java: 158) at org .springframework .beans .factory .config .PropertyResourceConfigurer .postProcessBeanFactory(PropertyResourceConfigurer.java:68) at org .springframework .context .support .AbstractApplicationContext .invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:467) at org .springframework .context .support .AbstractApplicationContext.refresh(AbstractApplicationContext.java:334) at org.springframework.web.context.ContextLoader.createWebApplicationContext (ContextLoader.java:245) at org.springframework.web.context.ContextLoader.initWebApplicationContext (ContextLoader.java:188) at org.springframework.web.context.ContextLoaderListener.contextInitialized (ContextLoaderListener.java:49) at org .cipres .treebase .web.listeners.StartupListener.contextInitialized(StartupListener.java: 45) at org .apache .catalina.core.StandardContext.listenerStart(StandardContext.java:3795) at org.apache.catalina.core.StandardContext.start(StandardContext.java: 4252) at org .apache .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: 740) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java: 544) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java: 831) at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java: 720) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java: 490) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: 311) at org .apache .catalina .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1022) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java: 700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 39) at sun .reflect .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 25) at java.lang.reflect.Method.invoke(Method.java:592) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) [main] ERROR org.apache.catalina.core.ContainerBase.[Catalina]. [localhost].[/treebase-web] - Exception sending context initialized event to listener instance of class org.cipres.treebase.web.listeners.StartupListener org.springframework.beans.factory.BeanInitializationException: Could not load properties; nested exception is java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist Caused by: java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist at org .springframework .core.io.ClassPathResource.getInputStream(ClassPathResource.java:135) at org .springframework .core .io .support .PropertiesLoaderSupport.loadProperties(PropertiesLoaderSupport.java: 179) at org .springframework .core .io .support .PropertiesLoaderSupport.mergeProperties(PropertiesLoaderSupport.java: 158) at org .springframework .beans .factory .config .PropertyResourceConfigurer .postProcessBeanFactory(PropertyResourceConfigurer.java:68) at org .springframework .context .support .AbstractApplicationContext .invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:467) at org .springframework .context .support .AbstractApplicationContext.refresh(AbstractApplicationContext.java:334) at org.springframework.web.context.ContextLoader.createWebApplicationContext (ContextLoader.java:245) at org.springframework.web.context.ContextLoader.initWebApplicationContext (ContextLoader.java:188) at org.springframework.web.context.ContextLoaderListener.contextInitialized (ContextLoaderListener.java:49) at org .cipres .treebase .web.listeners.StartupListener.contextInitialized(StartupListener.java: 45) at org .apache .catalina.core.StandardContext.listenerStart(StandardContext.java:3795) at org.apache.catalina.core.StandardContext.start(StandardContext.java: 4252) at org .apache .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java: 740) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java: 544) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java: 831) at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java: 720) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java: 490) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java: 311) at org .apache .catalina .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1022) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java: 1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java: 443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java: 700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 39) at sun .reflect .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: 25) at java.lang.reflect.Method.invoke(Method.java:592) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) Dec 15, 2009 2:31:16 PM org.apache.catalina.core.StandardContext start SEVERE: Error listenerStart Dec 15, 2009 2:31:16 PM org.apache.catalina.core.StandardContext start SEVERE: Context [/treebase-web] startup failed due to previous errors |
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From: Vladimir G. <vla...@du...> - 2009-12-15 19:19:04
