Re: [Treebase-devel] TreeBASE <=> Mesquite interaction

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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
>
>
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