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From 09/28/2014 to 10/27/2014

10/26/2014

05:29 PM Revision 14910: lib/sh/util.sh: added errexit_sig()
Aaron Marcuse-Kubitza
05:26 PM Revision 14909: lib/sh/util.sh: sig_e(): use new sig_num()
Aaron Marcuse-Kubitza
05:25 PM Revision 14908: lib/sh/util.sh: added sig_num()
Aaron Marcuse-Kubitza
05:21 PM Revision 14907: bin/import_all: `make -s`: removed no longer needed output_data=1
Aaron Marcuse-Kubitza
05:13 PM Revision 14906: bugfix: lib/sh/make.sh: make() wrapper: need to set output_data mode if -s is set, to match the behavior of the underlying make
Aaron Marcuse-Kubitza
04:58 PM Revision 14905: bugfix: bin/import_all: don't disable errexit because this prevents the program from being Ctrl-C'd. this functionality is no longer needed now that the README.TXT instructs to run bin/import_all in a subshell.
Aaron Marcuse-Kubitza
04:56 PM Revision 14904: bin/import_all: removed functionality now provided by util.run
Aaron Marcuse-Kubitza
04:56 PM Revision 14903: bin/import_all: converted to a runscript so it can use runscript functionality
Aaron Marcuse-Kubitza
01:22 PM Revision 14902: /README.TXT: Installation: `make install`: added alternative command to install a complete DB with all the datasources (instead of a blank DB)
Aaron Marcuse-Kubitza
01:16 PM Revision 14901: inputs/bien_web/observation/map.csv: updated
Aaron Marcuse-Kubitza
01:13 PM Revision 14900: bugfix: inputs/Makefile: install: need to use $(wildcard+suffix) to support Linux
Aaron Marcuse-Kubitza
01:13 PM Revision 14899: lib/common.Makefile: added $(wildcard+suffix), needed because on Linux, builtin $(wildcard) doesn't handle suffixes that don't exist
Aaron Marcuse-Kubitza
12:56 PM Revision 14898: inputs/Makefile: install: support $(all) mode like for download
Aaron Marcuse-Kubitza
12:51 PM Revision 14897: inputs/Makefile: download: don't download log files, to speed up installation on a new machine
Aaron Marcuse-Kubitza
12:48 PM Revision 14896: inputs/Makefile: download: don't download all the inputs by default, to speed up installation on a new machine. instead, enable this with the $(all) flag.
Aaron Marcuse-Kubitza
06:20 AM Revision 14895: bugfix: /README.TXT: Full database import: need to unlock hardlinked files
Aaron Marcuse-Kubitza
05:57 AM Revision 14894: /README.TXT: back up Postgres: backups/pg_snapshot: documented runtime when queries have been run (1 h)
Aaron Marcuse-Kubitza
04:33 AM Revision 14893: fix: /README.TXT: Full database import: also need to run `unset TMOUT` in the outer `screen` shell
Aaron Marcuse-Kubitza
04:20 AM Revision 14892: fix: /README.TXT: back up Postgres: needs to be run in `screen`
Aaron Marcuse-Kubitza
04:16 AM Revision 14891: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: update mtimes in Dropbox: preserve uncommitted changes
Aaron Marcuse-Kubitza
04:06 AM Revision 14890: 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
Aaron Marcuse-Kubitza
03:38 AM Revision 14889: fix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: TWiki: need to fix_perms after running this to reset perms on hardlinks
Aaron Marcuse-Kubitza
02:31 AM Revision 14888: /README.TXT: syncing: use del instead of overwrite where possible, to avoid overwriting newer files
Aaron Marcuse-Kubitza

