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From: Rutger V. <rut...@gm...> - 2009-12-15 16:35:02
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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 |
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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: 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: Rutger V. <rut...@gm...> - 2009-12-16 10:02:34
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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 18:04:22
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Hi all, Wayne's suggestion to pass mesquite's location programmatically works. I just managed to get it to parse a file through the web interface (and so this should also apply to the batch loader, which uses the same NexusServiceMesquite object). I still need to replicate the behaviour on the server, which means creating a bit of a Frankenstein system, unfortunately: * use the mesquite-2.01.tb.jar to compile against * place the class folder structure in treebase-core/lib in a location where tomcat sees it (e.g. in $CATALINA_HOME/shared/classes) * have the mesquite.folder_dir variable in jdbc.properties point to that location ...then the NexusServiceMesquite bean will be passed that location on instantiation, from where it can tell MesquiteModule where it lives. Phew. Rutger On Wed, Dec 16, 2009 at 10:02 AM, Rutger Vos <rut...@gm...> wrote: > 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 > -- 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 18:14:17
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Great!! Sounds like we're making progress wading through the mucky waters :-) -hilmar On Dec 16, 2009, at 1:04 PM, Rutger Vos wrote: > Hi all, > > Wayne's suggestion to pass mesquite's location programmatically works. > I just managed to get it to parse a file through the web interface > (and so this should also apply to the batch loader, which uses the > same NexusServiceMesquite object). I still need to replicate the > behaviour on the server, which means creating a bit of a Frankenstein > system, unfortunately: > > * use the mesquite-2.01.tb.jar to compile against > > * place the class folder structure in treebase-core/lib in a location > where tomcat sees it (e.g. in $CATALINA_HOME/shared/classes) > > * have the mesquite.folder_dir variable in jdbc.properties point to > that location > > ...then the NexusServiceMesquite bean will be passed that location on > instantiation, from where it can tell MesquiteModule where it lives. > > Phew. > > Rutger > > On Wed, Dec 16, 2009 at 10:02 AM, Rutger Vos <rut...@gm...> > wrote: >> 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 >> > > > > -- > 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 > > ------------------------------------------------------------------------------ > 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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