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From: youjun g. <you...@ya...> - 2009-12-17 13:21:47
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Vladimir, Congratulations! Youjun On Wed, Dec 16, 2009 at 2:32 PM, Vladimir Gapeyev <vla...@du... > wrote: > > On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > > > Vladimir, if you do an update on your end, will the source now build > > on your system? The complaints about mesquite.lib.* missing should go > > away. > > Uff, the easy step is done: I was able to build treebase-web.war that > runs on localhost (revision 398). I attach below the cumulative > instructions on how I did it. > > Now I need to figure out what are the most comfortable currently known > setups for (1) development and (2) server. The one I figured out so > far is not good for either, while the instructions on the wiki did not > work for me. Also, I am sure, there are many more details I need to > know about the project and now am in a position to start to understand. > > Who would be the best person to spend a few hours talking to me > sometime soon? Rutger, since Wednesday is probably over for you, > would you be able to start with me on this Thu morning, around 9am my > (US Eastern) time? > > --Vladimir > > > > ==Development environment in Eclipse== > > * Install Subclipse and Maven Integration plugins > > * Register Treebase SVN repository in Eclipse > ** Open SVN Repositories view: menu Window > Show View > Other ... > > SVN / SVN Repositories > ** Right-click > New > Repository Location > ** Enter https://treebase.svn.sourceforge.net/svnroot/treebase > > * Connect to the Maven project in SVN > ** In Project Explorer, Right-click > New > Project > Maven / Checkout > Maven Projects from SCM > ** SCM url: SVN as type, browse for the repository registered above, > and select the 'trunk' folder. > ** Next > ** Location: specify as desired (to an empty directory) > ** Finish (Takes awhile, not much action visible) > > * Place <tt>jdbc.properties</tt> file, containing appropriate > credentials, into <tt>treebase-core/src/main/resources</tt>. > > * Build the Maven project, skipping the tests. > ** On the 'treebase' project: Run As > m2 6 Maven build ... > > *** Goals: package > *** Skip tests: checkmark > *** Resolve Workspace artifacts: uncheck > *** Run > ** When successful, this creates treebase/treebase-web/target/treebase- > web.war > > * Deploy treebase-web.war under Tomcat > ** Place treebase-web.war into $CATALINA_HOME/webapps > ** Start Tomcat via $CATALINA_HOME/bin/startup.sh > ** The app should be available at http://localhost:8080/treebase-web/ > ** In case of trouble, check logs in $CATALINA_HOME/logs, especially > the <tt>catalina.out</tt> log. > > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and > easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > |
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From: Hilmar L. <hl...@ne...> - 2009-12-16 23:44:16
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On Dec 16, 2009, at 1:39 PM, Vladimir Gapeyev wrote: > move whatever settings are currently specified in treebase-core/src/ > main/resources/ > jdbc.properties out of the WAR file and into tomcat configuration. Ideally the .war file is actually as self-contained as possible, i.e., contains as much configuration as it can. Keep in mind that normally, only a system administrator can change the application server configuration, whereas a deployable is under the control of the developers. Also, looking toward the future, it is possible that a mirror site doesn't have any signifiant sysadmin support, or their sysadmin support may be reluctant to change the configuration of their application server. So normally the way this is done is that the deployment descriptor or configuration file that holds the necessarily machine-specific configuration is created fresh each time from a template when the .war (or whatever deployable) is built, and packaged along with it. This can be easily written as an ant task, and in fact we do this for several projects at NESCent (Vladimir, you can ask Xianhua to show you examples). There are ant tasks for replacing placeholder variables with actual values that can be specified on the ant command line or in a properties file. I would assume that maven can do the exact same thing, if not better. That said, if that complicates things too much for now, let's table that for after release, and hard-configure tomcat. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2009-12-16 23:46:04
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On Dec 16, 2009, at 2:32 PM, Vladimir Gapeyev wrote: > I was able to build treebase-web.war that runs on localhost > (revision 398). Cool! > I attach below the cumulative instructions on how I did it. Great, thanks for keeping track. Would you mind posting this to the TreeBASE wiki? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2009-12-17 09:29:38
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>> I attach below the cumulative instructions on how I did it. > > Great, thanks for keeping track. Would you mind posting this to the TreeBASE > wiki? Seconded! Could you try to fit it in with the current page structure? I.E. add your comments to the following pages: * IDE configuration: https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment * source code checkout: https://sourceforge.net/apps/mediawiki/treebase/index.php?title=SourceCode * maven dependency management: https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DependencyManagement * deployment to a servlet container: https://sourceforge.net/apps/mediawiki/treebase/index.php?title=WebServers -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Vladimir G. <vla...@du...> - 2009-12-17 14:01:05
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I should specify that the parameters I do care about are the likes of database URL, username, password, mesquite installation folder. (See https://sourceforge.net/apps/mediawiki/treebase/index.php?title=JdbcProperties for the rest, which I agree could be ok to hardwire into a build.) I think it would be highly unreasonable that a sysadmin would need to ask the developers to make a new build any time he changes the DB password (or that the developers should even know the password for the production DB server!) --Vladimir On Dec 16, 2009, at 6:44 PM, Hilmar Lapp wrote: > > On Dec 16, 2009, at 1:39 PM, Vladimir Gapeyev wrote: > >> move whatever settings are currently specified in treebase-core/src/ >> main/resources/ >> jdbc.properties out of the WAR file and into tomcat configuration. > > > Ideally the .war file is actually as self-contained as possible, > i.e., contains as much configuration as it can. > > Keep in mind that normally, only a system administrator can change > the application server configuration, whereas a deployable is under > the control of the developers. Also, looking toward the future, it > is possible that a mirror site doesn't have any signifiant sysadmin > support, or their sysadmin support may be reluctant to change the > configuration of their application server. > > So normally the way this is done is that the deployment descriptor > or configuration file that holds the necessarily machine-specific > configuration is created fresh each time from a template when > the .war (or whatever deployable) is built, and packaged along with > it. This can be easily written as an ant task, and in fact we do > this for several projects at NESCent (Vladimir, you can ask Xianhua > to show you examples). There are ant tasks for replacing placeholder > variables with actual values that can be specified on the ant > command line or in a properties file. I would assume that maven can > do the exact same thing, if not better. > > That said, if that complicates things too much for now, let's table > that for after release, and hard-configure tomcat. > > -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > |
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From: Hilmar L. <hl...@ne...> - 2009-12-17 14:28:56
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On Dec 17, 2009, at 9:00 AM, Vladimir Gapeyev wrote: > I think it would be highly unreasonable that a sysadmin would need > to ask the developers to make a new build any time he changes the DB > password (or that the developers should even know the password for > the production DB server!) I'm not sure it's highly unreasonable. It is though the way we've settled on doing things here. BTW even though they know password and user, developers still can't log into the production database because it is firewalled off from everywhere except the production application server (where the application connects from). -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Vladimir G. <vla...@du...> - 2009-12-17 14:05:02
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I'd need proper rights to the wiki to do that. The summary I've got would only go to the DeveloperEnvironment page -- I don't yet understand its implications for the others. --VG On Dec 17, 2009, at 4:29 AM, Rutger Vos wrote: >>> I attach below the cumulative instructions on how I did it. >> >> Great, thanks for keeping track. Would you mind posting this to the >> TreeBASE >> wiki? > > Seconded! Could you try to fit it in with the current page structure? > I.E. add your comments to the following pages: > > * IDE configuration: > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment > > * source code checkout: > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=SourceCode > > * maven dependency management: > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DependencyManagement > > * deployment to a servlet container: > https://sourceforge.net/apps/mediawiki/treebase/index.php?title=WebServers > > -- > 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...> - 2009-12-17 14:25:32
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I believe you should be able to log in on the wiki using your sf.net account. On Thu, Dec 17, 2009 at 2:04 PM, Vladimir Gapeyev <vla...@du...> wrote: > I'd need proper rights to the wiki to do that. > The summary I've got would only go to the DeveloperEnvironment page -- I > don't yet understand its implications for the others. > --VG > > > On Dec 17, 2009, at 4:29 AM, Rutger Vos wrote: > >>>> I attach below the cumulative instructions on how I did it. >>> >>> Great, thanks for keeping track. Would you mind posting this to the >>> TreeBASE >>> wiki? >> >> Seconded! Could you try to fit it in with the current page structure? >> I.E. add your comments to the following pages: >> >> * IDE configuration: >> >> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DeveloperEnvironment >> >> * source code checkout: >> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=SourceCode >> >> * maven dependency management: >> >> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=DependencyManagement >> >> * deployment to a servlet container: >> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=WebServers >> >> -- >> 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...> - 2009-12-17 15:07:15
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Vladimir and Youjun are now both also editors and admins on the wiki. On Thu, Dec 17, 2009 at 2:49 PM, Vladimir Gapeyev <vla...@du...> wrote: > I can log in, but I cannot edit pages. I probably should be assigned a > suitable user group within the wiki. --vg > > On Dec 17, 2009, at 9:25 AM, Rutger Vos wrote: > >> I believe you should be able to log in on the wiki using your sf.net >> account. >> >> On Thu, Dec 17, 2009 at 2:04 PM, Vladimir Gapeyev >> <vla...@du...> wrote: >>> >>> I'd need proper rights to the wiki to do that. >>> The summary I've got would only go to the DeveloperEnvironment page -- I >>> don't yet understand its implications for the others. >>> --VG >>> >>> > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@ne...> - 2009-12-17 21:19:15
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On Dec 16, 2009, at 1:22 PM, Jon Auman wrote: > I suggest that treebase-dev be configured to run from the treebase > account on the server. I agree. > CATALINA_HOME : /home/treebase/tomcat Ditto. > The environment for this user should be setup from scratch instead > of copied over from an existing user's home dir. Yes. Rutger, are the instructions for that now complete, including any Mesquite environment variables? > I'll create an initd script that starts tomcat on startup of the > server. All developers will be able to start and stop that instance > of tomcat as well. That sounds great. > BTW, I tired to start Rutger's instance of tomcat with sudo this > morning and was not able to because it needed some environment > variables to start. Will this be necessary on production? I would > prefer not. I usually put those variables in tomcat5.conf or in the > catalina.sh script. It sounds like we need to fix that too so they are indeed part of the tomcat startup configuration. Is that part of the documented instructions above? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2009-12-18 10:49:50
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>> The environment for this user should be setup from scratch instead of >> copied over from an existing user's home dir. > > Yes. Rutger, are the instructions for that now complete, including any > Mesquite environment variables? Yes. It's on the wiki, there's also a file with the same variables in /home/rvosa/vars >> BTW, I tired to start Rutger's instance of tomcat with sudo this morning >> and was not able to because it needed some environment variables to start. >> Will this be necessary on production? I would prefer not. I usually put >> those variables in tomcat5.conf or in the catalina.sh script. > > It sounds like we need to fix that too so they are indeed part of the tomcat > startup configuration. Is that part of the documented instructions above? Not yet. The configuration that is being suggested here is different from how I did it. I approached it as a programmer wanting to have all the required variables set in the shell, so I can run scripts, launch standalone mesquite, etc. What Jon is suggesting is a more sysadmin-oriented approach where everything is scoped inside tomcat so that there is no hidden "magic" in the outside environment. I guess the consensus is that that suggestion is better, so what we should probably do is set it up on tre...@tr..., then update the wiki. -- 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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