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From: Rutger V. <rut...@gm...> - 2009-12-17 16:57:23
|
Hi Wayne, thanks - I think we're not going to tinker with upgrading right now, though we definitely should later on. There are some situations where having a new mesquite on our server will significantly enhance the user experience (say, when they're uploading a massive set of bayesian trees) but right now we just want to roll out the Mission Accomplished banner and unveil TreeBASE2.0 Rutger On Thu, Dec 17, 2009 at 3:52 PM, Wayne Maddison <wma...@in...> wrote: > Hi Rutger, > Great! You might still want to look at MesquiteRunner, since it may turn > out that you could upgrade to Mesquite 2.72 via its methods. But, if your > current system ain't broke.... > Wayne > > At 5:58 PM +0000 16.12.2009, Rutger Vos wrote: >> >> Hi Wayne, >> >> it worked - hurrah! Thank you very much, high-fives all around. >> >> Rutger >> >> On Wed, Dec 16, 2009 at 3:28 PM, Wayne Maddison >> <wma...@in...> wrote: >>> >>> Rutger, >>> How about setting the static MesquiteModule.mesquiteDirectory before to >>> call >>> to Mesquite.main? >>> Wayne >>> >>>> Hi Wayne, >>>> >>>> On Tue, Dec 15, 2009 at 7:05 PM, Wayne Maddison >>>> <wma...@in...> wrote: >>>>> >>>>> This code is ancient -- probably has not been activated in 10 years! >>>>> Mesquite in general always knows where its home folder is, but we have >>>>> not >>>>> been trying server stuff. >>>> >>>> I know this code is ancient, which is why I was a little embarrassed >>>> to ask about it. Supposedly, Jin Ruan applied some slight patches to >>>> it to make it work with TreeBASE, but he didn't record anywhere what >>>> those changes were (and whether they're even still necessary: I notice >>>> a lot of work has gone into making mesquite more amenable to our sort >>>> of use cases). >>>> >>>> The hard part is that the server is quite a different environment that >>>> constructs its own class path and has its own way of loading classes. >>>> Also, the calling class lives inside a "war" file - a jar containing a >>>> web application - whereas mesquite lives inside >>>> $CATALINA_HOME/shared/classes, the location from whence shared classes >>>> are visible to web applications. >>>> >>>> Since "war" files are actually unpacked into a class folder the first >>>> time the server sees the archive I suppose I could copy the mesquite >>>> classes into that same folder structure and see what happens. Tomcat >>>> purists be damned. >>>> >>>>> mesquiteLocation.txt and the entries in Mesquite.xml don't help -- >>>>> they >>>>> are >>>>> a service to otehr programs. >>>> >>>> Ah, thanks, at least I can stop worrying about those then. >>>> >>>>> Is that the entire log file? >>>> >>>> The log file I sent you is the whole thing. >>>> >>>>> What version of Mesquite are you using? >>>> >>>> We're using version "2.01tb". >>>> >>>>> How exactly are you calling Mesquite? You might want to look into >>>>> svn.mesquiteproject.org, RMesquite, >>>>> src/java/mesquite/R/RCallsMesquite/lib/MesquiteRunner for an actively >>>>> developed class that instantiates and calls Mesquite. To tell you the >>>>> truth, now that I think about it, I'm not sure how this works -- I'm >>>>> not >>>>> sure how Mesquite knows its home directory if its in a different >>>>> classpath >>>>> than the one in which the class calling it lives. >>>> >>>> All we're doing is the following: >>>> >>>> Mesquite.main(new String[] {"-w"}); >>>> MesquiteProject project = >>>> MesquiteTrunk.mesquiteTrunk.openFile(pFile.getAbsolutePath()); >>>> >>>> I'll have a look at the R code, see if that gives me any pointers. >>>> >>>> Thanks! >>>> >>>> Rutger >>>> >>>> >>>>>> Hi Wayne, >>>>>> >>>>>> I'm having trouble launching mesquite programmatically as treebase's >>>>>> nexus file parser. Try as I might, the log keeps showing that it >>>>>> cannot find the Mesquite_Folder: it wants me to show where the >>>>>> manuals >>>>>> is located. Could you give me a hint as to which of the following >>>>>> moving parts are involved: >>>>>> >>>>>> * ~/Mesquite_Support_Files/Mesquite_Prefs/mesquiteLocation.txt - I >>>>>> set >>>>>> this to the right location >>>>>> >>>>>> * ~/Mesquite_Support_Files/Mesquite_Prefix/Mesquite.xml - I set >>>>>> mesquiteHeadlessPath and mesquitePath to the right location >>>>>> >>>>>> * system property "mesquite.folder_dir" - I set this to the right >>>>>> location >>>>>> >>>>>> What else can I do? Is there a programmatic way to set this? I'm >>>>>> hoping to have overlooked a Mesquite.setMesquiteDirectory() method, >>>>>> but there are probably good reasons why that doesn't exist. Can I >>>>>> pass >> >> >>>> it to the main method? >>>>>> >>>>>> 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 >>>>>> >>>>>> Content-type: application/octet-stream; name=Mesquite_Log >>>>>> Content-disposition: attachment; filename=Mesquite_Log >>>>>> X-Attachment-Id: f_g38tnpcj0 >>>>>> >>>>>> Attachment converted: Thrandina:Mesquite_Log 78 ( / ) >>>>>> (0078D979) >>>>> >>>>> >>>>> -- >>>>> -------------------------------------------------------- >>>>> Wayne Maddison >>>>> Professor and Canada Research Chair >>>>> Depts. of Zoology and Botany and >>>>> Biodiversity Research Centre >>>> >>>> > & Director >>>>> >>>>> Beaty Biodiversity Museum >>>>> 6270 University Boulevard >>>>> University of British Columbia >>>>> Vancouver, BC V6T 1Z4 Canada >>>>> >>>>> email: wma...@in... FAX: +1 604 822-2416 >>>>> >>>>> Mesquite: http://mesquiteproject.org >>>>> MacClade: http://macclade.org >>>>> Salticidae: http://salticidae.org >>>>> Tree of Life: http://tolweb.org >>>>> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca >>>>> Home page: http://salticidae.org/wpm/home.html >>>>> >>>> >>>> >>>> >>>> -- >>>> 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 >>> >>> >>> -- >>> -------------------------------------------------------- >>> Wayne Maddison >>> Professor and Canada Research Chair >>> Depts. of Zoology and Botany and >>> Biodiversity Research Centre >>> & Director >>> Beaty Biodiversity Museum >>> 6270 University Boulevard >>> University of British Columbia >>> Vancouver, BC V6T 1Z4 Canada >>> >>> email: wma...@in... FAX: +1 604 822-2416 >>> >>> Mesquite: http://mesquiteproject.org >>> MacClade: http://macclade.org >>> Salticidae: http://salticidae.org >>> Tree of Life: http://tolweb.org >>> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca >>> Home page: http://salticidae.org/wpm/home.html >>> >> >> >> >> -- >> 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 > > > -- > -------------------------------------------------------- > Wayne Maddison > Professor and Canada Research Chair > Depts. of Zoology and Botany and > Biodiversity Research Centre > & Director > Beaty Biodiversity Museum > 6270 University Boulevard > University of British Columbia > Vancouver, BC V6T 1Z4 Canada > > email: wma...@in... FAX: +1 604 822-2416 > > Mesquite: http://mesquiteproject.org > MacClade: http://macclade.org > Salticidae: http://salticidae.org > Tree of Life: http://tolweb.org > Beaty Biodiversity Museum: http://beatymuseum.ubc.ca > Home page: http://salticidae.org/wpm/home.html > -- 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: Wayne M. <wma...@in...> - 2009-12-17 15:53:03
|
