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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: Rutger V. <rut...@gm...> - 2009-12-15 09:52:54
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The mesquite-2.6+SNAPSHOT dependency shouldn't be there. I accidentally introduced it in a pom.xml to try to resolve the mesquite issues, but in actual fact we are using mesquite-2.01tb (an earlier version that was modified for TreeBASE), so the 2.6 dependency shouldn't be there. Having it commented out should address your build issues, as Youjun points out below. On Tue, Dec 15, 2009 at 1:16 AM, youjun guo <you...@ya...> wrote: > Vladimir, > > 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. > > Youjun > > On Mon, Dec 14, 2009 at 6:12 PM, Vladimir Gapeyev <vga...@ne...> > wrote: >> >> On Dec 14, 2009, at 5:13 PM, youjun guo wrote: >> >> The TreeBASE test suite may have some problem. You can skip the test for >> now by check the "skip test" boxes. >> >> I think I did this by: >> On treebase project, Run As > 6 Maven Build ... > in Main tab >> specify: >> Goals: package >> Skip tests - checkmark >> This fails: mesquite is missing as a "transitive dependency" for >> treebase-web (see log below). >> My only guess for solving this was putting treebase-core project on Java >> Build Path for treebase-web. It did not help. >> Recall that I do have mesquite in ~/.m2 >> --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] >> [INFO] >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] Reactor Summary: >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] Treebase .............................................. SUCCESS >> [0.973s] >> [INFO] treebase-core ......................................... SUCCESS >> [2.885s] >> [INFO] treebase-web .......................................... FAILED >> [0.651s] >> [INFO] >> ------------------------------------------------------------------------ >> [ERROR] >> Transitive dependency resolution for scope: compile has failed for your >> project. >> >> >> Error message: Missing: >> ---------- >> 1) mesquite:mesquite:jar:2.6+SNAPSHOT >> Try downloading the file manually from the project website. >> Then, install it using the command: >> mvn install:install-file -DgroupId=mesquite -DartifactId=mesquite >> -Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file >> Alternatively, if you host your own repository you can deploy the file >> there: >> mvn deploy:deploy-file -DgroupId=mesquite -DartifactId=mesquite >> -Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] >> -DrepositoryId=[id] >> Path to dependency: >> 1) org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT >> 2) org.nexml.model:nexml:jar:1.5-SNAPSHOT >> 3) mesquite:mesquite:jar:2.6+SNAPSHOT >> ---------- >> 1 required artifact is missing. >> for artifact: >> org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT >> from the specified remote repositories: >> Maven Snapshots (http://snapshots.maven.codehaus.org/maven2), >> m2.remote.repos (http://treebase.sourceforge.net/maven2/), >> central (http://repo1.maven.org/maven2), >> m2.nexml.repos (http://nexml-dev.nescent.org/.m2/repository/), >> repository.jboss.org (http://repository.jboss.org/maven2), >> maven2 (http://repo1.maven.org/maven2) >> Group-Id: org.cipres.treebase >> Artifact-Id: treebase-web >> Version: 1.0-SNAPSHOT >> From file: >> /Users/vgapeyev/Work/TreeBase/EclipseMaven/treebase/treebase-web/pom.xml >> >> >> >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] For more information, run with the -e flag >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] BUILD FAILED >> [INFO] >> ------------------------------------------------------------------------ >> [INFO] Total time: 4 seconds >> [INFO] Finished at: Mon Dec 14 17:59:49 EST 2009 >> [INFO] Final Memory: 3M/25M >> [INFO] >> ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------------ > 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...> - 2009-12-15 09:47:53
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> I think you did a wonderful job on the wiki page. Based on my understanding, > the purpose of "shell environment" is to run the script "publish", and it > will download, compile, build and deploy the source code. Yes, that is exactly the point. So for example on my machine I use both the "shell environment" configuration to run the scripts as well as the "developer environment" for when I'm coding in eclipse. The two configurations are just two ways to talk to the same code base, the former from the command line, the latter from within eclipse. > The way I work on TreeBASE is just a standard Tomcat deployment with Eclipse > & Maven build up. Do you think it will miss something specific for TreeBASE > project? No, this is fine. Rutger > On Mon, Dec 14, 2009 at 6:52 AM, Rutger Vos <rut...@gm...> wrote: >> >> Hi Youjun, >> >> since you have this fresh in your memory, could you check whether the >> wiki page >> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> is complete and correct? And add/update as needed? >> >> Thanks! >> >> >> On Fri, Dec 11, 2009 at 7:13 PM, youjun guo <you...@ya...> wrote: >> > Vladimir, >> > >> > Unless you are going to do the developing work directly on the >> > treebase-dev >> > server , or you want to remotely deploy from your workstation to the >> > treebase tomcat server, your eclipse set up have nothing to do with the >> > shell envelopment. >> > >> > m2eclipse is a mvn inatall for eclipse. >> > >> > Youjun >> > >> > >> > On Fri, Dec 11, 2009 at 1:26 PM, Vladimir Gapeyev <vga...@ne...> >> > wrote: >> >> >> >> Youjun, >> >> As I understand, you suggest to skip the (mvn install; Eclipse >> >> workspace >> >> at trunk; create Java projects from existing files) part of >> >> instructions >> >> >> >> at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> >> and instead start with an Eclipse workspace in a blank directory. >> >> I'll probably try that if nothing can make the above instructions work. >> >> However, it will be useful if we can make those wiki instructions >> >> work... >> >> --VG >> >> >> >> >> >> >> >> On Dec 11, 2009, at 11:35 AM, youjun guo wrote: >> >> >> >> Vladimir, >> >> >> >> 1st, make sure your eclipse have the maven plugin like m2eclipse and >> >> subversion plugin like subclipse installed. >> >> >> >> 2rd instead of creating a maven project, "import a maven project form >> >> remote reposotory" in other words - treebase sourceforge svn url. >> >> >> >> All the dependencies were defined in pom.xml, maven know how to find >> >> them >> >> online, even if they are missing from you local .m2 directory >> >> >> >> Youjun >> >> >> >> >> >> >> >> On Fri, Dec 11, 2009 at 11:06 AM, Vladimir Gapeyev >> >> <vga...@ne...> >> >> wrote: >> >>> >> >>> Yes, I followed the wiki instructions, including running mvn install - >> >>> Dmaven.test.skip=true in the proper shell environment. This appeared >> >>> to have created the repository in ~vgapeyev/.m2, which Eclipse does >> >>> see through the M2_REPO variable. >> >>> >> >>> Note that only a fraction of the dependencies is missing in Eclipse. >> >>> Is there a chance they are simply missing from the Maven config >> >>> files? That is, can someone check the status of the handful of the >> >>> dependencies I have mentioned? Again, I can supply the full list if >> >>> this turns out to be the right way to go. >> >>> >> >>> I also tried following Youjun's advice, to create Maven rather than >> >>> Java projects in Eclipse. The wizard asks questions (about group and >> >>> artifact IDs, which I, as a Maven novice, do not understand) and >> >>> finally stops with the error "A pom.xml file already exists in the >> >>> destination folder". >> >>> >> >>> --Vladimir >> >>> >> >>> >> >>> On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: >> >>> >> >>> > Yes, you have to do the maven build first (e.g. from the command >> >>> > line) >> >>> > and make sure in eclipse that the M2_REPO variable is configured >> >>> > correctly (i.e. points to your local repository in >> >>> > $HOME/.m2/repository) >> >>> > >> >>> > On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> >> >>> > wrote: >> >>> >> Make sure you import the project as maven project, it will find and >> >>> >> download >> >>> >> those dependencies for you. >> >>> >> >> >>> >> Youjun >> >>> >> >> >>> >> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev >> >>> >> <vga...@ne... >> >>> >> > >> >>> >> wrote: >> >>> >>> >> >>> >>> Going through the installation instructions >> >>> >>> at >> >>> >>> >> >>> >>> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> >>> >>> , >> >>> >>> I got to creation of Eclipse projects treebase-core and treebase- >> >>> >>> web. >> >>> >>> This gave me lots of missing buildpath entries: 11 in treebase- >> >>> >>> core and 39 >> >>> >>> in treebase-web. Please advise on how to proceed! >> >>> >>> Here are a few of the missing entries: >> >>> >>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- >> >>> >>> extensions-1.2.jar >> >>> >>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- >> >>> >>> framework-4.1.3.jar >> >>> >>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar >> >>> >>> >> >>> >>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- >> >>> >>> beanutils-1.7.0.jar >> >>> >>> I can work on putting together the whole list in case it will be >> >>> >>> useful. >> >>> >>> --Vladimir >> >>> >>> >> >>> >>> >> >>> >>> >> >>> >>> ------------------------------------------------------------------------------ >> >>> >>> 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 >> >>> >>> >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> ------------------------------------------------------------------------------ >> >>> >> 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 >> >>> >> >>> >> >>> >> >>> >> >>> ------------------------------------------------------------------------------ >> >>> 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 >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> 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 >> >> >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > 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: Rutger V. <rut...@gm...> - 2009-12-15 09:44:04
|
> I am not quite understand of this: > > # Headless mesquite needs a window server (a virtual one is OK)" This only applies to environments that don't normally have a windowing server (such as X11), i.e. this can only happen on something like a linux server without a display attached. So on your desktop or laptop you can ignore this. I noticed this issue because on the NESCent server, mesquite failed to launch because even in headless mode, mesquite uses awt, and it assumes it needs to spawn java widgets. (This is not to say that the mesquite issues are all fixed now, but it emerged that this was one of the hurdles.) > On Mon, Dec 14, 2009 at 6:52 AM, Rutger Vos <rut...@gm...> wrote: >> >> Hi Youjun, >> >> since you have this fresh in your memory, could you check whether the >> wiki page >> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> is complete and correct? And add/update as needed? >> >> Thanks! >> >> >> On Fri, Dec 11, 2009 at 7:13 PM, youjun guo <you...@ya...> wrote: >> > Vladimir, >> > >> > Unless you are going to do the developing work directly on the >> > treebase-dev >> > server , or you want to remotely deploy from your workstation to the >> > treebase tomcat server, your eclipse set up have nothing to do with the >> > shell envelopment. >> > >> > m2eclipse is a mvn inatall for eclipse. >> > >> > Youjun >> > >> > >> > On Fri, Dec 11, 2009 at 1:26 PM, Vladimir Gapeyev <vga...@ne...> >> > wrote: >> >> >> >> Youjun, >> >> As I understand, you suggest to skip the (mvn install; Eclipse >> >> workspace >> >> at trunk; create Java projects from existing files) part of >> >> instructions >> >> >> >> at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> >> and instead start with an Eclipse workspace in a blank directory. >> >> I'll probably try that if nothing can make the above instructions work. >> >> However, it will be useful if we can make those wiki instructions >> >> work... >> >> --VG >> >> >> >> >> >> >> >> On Dec 11, 2009, at 11:35 AM, youjun guo wrote: >> >> >> >> Vladimir, >> >> >> >> 1st, make sure your eclipse have the maven plugin like m2eclipse and >> >> subversion plugin like subclipse installed. >> >> >> >> 2rd instead of creating a maven project, "import a maven project form >> >> remote reposotory" in other words - treebase sourceforge svn url. >> >> >> >> All the dependencies were defined in pom.xml, maven know how to find >> >> them >> >> online, even if they are missing from you local .m2 directory >> >> >> >> Youjun >> >> >> >> >> >> >> >> On Fri, Dec 11, 2009 at 11:06 AM, Vladimir Gapeyev >> >> <vga...