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  • svn:ignore: extern

# Date Author Comment
13366 05/01/2014 03:22 AM Aaron Marcuse-Kubitza

bugfix: inputs/SALVIAS/validations.sql: need to cast character varying to text so that the types of each side of if() match

13365 05/01/2014 03:14 AM Aaron Marcuse-Kubitza

bugfix: lib/sh/db.sh: pg_dump(): need use_pg to import $pg_database before checking for existence of $database

13364 05/01/2014 03:11 AM Aaron Marcuse-Kubitza

lib/sh/util.sh: import_vars: documented that it's idempotent

13363 04/30/2014 07:10 PM Aaron Marcuse-Kubitza

/Makefile: python-Linux: removed ordereddict, since OrderedDict is now obtained from `collections`

13362 04/30/2014 07:06 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks: fixed broken links

13361 04/30/2014 06:58 PM Aaron Marcuse-Kubitza

bugfix: lib/util.py: use OrderedDict from collections rather than ordereddict to work with Mac OS X 10.8 Mountain Lion (http://vegpath.org/links/#OrderedDict)

13360 04/30/2014 06:42 PM Aaron Marcuse-Kubitza

/Makefile: apache-Linux: updated for Ubuntu 14.04, which includes Apache 2.4 in the distribution

13359 04/30/2014 06:23 PM Aaron Marcuse-Kubitza

/Makefile: install: documented that schemas/public/install also tests that a clean public schema will be installable by full-database import

13358 04/30/2014 06:12 PM Aaron Marcuse-Kubitza

/Makefile: install: skip the test step at the end because this is not needed for the installation (it can be run separately if desired)

13357 04/30/2014 05:46 PM Aaron Marcuse-Kubitza

bugfix: **/postprocess.sql: don't use the public schema, because this creates an unsatisfied dependency while the database is being installed, and breaks `make install`

13356 04/30/2014 05:36 PM Aaron Marcuse-Kubitza

schemas/public_.sql: _km_to_m(): made it a wrapper around util._km_to_m() so this function is only in one place

13355 04/30/2014 05:32 PM Aaron Marcuse-Kubitza

schemas/util.sql: added _km_to_m() for use when public._km_to_m() is not defined yet

13354 04/29/2014 11:36 PM Aaron Marcuse-Kubitza

bugfix: benign_does_not_exist_error(): removed ignore_e=3, because this exit status is also used for other errors

13353 04/29/2014 11:35 PM Aaron Marcuse-Kubitza

fix: lib/sh/db.sh: benign_does_not_exist_error(): use benign_error=1, which is now supported properly by stderr_matches()

13352 04/29/2014 11:34 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/util.sh: stderr_matches(): support $benign_error properly, by handling exit status logging in this func instead

13351 04/29/2014 11:03 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/db.sh: pg_schema_exists(): also need to benignify "does not exist" error if returns false

13350 04/29/2014 10:42 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/util.sh: stderr_matches(): need to separately display errors that were incorrectly suppressed due to $benign_error

13349 04/29/2014 10:36 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/util.sh: is_err(): rethrow must be inverted (rethrow->false if error)

13348 04/29/2014 10:32 PM Aaron Marcuse-Kubitza

lib/sh/util.sh: added is_err()

13347 04/29/2014 09:53 PM Aaron Marcuse-Kubitza

lib/sh/local.sh: public_schema_exists(): moved to lib/sh/db.sh since this no longer depends on BIEN-specific configurations

13346 04/29/2014 09:42 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/db.sh: public_schema_exists(): don't hide the function call tree so it's clear which function is running the psql commands

13345 04/29/2014 09:40 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/db.sh: public_schema_exists(): don't hide the function call tree so it's clear which function is running the psql commands

13344 04/29/2014 09:38 PM Aaron Marcuse-Kubitza

fix: *{.sh,run}: stderr_matches() callers: added benign_error=1 where needed

13343 04/29/2014 09:36 PM Aaron Marcuse-Kubitza

fix: *{.sh,run}: stderr_matches() callers: usage: documented that they may require benign_error=1