Hi Rutger, Great! You might still want to look at MesquiteRunner, since it may turn out that you could upgrade to Mesquite 2.72 via its methods. But, if your current system ain't broke.... Wayne At 5:58 PM +0000 16.12.2009, Rutger Vos wrote: >Hi Wayne, > >it worked - hurrah! Thank you very much, high-fives all around. > >Rutger > >On Wed, Dec 16, 2009 at 3:28 PM, Wayne Maddison ><wma...@in...> wrote: >> Rutger, >> How about setting the static MesquiteModule.mesquiteDirectory before to call >> to Mesquite.main? >> Wayne >> >>> Hi Wayne, >>> >>> On Tue, Dec 15, 2009 at 7:05 PM, Wayne Maddison >>> <wma...@in...> wrote: >>>> >>>> This code is ancient -- probably has not been activated in 10 years! >>>> Mesquite in general always knows where its home folder is, but we have >>>> not >>>> been trying server stuff. >>> >>> I know this code is ancient, which is why I was a little embarrassed >>> to ask about it. Supposedly, Jin Ruan applied some slight patches to >>> it to make it work with TreeBASE, but he didn't record anywhere what >>> those changes were (and whether they're even still necessary: I notice >>> a lot of work has gone into making mesquite more amenable to our sort >>> of use cases). >>> >>> The hard part is that the server is quite a different environment that >>> constructs its own class path and has its own way of loading classes. >>> Also, the calling class lives inside a "war" file - a jar containing a >>> web application - whereas mesquite lives inside >>> $CATALINA_HOME/shared/classes, the location from whence shared classes >>> are visible to web applications. >>> >>> Since "war" files are actually unpacked into a class folder the first >>> time the server sees the archive I suppose I could copy the mesquite >>> classes into that same folder structure and see what happens. Tomcat >>> purists be damned. >>> >>>> mesquiteLocation.txt and the entries in Mesquite.xml don't help -- they >>>> are >>>> a service to otehr programs. >>> >>> Ah, thanks, at least I can stop worrying about those then. >>> >>>> Is that the entire log file? >>> >>> The log file I sent you is the whole thing. >>> >>>> What version of Mesquite are you using? >>> >>> We're using version "2.01tb". >>> >>>> How exactly are you calling Mesquite? You might want to look into >>>> svn.mesquiteproject.org, RMesquite, >>>> src/java/mesquite/R/RCallsMesquite/lib/MesquiteRunner for an actively >>>> developed class that instantiates and calls Mesquite. To tell you the >>>> truth, now that I think about it, I'm not sure how this works -- I'm not >>>> sure how Mesquite knows its home directory if its in a different >>>> classpath >>>> than the one in which the class calling it lives. >>> >>> All we're doing is the following: >>> >>> Mesquite.main(new String[] {"-w"}); >>> MesquiteProject project = >>> MesquiteTrunk.mesquiteTrunk.openFile(pFile.getAbsolutePath()); >>> >>> I'll have a look at the R code, see if that gives me any pointers. >>> >>> Thanks! >>> >>> Rutger >>> >>> >>>>> Hi Wayne, >>>>> >>>>> I'm having trouble launching mesquite programmatically as treebase's >>>>> nexus file parser. Try as I might, the log keeps showing that it >>>>> cannot find the Mesquite_Folder: it wants me to show where the manuals >>>>> is located. Could you give me a hint as to which of the following >>>>> moving parts are involved: >>>>> >>>>> * ~/Mesquite_Support_Files/Mesquite_Prefs/mesquiteLocation.txt - I set >>>>> this to the right location >>>>> >>>>> * ~/Mesquite_Support_Files/Mesquite_Prefix/Mesquite.xml - I set >>>>> mesquiteHeadlessPath and mesquitePath to the right location >>>>> >>>>> * system property "mesquite.folder_dir" - I set this to the right >>>>> location >>>>> >>>>> What else can I do? Is there a programmatic way to set this? I'm >>>>> hoping to have overlooked a Mesquite.setMesquiteDirectory() method, >>>>> but there are probably good reasons why that doesn't exist. Can I pass > >>>> it to the main method? >>>>> >>>>> 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 >>>>> >>>>> Content-type: application/octet-stream; name=Mesquite_Log >>>>> Content-disposition: attachment; filename=Mesquite_Log >>>>> X-Attachment-Id: f_g38tnpcj0 >>>>> >>>>> Attachment converted: Thrandina:Mesquite_Log 78 ( / ) (0078D979) >>>> >>>> >>>> -- >>>> -------------------------------------------------------- >>>> Wayne Maddison >>>> Professor and Canada Research Chair >>>> Depts. of Zoology and Botany and >>>> Biodiversity Research Centre >>> >>> > & Director >>>> >>>> Beaty Biodiversity Museum >>>> 6270 University Boulevard >>>> University of British Columbia >>>> Vancouver, BC V6T 1Z4 Canada >>>> >>>> email: wma...@in... FAX: +1 604 822-2416 >>>> >>>> Mesquite: http://mesquiteproject.org >>>> MacClade: http://macclade.org >>>> Salticidae: http://salticidae.org >>>> Tree of Life: http://tolweb.org >>>> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca >>>> Home page: http://salticidae.org/wpm/home.html >>>> >>> >>> >>> >>> -- >>> 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 >> >> >> -- >> -------------------------------------------------------- >> Wayne Maddison >> Professor and Canada Research Chair >> Depts. of Zoology and Botany and >> Biodiversity Research Centre >> & Director >> Beaty Biodiversity Museum >> 6270 University Boulevard >> University of British Columbia >> Vancouver, BC V6T 1Z4 Canada >> >> email: wma...@in... FAX: +1 604 822-2416 >> >> Mesquite: http://mesquiteproject.org >> MacClade: http://macclade.org >> Salticidae: http://salticidae.org >> Tree of Life: http://tolweb.org >> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca >> Home page: http://salticidae.org/wpm/home.html >> > > > >-- >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 -- -------------------------------------------------------- Wayne Maddison Professor and Canada Research Chair Depts. of Zoology and Botany and Biodiversity Research Centre & Director Beaty Biodiversity Museum 6270 University Boulevard University of British Columbia Vancouver, BC V6T 1Z4 Canada email: wma...@in... FAX: +1 604 822-2416 Mesquite: http://mesquiteproject.org MacClade: http://macclade.org Salticidae: http://salticidae.org Tree of Life: http://tolweb.org Beaty Biodiversity Museum: http://beatymuseum.ubc.ca Home page: http://salticidae.org/wpm/home.html |
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From: Hilmar L. <hl...@ne...> - 2009-12-17 15:32:14
|
Just in case anyone forgot, we're starting our next follow-up release planning call now. Dial# as before. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2009-12-17 15:07:15
|
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 14:28:56
|
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: Rutger V. <rut...@gm...> - 2009-12-17 14:25:32
|
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: Vladimir G. <vla...@du...> - 2009-12-17 14:05:02
|
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: 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: Rutger V. <rut...@gm...> - 2009-12-17 13:49:52
|
Hi all, I summarized the benchmarking comparison. Here's what I did: * collected all matrix, study and tree IDs * wrote a perl script that fetches the PhyloWS URL for each data type, for each ID, for each server and recorded response time * wrote out the results in the attached files (e.g MATRICES.sdsc lists the response time in seconds for each matrix when downloaded from 8ball.sdsc.edu) * joined the equivalent files for both servers (e.g. $ join MATRICES.sdsc MATRICES.nescent > MATRICES.joined) * created box plots, which are the attached pdfs Conclusions: for pages where the main effort lies in tomcat returning JSPs (i.e. for studies and trees), NESCent outperforms SDSC (this is after I assigned more memory to tomcat). For pages where the main effort lies in the database returning data, SDSC (DB2) outperforms NESCent (postgres) by about 30%. The low hanging fruit for further optimization seems to be the database, not the servlet container. I consider this item on the release plan as 100% complete (green) and will now close issue #2899241 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: youjun g. <you...@ya...> - 2009-12-17 13:25:35
