fix: exports/.rsync_filter.upload: *.csv: don't allow test runs' exports to overwrite the backed up ones

fix: lib/sh/db.sh: psql(): removed debugging changes

bugfix: lib/sh/util.sh: highlight_log_msg(): when not can_highlight_log_msg, need to remove any surrounding formatting

fix: lib/sh/util.sh: die_error_hidden(): always log local vars at same log_level as echo_func

fix: *{.sh,run}: always log kw_params at same log_level as echo_func

lib/sh/util.sh: split_lines(): usage: matched up and synced different syntaxes

bugfix: lib/sh/util.sh: log_msg!(): split_lines does not support being invoked by wrapper; need to use `declare lines; wrapper "split_lines" str` instead

fix: lib/sh/util.sh: split_lines(): usage: documented different syntax for when using wrapper

bugfix: lib/sh/util.sh: die_error_hidden(): echo_func to assist debugging

bugfix: lib/sh/util.sh: split(): need to limit the effects of IFS to just the splitting, so it doesn't cause strange errors in other functions

bugfix: stderr2stdout(): fd 2 must be redirected back to fd 2, not log-filtered, in case there are other errors in addition to the benign error. this fixes a bug in pg_schema_exists(), where errors about the DB being down were not displayed because they were log-filtered out.

lib/sh/make.sh: set_make_vars: don't display make vars at verbosity 2 to avoid clutter

bugfix: lib/sh/make.sh: begin_target: don't echo_func twice

inputs/GBIF/_MySQL/.rsync_ignore: added GBIFPortalDB-*.data.sql.gz, because these are intermediate files

bugfix: /Makefile: $(pg_ctl-Darwin): need to call the command rather than echoing it, as is needed for the Linux version

bugfix: /Makefile: $(pg_ctl-Darwin): need to `cd /` because due to pg_ctl bug, current directory must be accessible by it

bugfix: lib/runscripts/util.run: a non-runscript should have all args passed to main(). this fixes a bug in backups/*_snapshot where "main" would need to be prepended to any args for the script to run correctly.

bugfix: lib/runscripts/util.run: $wrap_fn: invoked script must always run as runscript so that wrapped command is run

lib/runscripts/util.run: added $is_runscript, for use by $wrap_fn

bugfix: lib/runscripts/util.run: $wrap_fn: $top_script doesn't need to be world-executable for most uses of sudo (only if sudoing to non-root)

bin/in_place: diff: use --brief to avoid scanning the entire file for large files

bin/in_place: added $preserve_mtime flag

web/links/index.htm: updated to Firefox bookmarks: Ubuntu 14.04 upgrade: Apache: documented that MultiViews is actually only broken for redirects with the filename "index"

web/.htaccess: for dirs, redirect to index.*: document it is actually just the filename "index" that MultiViews is broken for, other filenames work fine

bugfix: web/index.php: full directory index: only display if invoked as "vegpath.org/", not "vegpath.org/index.php"

bugfix: web/.htaccess: for dirs, redirect to index.*: added workaround for Ubuntu 14.04, which breaks MultiViews

/Makefile: postgres-Linux: updated to use the official version that comes with Ubuntu 14.04

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