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  • svn:ignore: extern

# Date Author Comment
14086 07/16/2014 01:24 PM Aaron Marcuse-Kubitza

bugfix: schemas/public_.sql: analytical_stem_view_modify(): added columns: need to include COMMENT statements

14085 07/16/2014 01:21 PM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: comment(element oid): need `objsubid = 0` filter so this doesn't use comments for any other objsubids

14084 07/16/2014 12:53 PM Aaron Marcuse-Kubitza

schemas/public_.sql: added iucn_red_list_view_modify() and use it in iucn_red_list_view's "after updating this" instructions

14083 07/16/2014 12:47 PM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: rematerialize_view(): also need to handle the target table's dependent views

14082 07/16/2014 12:38 PM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: mk_drop_from_create(): need to use `IF EXISTS` so that the resulting statement also works if the target object does not yet exist

14081 07/16/2014 12:24 PM Aaron Marcuse-Kubitza

schemas/util.sql: mk_drop_from_create(): also support `SELECT util.drop_*()` statements, in addition to DROP

14080 07/16/2014 11:37 AM Aaron Marcuse-Kubitza

inputs/.TNRS/Source/test.xml.ref: updated

14079 07/15/2014 11:14 PM Aaron Marcuse-Kubitza

bugfix: /README.TXT: logs glob: don't unintentionally match . or ..

14078 07/15/2014 10:43 PM Aaron Marcuse-Kubitza

inputs/VegBank/stemlocation_/test.xml.ref: updated

14077 07/15/2014 10:41 PM Aaron Marcuse-Kubitza

/README.TXT: Full database import: `make test by_col=1`: updated runtime (1 h)

14076 07/15/2014 10:07 PM Aaron Marcuse-Kubitza

inputs/TEX/Specimen2/test.xml.ref: updated

14075 07/15/2014 09:35 PM Aaron Marcuse-Kubitza

inputs/GBIF/raw_occurrence_record_plants/test.xml.ref: updated

14074 07/15/2014 05:44 PM Aaron Marcuse-Kubitza

bugfix: lib/sql_io.py: put_table(): handle_MissingCastException(): when updating join_cols, don't add new entry for join_cols[out_col], only update existing one. this fixes #902 (import bug), and with #902 fixed, #887 (disk space leak) should no longer occur.

14073 07/15/2014 04:49 PM Aaron Marcuse-Kubitza

bin/import_all: delete_logs(): documented that `trap EXIT` doesn't run until shell exit

14072 07/15/2014 04:48 PM Aaron Marcuse-Kubitza

bin/import_all: delete_logs(): print when this happens, so it can be verified that it's happening properly

14071 07/15/2014 04:32 PM Aaron Marcuse-Kubitza

bugfix: bin/import_all: need to run delete_logs manually because `trap EXIT` doesn't run until bg cmds done

14070 07/15/2014 04:28 PM Aaron Marcuse-Kubitza

bin/import_all: delete_logs: moved testing of whether to delete logs to delete_logs() so that delete_logs() can be run regardless of the $delete_logs setting

14069 07/15/2014 03:58 PM Aaron Marcuse-Kubitza

bugfix: bin/import_all: delete_logs(): also need to match log filenames when n=""

14068 07/15/2014 03:11 PM Aaron Marcuse-Kubitza

bugfix: /Makefile: postgres_restart-*: argument to echo always needs quotes

14067 07/15/2014 03:05 PM Aaron Marcuse-Kubitza

bugfix: /Makefile: $(pg_ctl-*): tell user that if it doesn't work, need to run `rm $(macPostgresDir)/postmaster.pid` and retry

14066 07/15/2014 02:57 PM Aaron Marcuse-Kubitza

/Makefile: $(pg_ctl-Darwin): documented the pg_ctl version of this command in case `brew services` doesn't work

14065 07/15/2014 02:39 PM Aaron Marcuse-Kubitza

bugfix: bin/with_all: isset(): need to use `>&- 2>&-` because &> does not work with - as the dest

14064 07/15/2014 01:19 PM Aaron Marcuse-Kubitza

fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: determine if the revision works: use the in# of the query instead of waiting an arbitrary time, because this is more accurate in determining whether the import is successful

14063 07/15/2014 12:52 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: regressions that occurred during the revision range: named these "concurrent regressions"

14062 07/15/2014 12:45 PM Aaron Marcuse-Kubitza

fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: need to update system time so wait times can be calculated correctly

14061 07/15/2014 12:22 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: documented that the patches are specifically for regressions that occurred during the revision range, not all bugs that were fixed in that range