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Rutger, Good job. youjun On Wed, Dec 16, 2009 at 12:58 PM, Rutger Vos <rut...@gm...> wrote: > Hi Wayne, > > it worked - hurrah! Thank you very much, high-fives all around. > > Rutger > > On Wed, Dec 16, 2009 at 3:28 PM, Wayne Maddison > <wma...@in...> wrote: > > Rutger, > > How about setting the static MesquiteModule.mesquiteDirectory before to > call > > to Mesquite.main? > > Wayne > > > >> Hi Wayne, > >> > >> On Tue, Dec 15, 2009 at 7:05 PM, Wayne Maddison > >> <wma...@in...> wrote: > >>> > >>> This code is ancient -- probably has not been activated in 10 years! > >>> Mesquite in general always knows where its home folder is, but we have > >>> not > >>> been trying server stuff. > >> > >> I know this code is ancient, which is why I was a little embarrassed > >> to ask about it. Supposedly, Jin Ruan applied some slight patches to > >> it to make it work with TreeBASE, but he didn't record anywhere what > >> those changes were (and whether they're even still necessary: I notice > >> a lot of work has gone into making mesquite more amenable to our sort > >> of use cases). > >> > >> The hard part is that the server is quite a different environment that > >> constructs its own class path and has its own way of loading classes. > >> Also, the calling class lives inside a "war" file - a jar containing a > >> web application - whereas mesquite lives inside > >> $CATALINA_HOME/shared/classes, the location from whence shared classes > >> are visible to web applications. > >> > >> Since "war" files are actually unpacked into a class folder the first > >> time the server sees the archive I suppose I could copy the mesquite > >> classes into that same folder structure and see what happens. Tomcat > >> purists be damned. > >> > >>> mesquiteLocation.txt and the entries in Mesquite.xml don't help -- > they > >>> are > >>> a service to otehr programs. > >> > >> Ah, thanks, at least I can stop worrying about those then. > >> > >>> Is that the entire log file? > >> > >> The log file I sent you is the whole thing. > >> > >>> What version of Mesquite are you using? > >> > >> We're using version "2.01tb". > >> > >>> How exactly are you calling Mesquite? You might want to look into > >>> svn.mesquiteproject.org, RMesquite, > >>> src/java/mesquite/R/RCallsMesquite/lib/MesquiteRunner for an actively > >>> developed class that instantiates and calls Mesquite. To tell you the > >>> truth, now that I think about it, I'm not sure how this works -- I'm > not > >>> sure how Mesquite knows its home directory if its in a different > >>> classpath > >>> than the one in which the class calling it lives. > >> > >> All we're doing is the following: > >> > >> Mesquite.main(new String[] {"-w"}); > >> MesquiteProject project = > >> MesquiteTrunk.mesquiteTrunk.openFile(pFile.getAbsolutePath()); > >> > >> I'll have a look at the R code, see if that gives me any pointers. > >> > >> Thanks! > >> > >> Rutger > >> > >> > >>>> Hi Wayne, > >>>> > >>>> I'm having trouble launching mesquite programmatically as treebase's > >>>> nexus file parser. Try as I might, the log keeps showing that it > >>>> cannot find the Mesquite_Folder: it wants me to show where the > manuals > >>>> is located. Could you give me a hint as to which of the following > >>>> moving parts are involved: > >>>> > >>>> * ~/Mesquite_Support_Files/Mesquite_Prefs/mesquiteLocation.txt - I > set > >>>> this to the right location > >>>> > >>>> * ~/Mesquite_Support_Files/Mesquite_Prefix/Mesquite.xml - I set > >>>> mesquiteHeadlessPath and mesquitePath to the right location > >>>> > >>>> * system property "mesquite.folder_dir" - I set this to the right > >>>> location > >>>> > >>>> What else can I do? Is there a programmatic way to set this? I'm > >>>> hoping to have overlooked a Mesquite.setMesquiteDirectory() method, > >>>> but there are probably good reasons why that doesn't exist. Can I > pass > >>>> it to the main method? > >>>> > >>>> 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 > >>>> > >>>> Content-type: application/octet-stream; name=Mesquite_Log > >>>> Content-disposition: attachment; filename=Mesquite_Log > >>>> X-Attachment-Id: f_g38tnpcj0 > >>>> > >>>> Attachment converted: Thrandina:Mesquite_Log 78 ( / ) > (0078D979) > >>> > >>> > >>> -- > >>> -------------------------------------------------------- > >>> Wayne Maddison > >>> Professor and Canada Research Chair > >>> Depts. of Zoology and Botany and > >>> Biodiversity Research Centre > >> > >> > & Director > >>> > >>> Beaty Biodiversity Museum > >>> 6270 University Boulevard > >>> University of British Columbia > >>> Vancouver, BC V6T 1Z4 Canada > >>> > >>> email: wma...@in... FAX: +1 604 822-2416 > >>> > >>> Mesquite: http://mesquiteproject.org > >>> MacClade: http://macclade.org > >>> Salticidae: http://salticidae.org > >>> Tree of Life: http://tolweb.org > >>> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca > >>> Home page: http://salticidae.org/wpm/home.html > >>> > >> > >> > >> > >> -- > >> 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 > > > > > > -- > > -------------------------------------------------------- > > Wayne Maddison > > Professor and Canada Research Chair > > Depts. of Zoology and Botany and > > Biodiversity Research Centre > > & Director > > Beaty Biodiversity Museum > > 6270 University Boulevard > > University of British Columbia > > Vancouver, BC V6T 1Z4 Canada > > > > email: wma...@in... FAX: +1 604 822-2416 > > > > Mesquite: http://mesquiteproject.org > > MacClade: http://macclade.org > > Salticidae: http://salticidae.org > > Tree of Life: http://tolweb.org > > Beaty Biodiversity Museum: http://beatymuseum.ubc.ca > > Home page: http://salticidae.org/wpm/home.html > > > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and > easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > |
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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: Rutger V. <rut...@gm...> - 2009-12-17 09:37:02