@ne...> >> >> wrote: >> >>> >> >>> Yes, I followed the wiki instructions, including running mvn install - >> >>> Dmaven.test.skip=true in the proper shell environment. This appeared >> >>> to have created the repository in ~vgapeyev/.m2, which Eclipse does >> >>> see through the M2_REPO variable. >> >>> >> >>> Note that only a fraction of the dependencies is missing in Eclipse. >> >>> Is there a chance they are simply missing from the Maven config >> >>> files? That is, can someone check the status of the handful of the >> >>> dependencies I have mentioned? Again, I can supply the full list if >> >>> this turns out to be the right way to go. >> >>> >> >>> I also tried following Youjun's advice, to create Maven rather than >> >>> Java projects in Eclipse. The wizard asks questions (about group and >> >>> artifact IDs, which I, as a Maven novice, do not understand) and >> >>> finally stops with the error "A pom.xml file already exists in the >> >>> destination folder". >> >>> >> >>> --Vladimir >> >>> >> >>> >> >>> On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: >> >>> >> >>> > Yes, you have to do the maven build first (e.g. from the command >> >>> > line) >> >>> > and make sure in eclipse that the M2_REPO variable is configured >> >>> > correctly (i.e. points to your local repository in >> >>> > $HOME/.m2/repository) >> >>> > >> >>> > On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> >> >>> > wrote: >> >>> >> Make sure you import the project as maven project, it will find and >> >>> >> download >> >>> >> those dependencies for you. >> >>> >> >> >>> >> Youjun >> >>> >> >> >>> >> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev >> >>> >> <vga...@ne... >> >>> >> > >> >>> >> wrote: >> >>> >>> >> >>> >>> Going through the installation instructions >> >>> >>> at >> >>> >>> >> >>> >>> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> >>> >>> , >> >>> >>> I got to creation of Eclipse projects treebase-core and treebase- >> >>> >>> web. >> >>> >>> This gave me lots of missing buildpath entries: 11 in treebase- >> >>> >>> core and 39 >> >>> >>> in treebase-web. Please advise on how to proceed! >> >>> >>> Here are a few of the missing entries: >> >>> >>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- >> >>> >>> extensions-1.2.jar >> >>> >>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- >> >>> >>> framework-4.1.3.jar >> >>> >>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar >> >>> >>> >> >>> >>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- >> >>> >>> beanutils-1.7.0.jar >> >>> >>> I can work on putting together the whole list in case it will be >> >>> >>> useful. >> >>> >>> --Vladimir >> >>> >>> >> >>> >>> >> >>> >>> >> >>> >>> ------------------------------------------------------------------------------ >> >>> >>> 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 >> >>> >>> >> >>> >> >> >>> >> >> >>> >> >> >>> >> >> >>> >> ------------------------------------------------------------------------------ >> >>> >> 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 >> >>> >> >>> >> >>> >> >>> >> >>> ------------------------------------------------------------------------------ >> >>> 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 >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> 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 >> >> >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > 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: youjun g. <you...@ya...> - 2009-12-15 01:16:14
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Vladimir, 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. Youjun On Mon, Dec 14, 2009 at 6:12 PM, Vladimir Gapeyev <vga...@ne...>wrote: > > On Dec 14, 2009, at 5:13 PM, youjun guo wrote: > > The TreeBASE test suite may have some problem. You can skip the test for > now by check the "skip test" boxes. > > > I think I did this by: > > On treebase project, Run As > 6 Maven Build ... > in Main tab specify: > Goals: package > Skip tests - checkmark > > This fails: mesquite is missing as a "transitive dependency" for > treebase-web (see log below). > My only guess for solving this was putting treebase-core project on Java > Build Path for treebase-web. It did not help. > Recall that I do have mesquite in ~/.m2 > > --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] > [INFO] > [INFO] > ------------------------------------------------------------------------ > [INFO] Reactor Summary: > [INFO] > ------------------------------------------------------------------------ > [INFO] Treebase .............................................. SUCCESS > [0.973s] > [INFO] treebase-core ......................................... SUCCESS > [2.885s] > [INFO] treebase-web .......................................... FAILED > [0.651s] > [INFO] > ------------------------------------------------------------------------ > [ERROR] > > Transitive dependency resolution for scope: compile has failed for your > project. > > > > Error message: Missing: > ---------- > 1) mesquite:mesquite:jar:2.6+SNAPSHOT > > Try downloading the file manually from the project website. > > Then, install it using the command: > mvn install:install-file -DgroupId=mesquite -DartifactId=mesquite > -Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file > > Alternatively, if you host your own repository you can deploy the file > there: > mvn deploy:deploy-file -DgroupId=mesquite -DartifactId=mesquite > -Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] > -DrepositoryId=[id] > > Path to dependency: > 1) org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT > 2) org.nexml.model:nexml:jar:1.5-SNAPSHOT > 3) mesquite:mesquite:jar:2.6+SNAPSHOT > > ---------- > 1 required artifact is missing. > > for artifact: > org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT > > from the specified remote repositories: > Maven Snapshots (http://snapshots.maven.codehaus.org/maven2), > m2.remote.repos (http://treebase.sourceforge.net/maven2/), > central (http://repo1.maven.org/maven2), > m2.nexml.repos (http://nexml-dev.nescent.org/.m2/repository/), > repository.jboss.org (http://repository.jboss.org/maven2), > maven2 (http://repo1.maven.org/maven2) > > Group-Id: org.cipres.treebase > Artifact-Id: treebase-web > Version: 1.0-SNAPSHOT > From file: > /Users/vgapeyev/Work/TreeBase/EclipseMaven/treebase/treebase-web/pom.xml > > > > > [INFO] > ------------------------------------------------------------------------ > [INFO] For more information, run with the -e flag > [INFO] > ------------------------------------------------------------------------ > [INFO] BUILD FAILED > [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: 4 seconds > [INFO] Finished at: Mon Dec 14 17:59:49 EST 2009 > [INFO] Final Memory: 3M/25M > [INFO] > ------------------------------------------------------------------------ > > |
|
From: Vladimir G. <vga...@ne...> - 2009-12-14 23:12:17
|
On Dec 14, 2009, at 5:13 PM, youjun guo wrote:
> The TreeBASE test suite may have some problem. You can skip the test
> for now by check the "skip test" boxes.
I think I did this by:
On treebase project, Run As > 6 Maven Build ... > in Main tab
specify:
Goals: package
Skip tests - checkmark
This fails: mesquite is missing as a "transitive dependency" for
treebase-web (see log below).
My only guess for solving this was putting treebase-core project on
Java Build Path for treebase-web. It did not help.
Recall that I do have mesquite in ~/.m2
--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]
[INFO]
[INFO]
------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO]
------------------------------------------------------------------------
[INFO] Treebase .............................................. SUCCESS
[0.973s]
[INFO] treebase-core ......................................... SUCCESS
[2.885s]
[INFO] treebase-web .......................................... FAILED
[0.651s]
[INFO]
------------------------------------------------------------------------
[ERROR]
Transitive dependency resolution for scope: compile has failed for
your project.
Error message: Missing:
----------
1) mesquite:mesquite:jar:2.6+SNAPSHOT
Try downloading the file manually from the project website.
Then, install it using the command:
mvn install:install-file -DgroupId=mesquite -
DartifactId=mesquite -Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/
path/to/file
Alternatively, if you host your own repository you can deploy the
file there:
mvn deploy:deploy-file -DgroupId=mesquite -DartifactId=mesquite
-Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file -
Durl=[url] -DrepositoryId=[id]
Path to dependency:
1) org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT
2) org.nexml.model:nexml:jar:1.5-SNAPSHOT
3) mesquite:mesquite:jar:2.6+SNAPSHOT
----------
1 required artifact is missing.
for artifact:
org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT
from the specified remote repositories:
Maven Snapshots (http://snapshots.maven.codehaus.org/maven2),
m2.remote.repos (http://treebase.sourceforge.net/maven2/),
central (http://repo1.maven.org/maven2),
m2.nexml.repos (http://nexml-dev.nescent.org/.m2/repository/),
repository.jboss.org (http://repository.jboss.org/maven2),
maven2 (http://repo1.maven.org/maven2)
Group-Id: org.cipres.treebase
Artifact-Id: treebase-web
Version: 1.0-SNAPSHOT
From file: /Users/vgapeyev/Work/TreeBase/EclipseMaven/treebase/
treebase-web/pom.xml
[INFO]
------------------------------------------------------------------------
[INFO] For more information, run with the -e flag
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILED
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 4 seconds
[INFO] Finished at: Mon Dec 14 17:59:49 EST 2009
[INFO] Final Memory: 3M/25M
[INFO]
------------------------------------------------------------------------
|
|
From: youjun g. <you...@ya...> - 2009-12-14 22:13:46
|
Vladimir, The TreeBASE test suite may have some problem. You can skip the test for now by check the "skip test" boxes. Youjun On Mon, Dec 14, 2009 at 4:27 PM, Vladimir Gapeyev <vga...@ne...>wrote: > > On Dec 14, 2009, at 2:33 PM, youjun guo wrote: > > The TreeBASE is a whole Maven project with two modules treebase-core and > treebase-web, you need to run the "maven package" on project treebase > instead of treebase-web. > > To build treebase-web, the treebase-core need to be built first that's all > setup in the pom.xml, mesquite is one of the treebase-core's dependencies. > > Check your local .m2 directory see if there is a folder called mesquite. If > not then you can mannualy install it as maven dependency, our maven > dependency repository's url is: http://treebase.sourceforge.net/maven2/, > your Maven pom.xml have already pointed here every dependency should be > downloaded automaticly. > > > Ok, we are making some progress -- thanks Youjun! > > It turns out I did have ~/.m2/repository/mesquite/mesquite/2.6+SNAPSHOT. > So, after I *removed* the comment around the mesquite dependency in > treebase-core/pom.xml and did Run As > Maven package on the treebase > project, there was more progress: Maven started running tests. However, > there have been test failures and errors and the whole build failed. The > log's tail is copied below. Let me know if detailed info for any of the > failures or errors would be useful. > > --Vladimir > > > Results : > > Failed tests: > testValue_Study(org.cipres.treebase.auxdata.ValueStudyTest) > testDomainHome(org.cipres.treebase.service.admin.HelpServiceImplTest) > > Tests in error: > testFindColumnByIndices( > org.cipres.treebase.dao.matrix.MatrixElementDAOTest) > testCreateDelete(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testupdatePublishedFlagByStudy( > org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testfindKindByDescription(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindNodesByTaxonLabel(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindByAnyTaxonLabel(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindByStudy(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testfindQualityByDescription( > org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindTypeByDescription(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindTreeBlocksByNexusFileName( > org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindByTopology3(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testFindByTreeType(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) > testGetFormatInfo(org.cipres.treebase.domain.matrix.MatrixTest) > testGenerateNexusBlock(org.cipres.treebase.domain.matrix.MatrixTest) > testAddDelete(org.cipres.treebase.service.study.AnalysisServiceImplTest) > testFindTaxonLabelSets(org.cipres.treebase.dao.taxon.TaxonLabelDAOTest) > testJDBCConnection(org.cipres.treebase.core.CoreServiceLauncherTest) > testFindByDescription( > org.cipres.treebase.dao.matrix.MatrixDataTypeDAOTest) > testFindTaxonLabelSets( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindStudiesByTaxon( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindTreesByTaxon( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindMatricesByTaxon( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testCreateFromUBIOService( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testExpandTaxonVariant( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testExpandTaxonVariantSet( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindByExactString( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindTaxonVariantWithSubstring( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindByTaxonVariant( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testFindTaxonVariantByFullName( > org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) > testMesqutieFolderDir( > org.cipres.treebase.domain.nexus.NexusMesquiteDataSetTest) > testFindStatusInProgress( > org.cipres.treebase.dao.study.StudyStatusDAOTest) > testFindStatusReady(org.cipres.treebase.dao.study.StudyStatusDAOTest) > testFindStatusPublished(org.cipres.treebase.dao.study.StudyStatusDAOTest > ) > testFindPredefinedItemDefinition( > org.cipres.treebase.dao.matrix.ItemDefinitionDAOTest) > testFindByDescription( > org.cipres.treebase.dao.matrix.ItemDefinitionDAOTest) > testGetHelp(org.cipres.treebase.domain.admin.HelpTest) > testChangeMessage(org.cipres.treebase.domain.admin.HelpTest) > testDelete(org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindByMatrix(org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindByTree(org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindBySubmissionNumber( > org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindByReadyState(org.cipres.treebase.dao.study.SubmissionDAOTest) > testFindByCreateDateRange( > org.cipres.treebase.dao.study.SubmissionDAOTest) > testSetAuthors(org.cipres.treebase.domain.study.CitationTest) > testBuildNewickStringPerf(org.cipres.treebase.domain.tree.PhyloTreeTest) > testUpdateNewickString(org.cipres.treebase.domain.tree.PhyloTreeTest) > testDelete(org.cipres.treebase.dao.admin.PersonDAOTest) > testFindByID(org.cipres.treebase.dao.admin.PersonDAOTest) > testFindByExactMatch(org.cipres.treebase.dao.admin.PersonDAOTest) > testFindByLastName(org.cipres.treebase.dao.admin.PersonDAOTest) > testFindCompleteEmailAddress(org.cipres.treebase.dao.admin.PersonDAOTest > ) > testFindDuplicateWithFirstAndLastNames( > org.cipres.treebase.dao.admin.PersonDAOTest) > testFindDuplicateWithLastNames( > org.cipres.treebase.dao.admin.PersonDAOTest) > testCreateDelete(org.cipres.treebase.dao.admin.UserDAOTest) > testDelete_Negative(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByUserName(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByUserRole(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByPerson(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByEmailAddress(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByEmailAddressNegative(org.cipres.treebase.dao.admin.UserDAOTest > ) > testFindByEmailAddressLike(org.cipres.treebase.dao.admin.UserDAOTest) > testMerge(org.cipres.treebase.dao.admin.UserDAOTest) > testFindByUserName_Negative(org.cipres.treebase.dao.admin.UserDAOTest) > testAddDelete(org.cipres.treebase.service.study.StudyServiceImplTest) > testAddAnalysisByUpdate( > org.cipres.treebase.service.study.StudyServiceImplTest) > testAddAnalysis(org.cipres.treebase.service.study.StudyServiceImplTest) > testAddNexus(org.cipres.treebase.service.study.StudyServiceImplTest) > testAddNexusFile(org.cipres.treebase.service.study.StudyServiceImplTest) > testGenerateReconstructedNexusFile( > org.cipres.treebase.service.study.StudyServiceImplTest) > testSetAuthors(org.cipres.treebase.domain.study.StudyTest) > testGetAnalyses(org.cipres.treebase.domain.study.StudyTest) > testfindByNexusFileName(org.cipres.treebase.dao.matrix.MatrixDAOTest) > testfindRowAsString(org.cipres.treebase.dao.matrix.MatrixDAOTest) > testupdatePublishedFlagByStudy( > org.cipres.treebase.dao.matrix.MatrixDAOTest) > testfindKindByDescription(org.cipres.treebase.dao.matrix.MatrixDAOTest) > testgetInProgressSubmissions(org.cipres.treebase.domain.admin.UserTest) > testFindByMatrixID(org.cipres.treebase.dao.matrix.RowSegmentDAOTest) > testdeleteByMatrixAndColumnRange( > org.cipres.treebase.dao.matrix.RowSegmentDAOTest) > testFindBySubstring(org.cipres.treebase.domain.taxon.TaxonLabelTest) > testFindStudies(org.cipres.treebase.domain.taxon.TaxonLabelTest) > testFindMatricesByTaxonLabel( > org.cipres.treebase.domain.taxon.TaxonLabelTest) > testFindMatricesByTaxonVariant( > org.cipres.treebase.domain.taxon.TaxonLabelTest) > testFindByTopology3( > org.cipres.treebase.service.tree.PhyloTreeServiceImplTest) > testFindSomethingByRangeExpression( > org.cipres.treebase.service.tree.PhyloTreeServiceImplTest) > testupdateByRearrangeNodes( > org.cipres.treebase.service.tree.PhyloTreeServiceImplTest) > testFindByTag(org.cipres.treebase.service.admin.HelpServiceImplTest) > testEnumRowSegmentField( > org.cipres.treebase.service.matrix.RowSegmentServiceImplTest) > testCreateRowSegments( > org.cipres.treebase.service.matrix.RowSegmentServiceImplTest) > testFindSomethingByRangeExpression( > org.cipres.treebase.service.matrix.MatrixServiceImplTest) > testAddDelete(org.cipres.treebase.service.matrix.MatrixServiceImplTest) > testNull(org.cipres.treebase.RangeExpressionTest) > testParsingErrors(org.cipres.treebase.RangeExpressionTest) > testParsing(org.cipres.treebase.RangeExpressionTest) > testFindByLabel(org.cipres.treebase.dao.matrix.MatrixRowDAOTest) > testDeleteRows(org.cipres.treebase.dao.matrix.MatrixRowDAOTest) > testDeleteRowsEmpty(org.cipres.treebase.dao.matrix.MatrixRowDAOTest) > testAnalyzedDataDAO_1(org.cipres.treebase.dao.study.AnalyzedDataDAOTest) > testFindByMatrix_fixture_1( > org.cipres.treebase.dao.study.AnalyzedDataDAOTest) > testFindByTree_fixture_1( > org.cipres.treebase.dao.study.AnalyzedDataDAOTest) > testJDOMSerach(org.cipres.treebase.XMLTestCase) > testDOM4jSerach(org.cipres.treebase.XMLTestCase) > testTrivial(org.cipres.treebase.domain.search.SearchResultsTest) > testSearchService(org.cipres.treebase.domain.search.SearchResultsTest) > testQuickCheck(org.cipres.treebase.domain.search.SearchResultsTest) > testConvertToMatrices( > org.cipres.treebase.domain.search.SearchResultsTest) > testConvertFromMatrices( > org.cipres.treebase.domain.search.SearchResultsTest) > testConvertToTrees(org.cipres.treebase.domain.search.SearchResultsTest) > testConvertFromTrees(org.cipres.treebase.domain.search.SearchResultsTest > ) > testGetInfo(org.cipres.treebase.domain.matrix.SpecimenLabelTest) > testLoadPhyloDataSet(org.cipres.treebase.service.nexus.NexusParserTest) > testFinalAllUniqueAlgorithmDescriptions( > org.cipres.treebase.dao.study.AlgorithmDAOTest) > testNewickParsing(org.cipres.treebase.domain.nexus.NexusNCLDataSetTest) > testM1389Parsing(org.cipres.treebase.domain.nexus.NexusNCLDataSetTest) > testM12c11Parsing(org.cipres.treebase.domain.nexus.NexusNCLDataSetTest) > testGetMatrices(org.cipres.treebase.auxdata.AuxDataTest) > testGetTrees(org.cipres.treebase.auxdata.AuxDataTest) > testFindByAccessionNumber(org.cipres.treebase.dao.study.StudyDAOTest) > testFindByAbstract(org.cipres.treebase.dao.study.StudyDAOTest) > testFindByAuthor(org.cipres.treebase.dao.study.StudyDAOTest) > testFindBySubmitter(org.cipres.treebase.dao.study.StudyDAOTest) > testFindByCriteria(org.cipres.treebase.dao.study.StudyDAOTest) > testPersistNexusClob(org.cipres.treebase.dao.study.StudyDAOTest) > testFindByTBStudyID(org.cipres.treebase.dao.study.StudyDAOTest) > testC3p0(org.cipres.treebase.dao.EnvironmentTest) > testProperty(org.cipres.treebase.dao.EnvironmentTest) > testHibernateQueryStatement(org.cipres.treebase.dao.EnvironmentTest) > testGetGeneratedKey(org.cipres.treebase.dao.EnvironmentTest) > testSelectFromInsert(org.cipres.treebase.dao.EnvironmentTest) > testProcessNexusFile( > org.cipres.treebase.service.study.SubmissionServiceImplTest) > testGetSpecimenInfo(org.cipres.treebase.domain.matrix.RowSegmentTest) > > Tests run: 268, Failures: 2, Errors: 130, Skipped: 0 > > [INFO] > [INFO] > [INFO] > ------------------------------------------------------------------------ > [INFO] Reactor Summary: > [INFO] > ------------------------------------------------------------------------ > [INFO] Treebase .............................................. SUCCESS > [1.133s] > [INFO] treebase-core ......................................... FAILED > [18.360s] > [INFO] treebase-web .......................................... NOT BUILT > [INFO] > ------------------------------------------------------------------------ > [ERROR] > > Mojo: > > org.apache.maven.plugins:maven-surefire-plugin:2.4.2:test > > FAILED for project: > > org.cipres.treebase:treebase-core:jar:1.0-SNAPSHOT > > Reason: > > There are test failures. > > Please refer to > /Users/vgapeyev/Work/TreeBase/EclipseMaven/treebase/treebase-core/target/surefire-reports > for the individual test results. > > > > > [INFO] > ------------------------------------------------------------------------ > [INFO] For more information, run with the -e flag > [INFO] > ------------------------------------------------------------------------ > [INFO] BUILD FAILED > [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: 19 seconds > [INFO] Finished at: Mon Dec 14 16:09:04 EST 2009 > [INFO] Final Memory: 2M/22M > [INFO] > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > 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 > > |
|
From: Vladimir G. <vga...@ne...> - 2009-12-14 21:27:23
|
On Dec 14, 2009, at 2:33 PM, youjun guo wrote: > The TreeBASE is a whole Maven project with two modules treebase-core > and treebase-web, you need to run the "maven package" on project > treebase instead of treebase-web. > > To build treebase-web, the treebase-core need to be built first > that's all setup in the pom.xml, mesquite is one of the treebase- > core's dependencies. > > Check your local .m2 directory see if there is a folder called > mesquite. If not then you can mannualy install it as maven > dependency, our maven dependency repository's url is: http://treebase.sourceforge.net/maven2/ > , your Maven pom.xml have already pointed here every dependency > should be downloaded automaticly. Ok, we are making some progress -- thanks Youjun! It turns out I did have ~/.m2/repository/mesquite/mesquite/ 2.6+SNAPSHOT. So, after I *removed* the comment around the mesquite dependency in treebase-core/pom.xml and did Run As > Maven package on the treebase project, there was more progress: Maven started running tests. However, there have been test failures and errors and the whole build failed. The log's tail is copied below. Let me know if detailed info for any of the failures or errors would be useful. --Vladimir Results : Failed tests: testValue_Study(org.cipres.treebase.auxdata.ValueStudyTest) testDomainHome(org.cipres.treebase.service.admin.HelpServiceImplTest) Tests in error: testFindColumnByIndices (org.cipres.treebase.dao.matrix.MatrixElementDAOTest) testCreateDelete(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testupdatePublishedFlagByStudy (org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testfindKindByDescription(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testFindNodesByTaxonLabel(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testFindByAnyTaxonLabel(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testFindByStudy(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testfindQualityByDescription (org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testFindTypeByDescription(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testFindTreeBlocksByNexusFileName (org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testFindByTopology3(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testFindByTreeType(org.cipres.treebase.dao.tree.PhyloTreeDAOTest) testGetFormatInfo(org.cipres.treebase.domain.matrix.MatrixTest) testGenerateNexusBlock(org.cipres.treebase.domain.matrix.MatrixTest) testAddDelete(org.cipres.treebase.service.study.AnalysisServiceImplTest) testFindTaxonLabelSets(org.cipres.treebase.dao.taxon.TaxonLabelDAOTest) testJDBCConnection(org.cipres.treebase.core.CoreServiceLauncherTest) testFindByDescription (org.cipres.treebase.dao.matrix.MatrixDataTypeDAOTest) testFindTaxonLabelSets (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testFindStudiesByTaxon (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testFindTreesByTaxon (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testFindMatricesByTaxon (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testCreateFromUBIOService (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testExpandTaxonVariant (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testExpandTaxonVariantSet (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testFindByExactString (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testFindTaxonVariantWithSubstring (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testFindByTaxonVariant (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testFindTaxonVariantByFullName (org.cipres.treebase.service.taxon.TaxonLabelServiceImplTest) testMesqutieFolderDir (org.cipres.treebase.domain.nexus.NexusMesquiteDataSetTest) testFindStatusInProgress (org.cipres.treebase.dao.study.StudyStatusDAOTest) testFindStatusReady(org.cipres.treebase.dao.study.StudyStatusDAOTest) testFindStatusPublished (org.cipres.treebase.dao.study.StudyStatusDAOTest) testFindPredefinedItemDefinition (org.cipres.treebase.dao.matrix.ItemDefinitionDAOTest) testFindByDescription (org.cipres.treebase.dao.matrix.ItemDefinitionDAOTest) testGetHelp(org.cipres.treebase.domain.admin.HelpTest) testChangeMessage(org.cipres.treebase.domain.admin.HelpTest) testDelete(org.cipres.treebase.dao.study.SubmissionDAOTest) testFindByMatrix(org.cipres.treebase.dao.study.SubmissionDAOTest) testFindByTree(org.cipres.treebase.dao.study.SubmissionDAOTest) testFindBySubmissionNumber (org.cipres.treebase.dao.study.SubmissionDAOTest) testFindByReadyState(org.cipres.treebase.dao.study.SubmissionDAOTest) testFindByCreateDateRange (org.cipres.treebase.dao.study.SubmissionDAOTest) testSetAuthors(org.cipres.treebase.domain.study.CitationTest) testBuildNewickStringPerf(org.cipres.treebase.domain.tree.PhyloTreeTest) testUpdateNewickString(org.cipres.treebase.domain.tree.PhyloTreeTest) testDelete(org.cipres.treebase.dao.admin.PersonDAOTest) testFindByID(org.cipres.treebase.dao.admin.PersonDAOTest) testFindByExactMatch(org.cipres.treebase.dao.admin.PersonDAOTest) testFindByLastName(org.cipres.treebase.dao.admin.PersonDAOTest) testFindCompleteEmailAddress (org.cipres.treebase.dao.admin.PersonDAOTest) testFindDuplicateWithFirstAndLastNames (org.cipres.treebase.dao.admin.PersonDAOTest) testFindDuplicateWithLastNames (org.cipres.treebase.dao.admin.PersonDAOTest) testCreateDelete(org.cipres.treebase.dao.admin.UserDAOTest) testDelete_Negative(org.cipres.treebase.dao.admin.UserDAOTest) testFindByUserName(org.cipres.treebase.dao.admin.UserDAOTest) testFindByUserRole(org.cipres.treebase.dao.admin.UserDAOTest) testFindByPerson(org.cipres.treebase.dao.admin.UserDAOTest) testFindByEmailAddress(org.cipres.treebase.dao.admin.UserDAOTest) testFindByEmailAddressNegative (org.cipres.treebase.dao.admin.UserDAOTest) testFindByEmailAddressLike(org.cipres.treebase.dao.admin.UserDAOTest) testMerge(org.cipres.treebase.dao.admin.UserDAOTest) testFindByUserName_Negative(org.cipres.treebase.dao.admin.UserDAOTest) testAddDelete(org.cipres.treebase.service.study.StudyServiceImplTest) testAddAnalysisByUpdate (org.cipres.treebase.service.study.StudyServiceImplTest) testAddAnalysis(org.cipres.treebase.service.study.StudyServiceImplTest) testAddNexus(org.cipres.treebase.service.study.StudyServiceImplTest) testAddNexusFile(org.cipres.treebase.service.study.StudyServiceImplTest) testGenerateReconstructedNexusFile (org.cipres.treebase.service.study.StudyServiceImplTest) testSetAuthors(org.cipres.treebase.domain.study.StudyTest) testGetAnalyses(org.cipres.treebase.domain.study.StudyTest) testfindByNexusFileName(org.cipres.treebase.dao.matrix.MatrixDAOTest) testfindRowAsString(org.cipres.treebase.dao.matrix.MatrixDAOTest) testupdatePublishedFlagByStudy (org.cipres.treebase.dao.matrix.MatrixDAOTest) testfindKindByDescription(org.cipres.treebase.dao.matrix.MatrixDAOTest) testgetInProgressSubmissions(org.cipres.treebase.domain.admin.UserTest) testFindByMatrixID(org.cipres.treebase.dao.matrix.RowSegmentDAOTest) testdeleteByMatrixAndColumnRange (org.cipres.treebase.dao.matrix.RowSegmentDAOTest) testFindBySubstring(org.cipres.treebase.domain.taxon.TaxonLabelTest) testFindStudies(org.cipres.treebase.domain.taxon.TaxonLabelTest) testFindMatricesByTaxonLabel (org.cipres.treebase.domain.taxon.TaxonLabelTest) testFindMatricesByTaxonVariant (org.cipres.treebase.domain.taxon.TaxonLabelTest) testFindByTopology3 (org.cipres.treebase.service.tree.PhyloTreeServiceImplTest) testFindSomethingByRangeExpression (org.cipres.treebase.service.tree.PhyloTreeServiceImplTest) testupdateByRearrangeNodes (org.cipres.treebase.service.tree.PhyloTreeServiceImplTest) testFindByTag(org.cipres.treebase.service.admin.HelpServiceImplTest) testEnumRowSegmentField (org.cipres.treebase.service.matrix.RowSegmentServiceImplTest) testCreateRowSegments (org.cipres.treebase.service.matrix.RowSegmentServiceImplTest) testFindSomethingByRangeExpression (org.cipres.treebase.service.matrix.MatrixServiceImplTest) testAddDelete(org.cipres.treebase.service.matrix.MatrixServiceImplTest) testNull(org.cipres.treebase.RangeExpressionTest) testParsingErrors(org.cipres.treebase.RangeExpressionTest) testParsing(org.cipres.treebase.RangeExpressionTest) testFindByLabel(org.cipres.treebase.dao.matrix.MatrixRowDAOTest) testDeleteRows(org.cipres.treebase.dao.matrix.MatrixRowDAOTest) testDeleteRowsEmpty(org.cipres.treebase.dao.matrix.MatrixRowDAOTest) testAnalyzedDataDAO_1(org.cipres.treebase.dao.study.AnalyzedDataDAOTest) testFindByMatrix_fixture_1 (org.cipres.treebase.dao.study.AnalyzedDataDAOTest) testFindByTree_fixture_1 (org.cipres.treebase.dao.study.AnalyzedDataDAOTest) testJDOMSerach(org.cipres.treebase.XMLTestCase) testDOM4jSerach(org.cipres.treebase.XMLTestCase) testTrivial(org.cipres.treebase.domain.search.SearchResultsTest) testSearchService(org.cipres.treebase.domain.search.SearchResultsTest) testQuickCheck(org.cipres.treebase.domain.search.SearchResultsTest) testConvertToMatrices (org.cipres.treebase.domain.search.SearchResultsTest) testConvertFromMatrices (org.cipres.treebase.domain.search.SearchResultsTest) testConvertToTrees(org.cipres.treebase.domain.search.SearchResultsTest) testConvertFromTrees (org.cipres.treebase.domain.search.SearchResultsTest) testGetInfo(org.cipres.treebase.domain.matrix.SpecimenLabelTest) testLoadPhyloDataSet(org.cipres.treebase.service.nexus.NexusParserTest) testFinalAllUniqueAlgorithmDescriptions (org.cipres.treebase.dao.study.AlgorithmDAOTest) testNewickParsing(org.cipres.treebase.domain.nexus.NexusNCLDataSetTest) testM1389Parsing(org.cipres.treebase.domain.nexus.NexusNCLDataSetTest) testM12c11Parsing(org.cipres.treebase.domain.nexus.NexusNCLDataSetTest) testGetMatrices(org.cipres.treebase.auxdata.AuxDataTest) testGetTrees(org.cipres.treebase.auxdata.AuxDataTest) testFindByAccessionNumber(org.cipres.treebase.dao.study.StudyDAOTest) testFindByAbstract(org.cipres.treebase.dao.study.StudyDAOTest) testFindByAuthor(org.cipres.treebase.dao.study.StudyDAOTest) testFindBySubmitter(org.cipres.treebase.dao.study.StudyDAOTest) testFindByCriteria(org.cipres.treebase.dao.study.StudyDAOTest) testPersistNexusClob(org.cipres.treebase.dao.study.StudyDAOTest) testFindByTBStudyID(org.cipres.treebase.dao.study.StudyDAOTest) testC3p0(org.cipres.treebase.dao.EnvironmentTest) testProperty(org.cipres.treebase.dao.EnvironmentTest) testHibernateQueryStatement(org.cipres.treebase.dao.EnvironmentTest) testGetGeneratedKey(org.cipres.treebase.dao.EnvironmentTest) testSelectFromInsert(org.cipres.treebase.dao.EnvironmentTest) testProcessNexusFile (org.cipres.treebase.service.study.SubmissionServiceImplTest) testGetSpecimenInfo(org.cipres.treebase.domain.matrix.RowSegmentTest) Tests run: 268, Failures: 2, Errors: 130, Skipped: 0 [INFO] [INFO] [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary: [INFO] ------------------------------------------------------------------------ [INFO] Treebase .............................................. SUCCESS [1.133s] [INFO] treebase-core ......................................... FAILED [18.360s] [INFO] treebase-web .......................................... NOT BUILT [INFO] ------------------------------------------------------------------------ [ERROR] Mojo: org.apache.maven.plugins:maven-surefire-plugin:2.4.2:test FAILED for project: org.cipres.treebase:treebase-core:jar:1.0-SNAPSHOT Reason: There are test failures. Please refer to /Users/vgapeyev/Work/TreeBase/EclipseMaven/treebase/ treebase-core/target/surefire-reports for the individual test results. [INFO] ------------------------------------------------------------------------ [INFO] For more information, run with the -e flag [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILED [INFO] ------------------------------------------------------------------------ [INFO] Total time: 19 seconds [INFO] Finished at: Mon Dec 14 16:09:04 EST 2009 [INFO] Final Memory: 2M/22M [INFO] ------------------------------------------------------------------------ |
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From: youjun g. <you...@ya...> - 2009-12-14 19:33:56
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Vladimir, The TreeBASE is a whole Maven project with two modules treebase-core and treebase-web, you need to run the "maven package" on project treebase instead of treebase-web. To build treebase-web, the treebase-core need to be built first that's all setup in the pom.xml, mesquite is one of the treebase-core's dependencies. Check your local .m2 directory see if there is a folder called mesquite. If not then you can mannualy install it as maven dependency, our maven dependency repository's url is: http://treebase.sourceforge.net/maven2/, your Maven pom.xml have already pointed here every dependency should be downloaded automaticly. remember if you use my solution to build the war file, your java sdk version cannot be newer then the server's sdk. Youjun On Mon, Dec 14, 2009 at 2:02 PM, Vladimir Gapeyev <vga...@ne...>wrote: > > On Dec 11, 2009, at 8:00 PM, youjun guo wrote: > > Alternative solution is run "maven package" on the project from your > eclipse to build the war file then copy the treebase-web.war to your tomcat > webapp directory, then restart the tomcat if you didn't set the autodeploy. > > > On the treebase-web project, I did Run As > m2 Maven Package. This > failed due to the missing mesquite dependency -- see the partial log below. > I see that the dependency on mesquite is commented out from > treebase-core/pom.xml -- any idea why's the build failure then? > > --Vladimir > > > > > Downloading: > http://snapshots.maven.codehaus.org/maven2/mesquite/mesquite/2.6+SNAPSHOT/mesquite-2.6+SNAPSHOT.jar > [ERROR] > > Transitive dependency resolution for scope: compile has failed for your > project. > > > > Error message: Missing: > ---------- > 1) mesquite:mesquite:jar:2.6+SNAPSHOT > > Try downloading the file manually from the project website. > > Then, install it using the command: > mvn install:install-file -DgroupId=mesquite -DartifactId=mesquite > -Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file > > Alternatively, if you host your own repository you can deploy the file > there: > mvn deploy:deploy-file -DgroupId=mesquite -DartifactId=mesquite > -Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file -Durl=[url] > -DrepositoryId=[id] > > Path to dependency: > 1) org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT > 2) org.nexml.model:nexml:jar:1.5-SNAPSHOT > 3) mesquite:mesquite:jar:2.6+SNAPSHOT > > ---------- > 1 required artifact is missing. > > for artifact: > org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT > > from the specified remote repositories: > Maven Snapshots (http://snapshots.maven.codehaus.org/maven2), > m2.remote.repos (http://treebase.sourceforge.net/maven2/), > central (http://repo1.maven.org/maven2), > m2.nexml.repos (http://nexml-dev.nescent.org/.m2/repository/), > repository.jboss.org (http://repository.jboss.org/maven2), > maven2 (http://repo1.maven.org/maven2) > > Group-Id: org.cipres.treebase > Artifact-Id: treebase-web > Version: 1.0-SNAPSHOT > From file: > /Users/vgapeyev/Work/TreeBase/EclipseMaven/treebase/treebase-web/pom.xml > > > > > [INFO] > ------------------------------------------------------------------------ > [INFO] For more information, run with the -e flag > [INFO] > ------------------------------------------------------------------------ > [INFO] BUILD FAILED > [INFO] > ------------------------------------------------------------------------ > [INFO] Total time: 1 minute 11 seconds > [INFO] Finished at: Mon Dec 14 10:18:21 EST 2009 > [INFO] Final Memory: 2M/18M > [INFO] > ------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > 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...> - 2009-12-14 19:02:32
