web/links/index.htm: updated to Firefox bookmarks: Ubuntu 14.04 upgrade: Apache: documented that this breaks MultiViews, so you need to rewrite .htaccess files to avoid using MultiViews

web/links/index.htm: updated to Firefox bookmarks: Ubuntu 14.04 upgrade: added Postgres upgrading instructions

_license/non-open-source/applies_to.txt: Brad: added "anything he created while not working for iPlant, from 2013-7-1..10-31"

web/links/index.htm: updated to Firefox bookmarks: Ubuntu 14.04 upgrade

web/links/index.htm: updated to Firefox bookmarks: Ubuntu 14.04 upgrade: added phpMyAdmin fixing instructions

web/links/index.htm: updated to Firefox bookmarks: Ubuntu 14.04 upgrade: added phpMyAdmin fixing instructions

web/links/index.htm: updated to Firefox bookmarks: Ubuntu: Ubuntu 14.04 upgrade: added things broken by it. PostgreSQL: fixed links.

/Makefile: postgres-Linux: added warning that the install commands were designed to run on Ubuntu 12.04, which is no longer the version used by vegbiendev (it is now 14.04)

backups/mysql_snapshot: documented initial vegbiendev->jupiter upload time for GBIF/raw_occurrence_record.MYD (7 h for 91 GB = 3.7 MB/s)

fix: web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: backups: wal_keep_segments method: clarified how to determine the value of wal_keep_segments. filesystem-level backups: documented the advantages of filesystem-level backups over traditional database-level backups with pg_dump.

fix: web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: backups: wal_keep_segments: restored annotations

web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: backups: documented how to set up online and offline backups (with two possible approaches for online backups)

web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: backups: documented how to set up online and offline backups (with two possible approaches for online backups)

web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: backups: documented how to set up online and offline backups (with two possible approaches for online backups)

lib/sh/db.sh: pg_snapshot(): perform online backup if possible, to avoid needing to restart the server

lib/sh/db.sh: added pg_start_backup(), pg_stop_backup()

lib/sh/db.sh: psql(): only set redirs if can redirect

bugfix: psql(): when as_root is on, need to avoid redirections as these are not passed through by sudo

/README.TXT: use `sudo -u ... -i` instead of `sudo su - ...` to avoid using two commands to accomplish the login

bugfix: lib/sh/db.sh: psql(): don't use `--file /dev/fd/40` when can't redirect

fix: lib/sh/db.sh: psql(): when using sudo with custom $stdin, raise error that this is not supported

lib/sh/db.sh: psql(): $data_bypasses_filter: renamed to $data2stdout for clarity

lib/sh/db.sh: psql(): $bypass_ok: renamed to $can_redir for clarity

lib/sh/db.sh: psql(): usage: $stdin: documented that can also use process substitution for this

bugfix: lib/sh/util.sh: `type` calls: need -- before cmd in case it starts with -

lib/sh/util.sh: cmd2rel_path: use is_extern()

lib/sh/sync.sh: db_snapshot(): use `end_try` as specified in `try` usage

lib/sh/util.sh: try: usage: added location of finally block

schemas/postgresql.conf: wal_level: set to hot_standby to enable online backup with pg_start_backup()

lib/sh/sync.sh: upload(): always print the function and kw_params

added backups/mysql_snapshot, pg_snapshot

bugfix: lib/sh/util.sh: type(): need to handle options before command name

lib/sh/util.sh: added 1st_non_opt()

lib/sh/util.sh: unalias(): use self_builtin, which is now defined before it

lib/runscripts/util.run: sudo(): avoid slow $wrap_fn when using `command` (ie. always executable)

lib/sh/util.sh: unalias(): use self_builtin, which is now defined before it

bugfix: lib/sh/util.sh: commands: `type` calls: need to account for the fact that any alias is already expanded

lib/sh/util.sh: functions: moved before commands since commands are more complex

lib/sh/sync.sh: db_copy() and callers: pass args as rsync options

fix: lib/sh/sync.sh: db_copy(): need to exclude files which prevent tape backup

lib/sh/db.sh: added pg_ctl(), pg_snapshot()

lib/sh/sync.sh: db_snapshot(): copy changes before stopping DB to minimize the time that it's shut down

lib/sh/sync.sh: db_snapshot(): factored copy operation out into separate db_copy() function

lib/sh/db.sh: mysql_snapshot(): use new db_snapshot()

lib/sh/sync.sh: added db_snapshot()

lib/Firefox_bookmarks.reformat.csv: changed "page's own description" to "page's self-description" for clarity

web/links/index.htm: updated to Firefox bookmarks: removed dead links

web/links/index.htm: updated to Firefox bookmarks: updated favicons

web/links/index.htm: updated to Firefox bookmarks: modifying a running shell script: updated to document that `svn up` actually does use two-stage save automatically