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Ok, I managed to build treebase-web.war This required *unchecking* the 'Resolve Workspace artifacts' option in a Maven build configuration. Unless this resolution disturbs anyone, I suggest to close the current thread. I'll post further trouble under new titles. Thanks for all the help so far! --Vladimir On Dec 15, 2009, at 12:40 PM, Vladimir Gapeyev wrote: > > On Dec 14, 2009, at 8:16 PM, youjun guo wrote: > >> I checked the newest version of TreeBASE code, the mesquite is not >> among our dependencies anymore, it was commented, and Maven package >> running well. >> >> Check out the newest version and run, you may want to keep mesquite >> commented. > > I have started all over in a new Eclipse workspace, with a new Maven > project built from SVN. The new failure log is below. > I have also tried putting treebase-core on the Java Build Path for > treebase-web, with no change to the outcome. > > The log suggests "For more information, run with the -e flag". Is > this a Maven flag? How can I specify it in Eclipse? > > --Vladimir > > > > [INFO] Scanning for projects... > [INFO] Reactor build order: > [INFO] Treebase > [INFO] treebase-core > [INFO] treebase-web > [INFO] > ------------------------------------------------------------------------ > [INFO] Building Treebase > [INFO] > [INFO] Id: org.cipres.treebase:treebase:pom:1.0-SNAPSHOT > [INFO] task-segment: [package] > [INFO] > ------------------------------------------------------------------------ > [INFO] [site:attach-descriptor] > [INFO] > ------------------------------------------------------------------------ > [INFO] Building treebase-core > [INFO] > [INFO] Id: org.cipres.treebase:treebase-core:jar:1.0-SNAPSHOT > [INFO] task-segment: [package] > [INFO] > ------------------------------------------------------------------------ > [INFO] [resources:resources] > [INFO] Using default encoding to copy filtered resources. > [INFO] [compiler:compile] > [INFO] Nothing to compile - all classes are up to date > [INFO] [resources:testResources] > [INFO] Using default encoding to copy filtered resources. > [INFO] [compiler:testCompile] > [INFO] Not compiling test sources > [INFO] [surefire:test] > [INFO] Tests are skipped. > [INFO] [jar:jar] > [INFO] > ------------------------------------------------------------------------ > [INFO] Building treebase-web > [INFO] > [INFO] Id: org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT > [INFO] task-segment: [package] > [INFO] > ------------------------------------------------------------------------ > [INFO] [resources:resources] > [INFO] Using default encoding to copy filtered resources. > [INFO] [compiler:compile] > [INFO] Nothing to compile - all classes are up to date > [INFO] [resources:testResources] > [INFO] Using default encoding to copy filtered resources. > [INFO] [compiler:testCompile] > [INFO] Not compiling test sources > [INFO] [surefire:test] > [INFO] Tests are skipped. > [INFO] [war:war] > [INFO] Packaging webapp > [INFO] Assembling webapp[treebase-web] in [/Users/vgapeyev/Work/ > TreeBase/EclipseMaven2/maven.1260896355245/trunk/treebase-web/target/ > treebase-web] > [INFO] Processing war project > [INFO] > [INFO] > [INFO] > ------------------------------------------------------------------------ > [INFO] Reactor Summary: > [INFO] > ------------------------------------------------------------------------ > [INFO] Treebase .............................................. > SUCCESS [0.830s] > [INFO] treebase-core ......................................... > SUCCESS [2.405s] > [INFO] treebase-web .......................................... > FAILED [2.600s] > [INFO] > ------------------------------------------------------------------------ > [ERROR] > > The following mojo encountered an error while executing: > Group-Id: org.apache.maven.plugins > Artifact-Id: maven-war-plugin > Version: 2.1-alpha-1 > Mojo: war > brought in via: packaging: war > > While building project: > Group-Id: org.cipres.treebase > Artifact-Id: treebase-web > Version: 1.0-SNAPSHOT > From file: /Users/vgapeyev/Work/TreeBase/EclipseMaven2/maven. > 1260896355245/trunk/treebase-web/pom.xml > Reason: Failed to copy file for artifact[active project artifact: > artifact = org.cipres.treebase:treebase-core:jar:1.0- > SNAPSHOT:compile; > project: MavenProject: org.cipres.treebase:treebase-core:1.0- > SNAPSHOT @ /Users/vgapeyev/Work/TreeBase/EclipseMaven2/maven. > 1260896355245/trunk/treebase-core/pom.xml] > > > > [INFO] > ------------------------------------------------------------------------ > [INFO] For more information, run with the -e flag > [INFO] > ------------------------------------------------------------------------ > [INFO] BUILD FAILED > [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: 6 seconds > [INFO] Finished at: Tue Dec 15 12:26:47 EST 2009 > [INFO] Final Memory: 4M/27M > [INFO] > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Vladimir G. <vga...@ne...> - 2009-12-15 17:41:01
