Maintenance:

	on a live machine, you should put the following in your .profile:

--

# make svn files web-accessible. this does not affect unversioned files, because

# these get the right permissions on the local machine instead.

umask ug=rwx,o=rx

unset TMOUT # TMOUT causes screen to exit even with background processes

--

	if http://vegbiendev.nceas.ucsb.edu/phppgadmin/ goes down:

		on vegbiendev: make postgres-Linux

	to synchronize vegbiendev, jupiter, and your local machine:

		WARNING: pay careful attention to all files that will be deleted or

			overwritten!

		install put if needed:

			download https://uutils.googlecode.com/svn/trunk/bin/put to ~/bin/ and `chmod +x` it

		when changes are made on vegbiendev:

			on all machines: ./fix_perms

			on vegbiendev, upload:

				overwrite=1 bin/sync_upload

					then rerun with l=1 ...

			on your machine, download:

				overwrite=1 swap=1 src=. dest='aaronmk@jupiter:~/bien' put --exclude=.svn inputs/VegBIEN/TWiki

					then rerun with l=1 ...

				overwrite=1 swap=1 bin/sync_upload

					then rerun with l=1 ...

				make backups/TNRS.backup/download live=1

				overwrite=1 sync_remote_url=~/Dropbox/svn/ bin/sync_upload --existing --size-only # just update mtimes/perms

					then rerun with l=1 ...

	to synchronize a Mac's settings with my testing machine's:

		download:

			WARNING: this will overwrite all your user's settings!

			overwrite=1 swap=1 sync_local_dir=~/Library/ sync_remote_subdir=Library/ bin/sync_upload --exclude="/Saved Application State"

				then rerun with l=1 ...

		upload:

			do step when changes are made on vegbiendev > on your machine, download

			on jupiter: (cd ~/Dropbox/svn/; up)

			on your machine:

				overwrite=1 del= sync_local_dir=~/Dropbox/svn/ sync_remote_subdir=Dropbox/svn/ bin/sync_upload --size-only # just update mtimes

					then rerun with l=1 ...

				overwrite=1      sync_local_dir=~              sync_remote_subdir=             bin/sync_upload --exclude="/Library/Saved Application State" --exclude="/.Trash" --exclude="/bin" --exclude="/bin/pg_ctl" --exclude="/bin/unzip" --exclude="/Dropbox/home" --exclude="/.profile" --exclude="/.shrc" --exclude="/.bashrc"

					then rerun with l=1 ...

				overwrite=1      sync_local_dir=~              sync_remote_url=~/Dropbox/home  bin/sync_upload --exclude="/Library/Saved Application State" --exclude="/.Trash" --exclude="/.dropbox" --exclude="/Documents/BIEN" --exclude="/Dropbox" --exclude="/software" --exclude="/VirtualBox VMs/**.sav" --exclude="/VirtualBox VMs/**.vdi" --exclude="/VirtualBox VMs/**.vmdk"

					then rerun with l=1 ...

		upload just the VirtualBox VMs:

			on your machine:

				overwrite=1      sync_local_dir=~              sync_remote_subdir=             bin/sync_upload ~/"VirtualBox VMs/**"

					then rerun with l=1 ...

	to backup files not in Time Machine:

		pg_ctl. stop # stop the PostgreSQL server

		src=/ dest=/Volumes/Time\ Machine\ Backups/ sudo put Library/PostgreSQL/9.1/data/

			then rerun with l=1 ...

		pg_ctl. start # start the PostgreSQL server

	VegCore data dictionary:

		Regularly, or whenever the VegCore data dictionary page

			(https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore)

			is changed, regenerate mappings/VegCore.csv:

			make mappings/VegCore.htm-remake; make mappings/

			svn di mappings/VegCore.tables.redmine

			If there are changes, update the data dictionary's Tables section

			When moving terms, check that no terms were lost: svn di

			svn ci -m 'mappings/VegCore.htm: regenerated from wiki'

	Important: Whenever you install a system update that affects PostgreSQL or

		any of its dependencies, such as libc, you should restart the PostgreSQL

		server. Otherwise, you may get strange errors like "the database system

		is in recovery mode" which go away upon reimport, or you may not be able

		to access the database as the postgres superuser. This applies to both

		Linux and Mac OS X.

Backups:

	Archived imports:

		Back up: make backups/<version>.backup &

			Note: To back up the last import, you must archive it first:

				make schemas/rotate

		Test: make -s backups/<version>.backup/test &

		Restore: make backups/<version>.backup/restore &

		Remove: make backups/<version>.backup/remove

		Download: make backups/<version>.backup/download

	TNRS cache:

		Back up: make backups/TNRS.backup-remake &

			runtime: 3 min ("real 2m48.859s")

		Restore:

			yes|make inputs/.TNRS/uninstall

			make backups/TNRS.backup/restore &

				runtime: 5.5 min ("real 5m35.829s")

			yes|make schemas/public/reinstall

				Must come after TNRS restore to recreate tnrs_input_name view

	Full DB:

		Back up: make backups/vegbien.<version>.backup &

		Test: make -s backups/vegbien.<version>.backup/test &

		Restore: make backups/vegbien.<version>.backup/restore &

		Download: make backups/vegbien.<version>.backup/download

	Import logs:

		Download: make inputs/download-logs live=1