This includes all archived imports and staging tables.

Connecting to vegbiendev:

	cd /home/bien/svn # should happen automatically at login

Notes on system stability:

		http://vegpath.org/links/#**%20modifying%20a%20running%20shell%20script)

Single datasource import:

	(Re)import and scrub: make inputs/<datasrc>/reimport_scrub by_col=1 &

	(Re)import only: make inputs/<datasrc>/reimport by_col=1 &

	Note that these commands also work if the datasource is not yet imported

			if you encounter errors, they are most likely related to the

				PostgreSQL error parsing in /lib/sql.py parse_exception()

			See note under Testing below

	Ensure there are no local modifications: svn st

	up

	make inputs/download

				inputs/test_taxonomic_names/test_scrub # re-run TNRS

				rm=1 inputs/.TNRS/data.sql.run export_

				Commit

				If dropping a column, save the dependent views

				Make the same changes in the live TNRS.tnrs table on vegbiendev

				If dropping a column, recreate the dependent views

			Place the original .sql file in _src/ (*not* in _MySQL/)

			Follow the steps starting with Install the staging tables below.

				This is for an initial sync to get the file onto vegbiendev.

				Create a database for the MySQL export in phpMyAdmin

				Give the bien user all database-specific privileges *except*

					UPDATE, DELETE, ALTER, DROP. This prevents bugs in the

			./fix_perms

			make inputs/upload

			make inputs/upload live=1

			up

			make inputs/download

			make inputs/download live=1

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

--

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

			make phppgadmin-Linux

	regularly, re-run full-database import so that bugs in it don't pile up.

		it needs to be kept in working order so that it works when it's needed.

				on all machines:

				up

				./fix_perms

				upload:

				overwrite=1 bin/sync_upload --size-only

					then rerun with l=1 ...

		open Thunderbird

		click the All Mail folder for each account and wait for it to download the e-mails in it

	to back up the version history:

		svnsync sync file:///home/aaronmk/Dropbox/docs/BIEN/svn_repo/ # initial runtime: 1.5 h ("08:21:38" - "06:45:26") @vegbiendev

		(cd ~/Dropbox/docs/BIEN/git/; git svn fetch)

		overwrite=1        src=~ dest='aaronmk@jupiter.nceas.ucsb.edu:~' put Dropbox/docs/BIEN/svn_repo/ # runtime: 1 min ("1:05.08")

			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'

				perform the steps under "apply new data dict mappings to

					datasource mappings/staging tables" above

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

Backups:

	Archived imports:

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

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

				make schemas/rotate

		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 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 &

Datasource refreshing:

	VegBank:

		make inputs/VegBank/vegbank.sql-remake

		make inputs/VegBank/reinstall quiet=1 &

				This must be run *after* the datasources are installed, because

				views in public depend on some of the datasources

			sudo -E -u postgres psql <<<'DROP DATABASE vegbien_prev'

			repeat the above steps

			**WARNING**: Do not run this until reinstall_all runs successfully

			on the local machine, or the live DB may be unrestorable!

		on local machine:

			inputs/run postprocess # runtime: see inputs/run

			time yes|make inputs/{NVS,SALVIAS,TEAM}/test # old-style import; runtime: 1 min ("0m59.692s") @starscream

			manually apply schema changes to the live public schema

			do steps under "on local machine" above

	Sync ERD with vegbien.sql schema:

		make schemas/public/reinstall

		make inputs/ACAD/Specimen/logs/steps.by_col.log.sql

	To import and scrub just the test taxonomic names:

		inputs/test_taxonomic_names/test_scrub

General: