Menu
▾
▴
Re: [Treebase-devel] TreeBASE <=> Mesquite interaction
|
From: Rutger V. <rut...@gm...> - 2009-12-16 17:58:20
|
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 |