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On Dec 11, 2009, at 8:00 PM, youjun guo wrote: > Alternative solution is run "maven package" on the project from your > eclipse to build the war file then copy the treebase-web.war to your > tomcat webapp directory, then restart the tomcat if you didn't set > the autodeploy. On the treebase-web project, I did Run As > m2 Maven Package. This failed due to the missing mesquite dependency -- see the partial log below. I see that the dependency on mesquite is commented out from treebase-core/pom.xml -- any idea why's the build failure then? --Vladimir Downloading: http://snapshots.maven.codehaus.org/maven2/mesquite/mesquite/2.6+SNAPSHOT/mesquite-2.6+SNAPSHOT.jar [ERROR] Transitive dependency resolution for scope: compile has failed for your project. Error message: Missing: ---------- 1) mesquite:mesquite:jar:2.6+SNAPSHOT Try downloading the file manually from the project website. Then, install it using the command: mvn install:install-file -DgroupId=mesquite - DartifactId=mesquite -Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/ path/to/file Alternatively, if you host your own repository you can deploy the file there: mvn deploy:deploy-file -DgroupId=mesquite -DartifactId=mesquite -Dversion=2.6+SNAPSHOT -Dpackaging=jar -Dfile=/path/to/file - Durl=[url] -DrepositoryId=[id] Path to dependency: 1) org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT 2) org.nexml.model:nexml:jar:1.5-SNAPSHOT 3) mesquite:mesquite:jar:2.6+SNAPSHOT ---------- 1 required artifact is missing. for artifact: org.cipres.treebase:treebase-web:war:1.0-SNAPSHOT from the specified remote repositories: Maven Snapshots (http://snapshots.maven.codehaus.org/maven2), m2.remote.repos (http://treebase.sourceforge.net/maven2/), central (http://repo1.maven.org/maven2), m2.nexml.repos (http://nexml-dev.nescent.org/.m2/repository/), repository.jboss.org (http://repository.jboss.org/maven2), maven2 (http://repo1.maven.org/maven2) Group-Id: org.cipres.treebase Artifact-Id: treebase-web Version: 1.0-SNAPSHOT From file: /Users/vgapeyev/Work/TreeBase/EclipseMaven/treebase/ treebase-web/pom.xml [INFO] ------------------------------------------------------------------------ [INFO] For more information, run with the -e flag [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILED [INFO] ------------------------------------------------------------------------ [INFO] Total time: 1 minute 11 seconds [INFO] Finished at: Mon Dec 14 10:18:21 EST 2009 [INFO] Final Memory: 2M/18M [INFO] ------------------------------------------------------------------------ |
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From: youjun g. <you...@ya...> - 2009-12-14 15:41:24
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Hi, Vladimir The difference we talked about only affect developer's workstation setup but not server. Actually there are many different ways for a developer to setup their workstation. for example, use Maven and/or Subversion either via command line or with some eclipse plug ins, like me, or running a script like "publish", It is totally according to what they are preferred. The wiki page Rutger did is great for helping people set up their server and deploy via script "publish". Those other ways are just standard Eclipse, Maven, Subversion and Tomcat usage. Nothing special. Youjun On Mon, Dec 14, 2009 at 9:31 AM, Vladimir Gapeyev <vga...@ne...>wrote: > Also, since it appears that there are two different setups, for the > server and for a developer, maybe it would make sense to split the > wiki instructions accordingly? > --VG > > > On Dec 14, 2009, at 6:52 AM, Rutger Vos wrote: > > > Hi Youjun, > > > > since you have this fresh in your memory, could you check whether the > > wiki page > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > > is complete and correct? And add/update as needed? > > > > Thanks! > > > > > > On Fri, Dec 11, 2009 at 7:13 PM, youjun guo <you...@ya...> > > wrote: > >> Vladimir, > >> > >> Unless you are going to do the developing work directly on the > >> treebase-dev > >> server , or you want to remotely deploy from your workstation to the > >> treebase tomcat server, your eclipse set up have nothing to do with > >> the > >> shell envelopment. > >> > >> m2eclipse is a mvn inatall for eclipse. > >> > >> Youjun > >> > >> > >> On Fri, Dec 11, 2009 at 1:26 PM, Vladimir Gapeyev <vga...@ne... > >> > > >> wrote: > >>> > >>> Youjun, > >>> As I understand, you suggest to skip the (mvn install; Eclipse > >>> workspace > >>> at trunk; create Java projects from existing files) part of > >>> instructions > >>> at > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > >>> and instead start with an Eclipse workspace in a blank directory. > >>> I'll probably try that if nothing can make the above instructions > >>> work. > >>> However, it will be useful if we can make those wiki instructions > >>> work... > >>> --VG > >>> > >>> > >>> > >>> On Dec 11, 2009, at 11:35 AM, youjun guo wrote: > >>> > >>> Vladimir, > >>> > >>> 1st, make sure your eclipse have the maven plugin like m2eclipse and > >>> subversion plugin like subclipse installed. > >>> > >>> 2rd instead of creating a maven project, "import a maven project > >>> form > >>> remote reposotory" in other words - treebase sourceforge svn url. > >>> > >>> All the dependencies were defined in pom.xml, maven know how to > >>> find them > >>> online, even if they are missing from you local .m2 directory > >>> > >>> Youjun > >>> > >>> > >>> > >>> On Fri, Dec 11, 2009 at 11:06 AM, Vladimir Gapeyev < > vga...@ne... > >>> > > >>> wrote: > >>>> > >>>> Yes, I followed the wiki instructions, including running mvn > >>>> install - > >>>> Dmaven.test.skip=true in the proper shell environment. This > >>>> appeared > >>>> to have created the repository in ~vgapeyev/.m2, which Eclipse does > >>>> see through the M2_REPO variable. > >>>> > >>>> Note that only a fraction of the dependencies is missing in > >>>> Eclipse. > >>>> Is there a chance they are simply missing from the Maven config > >>>> files? That is, can someone check the status of the handful of the > >>>> dependencies I have mentioned? Again, I can supply the full list > >>>> if > >>>> this turns out to be the right way to go. > >>>> > >>>> I also tried following Youjun's advice, to create Maven rather than > >>>> Java projects in Eclipse. The wizard asks questions (about group > >>>> and > >>>> artifact IDs, which I, as a Maven novice, do not understand) and > >>>> finally stops with the error "A pom.xml file already exists in the > >>>> destination folder". > >>>> > >>>> --Vladimir > >>>> > >>>> > >>>> On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: > >>>> > >>>>> Yes, you have to do the maven build first (e.g. from the command > >>>>> line) > >>>>> and make sure in eclipse that the M2_REPO variable is configured > >>>>> correctly (i.e. points to your local repository in > >>>>> $HOME/.m2/repository) > >>>>> > >>>>> On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> > >>>>> wrote: > >>>>>> Make sure you import the project as maven project, it will find > >>>>>> and > >>>>>> download > >>>>>> those dependencies for you. > >>>>>> > >>>>>> Youjun > >>>>>> > >>>>>> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev > >>>>>> <vga...@ne... > >>>>>>> > >>>>>> wrote: > >>>>>>> > >>>>>>> Going through the installation instructions > >>>>>>> at > >>>>>>> > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > >>>>>>> , > >>>>>>> I got to creation of Eclipse projects treebase-core and > >>>>>>> treebase- > >>>>>>> web. > >>>>>>> This gave me lots of missing buildpath entries: 11 in treebase- > >>>>>>> core and 39 > >>>>>>> in treebase-web. Please advise on how to proceed! > >>>>>>> Here are a few of the missing entries: > >>>>>>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- > >>>>>>> extensions-1.2.jar > >>>>>>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- > >>>>>>> framework-4.1.3.jar > >>>>>>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar > >>>>>>> > >>>>>>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- > >>>>>>> beanutils-1.7.0.jar > >>>>>>> I can work on putting together the whole list in case it will be > >>>>>>> useful. > >>>>>>> --Vladimir > >>>>>>> > >>>>>>> > >>>>>>> > ------------------------------------------------------------------------------ > >>>>>>> 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 > >>>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> > ------------------------------------------------------------------------------ > >>>>>> 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 > >>>> > >>>> > >>>> > >>>> > ------------------------------------------------------------------------------ > >>>> 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 > >>> > >>> > >>> > >>> > >>> > ------------------------------------------------------------------------------ > >>> 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 > >>> > >> > >> > >> > ------------------------------------------------------------------------------ > >> 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 > > > > ------------------------------------------------------------------------------ > 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: youjun g. <you...@ya...> - 2009-12-14 15:13:29
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Hi, Rutger, I think you did a wonderful job on the wiki page. Based on my understanding, the purpose of "shell environment" is to run the script "publish", and it will download, compile, build and deploy the source code. I am not quite understand of this: # Headless mesquite needs a window server (a virtual one is OK)" Does this mean, for a new installation of TreeBASE, we also need to do some initial setup for mesquite? what about re-deploy after fixing a bug? The way I work on TreeBASE is just a standard Tomcat deployment with Eclipse & Maven build up. Do you think it will miss something specific for TreeBASE project? Thanks Youjun On Mon, Dec 14, 2009 at 6:52 AM, Rutger Vos <rut...@gm...> wrote: > Hi Youjun, > > since you have this fresh in your memory, could you check whether the > wiki page > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > is complete and correct? And add/update as needed? > > Thanks! > > > On Fri, Dec 11, 2009 at 7:13 PM, youjun guo <you...@ya...> wrote: > > Vladimir, > > > > Unless you are going to do the developing work directly on the > treebase-dev > > server , or you want to remotely deploy from your workstation to the > > treebase tomcat server, your eclipse set up have nothing to do with the > > shell envelopment. > > > > m2eclipse is a mvn inatall for eclipse. > > > > Youjun > > > > > > On Fri, Dec 11, 2009 at 1:26 PM, Vladimir Gapeyev <vga...@ne...> > > wrote: > >> > >> Youjun, > >> As I understand, you suggest to skip the (mvn install; Eclipse > workspace > >> at trunk; create Java projects from existing files) part of > instructions > >> at > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > >> and instead start with an Eclipse workspace in a blank directory. > >> I'll probably try that if nothing can make the above instructions work. > >> However, it will be useful if we can make those wiki instructions > work... > >> --VG > >> > >> > >> > >> On Dec 11, 2009, at 11:35 AM, youjun guo wrote: > >> > >> Vladimir, > >> > >> 1st, make sure your eclipse have the maven plugin like m2eclipse and > >> subversion plugin like subclipse installed. > >> > >> 2rd instead of creating a maven project, "import a maven project form > >> remote reposotory" in other words - treebase sourceforge svn url. > >> > >> All the dependencies were defined in pom.xml, maven know how to find > them > >> online, even if they are missing from you local .m2 directory > >> > >> Youjun > >> > >> > >> > >> On Fri, Dec 11, 2009 at 11:06 AM, Vladimir Gapeyev < > vga...@ne...