14060 07/15/2014 12:14 PM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: waiting for query: increased time to min. 10 min because some revisions take longer

14059 07/15/2014 12:09 PM Aaron Marcuse-Kubitza

fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bin/import_all: added step to type y and press ENTER

14058 07/15/2014 12:07 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added steps to determine if the revision works, and then stop the import

14057 07/15/2014 11:27 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: added r12994

14056 07/15/2014 11:09 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: use for loop to avoid needing to repeat the command

14055 07/15/2014 11:05 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: added r12760

14054 07/15/2014 10:54 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: --fuzz apparently needs to be 3 even though we have only 2 lines of context

14053 07/15/2014 10:52 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: use --fuzz to allow patching even when surrounding lines have changed

14052 07/15/2014 10:44 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: sorted by revision #

14051 07/15/2014 10:43 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: added r12865

14050 07/15/2014 10:33 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: patch: need to use --force to avoid prompting user

14049 07/15/2014 10:16 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: `svn revert`: need to use `--depth infinity` when reverting more than a file

14048 07/15/2014 10:14 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: use `patch` instead of `svn merge` because `svn merge` sometimes inexplicably doens't apply patches

14047 07/15/2014 09:43 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: `svn revert` all changes instead of specific files, to support bugfixes to other files

14046 07/15/2014 09:42 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: lib/sh/util.sh bugfix: use `svn merge` instead of `sed --in-place` because this can be used for more complex changes

14045 07/15/2014 09:41 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: lib/sh/util.sh bugfix: documented revision

14044 07/15/2014 09:20 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: need to apply r12872 bugfix to lib/sh/util.sh because it occurred after r12025

14043 07/15/2014 09:10 AM Aaron Marcuse-Kubitza

fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: `make` commands: use `yes|` to avoid needing to confirm prompts

14042 07/15/2014 09:08 AM Aaron Marcuse-Kubitza

fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: `make mk_db ...`: use `yes|` to avoid needing to confirm prompts

14041 07/15/2014 08:56 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: to test a different revision: added step that if any of the commands after `svn up` are broken, try a different revision

14040 07/15/2014 08:46 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: `make db`: need to run `schemas/reinstall` manually because older versions of the codebase just used `schemas/install`

14039 07/14/2014 11:30 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: documented the range from within the revision should be chosen

14038 07/14/2014 09:19 PM Aaron Marcuse-Kubitza

fix: inputs/.IRMNG/*/: added _no_import because this datasource is only used as a lookup table and does not need to be imported/scrubbed

14037 07/14/2014 09:18 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: `svn up`: documented runtime (1 min)

14036 07/14/2014 08:24 PM Aaron Marcuse-Kubitza

bugfix: added nodes/_no_import, because the NCBI import doesn't work due to a Postgres 9.3 bug (#859). _no_import used to not be needed because we didn't import the hidden sources.

14035 07/14/2014 08:05 PM Aaron Marcuse-Kubitza

fix: bin/with_all: removed debug statements

14034 07/14/2014 05:19 PM Aaron Marcuse-Kubitza

bugfix: bin/with_all: testing if @inputs is set: `"${inputs+isset}"` syntax doesn't work for empty arrays, so need to use `declare -p` instead

14033 07/14/2014 04:46 PM Aaron Marcuse-Kubitza

bugfix: to set up the VM: to use a database backup: also need to `make rm_initial_public` because initdb creates a non-empty DB

14032 07/14/2014 04:42 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added steps to test a different revision

14031 07/14/2014 04:40 PM Aaron Marcuse-Kubitza

/Makefile: db: use reinstall instead of install to allow running this on an existing DB

14030 07/14/2014 02:49 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: `sudo apt-get dist-upgrade`: documented runtime (12 min)

14029 07/14/2014 02:47 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: updated VM snapshot names

14028 07/14/2014 02:44 PM Aaron Marcuse-Kubitza

fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to install system updates: added step to restart, because some system updates require this

14027 07/14/2014 02:34 PM Aaron Marcuse-Kubitza

fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to install system updates: added step to restart, because some system updates require this

14026 07/14/2014 02:29 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: added instructions to install system updates

14025 07/14/2014 01:23 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bin/import_all: documented runtime (50 min)

14024 07/14/2014 01:07 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added steps to run the import

14023 07/14/2014 12:24 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to set up the VM: added steps to move vegbiendev.vdi to the internal hard drive

14022 07/14/2014 12:19 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added steps to start the VM

