to test the import:
# -> "to set up the VM"
# restore the "booted" snapshot under "+pg_restore"
# start the VM
ssh -t 128.111.220.240
# update system time so wait times can be calculated correctly:
sudo service ntp stop; sudo ntpdate -s time.nist.gov; sudo service ntp start
* to test a different revision:
# {
# pick [rev] from r12025 (2014-2-2, last success)..r13002 (2014-3-30, 1st failure)
svn revert --depth infinity .
svn up --force -r [rev] # runtime: 1 min ("0m50.945s")
# fix concurrent regressions (which occurred during the revision range):
for patch in r12689 r12760 r12865 r12872 r12994; do
	svn di -c "$patch"|patch --force --fuzz=3 -p 0
done
	# use `patch` instead of `svn merge` because `svn merge` sometimes inexplicably
	# doens't apply patches
	# --fuzz: allow patching even when surrounding lines have changed
# if any of the commands below are broken, try a different revision
yes|make mk_db rm_initial_public schemas/reinstall # mk_db: install new extensions
yes|make inputs/.TNRS/reinstall
yes|make schemas/public/reinstall # sanity check before running the import
# }
$0 # nested shell
export version=test_import
declare -ax inputs; inputs=(inputs/ARIZ/)
. bin/import_all # runtime: 50 min ("0:45:07.105389"+"4:05.03")
# at "This will delete the test_import schema", type y and press ENTER
# determine if the revision works:
# {
# wait 8-10 min
# wait until pg_stat_activity shows an in# query
# see if pg_stat_activity shows the buggy query
#  (https://projects.nceas.ucsb.edu/nceas/issues/902) -> the revision is broken,
#  or an in# query after in#6 -> the revision is OK
# }
# stop the import:
# {
kill % # cancel after_import()
. bin/stop_imports
sudo pkill -f 'postgres: bien vegbien'
# }

to set up the VM:
ln -s /Volumes/vegbiendev/vegbiendev.vdi ~/VirtualBox\ VMs/vegbiendev/vegbiendev.vdi
screen
# press ENTER
l=1 overwrite=1 inplace=1 src=/Volumes/vegbiendev/vegbiendev.vdi dest=~/VirtualBox\ VMs/vegbiendev/vegbiendev.file.vdi put # runtime: 5 h ("4:43:16")
	# move vegbiendev.vdi to the internal hard drive
# press Ctrl-D
(cd ~/VirtualBox\ VMs/vegbiendev/; mv vegbiendev.file.vdi vegbiendev.vdi)
# open VirtualBox
# select the vegbiendev VM
# restore the "+bootloader+VirtualBox Guest Additions+eth1" snapshot
# open Settings > System tab
# in the Motherboard subtab, set Base Memory to 2048 MB
# in the Processor subtab, set Processor(s) to 1
# boot the VM
# when asked whether to skip mounting, press S
ssh -t 128.111.220.240
rm inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql
sed --in-place -r 's/^(shared_buffers = )\S+/\11000MB/' schemas/postgresql.conf
	# = <1 GB; decrease to match VM's allocated memory (2 GB)
sudo mkdir -p /var/lib/postgresql/9.3/main/
sudo chown postgres:postgres /var/lib/postgresql/9.3/main/
sudo -E -u postgres /usr/lib/postgresql/9.3/bin/initdb -D /var/lib/postgresql/9.3/main/
sudo ln -sf /etc/postgresql/9.3/main/*.conf /var/lib/postgresql/9.3/main/
make postgres_reload
# at "Modifying postgresql.conf and pg_hba.conf", type y and press ENTER
# at "kernel.shmmax ... Press ENTER to continue", press ENTER
# at "restart PostgreSQL manually ... Press ENTER to continue":
# open a new window
ssh -t 128.111.220.240
# run what it says
# press Ctrl-D
# return to the previous window
# press ENTER
* to use a database backup:
# {
make mk_db rm_initial_public # do things that are not part of the backup
screen
# press ENTER
l=1 src='frenzy.nceas.ucsb.edu:~/bien/' dest=. put backups/vegbien.r12025.backup # runtime: 25 min ("0:25:24")
# press Ctrl-D
sudo chgrp postgres backups/vegbien.r12025.backup
sudo halt
# at "System halted", close the VM and *uncheck* Restore current snapshot
# create a VM snapshot named "+initdb+database backup file"
# boot the VM
# when asked whether to skip mounting, press S
ssh -t 128.111.220.240
screen
# press ENTER
time for schema in temp util py_util geoscrub herbaria IRMNG IUCN NCBI newWorld TNRS ARIZ; do
	bin/psql_verbose_vegbien <<<"CREATE SCHEMA \"$schema\";"
	"time" sudo -E -u postgres pg_restore --exit-on-error --verbose --dbname=vegbien --schema="$schema" backups/vegbien.r12025.backup
		# need to run as DB superuser to restore py_util
done # runtime: 15 min ("11:44:05" - ~11:30)
	# must use for loop because pg_restore doesn't support multiple --schema
	# options (it just uses the last one)
	# (http://postgresql.1045698.n5.nabble.com/pg-restore-should-accept-multiple-t-switches-td2399138.html)
# press Ctrl-D
sudo halt
# at "System halted", close the VM and *uncheck* Restore current snapshot
# create a VM snapshot named "+pg_restore"
# boot the VM
# when asked whether to skip mounting, press S
# create a VM snapshot named "booted"
# close the VM and *check* Restore current snapshot
# }
* to use a clean database:
# {
(cd inputs/; for dir in IRMNG IUCN newWorld; do mv "$dir" ."$dir"; done)
(cd inputs/; for dir in */; do dir="${dir%/}"; case "$dir" in analytical_db|ARIZ) : ;; *) mv "$dir" .archive/"$dir";; esac; done)
make misc-Linux db inputs/install schemas/public/reinstall # runtime: 15 min ("15:11:16".."15:26:28") @starscream.vegbiendev
# at "This will delete the current public schema of your VegBIEN DB", type y and press ENTER
# }

