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Re: [Treebase-devel] TreeBASE <=> Mesquite interaction
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From: Wayne M. <wma...@in...> - 2009-12-17 15:53:03
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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 |