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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. I need to be able to programatically > recreate this environment on the staging and production server, so I'll need > instructions on how to set everything up. I think those instructions > currently exist except for some mesquite issues. That's right, on the wiki I describe my user environment on treebase-dev.nescent.org. A fairly important part in this is played by a number of environment variables (https://sourceforge.net/apps/mediawiki/treebase/index.php?title=HostEnvironment), as you've noticed. If you prefer it's not done this way we may have to split these into variables to do with building and maintenance and variables to do with deployment (which would go into catalina.sh or tomcat5.conf). > On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > >> http://treebasedb-dev.nescent.org:6666/treebase-web is up and running >> again, though the mesquite runtime issue is still not resolved. I >> fixed the compile time issue by putting the dependency on >> treebase-2.01.tb.jar back in the pom.xml (and committed this). >> >> I just got an email from Wayne suggesting a programmatic way to tell >> mesquite its location at runtime, I still have to try this. >> >> I am quite happy to "reconfigure" my account by sharing my login >> credentials with Youjun and Vladimir off-list (or is there a better >> way to do this)? >> >> I thought Youjun was capable locally of building and deploying the war >> (while talking to the remote db). I certainly can so I don't *have* to >> use the rv...@tr... account to get any work done. >> Vladimir, if you do an update on your end, will the source now build >> on your system? The complaints about mesquite.lib.* missing should go >> away. >> >> Rutger >> >> On Wed, Dec 16, 2009 at 5:07 PM, Hilmar Lapp <hl...@ne...> wrote: >>> >>> Rutger - >>> >>> it looks like at this point we do not have a second deployment-capable >>> installation on treebase-dev, and I get the sense that no one has one >>> local >>> to their lap/desktop either. >>> >>> Since Jon is on parental leave, can you reconfigure your account so that >>> it >>> can function as the shared developer account for now until Jon gets a >>> minute >>> to create that? >>> >>> Also, given that we want to do development work on the web-application in >>> parallel, I'd consider it high priority that we work out local >>> deployments >>> of the web-application on the developers' own machines. Vladimir seems to >>> be >>> almost there - what is missing right now? >>> >>> -hilmar >>> >>> On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: >>> >>>> Didn't we talk about this already, that we wanted to create a shared >>>> developer account or group so that we're all talking about the same >>>> environment with the same configuration? I'm not sure what the best >>>> way would be to set this up. >>>> >>>> On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> wrote: >>>>> >>>>> Except that that person can't remain Rutger. -hilmar >>>>> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >>>>> >>>>> Now I kind of understand, once other developers finish a task and pass >>>>> the >>>>> testing on their own environment, just submit the code to sourceforg, >>>>> Rutger >>>>> will be the person who redeploy the new code. >>>>> >>>>> Thanks >>>>> >>>>> Youjun >>>>> >>>>> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev >>>>> <vga...@ne...> >>>>> wrote: >>>>>> >>>>>> http://treebase-dev.nescent.org:6666/treebase-web is the only common >>>>>> TreeBase instance I am aware of. I presumed everyone had their own >>>>>> local >>>>>> tomcats for development purposes -- that's what I have been trying to >>>>>> set up >>>>>> for myself for the past two days... >>>>>> --Vladimir >>>>>> >>>>>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>>>>> >>>>>> Do you know which Tomcat server is assigned for all the TreeBASE >>>>>> developers? >>>>>> >>>>>> Youjun >>>>>> >>>>>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev >>>>>> <vga...@ne...> >>>>>> wrote: >>>>>>> >>>>>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>>>>> >>>>>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>>>>> >>>>>>> Vladimir, >>>>>>> >>>>>>> Do you know why I cannot access the treebase-web @ >>>>>>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>>>>>> >>>>>>> Youjun >>>>>>> >>>>>>> The server itself is up: http://treebase-dev.nescent.org/. My first >>>>>>> guess that 6666 is down due to Rutger's ongoing experimentation with >>>>>>> Mesquite. (The same reasons I could not set up my deployment >>>>>>> yesterday?) >>>>>>> I'll try to find and check the logs. >>>>>>> >>>>>>> Il'' take the last one back: according to the notes Jon gave me, 6666 >>>>>>> starts from Rutger's homedir, to which only he has access. >>>>>>> --Vladimir >>>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.Net email is sponsored by the Verizon Developer Community >>>>> Take advantage of Verizon's best-in-class app development support >>>>> A streamlined, 14 day to market process makes app distribution fast and >>>>> easy >>>>> Join now and get one step closer to millions of Verizon customers >>>>> http://p.sf.net/sfu/verizon-dev2dev >>>>> _______________________________________________ >>>>> Treebase-devel mailing list >>>>> Tre...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>>> >>>>> -- >>>>> =========================================================== >>>>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>>>> =========================================================== >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.Net email is sponsored by the Verizon Developer Community >>>>> Take advantage of Verizon's best-in-class app development support >>>>> A streamlined, 14 day to market process makes app distribution fast and >>>>> easy >>>>> Join now and get one step closer to millions of Verizon customers >>>>> http://p.sf.net/sfu/verizon-dev2dev >>>>> _______________________________________________ >>>>> Treebase-devel mailing list >>>>> Tre...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Dr. Rutger A. Vos >>>> School of Biological Sciences >>>> Philip Lyle Building, Level 4 >>>> University of Reading >>>> Reading >>>> RG6 6BX >>>> United Kingdom >>>> Tel: +44 (0) 118 378 7535 >>>> http://www.nexml.org >>>> http://rutgervos.blogspot.com >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>> =========================================================== >>> >>> >>> >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> >> >> ------------------------------------------------------------------------------ >> 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 > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > -- 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 09:31:08
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> 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? Sure, I always have gmail chat open (user rutgeraldo) so that's the best way to reach me - or do you really prefer some other means? -- 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 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: 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: 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: Vladimir G. <vla...@du...> - 2009-12-16 19:33:02
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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. |
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From: Vladimir G. <vla...@du...> - 2009-12-16 18:39:35