10/25/2014

07:32 PM Revision 14887: /README.TXT: Full database import: should also snapshot Postgres before starting import
Aaron Marcuse-Kubitza
06:52 PM Revision 14886: bugfix: inputs/import.stats.xls: need to exclude postprocessing from the ms/row and Change formulas, also for the "<2014-2-2" tab
Aaron Marcuse-Kubitza
06:51 PM Revision 14885: inputs/import.stats.xls: updated import times
Aaron Marcuse-Kubitza
06:42 PM Revision 14884: inputs/import.stats.xls: updated import times
Aaron Marcuse-Kubitza
06:08 PM Revision 14883: /README.TXT: record the import times: documented how to update the Postprocessing times
Aaron Marcuse-Kubitza
06:07 PM Revision 14882: bugfix: /README.TXT: globs that list all the datasources: this was incorrectly excluding U, so fixed to match bin/with_all $hidden_srcs
Aaron Marcuse-Kubitza
05:29 PM Revision 14881: fix: inputs/VegBank/project/: added _no_import because this is imported as part of taxon_observation.**
Aaron Marcuse-Kubitza
05:08 PM Revision 14880: bugfix: inputs/import.stats.xls: need to exclude postprocessing from the ms/row and Change formulas. removed deleted rows that don't apply to the most recent imports. updated runtime formulas to match bin/import_all.
Aaron Marcuse-Kubitza
04:41 PM Revision 14879: bugfix: inputs/import.stats.xls: restored missing formatting for multi-day times. prepped tabs to have new import stats data added.
Aaron Marcuse-Kubitza
04:18 PM Revision 14878: fix: /README.TXT: record the import times: need to first click the "current" tab
Aaron Marcuse-Kubitza
03:19 PM Revision 14877: /README.TXT: To re-run geoscrubbing: updated runtimes and revision #s
Aaron Marcuse-Kubitza

10/24/2014

06:33 PM Revision 14876: bugfix: /README.TXT: To re-run geoscrubbing: don't close subshell because it closes automatically (this would instead exit `screen`)
Aaron Marcuse-Kubitza
06:31 PM Revision 14875: /README.TXT: To re-run geoscrubbing: updated runtimes
Aaron Marcuse-Kubitza
05:38 PM Revision 14874: _license/VegBank_schema/applies_to.txt: added exports/sPlot/BIEN-sPLot-Skype-finalNotes.docx
Aaron Marcuse-Kubitza
05:36 PM Revision 14873: added exports/sPlot/BIEN-sPLot-Skype-finalNotes.docx from Bob
Aaron Marcuse-Kubitza
04:10 PM Revision 14872: /README.TXT: To re-run geoscrubbing: updated runtimes
Aaron Marcuse-Kubitza
03:58 PM Revision 14871: bugfix: /README.TXT: To re-run geoscrubbing: "press Enter" and `unset TMOUT` steps are reversed
Aaron Marcuse-Kubitza
03:50 PM Revision 14870: bugfix: schemas/public_.sql: geoscrub_input_new: need to join on the ARRAY[] of each column, to compare NULLs properly
Aaron Marcuse-Kubitza
03:32 PM Revision 14869: bugfix: lib/sh/util.sh: become_sudo don't continue running function after self_sudo finishes
Aaron Marcuse-Kubitza
01:29 PM Revision 14868: /README.TXT: datasource removal: linked to runtimes on the wiki
Aaron Marcuse-Kubitza
12:33 PM Revision 14867: bugfix: inputs/input.Makefile: %/map.csv: need to save it if errors occur in unmapped_terms.csv, new_terms.csv
Aaron Marcuse-Kubitza
12:05 PM Revision 14866: fix: inputs/FIA/PLOT/map.csv: added plotArea_ha, requested by Brian McGill
Aaron Marcuse-Kubitza
12:04 PM Revision 14865: fix: inputs/FIA/PLOT/map.csv: added plotArea_ha, requested by Brian McGill
Aaron Marcuse-Kubitza
11:05 AM Revision 14864: added backups/old_backups.txt
Aaron Marcuse-Kubitza
10:49 AM Revision 14863: added backups/TNRS.2014-6-2.backup.md5
Aaron Marcuse-Kubitza

10/23/2014

05:37 PM Revision 14862: _license/non-open-source/applies_to.txt: clarified that the things in this list are not embargoed, the issue is just that they are not formally open-source
Aaron Marcuse-Kubitza
03:43 PM Revision 14861: schemas/public_.sql: view_full_occurrence_individual_view: join to taxonoccurrence: can use a USING join for this because plot.** only exports one locationevent_id column
Aaron Marcuse-Kubitza

10/20/2014

03:33 PM Revision 14860: inputs/Cyrille_traits/trait_observation/postprocess.sql: accessRights index: added vegbiendev runtime
Aaron Marcuse-Kubitza
03:29 PM Revision 14859: fix: inputs/Cyrille_traits/trait_observation/postprocess.sql: need to remove private data, as clarified by Cyrille
Aaron Marcuse-Kubitza
03:13 PM Revision 14858: inputs/publishable datasources.xlsx: updated: Cyrille traits: updated with Cyrille's clarifications on publishability
Aaron Marcuse-Kubitza