14021 07/14/2014 12:16 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: moved "set up the VM" steps to separate section

14020 07/14/2014 12:06 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: added steps to create a booted snapshot

14019 07/14/2014 12:01 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: moved creation of pg_restore snapshot to be part of just the database backup section

14018 07/14/2014 11:52 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: documented runtime (15 min)

14017 07/14/2014 11:51 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: time the operation

14016 07/14/2014 11:32 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: added name for VM snapshot after this step

14015 07/14/2014 11:31 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: need to run as DB superuser to restore py_util

14014 07/14/2014 11:24 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: rsync: updated runtime (25 min)

14013 07/14/2014 11:24 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: added steps to create snapshot before running pg_restore

14012 07/14/2014 10:55 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: added steps to configure the VM before booting

14011 07/14/2014 10:53 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: added instructions for selecting the initial snapshot and booting the VM

14010 07/14/2014 10:36 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: perform long-running operations inside `screen`

14009 07/14/2014 10:35 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to use a database backup: only run mk_db, not db, to avoid restoring schemas that are part of the backup

14008 07/14/2014 09:33 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: schemas must be in dependency order

14007 07/14/2014 09:21 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: don't restore analytical_db schema because we don't use it and it depends on public, which we're not restoring

14006 07/14/2014 09:16 AM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks: WebEx: added steps to join a test meeting. pg_restore: documented that you need to create the schema before you restore into it, or else you will get a cryptic error message that it's using pg_catalog instead. added Homebrew links, including instructions for setting psycopg2 up with it. added PostGIS links. username URLs: documented how to enable these in Internet Explorer. TWiki: documented what to do when moving the TWiki install dir.

14005 07/14/2014 09:06 AM Aaron Marcuse-Kubitza

bugfix: lib/Firefox_bookmarks.reformat.csv: updated for new Firefox bookmarks format, which indents the <DD> tag

14004 07/14/2014 08:36 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: need to create the schema before you restore into it, to avoid cryptic error messages

14003 07/14/2014 08:33 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: schemas/postgresql.conf: need to decrease shared_buffers to match VM's allocated memory (1 GB)

14002 07/14/2014 08:18 AM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: schemas/postgresql.conf: need to decrease shared_buffers to match VM's allocated memory (1 GB)

14001 07/13/2014 11:50 PM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: need to run `make db` to restore users, which are not part of the backup

14000 07/13/2014 11:40 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: rsync: updated runtime (35 min)

13999 07/11/2014 04:54 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: turning off of non-ARIZ inputs: removed metadata datasources because these have been renamed to start with ".", and so aren't included in */

13998 07/11/2014 04:48 PM Aaron Marcuse-Kubitza

bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: pg_restore: need to use for loop because pg_restore doesn't support multiple --schema options (it just uses the last one)

13997 07/11/2014 04:35 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: added step to restore the necessary schemas from the DB

13996 07/11/2014 04:32 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: rsync: documented runtime (13 min)

13995 07/11/2014 04:11 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: added step to fetch the database backup via rsync

13994 07/11/2014 04:04 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: moved steps to enable the user to access VirtualBox shared folders to separate section because VirtualBox shared folders currently don't work, likely because of a bug in VirtualBox Guest Additions when installed on something other than a clean Linux install

13993 07/11/2014 03:54 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: added steps to enable the user to access VirtualBox shared folders

13992 07/11/2014 03:06 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added section for database backup approach, as alternative to clean database approach

13991 07/11/2014 10:32 AM Aaron Marcuse-Kubitza

fix: config/VirtualBox_VMs/vegbiendev/README.TXT: use ".." instead of - to indicate a range, to avoid this being confused for a minus sign

13990 07/11/2014 10:26 AM Aaron Marcuse-Kubitza

bugfix: /Makefile: postgres_restart-Darwin: need to have the user run the command outside of make because it doesn't appear to do anything when run inside make (this is the same problem as on Linux)

13989 07/11/2014 10:25 AM Aaron Marcuse-Kubitza

/Makefile: $(pg_ctl-Darwin): use simpler `brew services` instead of `launchctl __/homebrew.mxcl.postgresql.plist`

13988 07/11/2014 10:03 AM Aaron Marcuse-Kubitza

bugfix: bin/stop_imports: also need to include `bin/after_import`

13987 07/11/2014 09:56 AM Aaron Marcuse-Kubitza

inputs/.TNRS/Source/map.csv: datasetURL: updated to indicate that this uses the TNRS dev server (the actual URL is private)