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I hope we can agree that what Jon suggests is worthwhile doing. I also hope we can do one more thing alongside this: move whatever settings are currently specified in treebase-core/src/main/resources/ jdbc.properties out of the WAR file and into tomcat configuration. This should enable deploying the same WAR in multiple installations and make everyone's life much easier. --VG 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 think all the developers have the login info > for that user. I further suggest > > CATALINA_HOME : /home/treebase/tomcat > Tomcat can run from this location with default ports (8080, for web, > for example) as long as the 6666 instance is not running (which uses > some of the non-web interface default ports) > > The environment for this user should be setup from scratch instead of > copied over from an existing user's home dir. I need to be able to > programatically recreate this environment on the staging and > production server, so I'll need instructions on how to set everything > up. I think those instructions currently exist except for some > mesquite issues. > > Once that is setup, 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. > > Before I left fro parental leave, I created both a staging and a > production environment like this for Vladimir. > > 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. > > Ok, I'll probably check email again tonight or tomorrow. > > -Jon > > > > On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > >> http://treebasedb-dev.nescent.org:6666/treebase-web is up and running >> again, though the mesquite runtime issue is still not resolved. I >> fixed the compile time issue by putting the dependency on >> treebase-2.01.tb.jar back in the pom.xml (and committed this). >> >> I just got an email from Wayne suggesting a programmatic way to tell >> mesquite its location at runtime, I still have to try this. >> >> I am quite happy to "reconfigure" my account by sharing my login >> credentials with Youjun and Vladimir off-list (or is there a better >> way to do this)? >> >> I thought Youjun was capable locally of building and deploying the >> war >> (while talking to the remote db). I certainly can so I don't *have* >> to >> use the rv...@tr... account to get any work done. >> Vladimir, if you do an update on your end, will the source now build >> on your system? The complaints about mesquite.lib.* missing should go >> away. >> >> Rutger >> >> On Wed, Dec 16, 2009 at 5:07 PM, Hilmar Lapp <hl...@ne...> >> wrote: >>> Rutger - >>> >>> it looks like at this point we do not have a second deployment- >>> capable >>> installation on treebase-dev, and I get the sense that no one has >>> one local >>> to their lap/desktop either. >>> >>> Since Jon is on parental leave, can you reconfigure your account so >>> that it >>> can function as the shared developer account for now until Jon gets >>> a minute >>> to create that? >>> >>> Also, given that we want to do development work on the web- >>> application in >>> parallel, I'd consider it high priority that we work out local >>> deployments >>> of the web-application on the developers' own machines. Vladimir >>> seems to be >>> almost there - what is missing right now? >>> >>> -hilmar >>> >>> On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: >>> >>>> Didn't we talk about this already, that we wanted to create a >>>> shared >>>> developer account or group so that we're all talking about the same >>>> environment with the same configuration? I'm not sure what the best >>>> way would be to set this up. >>>> >>>> On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> >>>> wrote: >>>>> >>>>> Except that that person can't remain Rutger. -hilmar >>>>> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >>>>> >>>>> Now I kind of understand, once other developers finish a task and >>>>> pass >>>>> the >>>>> testing on their own environment, just submit the code to >>>>> sourceforg, >>>>> Rutger >>>>> will be the person who redeploy the new code. >>>>> >>>>> Thanks >>>>> >>>>> Youjun >>>>> >>>>> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... >>>>>> >>>>> wrote: >>>>>> >>>>>> http://treebase-dev.nescent.org:6666/treebase-web is the only >>>>>> common >>>>>> TreeBase instance I am aware of. I presumed everyone had their >>>>>> own >>>>>> local >>>>>> tomcats for development purposes -- that's what I have been >>>>>> trying to >>>>>> set up >>>>>> for myself for the past two days... >>>>>> --Vladimir >>>>>> >>>>>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>>>>> >>>>>> Do you know which Tomcat server is assigned for all the TreeBASE >>>>>> developers? >>>>>> >>>>>> Youjun >>>>>> >>>>>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev >>>>>> <vga...@ne...> >>>>>> wrote: >>>>>>> >>>>>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>>>>> >>>>>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>>>>> >>>>>>> Vladimir, >>>>>>> >>>>>>> Do you know why I cannot access the treebase-web @ >>>>>>> treebase-dev.nescent.org:6666? I saw the home page flash and >>>>>>> gone. >>>>>>> >>>>>>> Youjun >>>>>>> >>>>>>> The server itself is up: http://treebase-dev.nescent.org/. My >>>>>>> first >>>>>>> guess that 6666 is down due to Rutger's ongoing experimentation >>>>>>> with >>>>>>> Mesquite. (The same reasons I could not set up my deployment >>>>>>> yesterday?) >>>>>>> I'll try to find and check the logs. >>>>>>> >>>>>>> Il'' take the last one back: according to the notes Jon gave >>>>>>> me, 6666 >>>>>>> starts from Rutger's homedir, to which only he has access. >>>>>>> --Vladimir >>>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.Net email is sponsored by the Verizon Developer Community >>>>> Take advantage of Verizon's best-in-class app development support >>>>> A streamlined, 14 day to market process makes app distribution >>>>> fast and >>>>> easy >>>>> Join now and get one step closer to millions of Verizon customers >>>>> http://p.sf.net/sfu/verizon-dev2dev >>>>> _______________________________________________ >>>>> Treebase-devel mailing list >>>>> Tre...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>>> >>>>> -- >>>>> =========================================================== >>>>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>>>> =========================================================== >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.Net email is sponsored by the Verizon Developer Community >>>>> Take advantage of Verizon's best-in-class app development support >>>>> A streamlined, 14 day to market process makes app distribution >>>>> fast and >>>>> easy >>>>> Join now and get one step closer to millions of Verizon customers >>>>> http://p.sf.net/sfu/verizon-dev2dev >>>>> _______________________________________________ >>>>> Treebase-devel mailing list >>>>> Tre...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Dr. Rutger A. Vos >>>> School of Biological Sciences >>>> Philip Lyle Building, Level 4 >>>> University of Reading >>>> Reading >>>> RG6 6BX >>>> United Kingdom >>>> Tel: +44 (0) 118 378 7535 >>>> http://www.nexml.org >>>> http://rutgervos.blogspot.com >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>> =========================================================== >>> >>> >>> >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> >> ------------------------------------------------------------------------------ >> 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 > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > ------------------------------------------------------------------------------ > 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: Jon A. <jon...@du...> - 2009-12-16 18:22:24