> > >> wrote: > >>> > >>> Yes, I followed the wiki instructions, including running mvn install - > >>> Dmaven.test.skip=true in the proper shell environment. This appeared > >>> to have created the repository in ~vgapeyev/.m2, which Eclipse does > >>> see through the M2_REPO variable. > >>> > >>> Note that only a fraction of the dependencies is missing in Eclipse. > >>> Is there a chance they are simply missing from the Maven config > >>> files? That is, can someone check the status of the handful of the > >>> dependencies I have mentioned? Again, I can supply the full list if > >>> this turns out to be the right way to go. > >>> > >>> I also tried following Youjun's advice, to create Maven rather than > >>> Java projects in Eclipse. The wizard asks questions (about group and > >>> artifact IDs, which I, as a Maven novice, do not understand) and > >>> finally stops with the error "A pom.xml file already exists in the > >>> destination folder". > >>> > >>> --Vladimir > >>> > >>> > >>> On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: > >>> > >>> > Yes, you have to do the maven build first (e.g. from the command > line) > >>> > and make sure in eclipse that the M2_REPO variable is configured > >>> > correctly (i.e. points to your local repository in > >>> > $HOME/.m2/repository) > >>> > > >>> > On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> > >>> > wrote: > >>> >> Make sure you import the project as maven project, it will find and > >>> >> download > >>> >> those dependencies for you. > >>> >> > >>> >> Youjun > >>> >> > >>> >> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev > >>> >> <vga...@ne... > >>> >> > > >>> >> wrote: > >>> >>> > >>> >>> Going through the installation instructions > >>> >>> at > >>> >>> > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > >>> >>> , > >>> >>> I got to creation of Eclipse projects treebase-core and treebase- > >>> >>> web. > >>> >>> This gave me lots of missing buildpath entries: 11 in treebase- > >>> >>> core and 39 > >>> >>> in treebase-web. Please advise on how to proceed! > >>> >>> Here are a few of the missing entries: > >>> >>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- > >>> >>> extensions-1.2.jar > >>> >>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- > >>> >>> framework-4.1.3.jar > >>> >>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar > >>> >>> > >>> >>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- > >>> >>> beanutils-1.7.0.jar > >>> >>> I can work on putting together the whole list in case it will be > >>> >>> useful. > >>> >>> --Vladimir > >>> >>> > >>> >>> > >>> >>> > ------------------------------------------------------------------------------ > >>> >>> 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 > >>> >>> > >>> >> > >>> >> > >>> >> > >>> >> > ------------------------------------------------------------------------------ > >>> >> 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 > >>> > >>> > >>> > >>> > ------------------------------------------------------------------------------ > >>> 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 > >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ > >> 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 > >> > > > > > > > ------------------------------------------------------------------------------ > > 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: Vladimir G. <vga...@ne...> - 2009-12-14 14:31:57
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Also, since it appears that there are two different setups, for the server and for a developer, maybe it would make sense to split the wiki instructions accordingly? --VG On Dec 14, 2009, at 6:52 AM, Rutger Vos wrote: > Hi Youjun, > > since you have this fresh in your memory, could you check whether the > wiki page https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > is complete and correct? And add/update as needed? > > Thanks! > > > On Fri, Dec 11, 2009 at 7:13 PM, youjun guo <you...@ya...> > wrote: >> Vladimir, >> >> Unless you are going to do the developing work directly on the >> treebase-dev >> server , or you want to remotely deploy from your workstation to the >> treebase tomcat server, your eclipse set up have nothing to do with >> the >> shell envelopment. >> >> m2eclipse is a mvn inatall for eclipse. >> >> Youjun >> >> >> On Fri, Dec 11, 2009 at 1:26 PM, Vladimir Gapeyev <vga...@ne... >> > >> wrote: >>> >>> Youjun, >>> As I understand, you suggest to skip the (mvn install; Eclipse >>> workspace >>> at trunk; create Java projects from existing files) part of >>> instructions >>> at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >>> and instead start with an Eclipse workspace in a blank directory. >>> I'll probably try that if nothing can make the above instructions >>> work. >>> However, it will be useful if we can make those wiki instructions >>> work... >>> --VG >>> >>> >>> >>> On Dec 11, 2009, at 11:35 AM, youjun guo wrote: >>> >>> Vladimir, >>> >>> 1st, make sure your eclipse have the maven plugin like m2eclipse and >>> subversion plugin like subclipse installed. >>> >>> 2rd instead of creating a maven project, "import a maven project >>> form >>> remote reposotory" in other words - treebase sourceforge svn url. >>> >>> All the dependencies were defined in pom.xml, maven know how to >>> find them >>> online, even if they are missing from you local .m2 directory >>> >>> Youjun >>> >>> >>> >>> On Fri, Dec 11, 2009 at 11:06 AM, Vladimir Gapeyev <vga...@ne... >>> > >>> wrote: >>>> >>>> Yes, I followed the wiki instructions, including running mvn >>>> install - >>>> Dmaven.test.skip=true in the proper shell environment. This >>>> appeared >>>> to have created the repository in ~vgapeyev/.m2, which Eclipse does >>>> see through the M2_REPO variable. >>>> >>>> Note that only a fraction of the dependencies is missing in >>>> Eclipse. >>>> Is there a chance they are simply missing from the Maven config >>>> files? That is, can someone check the status of the handful of the >>>> dependencies I have mentioned? Again, I can supply the full list >>>> if >>>> this turns out to be the right way to go. >>>> >>>> I also tried following Youjun's advice, to create Maven rather than >>>> Java projects in Eclipse. The wizard asks questions (about group >>>> and >>>> artifact IDs, which I, as a Maven novice, do not understand) and >>>> finally stops with the error "A pom.xml file already exists in the >>>> destination folder". >>>> >>>> --Vladimir >>>> >>>> >>>> On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: >>>> >>>>> Yes, you have to do the maven build first (e.g. from the command >>>>> line) >>>>> and make sure in eclipse that the M2_REPO variable is configured >>>>> correctly (i.e. points to your local repository in >>>>> $HOME/.m2/repository) >>>>> >>>>> On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> >>>>> wrote: >>>>>> Make sure you import the project as maven project, it will find >>>>>> and >>>>>> download >>>>>> those dependencies for you. >>>>>> >>>>>> Youjun >>>>>> >>>>>> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev >>>>>> <vga...@ne... >>>>>>> >>>>>> wrote: >>>>>>> >>>>>>> Going through the installation instructions >>>>>>> at >>>>>>> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >>>>>>> , >>>>>>> I got to creation of Eclipse projects treebase-core and >>>>>>> treebase- >>>>>>> web. >>>>>>> This gave me lots of missing buildpath entries: 11 in treebase- >>>>>>> core and 39 >>>>>>> in treebase-web. Please advise on how to proceed! >>>>>>> Here are a few of the missing entries: >>>>>>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- >>>>>>> extensions-1.2.jar >>>>>>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- >>>>>>> framework-4.1.3.jar >>>>>>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar >>>>>>> >>>>>>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- >>>>>>> beanutils-1.7.0.jar >>>>>>> I can work on putting together the whole list in case it will be >>>>>>> useful. >>>>>>> --Vladimir >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> 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 >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> 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 >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> >> >> >> ------------------------------------------------------------------------------ >> 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...> - 2009-12-14 11:52:21
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Hi Youjun, since you have this fresh in your memory, could you check whether the wiki page https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment is complete and correct? And add/update as needed? Thanks! On Fri, Dec 11, 2009 at 7:13 PM, youjun guo <you...@ya...> wrote: > Vladimir, > > Unless you are going to do the developing work directly on the treebase-dev > server , or you want to remotely deploy from your workstation to the > treebase tomcat server, your eclipse set up have nothing to do with the > shell envelopment. > > m2eclipse is a mvn inatall for eclipse. > > Youjun > > > On Fri, Dec 11, 2009 at 1:26 PM, Vladimir Gapeyev <vga...@ne...> > wrote: >> >> Youjun, >> As I understand, you suggest to skip the (mvn install; Eclipse workspace >> at trunk; create Java projects from existing files) part of instructions >> at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> and instead start with an Eclipse workspace in a blank directory. >> I'll probably try that if nothing can make the above instructions work. >> However, it will be useful if we can make those wiki instructions work... >> --VG >> >> >> >> On Dec 11, 2009, at 11:35 AM, youjun guo wrote: >> >> Vladimir, >> >> 1st, make sure your eclipse have the maven plugin like m2eclipse and >> subversion plugin like subclipse installed. >> >> 2rd instead of creating a maven project, "import a maven project form >> remote reposotory" in other words - treebase sourceforge svn url. >> >> All the dependencies were defined in pom.xml, maven know how to find them >> online, even if they are missing from you local .m2 directory >> >> Youjun >> >> >> >> On Fri, Dec 11, 2009 at 11:06 AM, Vladimir Gapeyev <vga...@ne...> >> wrote: >>> >>> Yes, I followed the wiki instructions, including running mvn install - >>> Dmaven.test.skip=true in the proper shell environment. This appeared >>> to have created the repository in ~vgapeyev/.m2, which Eclipse does >>> see through the M2_REPO variable. >>> >>> Note that only a fraction of the dependencies is missing in Eclipse. >>> Is there a chance they are simply missing from the Maven config >>> files? That is, can someone check the status of the handful of the >>> dependencies I have mentioned? Again, I can supply the full list if >>> this turns out to be the right way to go. >>> >>> I also tried following Youjun's advice, to create Maven rather than >>> Java projects in Eclipse. The wizard asks questions (about group and >>> artifact IDs, which I, as a Maven novice, do not understand) and >>> finally stops with the error "A pom.xml file already exists in the >>> destination folder". >>> >>> --Vladimir >>> >>> >>> On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: >>> >>> > Yes, you have to do the maven build first (e.g. from the command line) >>> > and make sure in eclipse that the M2_REPO variable is configured >>> > correctly (i.e. points to your local repository in >>> > $HOME/.m2/repository) >>> > >>> > On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> >>> > wrote: >>> >> Make sure you import the project as maven project, it will find and >>> >> download >>> >> those dependencies for you. >>> >> >>> >> Youjun >>> >> >>> >> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev >>> >> <vga...@ne... >>> >> > >>> >> wrote: >>> >>> >>> >>> Going through the installation instructions >>> >>> at >>> >>> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >>> >>> , >>> >>> I got to creation of Eclipse projects treebase-core and treebase- >>> >>> web. >>> >>> This gave me lots of missing buildpath entries: 11 in treebase- >>> >>> core and 39 >>> >>> in treebase-web. Please advise on how to proceed! >>> >>> Here are a few of the missing entries: >>> >>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- >>> >>> extensions-1.2.jar >>> >>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- >>> >>> framework-4.1.3.jar >>> >>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar >>> >>> >>> >>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- >>> >>> beanutils-1.7.0.jar >>> >>> I can work on putting together the whole list in case it will be >>> >>> useful. >>> >>> --Vladimir >>> >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> 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 >>> >>> >>> >> >>> >> >>> >> >>> >> ------------------------------------------------------------------------------ >>> >> 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 >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >> >> >> >> >> ------------------------------------------------------------------------------ >> 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 >> > > > ------------------------------------------------------------------------------ > 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: youjun g. <you...@ya...> - 2009-12-12 01:00:34