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On Dec 14, 2009, at 8:16 PM, youjun guo wrote: > I checked the newest version of TreeBASE code, the mesquite is not > among our dependencies anymore, it was commented, and Maven package > running well. > > Check out the newest version and run, you may want to keep mesquite > commented. I have started all over in a new Eclipse workspace, with a new Maven project built from SVN. The new failure log is below. I have also tried putting treebase-core on the Java Build Path for treebase-web, with no change to the outcome. The log suggests "For more information, run with the -e flag". Is this a Maven flag? How can I specify it in Eclipse? --Vladimir [INFO] Scanning for projects... [INFO] Reactor build order: [INFO] Treebase [INFO] treebase-core [INFO] treebase-web [INFO] ------------------------------------------------------------------------ [INFO] Building Treebase [INFO] [INFO] Id: org.cipres.treebase:treebase:pom:1.0-SNAPSHOT [INFO] task-segment: [package] [INFO] ------------------------------------------------------------------------ [INFO] [site:attach-descriptor] [INFO] ------------------------------------------------------------------------ [INFO] Building treebase-core [INFO] [INFO] Id: org.cipres.treebase:treebase-core:jar:1.0-SNAPSHOT [INFO] task-segment: [package] [INFO] ------------------------------------------------------------------------ [INFO] [resources:resources] [INFO] Using default encoding to copy filtered resources. [INFO] [compiler:compile] [INFO] Nothing to compile - all classes are up to date [INFO] [resources:testResources] [INFO] Using default encoding to copy filtered resources. [INFO] [compiler:testCompile] [INFO] Not compiling test sources [INFO] [surefire:test] [INFO] Tests are skipped. [INFO] [jar:jar] [INFO] ------------------------------------------------------------------------ [INFO] Building treebase-web [INFO] [INFO] Id: org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT [INFO] task-segment: [package] [INFO] ------------------------------------------------------------------------ [INFO] [resources:resources] [INFO] Using default encoding to copy filtered resources. [INFO] [compiler:compile] [INFO] Nothing to compile - all classes are up to date [INFO] [resources:testResources] [INFO] Using default encoding to copy filtered resources. [INFO] [compiler:testCompile] [INFO] Not compiling test sources [INFO] [surefire:test] [INFO] Tests are skipped. [INFO] [war:war] [INFO] Packaging webapp [INFO] Assembling webapp[treebase-web] in [/Users/vgapeyev/Work/ TreeBase/EclipseMaven2/maven.1260896355245/trunk/treebase-web/target/ treebase-web] [INFO] Processing war project [INFO] [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] ------------------------------------------------------------------------ [INFO] Treebase .............................................. SUCCESS [0.830s] [INFO] treebase-core ......................................... SUCCESS [2.405s] [INFO] treebase-web .......................................... FAILED [2.600s] [INFO] ------------------------------------------------------------------------ [ERROR] The following mojo encountered an error while executing: Group-Id: org.apache.maven.plugins Artifact-Id: maven-war-plugin Version: 2.1-alpha-1 Mojo: war brought in via: packaging: war While building project: Group-Id: org.cipres.treebase Artifact-Id: treebase-web Version: 1.0-SNAPSHOT From file: /Users/vgapeyev/Work/TreeBase/EclipseMaven2/maven. 1260896355245/trunk/treebase-web/pom.xml Reason: Failed to copy file for artifact[active project artifact: artifact = org.cipres.treebase:treebase-core:jar:1.0-SNAPSHOT:compile; project: MavenProject: org.cipres.treebase:treebase-core:1.0-SNAPSHOT @ /Users/vgapeyev/Work/TreeBase/EclipseMaven2/maven.1260896355245/ trunk/treebase-core/pom.xml] [INFO] ------------------------------------------------------------------------ [INFO] For more information, run with the -e flag [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILED [INFO] ------------------------------------------------------------------------ [INFO] Total time: 6 seconds [INFO] Finished at: Tue Dec 15 12:26:47 EST 2009 [INFO] Final Memory: 4M/27M [INFO] ------------------------------------------------------------------------ |
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