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I suggest that treebase-dev be configured to run from the treebase account on the server. I think all the developers have the login info for that user. I further suggest CATALINA_HOME : /home/treebase/tomcat Tomcat can run from this location with default ports (8080, for web, for example) as long as the 6666 instance is not running (which uses some of the non-web interface default ports) The environment for this user should be setup from scratch instead of copied over from an existing user's home dir. I need to be able to programatically recreate this environment on the staging and production server, so I'll need instructions on how to set everything up. I think those instructions currently exist except for some mesquite issues. Once that is setup, 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. Before I left fro parental leave, I created both a staging and a production environment like this for Vladimir. 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. Ok, I'll probably check email again tonight or tomorrow. -Jon On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > http://treebasedb-dev.nescent.org:6666/treebase-web is up and running > again, though the mesquite runtime issue is still not resolved. I > fixed the compile time issue by putting the dependency on > treebase-2.01.tb.jar back in the pom.xml (and committed this). > > I just got an email from Wayne suggesting a programmatic way to tell > mesquite its location at runtime, I still have to try this. > > I am quite happy to "reconfigure" my account by sharing my login > credentials with Youjun and Vladimir off-list (or is there a better > way to do this)? > > I thought Youjun was capable locally of building and deploying the war > (while talking to the remote db). I certainly can so I don't *have* to > use the rv...@tr... account to get any work done. > Vladimir, if you do an update on your end, will the source now build > on your system? The complaints about mesquite.lib.* missing should go > away. > > Rutger > > On Wed, Dec 16, 2009 at 5:07 PM, Hilmar Lapp <hl...@ne...> > wrote: >> Rutger - >> >> it looks like at this point we do not have a second deployment- >> capable >> installation on treebase-dev, and I get the sense that no one has >> one local >> to their lap/desktop either. >> >> Since Jon is on parental leave, can you reconfigure your account so >> that it >> can function as the shared developer account for now until Jon gets >> a minute >> to create that? >> >> Also, given that we want to do development work on the web- >> application in >> parallel, I'd consider it high priority that we work out local >> deployments >> of the web-application on the developers' own machines. Vladimir >> seems to be >> almost there - what is missing right now? >> >> -hilmar >> >> On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: >> >>> Didn't we talk about this already, that we wanted to create a shared >>> developer account or group so that we're all talking about the same >>> environment with the same configuration? I'm not sure what the best >>> way would be to set this up. >>> >>> On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> >>> wrote: >>>> >>>> Except that that person can't remain Rutger. -hilmar >>>> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >>>> >>>> Now I kind of understand, once other developers finish a task and >>>> pass >>>> the >>>> testing on their own environment, just submit the code to >>>> sourceforg, >>>> Rutger >>>> will be the person who redeploy the new code. >>>> >>>> Thanks >>>> >>>> Youjun >>>> >>>> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... >>>> > >>>> wrote: >>>>> >>>>> http://treebase-dev.nescent.org:6666/treebase-web is the only >>>>> common >>>>> TreeBase instance I am aware of. I presumed everyone had their >>>>> own >>>>> local >>>>> tomcats for development purposes -- that's what I have been >>>>> trying to >>>>> set up >>>>> for myself for the past two days... >>>>> --Vladimir >>>>> >>>>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>>>> >>>>> Do you know which Tomcat server is assigned for all the TreeBASE >>>>> developers? >>>>> >>>>> Youjun >>>>> >>>>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev >>>>> <vga...@ne...> >>>>> wrote: >>>>>> >>>>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>>>> >>>>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>>>> >>>>>> Vladimir, >>>>>> >>>>>> Do you know why I cannot access the treebase-web @ >>>>>> treebase-dev.nescent.org:6666? I saw the home page flash and >>>>>> gone. >>>>>> >>>>>> Youjun >>>>>> >>>>>> The server itself is up: http://treebase-dev.nescent.org/. My >>>>>> first >>>>>> guess that 6666 is down due to Rutger's ongoing experimentation >>>>>> with >>>>>> Mesquite. (The same reasons I could not set up my deployment >>>>>> yesterday?) >>>>>> I'll try to find and check the logs. >>>>>> >>>>>> Il'' take the last one back: according to the notes Jon gave >>>>>> me, 6666 >>>>>> starts from Rutger's homedir, to which only he has access. >>>>>> --Vladimir >>>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> This SF.Net email is sponsored by the Verizon Developer Community >>>> Take advantage of Verizon's best-in-class app development support >>>> A streamlined, 14 day to market process makes app distribution >>>> fast and >>>> easy >>>> Join now and get one step closer to millions of Verizon customers >>>> http://p.sf.net/sfu/verizon-dev2dev >>>> _______________________________________________ >>>> Treebase-devel mailing list >>>> Tre...@li... >>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>> >>>> -- >>>> =========================================================== >>>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>>> =========================================================== >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> This SF.Net email is sponsored by the Verizon Developer Community >>>> Take advantage of Verizon's best-in-class app development support >>>> A streamlined, 14 day to market process makes app distribution >>>> fast and >>>> easy >>>> Join now and get one step closer to millions of Verizon customers >>>> http://p.sf.net/sfu/verizon-dev2dev >>>> _______________________________________________ >>>> Treebase-devel mailing list >>>> Tre...@li... >>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>> >>>> >>> >>> >>> >>> -- >>> Dr. Rutger A. Vos >>> School of Biological Sciences >>> Philip Lyle Building, Level 4 >>> University of Reading >>> Reading >>> RG6 6BX >>> United Kingdom >>> Tel: +44 (0) 118 378 7535 >>> http://www.nexml.org >>> http://rutgervos.blogspot.com >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > 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 ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: Hilmar L. <hl...@ne...> - 2009-12-16 18:20:08
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Yes we are, at 10.30am EST. -hilmar On Dec 16, 2009, at 1:15 PM, Rutger Vos wrote: > Hi, > > are we calling in on Thursday 12/16 again? I'm not sure anymore > whether that was the plan. Presumably there will be a reminder if we > are? > > Rutger > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2009-12-16 18:15:14
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Hi, are we calling in on Thursday 12/16 again? I'm not sure anymore whether that was the plan. Presumably there will be a reminder if we are? Rutger |
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From: Hilmar L. <hl...@ne...> - 2009-12-16 18:14:17
