bugfix: /README.TXT: to back up the local machine's hard drive: first need to resize the BIEN3.**SAVE** partition so there is enough space
bugfix: /README.TXT: to backup files not in Time Machine: need to use `brew services _ postgresql` instead of `launchctl _ ~/Library/LaunchAgents/homebrew.mxcl.postgresql.plist`
bugfix: /README.TXT: to back up the local machine's hard drive: need to use `brew services _ postgresql` instead of `launchctl _ ~/Library/LaunchAgents/homebrew.mxcl.postgresql.plist`
bugfix: /README.TXT: to back up vegbiendev: can't use inplace=1 optimization because this messes up the shared hardlinks used by ~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT*/
bugfix: /README.TXT: to back up vegbiendev: also need to lock hardlinked files at end
/README.TXT: Installation: `make install`: added alternative command to install a complete DB with all the datasources (instead of a blank DB)
bugfix: /README.TXT: Full database import: need to unlock hardlinked files
/README.TXT: back up Postgres: backups/pg_snapshot: documented runtime when queries have been run (1 h)
fix: /README.TXT: Full database import: also need to run `unset TMOUT` in the outer `screen` shell
fix: /README.TXT: back up Postgres: needs to be run in `screen`
/README.TXT: to synchronize vegbiendev, jupiter, and your local machine: update mtimes in Dropbox: preserve uncommitted changes
fix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: update mtimes in Dropbox: don't update perms because this would incorrectly transfer the hardlink lock status
fix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: TWiki: need to fix_perms after running this to reset perms on hardlinks
/README.TXT: syncing: use del instead of overwrite where possible, to avoid overwriting newer files
/README.TXT: Full database import: should also snapshot Postgres before starting import
/README.TXT: record the import times: documented how to update the Postprocessing times
bugfix: /README.TXT: globs that list all the datasources: this was incorrectly excluding U, so fixed to match bin/with_all $hidden_srcs
fix: /README.TXT: record the import times: need to first click the "current" tab
/README.TXT: To re-run geoscrubbing: updated runtimes and revision #s
bugfix: /README.TXT: To re-run geoscrubbing: don't close subshell because it closes automatically (this would instead exit `screen`)
/README.TXT: To re-run geoscrubbing: updated runtimes
bugfix: /README.TXT: To re-run geoscrubbing: "press Enter" and `unset TMOUT` steps are reversed
/README.TXT: datasource removal: linked to runtimes on the wiki
/README.TXT: To re-run geoscrubbing: re-create public-schema views that were cascadingly deleted: listed which views these currently are
bugfix: /README.TXT: Datasource setup: For MS Access databases: also need to comment out `CREATE DATABASE` because pg_dump_limit is only applied to data.sql (due to requirements of the TNRS datasource)
/README.TXT: To re-run geoscrubbing: also need to `unset TMOUT` because TMOUT causes shell to exit even with background processes
/README.TXT: To re-run geoscrubbing: `rm=1 inputs/.geoscrub/run`: should just need to reinstall the geoscrub_output table
/README.TXT: To re-run geoscrubbing: updated runtimes. note that these are faster on the new hardware.
fix: /README.TXT: To re-run geoscrubbing: `rm=1 inputs/.geoscrub/geoscrub_output/geoscrub.csv.run`: use a subshell to avoid closing screen on errexit
fix: /README.TXT: Single datasource refresh: also back up DB after this
/README.TXT: datasource removal: documented bien2_traits runtime
/README.TXT: added datasource removal instructions
fix: /README.TXT: Single datasource refresh: place updated extract: generalized datasrc name
/README.TXT: Installation: added instructions for inputs/download/live prompts
/README.TXT: Installation: added instructions for MySQL installation prompts
fix: /README.TXT: Installation: "Are you sure you want to continue connecting" prompt comes before "aaronmk@jupiter's password" prompt
fix: /README.TXT: Installation: added instructions for "aaronmk@jupiter's password" prompt
/README.TXT: Installation: added step to open a terminal window
fix: /README.TXT: Installation: added instructions for "Are you sure you want to continue connecting" prompt
fix: /README.TXT: Installation: need instructions for "reload PATH" prompt
fix: /README.TXT: Installation: `apt-get install subversion`: need --yes
README.TXT: bin/sync_upload calls as root: don't need to set $USER because this is now set to the correct value in bin/sync_upload's scripts
/README.TXT: Installation: `make install`: added instructions for what to do at each prompt
/README.TXT: Installation: Check out svn: need to install svn first as this does not come preinstalled on Ubuntu
/README.TXT: to back up the local machine's hard drive: just do a single pass, to avoid the numerous different steps
fix: /README.TXT: to back up the local machine's settings: to jupiter: need `sudo -E` for new Documents/BIEN/vegbiendev*/
/README.TXT: backups of ~/.dropbox/: just pause and resume Dropbox instead of quitting and restarting it
/README.TXT: to back up the local machine's settings: to Dropbox: exclude gmvault-db/ to save space in Dropbox
/README.TXT: to back up the local machine's settings: don't need to exclude ~/Library/Thunderbird/Profiles/9oo8rcyn.default/global-messages-db.sqlite because the disk that was corrupting this file has been replaced (#907)
/README.TXT: to back up e-mails: don't need to also sync aaronmk@nceas.ucsb.edu because these e-mails are also in aaronmk.nceas@gmail.com (auto-forwarded)