13342 04/29/2014 09:35 PM Aaron Marcuse-Kubitza

fix: lib/sh/util.sh: stderr_matches(): usage: documented that this may require benign_error=1

13341 04/29/2014 09:33 PM Aaron Marcuse-Kubitza

fix: /README.TXT: Mac backup: exclude ~/VirtualBox VMs/Ubuntu/Ubuntu.vdi, to avoid it being re-uploaded twice each time, due to an rsync verification error (https://projects.nceas.ucsb.edu/nceas/issues/907)

13340 04/29/2014 09:23 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/db.sh: pg_cmd(): updated for new echo_vars log_level

13339 04/29/2014 09:14 PM Aaron Marcuse-Kubitza

fix: lib/sh/db.sh: pg_schema_exists(): display the function name so it's clear which function is running the psql commands

13338 04/29/2014 05:37 PM Aaron Marcuse-Kubitza

fix: lib/sh/db.sh: pg_schema_exists(): don't use log++ because it hides the command that produces the benign error

13337 04/29/2014 04:42 PM Aaron Marcuse-Kubitza

/README.TXT: changed "then rerun with l=1 ..." to "then review diff, and rerun with `l=1` prepended" to ensure that user reviews diff before syncing

13336 04/29/2014 04:40 PM Aaron Marcuse-Kubitza

/README.TXT: to synchronize a Mac's settings with my testing machine's: removed separate step to upload just the VirtualBox VMs, because that is now part of the main upload

13335 04/29/2014 04:40 PM Aaron Marcuse-Kubitza

fix: /README.TXT: to synchronize a Mac's settings with my testing machine's: need to sync VirtualBox VMs with inplace=1 because they are very large files

13334 04/29/2014 03:47 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks: Ubuntu 14.04 upgrade: rsync: documented that this breaks use of ~ to reference the remote user's home dir

13333 04/29/2014 03:26 PM Aaron Marcuse-Kubitza

/README.TXT: to back up the version history: back up first on the local machine, because often only the svnsync command gets run, and that way it will get backed up immediately to Dropbox (and hourly to Time Machine), while vegbiendev only gets backed up daily to tape

13332 04/29/2014 03:23 PM Aaron Marcuse-Kubitza

bugfix: /README.TXT: to back up the version history: use absolute path for vegbiendev commands because the Ubuntu 14.04 version of rsync doesn't expand ~ properly

13331 04/29/2014 02:36 PM Aaron Marcuse-Kubitza

/README.TXT: to back up the version history: use $HOME to make paths platform-independent

13330 04/29/2014 01:18 PM Aaron Marcuse-Kubitza

bugfix: exports/.rsync_filter.upload: *.csv: need to use `protect` rather than `hide` to prevent overwriting

13329 04/28/2014 11:11 PM Aaron Marcuse-Kubitza

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

13328 04/25/2014 11:38 PM Aaron Marcuse-Kubitza

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

13327 04/25/2014 11:36 PM Aaron Marcuse-Kubitza

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

13326 04/25/2014 11:01 PM Aaron Marcuse-Kubitza

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

13325 04/25/2014 10:56 PM Aaron Marcuse-Kubitza

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

13324 04/25/2014 06:27 PM Aaron Marcuse-Kubitza

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

13323 04/25/2014 06:22 PM Aaron Marcuse-Kubitza

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

13322 04/25/2014 06:21 PM Aaron Marcuse-Kubitza

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

13321 04/25/2014 06:09 PM Aaron Marcuse-Kubitza

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

13320 04/25/2014 06:07 PM Aaron Marcuse-Kubitza

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

13319 04/25/2014 03:20 PM Aaron Marcuse-Kubitza

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.

13318 04/25/2014 06:15 AM Aaron Marcuse-Kubitza

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

13317 04/24/2014 05:34 PM Aaron Marcuse-Kubitza

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

13316 04/24/2014 05:29 PM Aaron Marcuse-Kubitza

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

13315 04/24/2014 05:02 PM Aaron Marcuse-Kubitza

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

13314 04/24/2014 04:59 PM Aaron Marcuse-Kubitza

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

13313 04/24/2014 03:49 PM Aaron Marcuse-Kubitza

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.