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Great!! Sounds like we're making progress wading through the mucky waters :-) -hilmar On Dec 16, 2009, at 1:04 PM, Rutger Vos wrote: > Hi all, > > Wayne's suggestion to pass mesquite's location programmatically works. > I just managed to get it to parse a file through the web interface > (and so this should also apply to the batch loader, which uses the > same NexusServiceMesquite object). I still need to replicate the > behaviour on the server, which means creating a bit of a Frankenstein > system, unfortunately: > > * use the mesquite-2.01.tb.jar to compile against > > * place the class folder structure in treebase-core/lib in a location > where tomcat sees it (e.g. in $CATALINA_HOME/shared/classes) > > * have the mesquite.folder_dir variable in jdbc.properties point to > that location > > ...then the NexusServiceMesquite bean will be passed that location on > instantiation, from where it can tell MesquiteModule where it lives. > > Phew. > > Rutger > > On Wed, Dec 16, 2009 at 10:02 AM, Rutger Vos <rut...@gm...> > wrote: >> Yes, you are both right: the mesquite jar is "needed", but unless you >> clean up your work environment (local repo) it will stick around and >> so you won't notice. >> >> Unfortunately, leaving it in won't help us because the issue is that >> the jar only works at compile time in that you can build against it, >> but at runtime mesquite won't work inside a jar (because of its own >> extension loading and bootstrapping implementation). >> >> What I'm doing instead is now committing the unpacked class folder >> for >> mesquite into /treebase-core/lib, and setting my eclipse .project to >> use that, which should amount to the same thing as having the jar >> file >> in your classpath. >> >> From this point, we have to figure out how to correctly deploy this >> class folder into our web application. I've tried placing it in >> $CATALINA_HOME/shared/classes but it's not quite happy with that >> (same >> error as before). >> >> Next I'll try and see what happens if I place it directly inside the >> folder structure that is created when tomcat unpacks the >> treebase-web.war. Not an ideal solution of course, but at this >> point I >> just want to narrow down the variables. >> >> Rutger >> >> On Tue, Dec 15, 2009 at 10:57 PM, youjun guo <you...@ya...> >> wrote: >>> Rutger, >>> >>> I Just noticed the mesquite jar, which was commented by you in the >>> pom.xml >>> of treebase-core, is actually needed for the project. Sometimes >>> you can get >>> the system compiled without it is because it already got >>> downloaded to the >>> classpath, >>> >>> But for a newly check out project, it will not compile without it. >>> >>> Youjun >>> >>> On Tue, Dec 15, 2009 at 11:34 AM, Rutger Vos >>> <rut...@gm...> wrote: >>>> >>>> Hi all, >>>> >>>> I'm still having trouble getting mesquite to play nice, so this >>>> email >>>> is a cry for help! >>>> >>>> I'm hoping that Vladimir and/or Youjun can give this some thought >>>> as >>>> well, because maybe I'm just overlooking something obvious. What >>>> continues to happen is that mesquite can't figure out where it is >>>> located when I run it inside tomcat. It then tries to ask the user >>>> where the mesquite manual is located (so that it can compute the >>>> correct path relative to the manual file), but because in headless >>>> mode we default to "OK" on all user queries everything breaks down >>>> from then on. >>>> >>>> Here's what I've done recently: >>>> >>>> * I added anything that seems pertinent w.r.t. mesquite <=> >>>> treebase >>>> interaction to the wiki page: >>>> >>>> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=HeadlessMesquite >>>> >>>> * I committed the treebase class files to /treebase-core/lib >>>> >>>> * I removed all reference to mesquite from the pom.xml files >>>> (apologies for adding them in the first place, I was hoping we >>>> could >>>> integrate it in the maven system) >>>> >>>> * I emailed Jin Ruan, Peter Midford, Mark-Jason Dominus and Wayne >>>> Maddison. >>>> >>>> Is Peter at nescent right now? Could someone knock on his door and >>>> plead for his help? He knows a lot about mesquite! >>>> >>>> Thanks, >>>> >>>> Rutger >>>> >>>> -- >>>> Dr. Rutger A. Vos >>>> School of Biological Sciences >>>> Philip Lyle Building, Level 4 >>>> University of Reading >>>> Reading >>>> RG6 6BX >>>> United Kingdom >>>> Tel: +44 (0) 118 378 7535 >>>> http://www.nexml.org >>>> http://rutgervos.blogspot.com >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Return on Information: >>>> Google Enterprise Search pays you back >>>> Get the facts. >>>> http://p.sf.net/sfu/google-dev2dev >>>> _______________________________________________ >>>> Treebase-devel mailing list >>>> Tre...@li... >>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>> >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2009-12-16 18:04:22
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Hi all, Wayne's suggestion to pass mesquite's location programmatically works. I just managed to get it to parse a file through the web interface (and so this should also apply to the batch loader, which uses the same NexusServiceMesquite object). I still need to replicate the behaviour on the server, which means creating a bit of a Frankenstein system, unfortunately: * use the mesquite-2.01.tb.jar to compile against * place the class folder structure in treebase-core/lib in a location where tomcat sees it (e.g. in $CATALINA_HOME/shared/classes) * have the mesquite.folder_dir variable in jdbc.properties point to that location ...then the NexusServiceMesquite bean will be passed that location on instantiation, from where it can tell MesquiteModule where it lives. Phew. Rutger On Wed, Dec 16, 2009 at 10:02 AM, Rutger Vos <rut...@gm...> wrote: > Yes, you are both right: the mesquite jar is "needed", but unless you > clean up your work environment (local repo) it will stick around and > so you won't notice. > > Unfortunately, leaving it in won't help us because the issue is that > the jar only works at compile time in that you can build against it, > but at runtime mesquite won't work inside a jar (because of its own > extension loading and bootstrapping implementation). > > What I'm doing instead is now committing the unpacked class folder for > mesquite into /treebase-core/lib, and setting my eclipse .project to > use that, which should amount to the same thing as having the jar file > in your classpath. > > From this point, we have to figure out how to correctly deploy this > class folder into our web application. I've tried placing it in > $CATALINA_HOME/shared/classes but it's not quite happy with that (same > error as before). > > Next I'll try and see what happens if I place it directly inside the > folder structure that is created when tomcat unpacks the > treebase-web.war. Not an ideal solution of course, but at this point I > just want to narrow down the variables. > > Rutger > > On Tue, Dec 15, 2009 at 10:57 PM, youjun guo <you...@ya...> wrote: >> Rutger, >> >> I Just noticed the mesquite jar, which was commented by you in the pom.xml >> of treebase-core, is actually needed for the project. Sometimes you can get >> the system compiled without it is because it already got downloaded to the >> classpath, >> >> But for a newly check out project, it will not compile without it. >> >> Youjun >> >> On Tue, Dec 15, 2009 at 11:34 AM, Rutger Vos <rut...@gm...