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If you want to run Rutger's publish script and deploy treebase to a tomcat in your workstation you do need to set up environment variables based on the wiki. Alternative solution is run "maven package" on the project from your eclipse to build the war file then copy the treebase-web.war to your tomcat webapp directory, then restart the tomcat if you didn't set the autodeploy. On Fri, Dec 11, 2009 at 5:26 PM, Vladimir Gapeyev <vga...@ne...>wrote: > Ok, I followed Youjun's advice to create an Eclipse project via the Maven > plugin, which did its own SVn checkout into an empty workspace. Eclipse > gave pleasantly few red marks to the result: > - Missing indirectly referenced artifact > mesquite:mesquite:jar:2.6+SNAPSHOT:compile > - and something cryptic at the end > of treebase-web/src/main/webapp/WEB-INF/pages/search/study/analyses.jsp > I presume these are benign. > > From this point, however, I am at a loss what needs to be configured so > that I have a functional web site at my localhost:8080 that connects to the > postgres instance. > > Starting Tomcat via the Servers view, as > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment recommends, > was not successful. (Tomcat startup log attached > > ) > > Thanks for further guidance, > > --Vladimir > > > On Dec 11, 2009, at 2:13 PM, youjun guo wrote: > > Vladimir, > > Unless you are going to do the developing work directly on the treebase-dev > server , or you want to remotely deploy from your workstation to the > treebase tomcat server, your eclipse set up have nothing to do with the > shell envelopment. > > m2eclipse is a mvn inatall for eclipse. > > Youjun > > > On Fri, Dec 11, 2009 at 1:26 PM, Vladimir Gapeyev <vga...@ne...>wrote: > >> Youjun, >> >> As I understand, you suggest to skip the (mvn install; Eclipse workspace >> at trunk; create Java projects from existing files) part of instructions >> at >> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> and instead start with an Eclipse workspace in a blank directory. >> >> I'll probably try that if nothing can make the above instructions work. >> However, it will be useful if we can make those wiki instructions work... >> >> --VG >> >> >> >> > > > > ------------------------------------------------------------------------------ > 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...> - 2009-12-11 22:26:48
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Ok, I followed Youjun's advice to create an Eclipse project via the Maven plugin, which did its own SVn checkout into an empty workspace. Eclipse gave pleasantly few red marks to the result: - Missing indirectly referenced artifact mesquite:mesquite:jar: 2.6+SNAPSHOT:compile - and something cryptic at the end of treebase-web/src/main/webapp/ WEB-INF/pages/search/study/analyses.jsp I presume these are benign. From this point, however, I am at a loss what needs to be configured so that I have a functional web site at my localhost:8080 that connects to the postgres instance. Starting Tomcat via the Servers view, as https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment recommends, was not successful. (Tomcat startup log attached ) Thanks for further guidance, --Vladimir On Dec 11, 2009, at 2:13 PM, youjun guo wrote: > Vladimir, > > Unless you are going to do the developing work directly on the > treebase-dev server , or you want to remotely deploy from your > workstation to the treebase tomcat server, your eclipse set up have > nothing to do with the shell envelopment. > > m2eclipse is a mvn inatall for eclipse. > > Youjun > > > On Fri, Dec 11, 2009 at 1:26 PM, Vladimir Gapeyev <vga...@ne... > > wrote: > Youjun, > > As I understand, you suggest to skip the (mvn install; Eclipse > workspace at trunk; create Java projects from existing files) part > of instructions at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > and instead start with an Eclipse workspace in a blank directory. > > I'll probably try that if nothing can make the above instructions > work. However, it will be useful if we can make those wiki > instructions work... > > --VG > > > > |
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From: youjun g. <you...@ya...> - 2009-12-11 19:13:23
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Vladimir, Unless you are going to do the developing work directly on the treebase-dev server , or you want to remotely deploy from your workstation to the treebase tomcat server, your eclipse set up have nothing to do with the shell envelopment. m2eclipse is a mvn inatall for eclipse. Youjun On Fri, Dec 11, 2009 at 1:26 PM, Vladimir Gapeyev <vga...@ne...>wrote: > Youjun, > > As I understand, you suggest to skip the (mvn install; Eclipse workspace > at trunk; create Java projects from existing files) part of instructions > at > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > and instead start with an Eclipse workspace in a blank directory. > > I'll probably try that if nothing can make the above instructions work. > However, it will be useful if we can make those wiki instructions work... > > --VG > > > > > On Dec 11, 2009, at 11:35 AM, youjun guo wrote: > > Vladimir, > > 1st, make sure your eclipse have the maven plugin like m2eclipse and > subversion plugin like subclipse installed. > > 2rd instead of creating a maven project, "import a maven project form > remote reposotory" in other words - treebase sourceforge svn url. > > All the dependencies were defined in pom.xml, maven know how to find them > online, even if they are missing from you local .m2 directory > > Youjun > > > > On Fri, Dec 11, 2009 at 11:06 AM, Vladimir Gapeyev <vga...@ne...>wrote: > >> Yes, I followed the wiki instructions, including running mvn install - >> Dmaven.test.skip=true in the proper shell environment. This appeared >> to have created the repository in ~vgapeyev/.m2, which Eclipse does >> see through the M2_REPO variable. >> >> Note that only a fraction of the dependencies is missing in Eclipse. >> Is there a chance they are simply missing from the Maven config >> files? That is, can someone check the status of the handful of the >> dependencies I have mentioned? Again, I can supply the full list if >> this turns out to be the right way to go. >> >> I also tried following Youjun's advice, to create Maven rather than >> Java projects in Eclipse. The wizard asks questions (about group and >> artifact IDs, which I, as a Maven novice, do not understand) and >> finally stops with the error "A pom.xml file already exists in the >> destination folder". >> >> --Vladimir >> >> >> On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: >> >> > Yes, you have to do the maven build first (e.g. from the command line) >> > and make sure in eclipse that the M2_REPO variable is configured >> > correctly (i.e. points to your local repository in >> > $HOME/.m2/repository) >> > >> > On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> >> > wrote: >> >> Make sure you import the project as maven project, it will find and >> >> download >> >> those dependencies for you. >> >> >> >> Youjun >> >> >> >> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev < >> vga...@ne... >> >> > >> >> wrote: >> >>> >> >>> Going through the installation instructions >> >>> at >> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> >>> , >> >>> I got to creation of Eclipse projects treebase-core and treebase- >> >>> web. >> >>> This gave me lots of missing buildpath entries: 11 in treebase- >> >>> core and 39 >> >>> in treebase-web. Please advise on how to proceed! >> >>> Here are a few of the missing entries: >> >>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- >> >>> extensions-1.2.jar >> >>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- >> >>> framework-4.1.3.jar >> >>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar >> >>> >> >>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- >> >>> beanutils-1.7.0.jar >> >>> I can work on putting together the whole list in case it will be >> >>> useful. >> >>> --Vladimir >> >>> >> >>> >> ------------------------------------------------------------------------------ >> >>> 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 >> >>> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> 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 >> >> >> >> ------------------------------------------------------------------------------ >> 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 >> > > > > > ------------------------------------------------------------------------------ > 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...> - 2009-12-11 18:26:58
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Youjun, As I understand, you suggest to skip the (mvn install; Eclipse workspace at trunk; create Java projects from existing files) part of instructions at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment and instead start with an Eclipse workspace in a blank directory. I'll probably try that if nothing can make the above instructions work. However, it will be useful if we can make those wiki instructions work... --VG On Dec 11, 2009, at 11:35 AM, youjun guo wrote: > Vladimir, > > 1st, make sure your eclipse have the maven plugin like m2eclipse and > subversion plugin like subclipse installed. > > 2rd instead of creating a maven project, "import a maven project > form remote reposotory" in other words - treebase sourceforge svn > url. > > All the dependencies were defined in pom.xml, maven know how to find > them online, even if they are missing from you local .m2 directory > > Youjun > > > > On Fri, Dec 11, 2009 at 11:06 AM, Vladimir Gapeyev <vga...@ne... > > wrote: > Yes, I followed the wiki instructions, including running mvn install - > Dmaven.test.skip=true in the proper shell environment. This appeared > to have created the repository in ~vgapeyev/.m2, which Eclipse does > see through the M2_REPO variable. > > Note that only a fraction of the dependencies is missing in Eclipse. > Is there a chance they are simply missing from the Maven config > files? That is, can someone check the status of the handful of the > dependencies I have mentioned? Again, I can supply the full list if > this turns out to be the right way to go. > > I also tried following Youjun's advice, to create Maven rather than > Java projects in Eclipse. The wizard asks questions (about group and > artifact IDs, which I, as a Maven novice, do not understand) and > finally stops with the error "A pom.xml file already exists in the > destination folder". > > --Vladimir > > > On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: > > > Yes, you have to do the maven build first (e.g. from the command > line) > > and make sure in eclipse that the M2_REPO variable is configured > > correctly (i.e. points to your local repository in > > $HOME/.m2/repository) > > > > On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> > > wrote: > >> Make sure you import the project as maven project, it will find and > >> download > >> those dependencies for you. > >> > >> Youjun > >> > >> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev <vga...@ne... > >> > > >> wrote: > >>> > >>> Going through the installation instructions > >>> at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > >>> , > >>> I got to creation of Eclipse projects treebase-core and treebase- > >>> web. > >>> This gave me lots of missing buildpath entries: 11 in treebase- > >>> core and 39 > >>> in treebase-web. Please advise on how to proceed! > >>> Here are a few of the missing entries: > >>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- > >>> extensions-1.2.jar > >>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- > >>> framework-4.1.3.jar > >>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar > >>> > >>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- > >>> beanutils-1.7.0.jar > >>> I can work on putting together the whole list in case it will be > >>> useful. > >>> --Vladimir > >>> > >>> > ------------------------------------------------------------------------------ > >>> 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 > >>> > >> > >> > >> > ------------------------------------------------------------------------------ > >> 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 > > > ------------------------------------------------------------------------------ > 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: youjun g. <you...@ya...> - 2009-12-11 16:36:00