13312 04/24/2014 03:43 PM Aaron Marcuse-Kubitza

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

13311 04/24/2014 03:40 PM Aaron Marcuse-Kubitza

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

13310 04/24/2014 03:36 PM Aaron Marcuse-Kubitza

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)

13309 04/23/2014 10:01 PM Aaron Marcuse-Kubitza

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

13308 04/23/2014 09:57 PM Aaron Marcuse-Kubitza

bin/in_place: added $preserve_mtime flag

13307 04/23/2014 07:16 PM Aaron Marcuse-Kubitza

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"

13306 04/23/2014 07:11 PM Aaron Marcuse-Kubitza

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

13305 04/23/2014 06:02 PM Aaron Marcuse-Kubitza

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

13304 04/23/2014 05:58 PM Aaron Marcuse-Kubitza

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

13303 04/23/2014 05:56 PM Aaron Marcuse-Kubitza

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

13302 04/23/2014 05:53 PM Aaron Marcuse-Kubitza

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

13301 04/23/2014 05:24 PM Aaron Marcuse-Kubitza

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

13300 04/23/2014 05:05 PM Aaron Marcuse-Kubitza

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

13299 04/23/2014 04:53 PM Aaron Marcuse-Kubitza

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

13298 04/23/2014 04:47 PM Aaron Marcuse-Kubitza

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

13297 04/23/2014 04:45 PM Aaron Marcuse-Kubitza

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

13296 04/23/2014 04:31 PM Aaron Marcuse-Kubitza

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

13295 04/23/2014 01:08 PM Aaron Marcuse-Kubitza

/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)

13294 04/23/2014 12:09 PM Aaron Marcuse-Kubitza

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

13293 04/23/2014 12:12 AM Aaron Marcuse-Kubitza

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.

13292 04/22/2014 11:32 PM Aaron Marcuse-Kubitza

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

13291 04/22/2014 11:26 PM Aaron Marcuse-Kubitza

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)

13290 04/22/2014 11:24 PM Aaron Marcuse-Kubitza

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)

13289 04/22/2014 11:21 PM Aaron Marcuse-Kubitza

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)

13288 04/22/2014 10:33 PM Aaron Marcuse-Kubitza

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

13287 04/22/2014 10:31 PM Aaron Marcuse-Kubitza

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

13286 04/22/2014 10:29 PM Aaron Marcuse-Kubitza

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

13285 04/22/2014 10:17 PM Aaron Marcuse-Kubitza

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

13284 04/22/2014 08:14 PM Aaron Marcuse-Kubitza

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

13283 04/22/2014 06:01 PM Aaron Marcuse-Kubitza

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

13282 04/22/2014 05:59 PM Aaron Marcuse-Kubitza

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

13281 04/22/2014 05:50 PM Aaron Marcuse-Kubitza

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

13280 04/22/2014 05:29 PM Aaron Marcuse-Kubitza

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

13279 04/22/2014 05:22 PM Aaron Marcuse-Kubitza

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

13278 04/22/2014 04:45 PM Aaron Marcuse-Kubitza

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

13277 04/22/2014 04:44 PM Aaron Marcuse-Kubitza

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

13276 04/22/2014 04:00 PM Aaron Marcuse-Kubitza

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

13275 04/22/2014 03:59 PM Aaron Marcuse-Kubitza

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

13274 04/22/2014 03:57 PM Aaron Marcuse-Kubitza

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

13273 04/22/2014 03:04 PM Aaron Marcuse-Kubitza

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

13272 04/22/2014 04:00 AM Aaron Marcuse-Kubitza

added backups/mysql_snapshot, pg_snapshot

13271 04/21/2014 08:21 PM Aaron Marcuse-Kubitza

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

13270 04/21/2014 08:21 PM Aaron Marcuse-Kubitza

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

13269 04/21/2014 08:07 PM Aaron Marcuse-Kubitza

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

13268 04/21/2014 08:01 PM Aaron Marcuse-Kubitza

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

13267 04/21/2014 07:59 PM Aaron Marcuse-Kubitza

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