to install system updates:
# boot the VM
# when asked whether to skip mounting, press S
sudo apt-get update
sudo apt-get dist-upgrade # runtime: 12 min ("14:20:15".."14:31:50") @starscream.vegbiendev
sudo reboot # some system updates require system restart
# when asked whether to skip mounting, press S
sudo halt
# at "System halted", close the VM and *uncheck* Restore current snapshot
# create a VM snapshot named "+system updates"
# boot the VM
# when asked whether to skip mounting, press S
# create a VM snapshot named "booted"

to enable VM to access VirtualBox shared folders:
(currently doesn't work, likely because of a bug in VirtualBox Guest Additions when installed on something other than a clean Linux install)
sudo sed --in-place -r 's/^vboxsf:.*:$/&aaronmk/' /etc/group
# press Ctrl-D
ssh -t 128.111.220.240

to retrieve the original contents of the backup from the VM:
# open VirtualBox
# select the vegbiendev VM
# restore the "+LiveCD+ssh+root pw+mount" snapshot
# **IMPORTANT**: can't use inplace=1 optimization because this messes up the
#  shared hardlinks used by ~/Documents/BIEN/vegbiendev/
# --link-dest: relative to dest, not currdir, so need abs path
l=1 overwrite=1 src=root@128.111.220.198:/mnt/ dest=~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT/ sudo -E put --link-dest="$HOME"/Documents/BIEN/vegbiendev/ --exclude=/home/bien/svn/ --exclude=/home/aaronmk/Dropbox/
	# --exclude=/home/aaronmk/Dropbox/: this is not used by the BIEN scripts
sudo mkdir ~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT/home/bien/svn/
# --exclude of specific files: these have compressed versions
l=1 overwrite=1 src=root@128.111.220.198:/mnt/ dest=~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT/ sudo -E put --link-dest="$HOME"/Documents/BIEN/vegbiendev/home/aaronmk/bien/ --no-owner --no-group --exclude=/backups/.vegbien.r10848.backup.aYCFxI --exclude='/backups/vegbien.*.backup' --exclude=/inputs/GBIF/_archive/Specimen/GBIF.txt --exclude=/inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql --exclude=/inputs/GBIF/raw_occurrence_record_plants/_archive/table.2013-5-13.tsv --exclude=/inputs/GBIF/raw_occurrence_record_plants/table.tsv --exclude=/inputs/VegBank/_archive/2012-8-30/vegbank.sql --exclude='/inputs/FIA/_archive/2011-10-17/Organism/*_Extract.csv' --exclude='*.CSV' --exclude='*.gz' --exclude='*.log.sql' --exclude='*.zip'                                          home/bien/svn/
l=1 overwrite=1 src=root@128.111.220.198:/mnt/ dest=~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT/ sudo -E put --link-dest="$HOME"/Documents/BIEN/vegbiendev/home/aaronmk/bien/ --no-owner --no-group --exclude=/backups/.vegbien.r10848.backup.aYCFxI --exclude='/backups/vegbien.*.backup' --exclude=/inputs/GBIF/_archive/Specimen/GBIF.txt --exclude=/inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql --exclude=/inputs/GBIF/raw_occurrence_record_plants/_archive/table.2013-5-13.tsv --exclude=/inputs/GBIF/raw_occurrence_record_plants/table.tsv --exclude=/inputs/VegBank/_archive/2012-8-30/vegbank.sql --include='/inputs/FIA/_archive/2011-10-17/Organism/*_Extract.csv' --include='*.CSV' --include='*.gz' --include='*.log.sql' --include='*.zip' --include='*/' --exclude='**' --no-perms home/bien/svn/
	# --no-perms: enable --link-dest to work in spite of perms changes (the
	#  perms on these files are not important to the BIEN scripts)
# generate list of all the files whose permissions were changed since the
#  backup, but which are extracted with their changed permissions instead of
#  their original ones in the backup:
l=  overwrite=1 src=root@128.111.220.198:/mnt/ dest=~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT/ sudo -E put --link-dest="$HOME"/Documents/BIEN/vegbiendev/home/aaronmk/bien/ --no-owner --no-group --exclude=/backups/.vegbien.r10848.backup.aYCFxI --exclude='/backups/vegbien.*.backup' --exclude=/inputs/GBIF/_archive/Specimen/GBIF.txt --exclude=/inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql --exclude=/inputs/GBIF/raw_occurrence_record_plants/_archive/table.2013-5-13.tsv --exclude=/inputs/GBIF/raw_occurrence_record_plants/table.tsv --exclude=/inputs/VegBank/_archive/2012-8-30/vegbank.sql home/bien/svn/ >~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT.perms_changed.txt