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Vladimir, 1st, make sure your eclipse have the maven plugin like m2eclipse and subversion plugin like subclipse installed. 2rd instead of creating a maven project, "import a maven project form remote reposotory" in other words - treebase sourceforge svn url. All the dependencies were defined in pom.xml, maven know how to find them online, even if they are missing from you local .m2 directory Youjun On Fri, Dec 11, 2009 at 11:06 AM, Vladimir Gapeyev <vga...@ne...>wrote: > Yes, I followed the wiki instructions, including running mvn install - > Dmaven.test.skip=true in the proper shell environment. This appeared > to have created the repository in ~vgapeyev/.m2, which Eclipse does > see through the M2_REPO variable. > > Note that only a fraction of the dependencies is missing in Eclipse. > Is there a chance they are simply missing from the Maven config > files? That is, can someone check the status of the handful of the > dependencies I have mentioned? Again, I can supply the full list if > this turns out to be the right way to go. > > I also tried following Youjun's advice, to create Maven rather than > Java projects in Eclipse. The wizard asks questions (about group and > artifact IDs, which I, as a Maven novice, do not understand) and > finally stops with the error "A pom.xml file already exists in the > destination folder". > > --Vladimir > > > On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: > > > Yes, you have to do the maven build first (e.g. from the command line) > > and make sure in eclipse that the M2_REPO variable is configured > > correctly (i.e. points to your local repository in > > $HOME/.m2/repository) > > > > On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> > > wrote: > >> Make sure you import the project as maven project, it will find and > >> download > >> those dependencies for you. > >> > >> Youjun > >> > >> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev <vga...@ne... > >> > > >> wrote: > >>> > >>> Going through the installation instructions > >>> at > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > >>> , > >>> I got to creation of Eclipse projects treebase-core and treebase- > >>> web. > >>> This gave me lots of missing buildpath entries: 11 in treebase- > >>> core and 39 > >>> in treebase-web. Please advise on how to proceed! > >>> Here are a few of the missing entries: > >>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- > >>> extensions-1.2.jar > >>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- > >>> framework-4.1.3.jar > >>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar > >>> > >>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- > >>> beanutils-1.7.0.jar > >>> I can work on putting together the whole list in case it will be > >>> useful. > >>> --Vladimir > >>> > >>> > ------------------------------------------------------------------------------ > >>> 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 > >>> > >> > >> > >> > ------------------------------------------------------------------------------ > >> 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 > > > > ------------------------------------------------------------------------------ > 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...> - 2009-12-11 16:06:48
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Yes, I followed the wiki instructions, including running mvn install - Dmaven.test.skip=true in the proper shell environment. This appeared to have created the repository in ~vgapeyev/.m2, which Eclipse does see through the M2_REPO variable. Note that only a fraction of the dependencies is missing in Eclipse. Is there a chance they are simply missing from the Maven config files? That is, can someone check the status of the handful of the dependencies I have mentioned? Again, I can supply the full list if this turns out to be the right way to go. I also tried following Youjun's advice, to create Maven rather than Java projects in Eclipse. The wizard asks questions (about group and artifact IDs, which I, as a Maven novice, do not understand) and finally stops with the error "A pom.xml file already exists in the destination folder". --Vladimir On Dec 11, 2009, at 8:37 AM, Rutger Vos wrote: > Yes, you have to do the maven build first (e.g. from the command line) > and make sure in eclipse that the M2_REPO variable is configured > correctly (i.e. points to your local repository in > $HOME/.m2/repository) > > On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> > wrote: >> Make sure you import the project as maven project, it will find and >> download >> those dependencies for you. >> >> Youjun >> >> On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev <vga...@ne... >> > >> wrote: >>> >>> Going through the installation instructions >>> at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >>> , >>> I got to creation of Eclipse projects treebase-core and treebase- >>> web. >>> This gave me lots of missing buildpath entries: 11 in treebase- >>> core and 39 >>> in treebase-web. Please advise on how to proceed! >>> Here are a few of the missing entries: >>> M2_REPO/apple/apple-java-extensions/1.2/apple-java- >>> extensions-1.2.jar >>> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- >>> framework-4.1.3.jar >>> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar >>> >>> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- >>> beanutils-1.7.0.jar >>> I can work on putting together the whole list in case it will be >>> useful. >>> --Vladimir >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> >> >> >> ------------------------------------------------------------------------------ >> 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...> - 2009-12-11 14:06:51
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Yes, you have to do the maven build first (e.g. from the command line) and make sure in eclipse that the M2_REPO variable is configured correctly (i.e. points to your local repository in $HOME/.m2/repository) On Thu, Dec 10, 2009 at 11:39 PM, youjun guo <you...@ya...> wrote: > Make sure you import the project as maven project, it will find and download > those dependencies for you. > > Youjun > > On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev <vga...@ne...> > wrote: >> >> Going through the installation instructions >> at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment, >> I got to creation of Eclipse projects treebase-core and treebase-web. >> This gave me lots of missing buildpath entries: 11 in treebase-core and 39 >> in treebase-web. Please advise on how to proceed! >> Here are a few of the missing entries: >> M2_REPO/apple/apple-java-extensions/1.2/apple-java-extensions-1.2.jar >> M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon-framework-4.1.3.jar >> M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar >> >> M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons-beanutils-1.7.0.jar >> I can work on putting together the whole list in case it will be useful. >> --Vladimir >> >> ------------------------------------------------------------------------------ >> 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 >> > > > ------------------------------------------------------------------------------ > 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: youjun g. <you...@ya...> - 2009-12-10 23:39:58
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Make sure you import the project as maven project, it will find and download those dependencies for you. Youjun On Thu, Dec 10, 2009 at 6:18 PM, Vladimir Gapeyev <vga...@ne...>wrote: > > Going through the installation instructions at > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment, > I got to creation of Eclipse projects treebase-core and treebase-web. > * > * > This gave me lots of missing buildpath entries: 11 in treebase-core and 39 > in treebase-web. Please advise on how to proceed! > Here are a few of the missing entries: > > M2_REPO/apple/apple-java-extensions/1.2/apple-java-extensions-1.2.jar > M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon-framework-4.1.3.jar > M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar > > M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons-beanutils-1.7.0.jar > > I can work on putting together the whole list in case it will be useful. > > --Vladimir > > > ------------------------------------------------------------------------------ > 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...> - 2009-12-10 23:18:27
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Going through the installation instructions at https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment , I got to creation of Eclipse projects treebase-core and treebase-web. This gave me lots of missing buildpath entries: 11 in treebase-core and 39 in treebase-web. Please advise on how to proceed! Here are a few of the missing entries: M2_REPO/apple/apple-java-extensions/1.2/apple-java-extensions-1.2.jar M2_REPO/avalon-framework/avalon-framework/4.1.3/avalon- framework-4.1.3.jar M2_REPO/com/lowagie/itext/1.3/itext-1.3.jar M2_REPO/commons-beanutils/commons-beanutils/1.7.0/commons- beanutils-1.7.0.jar I can work on putting together the whole list in case it will be useful. --Vladimir |
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From: youjun g. <you...@ya...> - 2009-12-10 19:45:57
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Sorry, I think I failed to describe this issue clearly in last email. We have 3 Type of citations: type "A" article; type "B" book; type "I" inbook (charpter?) In database they are all in the same table (citation) with column "type" mark their catogory (In java they are 4 different types). I found 4 type "B" citations records in table citation.treebase-dev. 2 of them have null value on column "tittle" , the other 2 have null value on column "booktittle". So return "booktittle" on type "B" will also cause null. Youjun On Thu, Dec 10, 2009 at 11:17 AM, youjun guo <you...@ya...> wrote: > Hi, Rutger, > > I git your comments on this issue: > > Added a getTitle() override. We always want getTitle() to return something. > For ArticleCitations, this field would normally be set with the name of the > > article. For InBookCitation, this field is populated with the section title, > so InBookCitation.getSectionTitle() calls the getTitle() method defined here, > from whence we need to go up the inheritance tree to the parent Citation class. > > For BookCitations, the title field is unset, so we return the BookTitle field > instead. This should resolve issue #2903172. > > > I am working on this bug: [ treebase-Bugs-2902650 ] Book titles don't > appear under study tab and found totally 4 published citations records in > our citation.treebase-dev. Two of them have booktiltle without tittle, and > the other 2 have tilttle without booktittle. So > "return the BookTitle field" may cause new problem. > > We may need to fix the table data, or return tiltte/booktittle whichever is > not null. > > Youjun > >> >> >> > |
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From: youjun g. <you...@ya...> - 2009-12-10 16:17:15
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Hi, Rutger, I git your comments on this issue: Added a getTitle() override. We always want getTitle() to return something. For ArticleCitations, this field would normally be set with the name of the article. For InBookCitation, this field is populated with the section title, so InBookCitation.getSectionTitle() calls the getTitle() method defined here, from whence we need to go up the inheritance tree to the parent Citation class. For BookCitations, the title field is unset, so we return the BookTitle field instead. This should resolve issue #2903172. I am working on this bug: [ treebase-Bugs-2902650 ] Book titles don't appear under study tab and found totally 4 published citations records in our citation.treebase-dev. Two of them have booktiltle without tittle, and the other 2 have tilttle without booktittle. So "return the BookTitle field" may cause new problem. We may need to fix the table data, or return tiltte/booktittle whichever is not null. Youjun > > > |
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