lib/sh/db.sh: mysql_snapshot(): for large files, don't re-copy entire file

lib/sh/db.sh: mysql_snapshot(): use live mode as the default

fix: lib/sh/db.sh: mysql_snapshot(): need to create dest dir if doesn't exist

bugfix: lib/sh/db.sh: mysql_snapshot(): try: need to use split syntax with prep_try instead, to work with prefix vars

bugfix: lib/sh/db.sh: mysql_snapshot(): try: need to use split syntax with prep_try instead, to work with prefix vars

fix: lib/sh/util.sh: try usage: documented that the split syntax with prep_try is meant to be used with vars before the cmd

fix: lib/sh/util.sh: echo_vars(): also need to print unset vars (including unset kw_params)

lib/sh/util.sh: echo_vars(): put loop var on same line as `for`

bugfix: lib/sh/util.sh: sudo(): need to preserve PATH separately because -E does not preserve this

lib/sh/util.sh: echo_redirs_cmd(): inline the function alias since it's only used in one place

bugfix: lib/sh/util.sh: redir(): need to load new aliases before it

lib/sh/util.sh: echo_redirs_cmd(): log $PATH to facilitate troubleshooting

lib/sh/util.sh: echo_redirs_cmd(): documented what the $(...) section does

lib/sh/util.sh: echo_redirs_cmd(): moved comment about <>file redirs to line that it applies to

lib/sh/util.sh: moved echo_redirs_cmd() to right before redir() which uses it

lib/sh/util.sh: catch(): log at higher log_level, since this is internal code

fix: lib/sh/util.sh: die_e(): treat SIGPIPE as benign error

lib/sh/util.sh: removed no longer used ignore_sig(). use ignore() instead, which now supports SIG*.

lib/sh/util.sh: piped_cmd(): use ignore, which now supports SIG*

lib/sh/util.sh: signals: catch(): added echo_func

lib/sh/util.sh: set_global_fds(): debug to global stderr in case stderr filtered

lib/sh/util.sh: debugging: use configurable debug_fd (set to $err_fd)

lib/sh/util.sh: signals: override catch() to support SIG* as exception type

lib/sh/util.sh: moved primitives sections before more complex sections that depend on them

lib/sh/util.sh: 2nd functions section: moved to 1st functions section

bugfix: lib/sh/util.sh: added workaround for bash bug where exit sometimes inxeplicably ignores $?

fix: lib/sh/util.sh: self_builtin: avoid $() so that $? isn't modified

lib/sh/util.sh: use new self_builtin

lib/sh/util.sh: added self_builtin

lib/sh/util.sh: pv(), pf(): moved to debugging section

bugfix: lib/sh/util.sh: stderr_matches(): also need to handle any filter error, such as caused by Ctrl+C

lib/sh/util.sh: stderr_matches(): echo_vars @PIPESTATUS_ to assist debugging

bugfix: lib/sh/util.sh: stderr2stdout(): use piped_cmd to ignore SIGPIPE since the output of this will piped to another command

lib/sh/util.sh: setup_log_fd(): $log_fd: use 3 (stdlog) since other scripts are likely to use this for logging as well

fix: lib/sh/util.sh: setup_log_fd(): fd_set_default(): use $log_fd instead of repeating the value of it

lib/sh/util.sh: die(): log at higher log_level, since this is logging code

lib/sh/util.sh: highlight_log_msg(): log at higher log_level, since this is logging code

bugfix: lib/runscripts/util.run: $subdirs: adjusted log_level now that echo_vars is one log_level lower

bugfix: lib/sh/util.sh: stderr_matches(): only set benign_error=1 if the matched error occurred

lib/sh/util.sh: ignore_e(): also set benign_error=1

fix: lib/sh/util.sh: prep_try alias: removed inaccurate comment

bugfix: lib/sh/util.sh: stdout2fd(): moved after redir() which it depends on

fix: lib/sh/util.sh: command(): moved `|| die_e` to command__exec so it would be properly indented under the echoed command

lib/sh/util.sh: verbosity_compat(): log at higher log_level because it's logging code

lib/sh/util.sh: $benign_error: log at higher log_level because it's logging code

lib/runscripts/util.run: $wrap_fn: log at higher log_level because it's startup code

lib/sh/util.sh: $top_* vars, $is_outermost: log at higher log_level because it's startup code

lib/sh/util.sh: $top_script: echo_vars this like the other $top_* vars

lib/sh/util.sh: .(): log at higher log_level because it's startup code

lib/sh/util.sh: is_dot_script(): run with higher log_level since this is run at the beginning of the script

lib/sh/util.sh, runscripts/util.run: set_paths(): run with higher log_level to hide all the paths that are set at the beginning of the script