Michael Lee's notes on installing VegBank on a new server (vegbankVM)
First, the current instance of VegBank was copied from to VegBankVM
Then I tested functions, redeployed bits of the website, and addressed what failed.  
This is a log of what happened.

As of 12/21/2010, VegBankVM is up and running and is our production server!

reinstalling VegBank on VegBankVM

problems:

   build.properties are all different on the new server
     googlemaps_apikey needed a new key generated from google's webserver (http://code.google.com/apis/maps/signup.html)
     
     THESE were also changed from comments out values to new values:
     apache.document.root=/usr/www/vegbank/htdocs
     vegbank.export.dir=export
     #webapps.dir=/usr/local/devtools/jakarta-tomcat/webapps
     webapps.dir=/var/lib/tomcat6/webapps
     #vegbank.web.dir=/usr/local/devtools/jakarta-tomcat/webapps/vegbank
     vegbank.web.dir=/var/lib/tomcat6/webapps/vegbank
     #tomcat=/usr/local/devtools/jakarta-tomcat
     tomcat=/var/lib/tomcat6

permissions:
   When running the ant install and web-install, I ran into problems with not having permissions
     to write to the files on the server.
     
     To fix this, I created a new linux user group (vegbank), and added the users (including tomcat) to this group
     then I did a chgrp for any dirs that didn't deploy from ant
     
     Matt Jones helped me set the sticky bits for the directory to remain a vegbank group.
     This still doesn't work perfectly, as the deployed vegbank directory doesn't have group write permissions by default.
     This needs to be fixed by adding the rest of the vegbank website to the vegbank.war file and only distribute files through the .war file.
          
writeviews didn't cooperate from /web/views/build.xml, as it complained the a .jsp file didn't exist.
  I switched force="true" to force="false" and ran ant as ant -v writeviews from web/views/, and it worked!
  
tokens are said to be recursive, ant version issue? : yes new ant 1.8 fixed this

I had some problems with redirect:write not working as predicted.  Reworked some xsl files and commited to SVN.

  The redirect:write is adding garbage to the jsps that are messing them up, they fail to compile
  fixed this by adding an ant task called "replace" that looks for xmnls:[jsp|vegbank|logic|bean]="http://vegbank.org" and replaces when with " "
  
  tested various functions on the site:
    vegbank_qa.xlsx
    
    particular fails: /get/std/[entity] is not always pulling up the correct view
    taxonObservation and observation fail and get 404 errors, but work if you adjust the jsp name
    
    big problem: observation_comprehensive failing due to "LocalVariableTable has wrong length in class file"
      but annoyingly this was not an issue on the old server
    fixed this by splitting observation_comprehensive into two files.
  
    old server can allow download of 850+ plots.  New server does too, and fast, but at 1,050 plots, the download fails :(
    Matt Jones increased the memory allowance of memory for tomcat: the memory was set to 128 MB for tomcat -- I increased it to 2048 MB.
    Now downloads of over 10,000 plots are successful!
      
   
   ONE TIME ISSUES RELATED TO CVS->SVN migration:
   checked out new copy of SVN repo!
      
      but date format is different.  following command fixed:
      find ./ -type f | xargs sed -i "s/\('\$Date: [0-9][0-9][0-9][0-9]\)\/\([0-9][0-9]\)\/\([0-9][0-9] [0-9][0-9]\:[0-9][0-9]\:[0-9][0-9] \$'$\)/\1-\2-\3/"
   no, that didn't work!
   
   this did work:
   grep -lr -e 'Date: ' * | xargs sed -i 's/\(''\$Date: [0-9][0-9][0-9][0-9]\)\/\([0-9][0-9]\)\/\([0-9][0-9] [0-9][0-9]:[0-9][0-9]:[0-9][0-9] \$''\)/\1-\2-\3/' 
  
   trying to fix this:
   
   < # $Id: vegbank.properties,v 1.21 2006-09-01 23:39:47 mlee Exp $
   ---
   > # $Id: vegbank.properties,v 1.21 2006/09/01 23:39:47 mlee Exp $
   
   just a couple, so I did it manually!  
   
   
   
   
   
   Matt Jones phone call 11/11/2010:
   
   autogen-views script not part of deploy
   (had to fix this anyway)
   
   1) stop tomcat
   2) make changes to permissions in webapps dir
   3) start tomcat
   
   partial reload due to war file not being able to write to vegbank dir
   
   fixed with umask 0002 in .bashrc
   
   fixed also with sticky bits:
     as root, in webapps dir, ran:
     chgrp vegbank .
     chmod g+s .
     (make the group sticky (the default for new files/folders)
     
     when tomcat creates the vegbank dir, it's not set as vegbank grp, so had to chgrp -R vegbank vegbank
     
     this fixed A LOT of the problems when we redeployed (so still a permissions issue)
     
     still having queries not run correctly.: 
      ERROR taglib.VegbankGetTag: Problem running GenericCommand
        java.lang.ClassCastException: [Ljava.lang.String; cannot be cast to java.lang.String
            at org.vegbank.ui.struts.taglib.Xwhere.doSwap(Xwhere.java:311)
            at org.vegbank.ui.struts.taglib.Xwhere.appendToClause(Xwhere.java:335)
            at org.vegbank.ui.struts.taglib.Xwhere.buildXwhereClause(Xwhere.java:97)
     (this resolved itself, apparently)


## BEFORE TRANSER OF DNS ENTRY, I rebuilt the VegBankVM site using vegbank.org as the machine url and google maps API key in build.properties.



  TRANSFER OF DATABASE FROM OLD VEGBANK TO NEW:
 /usr/bin/pg_dump -U vegbank --no-owner --no-privileges vegbank > /usr/vegbank/backup/migrate_new_server_xfer_2010_12_21.sql

now scp to new vegbank:
scp /usr/vegbank/backup/migrate_new_server_xfer_2010_12_21.sql lee@vegbankvm.nceas.ucsb.edu:/usr/vegbank/backup/migrate_new_server_xfer_2010_12_21.sql

ON NEW VEGBANK:
become root and stop tomcat:
su -
cd /etc/init.d
./tomcat6 stop

#then become postgres:
su postgres
# drop vegbank database
dropdb vegbank
# create database:
createdb -E UNICODE vegbank
createuser vegbank
#grant vegbank user permissions:
psql
grant all on database vegbank to vegbank;

#restore data:
su (yourself)
cd /usr/vegbank/backup
### this is super super slow: more than a day, thus far:
## can't get that to work at all /usr/bin/pg_restore -x -O -C -U vegbank -f /usr/vegbank/backup/migrate_new_server_xfer_2010_12_21.sql 

does work in minutes, too:
cd /usr/vegbank/backup/
psql -U vegbank vegbank < migrate_new_server_xfer_2010_12_21.sql > manualRestore_2010_12_21_real.log

then do psql -U vegbank vegbank
analyze;

# now start tomcat:
su -
cd /etc/init.d
./tomcat6 start