> wrote: >>> >>> Hi all, >>> >>> I'm still having trouble getting mesquite to play nice, so this email >>> is a cry for help! >>> >>> I'm hoping that Vladimir and/or Youjun can give this some thought as >>> well, because maybe I'm just overlooking something obvious. What >>> continues to happen is that mesquite can't figure out where it is >>> located when I run it inside tomcat. It then tries to ask the user >>> where the mesquite manual is located (so that it can compute the >>> correct path relative to the manual file), but because in headless >>> mode we default to "OK" on all user queries everything breaks down >>> from then on. >>> >>> Here's what I've done recently: >>> >>> * I added anything that seems pertinent w.r.t. mesquite <=> treebase >>> interaction to the wiki page: >>> >>> https://sourceforge.net/apps/mediawiki/treebase/index.php?title=HeadlessMesquite >>> >>> * I committed the treebase class files to /treebase-core/lib >>> >>> * I removed all reference to mesquite from the pom.xml files >>> (apologies for adding them in the first place, I was hoping we could >>> integrate it in the maven system) >>> >>> * I emailed Jin Ruan, Peter Midford, Mark-Jason Dominus and Wayne >>> Maddison. >>> >>> Is Peter at nescent right now? Could someone knock on his door and >>> plead for his help? He knows a lot about mesquite! >>> >>> Thanks, >>> >>> Rutger >>> >>> -- >>> Dr. Rutger A. Vos >>> School of Biological Sciences >>> Philip Lyle Building, Level 4 >>> University of Reading >>> Reading >>> RG6 6BX >>> United Kingdom >>> Tel: +44 (0) 118 378 7535 >>> http://www.nexml.org >>> http://rutgervos.blogspot.com >>> >>> >>> ------------------------------------------------------------------------------ >>> Return on Information: >>> Google Enterprise Search pays you back >>> Get the facts. >>> http://p.sf.net/sfu/google-dev2dev >>> _______________________________________________ >>> Treebase-devel mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Rutger V. <rut...@gm...> - 2009-12-16 17:58:20
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Hi Wayne, it worked - hurrah! Thank you very much, high-fives all around. Rutger On Wed, Dec 16, 2009 at 3:28 PM, Wayne Maddison <wma...@in...> wrote: > Rutger, > How about setting the static MesquiteModule.mesquiteDirectory before to call > to Mesquite.main? > Wayne > >> Hi Wayne, >> >> On Tue, Dec 15, 2009 at 7:05 PM, Wayne Maddison >> <wma...@in...> wrote: >>> >>> This code is ancient -- probably has not been activated in 10 years! >>> Mesquite in general always knows where its home folder is, but we have >>> not >>> been trying server stuff. >> >> I know this code is ancient, which is why I was a little embarrassed >> to ask about it. Supposedly, Jin Ruan applied some slight patches to >> it to make it work with TreeBASE, but he didn't record anywhere what >> those changes were (and whether they're even still necessary: I notice >> a lot of work has gone into making mesquite more amenable to our sort >> of use cases). >> >> The hard part is that the server is quite a different environment that >> constructs its own class path and has its own way of loading classes. >> Also, the calling class lives inside a "war" file - a jar containing a >> web application - whereas mesquite lives inside >> $CATALINA_HOME/shared/classes, the location from whence shared classes >> are visible to web applications. >> >> Since "war" files are actually unpacked into a class folder the first >> time the server sees the archive I suppose I could copy the mesquite >> classes into that same folder structure and see what happens. Tomcat >> purists be damned. >> >>> mesquiteLocation.txt and the entries in Mesquite.xml don't help -- they >>> are >>> a service to otehr programs. >> >> Ah, thanks, at least I can stop worrying about those then. >> >>> Is that the entire log file? >> >> The log file I sent you is the whole thing. >> >>> What version of Mesquite are you using? >> >> We're using version "2.01tb". >> >>> How exactly are you calling Mesquite? You might want to look into >>> svn.mesquiteproject.org, RMesquite, >>> src/java/mesquite/R/RCallsMesquite/lib/MesquiteRunner for an actively >>> developed class that instantiates and calls Mesquite. To tell you the >>> truth, now that I think about it, I'm not sure how this works -- I'm not >>> sure how Mesquite knows its home directory if its in a different >>> classpath >>> than the one in which the class calling it lives. >> >> All we're doing is the following: >> >> Mesquite.main(new String[] {"-w"}); >> MesquiteProject project = >> MesquiteTrunk.mesquiteTrunk.openFile(pFile.getAbsolutePath()); >> >> I'll have a look at the R code, see if that gives me any pointers. >> >> Thanks! >> >> Rutger >> >> >>>> Hi Wayne, >>>> >>>> I'm having trouble launching mesquite programmatically as treebase's >>>> nexus file parser. Try as I might, the log keeps showing that it >>>> cannot find the Mesquite_Folder: it wants me to show where the manuals >>>> is located. Could you give me a hint as to which of the following >>>> moving parts are involved: >>>> >>>> * ~/Mesquite_Support_Files/Mesquite_Prefs/mesquiteLocation.txt - I set >>>> this to the right location >>>> >>>> * ~/Mesquite_Support_Files/Mesquite_Prefix/Mesquite.xml - I set >>>> mesquiteHeadlessPath and mesquitePath to the right location >>>> >>>> * system property "mesquite.folder_dir" - I set this to the right >>>> location >>>> >>>> What else can I do? Is there a programmatic way to set this? I'm >>>> hoping to have overlooked a Mesquite.setMesquiteDirectory() method, >>>> but there are probably good reasons why that doesn't exist. Can I pass >>>> it to the main method? >>>> >>>> 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 >>>> >>>> Content-type: application/octet-stream; name=Mesquite_Log >>>> Content-disposition: attachment; filename=Mesquite_Log >>>> X-Attachment-Id: f_g38tnpcj0 >>>> >>>> Attachment converted: Thrandina:Mesquite_Log 78 ( / ) (0078D979) >>> >>> >>> -- >>> -------------------------------------------------------- >>> Wayne Maddison >>> Professor and Canada Research Chair >>> Depts. of Zoology and Botany and >>> Biodiversity Research Centre >> >> > & Director >>> >>> Beaty Biodiversity Museum >>> 6270 University Boulevard >>> University of British Columbia >>> Vancouver, BC V6T 1Z4 Canada >>> >>> email: wma...@in... FAX: +1 604 822-2416 >>> >>> Mesquite: http://mesquiteproject.org >>> MacClade: http://macclade.org >>> Salticidae: http://salticidae.org >>> Tree of Life: http://tolweb.org >>> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca >>> Home page: http://salticidae.org/wpm/home.html >>> >> >> >> >> -- >> 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 > > > -- > -------------------------------------------------------- > Wayne Maddison > Professor and Canada Research Chair > Depts. of Zoology and Botany and > Biodiversity Research Centre > & Director > Beaty Biodiversity Museum > 6270 University Boulevard > University of British Columbia > Vancouver, BC V6T 1Z4 Canada > > email: wma...@in... FAX: +1 604 822-2416 > > Mesquite: http://mesquiteproject.org > MacClade: http://macclade.org > Salticidae: http://salticidae.org > Tree of Life: http://tolweb.org > Beaty Biodiversity Museum: http://beatymuseum.ubc.ca > Home page: http://salticidae.org/wpm/home.html > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Rutger V. <rut...@gm...> - 2009-12-16 17:42:51
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>> I just got an email from Wayne suggesting a programmatic way to tell >> mesquite its location at runtime, I still have to try this. > > Has Jin Ruan responded? I'd imagine that he might be very useful, seeing as he modified Mesquite in the first place. If you think it would help, Val or I can write to him separately. Jin has not yet responded. If he has a good memory he's most likely to be the most useful person so if you or Val could write him that would be excellent. -- 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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