to retrieve the contents of the VM, with the VirtualBox changes added:
# open VirtualBox
# select the vegbiendev VM
# restore the "(+VirtualBox changes)+root pw" snapshot
# boot the VM
# **IMPORTANT**: can't use inplace=1 optimization because this messes up the
#  shared hardlinks used by ~/Documents/BIEN/vegbiendev/
# --link-dest: relative to dest, not currdir, so need abs path
l=1 overwrite=1 src=root@128.111.220.240:/ dest=~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT.VirtualBox/ sudo -E put --link-dest="$HOME"/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT/ --exclude=/home/bien/svn/ --exclude=/home/aaronmk/Dropbox/
	# --exclude=/home/aaronmk/Dropbox/: this is not used by the BIEN scripts
sudo mkdir ~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT.VirtualBox/home/bien/svn/
# --exclude of specific files: these have compressed versions
l=1 overwrite=1 src=root@128.111.220.240:/ dest=~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT.VirtualBox/ sudo -E put --link-dest="$HOME"/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT/home/bien/svn/ --no-owner --no-group --exclude=/backups/.vegbien.r10848.backup.aYCFxI --exclude='/backups/vegbien.*.backup' --exclude=/inputs/GBIF/_archive/Specimen/GBIF.txt --exclude=/inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql --exclude=/inputs/GBIF/raw_occurrence_record_plants/_archive/table.2013-5-13.tsv --exclude=/inputs/GBIF/raw_occurrence_record_plants/table.tsv --exclude=/inputs/VegBank/_archive/2012-8-30/vegbank.sql --exclude='/inputs/FIA/_archive/2011-10-17/Organism/*_Extract.csv' --exclude='*.CSV' --exclude='*.gz' --exclude='*.log.sql' --exclude='*.zip'                                          home/bien/svn/
l=1 overwrite=1 src=root@128.111.220.240:/ dest=~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT.VirtualBox/ sudo -E put --link-dest="$HOME"/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT/home/bien/svn/ --no-owner --no-group --exclude=/backups/.vegbien.r10848.backup.aYCFxI --exclude='/backups/vegbien.*.backup' --exclude=/inputs/GBIF/_archive/Specimen/GBIF.txt --exclude=/inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql --exclude=/inputs/GBIF/raw_occurrence_record_plants/_archive/table.2013-5-13.tsv --exclude=/inputs/GBIF/raw_occurrence_record_plants/table.tsv --exclude=/inputs/VegBank/_archive/2012-8-30/vegbank.sql --include='/inputs/FIA/_archive/2011-10-17/Organism/*_Extract.csv' --include='*.CSV' --include='*.gz' --include='*.log.sql' --include='*.zip' --include='*/' --exclude='**' --no-perms home/bien/svn/
	# --no-perms: enable --link-dest to work in spite of perms changes (the
	#  perms on these files are not important to the BIEN scripts)
l=  overwrite=1 src=root@128.111.220.240:/ dest=~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT.VirtualBox/ sudo -E put --link-dest="$HOME"/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT/home/bien/svn/ --no-owner --no-group --exclude=/backups/.vegbien.r10848.backup.aYCFxI --exclude='/backups/vegbien.*.backup' --exclude=/inputs/GBIF/_archive/Specimen/GBIF.txt --exclude=/inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql --exclude=/inputs/GBIF/raw_occurrence_record_plants/_archive/table.2013-5-13.tsv --exclude=/inputs/GBIF/raw_occurrence_record_plants/table.tsv --exclude=/inputs/VegBank/_archive/2012-8-30/vegbank.sql home/bien/svn/|diff /dev/stdin ~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT.perms_changed.txt 
# ensure there are no file changes

to configure the VM to support VirtualBox:
# open VirtualBox
# select the vegbiendev VM
# restore the "restore of 2014-02-02 01:07:32 backup (DO NOT DELETE)" snapshot
# boot the VM from ~/software/ubuntu-12.04.4-desktop-amd64.iso
# install a bootloader
# shut down the VM
# eject the CD image
# boot the VM
# when asked whether to skip mounting, press S
# install VirtualBox Guest Additions
# set up the network connection:
# {
ssh -t aaronmk@128.111.220.240
sudo nano /etc/network/interfaces
# remove the entry for eth0 (which doesn't work under VirtualBox)
# add the following entry:
---
auto eth1
iface eth1 inet dhcp
---
# }