/README.TXT: Notes on system stability: removed no longer applicable warning about system upgrades, which is now incorrect because the disk space overrun bug (#887) was found not to have been caused by a system upgrade
/README.TXT: to synchronize vegbiendev, jupiter, and your local machine: avoid extraneous diffs when rsyncing: clarified the machines that the command should be run on
fix: /README.TXT: to backup files not in Time Machine: need to use 2 TB external hard drive instead of Time Machine drive because Time Machine drive does not have ~/Documents/BIEN/ in a location where it can be hardlinked against
/README.TXT: Datasource setup: For MS Access databases: added that one should use the settings in the associated .ini file where available
/README.TXT: Datasource setup: For MS Access databases: program link: added page subsections
/README.TXT: to backup files not in Time Machine: note that Time Machine dereferences hard links: added commands documenting that this is the case
fix: /README.TXT: to backup files not in Time Machine: on first run, create parent dirs: added mkdir for Postgres
bugfix: /README.TXT: to backup files not in Time Machine: on first run, create parent dirs: mkdir: need sudo
/README.TXT: to backup files not in Time Machine: moved to root/ subdir to group the multiple top-level dirs together
/README.TXT: to backup files not in Time Machine: added the vegbiendev archival backups, which cannot be backed up by Time Machine because it dereferences hard links
/README.TXT: to backup files not in Time Machine: documented why Postgres cannot be backed up by Time Machine
/README.TXT: Single datasource refresh: added steps to place the updated extract and extracted flat file(s)
/README.TXT: Single datasource refresh: connect to vegbiendev first, even though steps before it have their own step to do this
/README.TXT: Single datasource refresh: reimport_scrub: added step to view progress
/README.TXT: Single datasource refresh: moved to top since these steps are performed more often
/README.TXT: Single datasource import: renamed to Single datasource refresh since it works on existing datasources
/README.TXT: Single datasource import: also need to reload staging tables
/README.TXT: Single datasource import: added steps to re-run geoscrubbing and back up the vegbiendev database
: renamed 2TB drive's BIEN3 partition to BIEN3.**SAVE since one might not see the SAVE file in it
/README.TXT: to back up the local machine's hard drive: also exclude *-files indicating the (differing) retention statuses of the partitions involved
/README.TXT: to back up the local machine's hard drive: renamed backup partition to BIEN3 to make clear what the backup drive contains
fix: /README.TXT: to back up the local machine's hard drive: updated location of `screen` for added commands
/README.TXT: added trailing / on dirs to make clear that they're dirs
fix: /README.TXT: to back up vegbiendev: also back up /home/aaronmk/bien/ (instead of just symlinking to the local copy), since this can be done space-efficiently with hardlinks. this ensures that the vegbiendev backup will not be modified when the local copy of bien/ is.
/README.TXT: to backup files not in Time Machine: don't need to review diff because command is unidirectional
fix: /README.TXT: to back up the local machine's hard drive: "repeat until only minimal changes" should refer to the first sync command
/README.TXT: to back up vegbiendev: use inplace=1 to speed stopping and resuming transfer
fix: /README.TXT: to back up the local machine's hard drive: removed --extended-attributes (after initial sync) because rsync apparently has to visit every file for this
fix: /README.TXT: to back up the local machine's hard drive: also need --extended-attributes
/README.TXT: to back up the local machine's hard drive: removed --delete-before now that that partition has been expanded
fix: /README.TXT: to back up vegbiendev: exclude /var/lib/mysql.bak,postgresql.bak because the local machine doesn't need 2 copies of this information
/README.TXT: to back up vegbiendev: removed no longer needed exclude of Dropbox subdir backup
fix: /README.TXT: to back up vegbiendev: also need to do steps under Maintenance > "to synchronize vegbiendev, jupiter, and your local machine" because /home/aaronmk/bien is not synced here
bugfix: /README.TXT: to back up vegbiendev: need `overwrite=1`
/README.TXT: to back up the version history: don't also need this on vegbiendev because it's already on jupiter and the local machine
bugfix: /README.TXT: to back up vegbiendev: need to include Postgres config files
/README.TXT: to back up the local machine's hard drive: don't back up temp files: added /.fseventsd/
fix: /README.TXT: to back up the local machine's hard drive: initial runtime: use range instead because some of the later runtime might have been from the same files
/README.TXT: to back up the local machine's hard drive: updated initial runtime to include additional transferred files (17 h)
fix: /README.TXT: to back up the local machine's hard drive: need to use --delete-before because the backup partition is near capacity
/README.TXT: to back up the local machine's hard drive: don't back up temp files such as /private/var/vm/*
fix: /README.TXT: to back up the local machine's hard drive: back up most Dropbox/Postgres files before stopping processes, to minimize downtime
bugfix: /README.TXT: to back up the local machine's hard drive: can't use ~ with --exclude
/README.TXT: to back up the local machine's hard drive: back up the non-Dropbox, non-Postgres files separately to minimize the Dropbox and Postgres downtime
/README.TXT: to back up the vegbiendev databases: don't need to review diff for these as it's always unidirectional
/README.TXT: added instructions to back up vegbiendev
