fix: /README.TXT: Full database import: Check # observations: updated to use view_full_occurrence_individual instead of analytical_stem
fix: /README.TXT: Full database import: Check that source contains the right datasources: use explicit list instead of checking just the count of datasources
bugfix: /README.TXT: to back up the local machine's settings: backing up / to vegbiendev: also need standard excludes from "to back up the local machine's hard drive"
/README.TXT: to back up the local machine's settings: also back up / to vegbiendev
/README.TXT: `sudo find / -name .DS_Store -print -delete`: documented runtime (23 min)
bugfix: /README.TXT: to back up the local machine's hard drive: need to turn off Time Machine to prevent Time Machine from running when the backup is booted, which messes up the Time Machine backup because the partition UUID is different
fix: /README.TXT: to back up the local machine's hard drive: don't need to pause Dropbox, since it will be reinitialized for the new partition UUID anyway
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)