10/19/2014

03:24 PM Revision 14857: bugfix: lib/sh/sync.sh, db.sh: *_snapshot() commands that run multiple sudo commands: use become_sudo so that the program won't hang at later sudo prompts. for pg_snapshot() with pg_start_backup(), this also prevents the backup from staying open at the end waiting on a sudo prompt, causing excess WAL logs to accrue.
Aaron Marcuse-Kubitza
03:16 PM Revision 14856: lib/sh/util.sh: become_sudo: documented that this is for funcs that run multiple sudo commands
Aaron Marcuse-Kubitza
03:15 PM Revision 14855: lib/sh/util.sh: $sudo_cmd_wrapper: use esc() so this does not need to be embedded with [@] array notation
Aaron Marcuse-Kubitza
03:09 PM Revision 14854: bugfix: lib/runscripts/util.run: $wrap_fn: this *always* needs to contain `is_runscript=1` because $is_runscript is not (and cannot be) exported
Aaron Marcuse-Kubitza
03:06 PM Revision 14853: bugfix: lib/sh/util.sh: sudo(): when don't need sudo: do need `command` to have effects of invoking external command
Aaron Marcuse-Kubitza
03:00 PM Revision 14852: fix: lib/sh/db.sh: pg_snapshot(): first need to run pg_stop_backup() in case a backup was not stopped cleanly
Aaron Marcuse-Kubitza
03:00 PM Revision 14851: fix: lib/sh/db.sh: pg_stop_backup(): ignore benign "a backup is not in progress" error
Aaron Marcuse-Kubitza
01:19 PM Revision 14850: lib/sh/util.sh: sudo(): only run sudo if needed
Aaron Marcuse-Kubitza
01:10 PM Revision 14849: lib/sh/util.sh: sudo(): factored PATH-preserving code out into separate wrapper var that can also be used separately, eg. with `sudo -u`
Aaron Marcuse-Kubitza
01:03 PM Revision 14848: lib/sh/util.sh: sudo(): moved addition of -E (which should always happen) to separate, overridden sudo() function
Aaron Marcuse-Kubitza
12:51 PM Revision 14847: lib/sh/util.sh: moved -E to is_callable section because it just applies to that
Aaron Marcuse-Kubitza
11:35 AM Revision 14846: fix: inputs/input.Makefile: $(svnFilesGlob): only svn:ignore *.log in the top-level dir
Aaron Marcuse-Kubitza

10/18/2014

07:32 PM Revision 14845: added inputs/XAL/Specimen/data.csv (empty template)
Aaron Marcuse-Kubitza
05:03 PM Revision 14844: fix: inputs/input.Makefile: add!: verify/: also svn:ignore .zip
Aaron Marcuse-Kubitza
05:03 PM Revision 14843: fix: inputs/input.Makefile: add!: verify/: also svn:ignore .zip
Aaron Marcuse-Kubitza
04:24 PM Revision 14842: lib/sh/util.sh: added become_sudo alias
Aaron Marcuse-Kubitza
04:21 PM Revision 14841: lib/sh/util.sh: added $is_root
Aaron Marcuse-Kubitza

10/17/2014

02:52 PM Revision 14840: inputs/publishable datasources.xlsx: updated: replaced BIEN2 traits with Cyrille traits
Aaron Marcuse-Kubitza
01:02 PM Revision 14839: exports/view_full_occurrence_CVS.csv.run: documented runtime (2 min for 5000 rows)
Aaron Marcuse-Kubitza

10/16/2014

01:51 PM Revision 14838: fix: inputs/publishable datasources.xlsx: updated: conditions of use: Canadensys sources: these should actually be marked as no restrictions, in contrast to Brian E's earlier annotations, because they are public domain: the citation is requested, but not legally required
Aaron Marcuse-Kubitza
01:46 PM Revision 14837: inputs/publishable datasources.xlsx: updated
Aaron Marcuse-Kubitza
01:40 PM Revision 14836: inputs/publishable datasources.xlsx: updated: conditions of use: indicated which datasources have no restrictions
Aaron Marcuse-Kubitza
10:55 AM Revision 14835: web/BIEN3/Redmine/issues/.htaccess: dest: decoded chars that don't need to be escaped, for clarity
Aaron Marcuse-Kubitza
10:51 AM Revision 14834: bugfix: web/BIEN3/Redmine/issues/.htaccess: need to store dest in separate var because % is treated specially in the replacement str
Aaron Marcuse-Kubitza
10:49 AM Revision 14833: inputs/CVS/^taxon_observation.**.sample/test.xml.ref: updated
Aaron Marcuse-Kubitza
10:49 AM Revision 14832: fix: inputs/CVS/plantConcept_/header.csv: regenerated after fixing the postprocess/cleanup ordering bug (r14827), which had caused header.csv to be incorrectly generated after renames in postprocess.sql were applied
Aaron Marcuse-Kubitza
10:33 AM Revision 14831: web/BIEN3/Redmine/issues/.htaccess: main page: sort by priority
Aaron Marcuse-Kubitza
10:14 AM Revision 14830: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza

10/15/2014

05:14 PM Revision 14829: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza
04:08 PM Revision 14828: planning/meetings/BIEN conference call availability.xlsx: updated: added and populated fall 2014 tab
Aaron Marcuse-Kubitza

10/14/2014

02:50 PM Revision 14827: bugfix: inputs/input.Makefile: postprocess must be run *after* cleanup rather than before because it depends on the cleanup having been performed.
this bug was not previously detected because this is only a problem when refreshing a datasource to data in the *same... Aaron Marcuse-Kubitza
12:36 PM Revision 14826: lib/sql_io.py: cleanup_table(): trim(): documented that this also converts character varying fields to text
Aaron Marcuse-Kubitza
11:05 AM Revision 14825: bugfix: inputs/input.Makefile: $(dbExports): also need to put data.sql before clean_up.sql, etc. previously, this ordering had to be done by naming clean_up.sql, etc so they would sort after data.sql alphabetically, but it can be confusing to have to remember to do this. this fixes a bug in the CVS refresh where cvs.~.clean_up.sql was being run before data.sql, causing some private columns to have been deleted before the data was imported into the tables, creating a column mismatch error.
Aaron Marcuse-Kubitza
10:34 AM Revision 14824: /README.TXT: To re-run geoscrubbing: re-create public-schema views that were cascadingly deleted: listed which views these currently are
Aaron Marcuse-Kubitza
10:26 AM Revision 14823: /README.TXT: To re-run geoscrubbing: updated runtimes
Aaron Marcuse-Kubitza
10:09 AM Revision 14822: bugfix: lib/sql_io.py: null_strs_str_default: removed "NA" because this is the abbr for a Spanish province (Navarra). this fixes the 2nd bug of #955, geovalidation duplicated rows.
Aaron Marcuse-Kubitza
10:00 AM Revision 14821: lib/sql_io.py: cleanup_table(): debug-print null_strs
Aaron Marcuse-Kubitza
09:56 AM Revision 14820: lib/sql_io.py: null_strs: made it customizable from an env var, since the same list of null_strs doesn't work for all datasources (see #957)
Aaron Marcuse-Kubitza
09:54 AM Revision 14819: inputs/Cyrille_traits/Makefile: set custom $(null_strs) which handles "NA"
Aaron Marcuse-Kubitza
09:49 AM Revision 14818: inputs/input.Makefile: pass make var $(null_strs) to invoked commands so it can be used by lib/sql_io.py
Aaron Marcuse-Kubitza
09:39 AM Revision 14817: fix: *Makefile: changed line endings to \n so that `patch` can work with pasted input. use `svn di --extensions --ignore-eol-style` to verify no diff.
Aaron Marcuse-Kubitza
08:35 AM Revision 14816: lib/sql_io.py: null_strs: made it customizable from an env var, since the same list of null_strs doesn't work for all datasources (see #957)
Aaron Marcuse-Kubitza

10/13/2014

07:40 AM Revision 14815: bugfix: web/links/index.htm: updated to Firefox bookmarks: Mac: automatic restart on power loss: also need to disable the UPSShutdownAtLevel/UPSShutdownAtMinutesLeft functions because an orderly shutdown prevents the computer from auto-restarting on power loss. Bookmarks Toolbar: reordered links to put those most relevant to VegBIEN users first.
Aaron Marcuse-Kubitza
07:25 AM Revision 14814: bugfix: config/dev_machine/com.apple.PowerManagement.plist: disable the UPSShutdownAtLevel/UPSShutdownAtMinutesLeft functions because an orderly shutdown prevents the computer from auto-restarting on power loss
Aaron Marcuse-Kubitza
07:17 AM Revision 14813: 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)
Aaron Marcuse-Kubitza
06:31 AM Revision 14812: added inputs/CVS/_src/cvs-eep-archive-2014-10-07-correctedCVSData.{data,schema}.sql.ini
Aaron Marcuse-Kubitza
06:31 AM Revision 14811: bugfix: inputs/CVS/_src/{data,schema}.sql.ini: sourcefilename: this needs to be on the VM's own HD to avoid crashing MSAccess to PostgreSQL. destinationdatabase: added this back since it is fine to leave this blank.
Aaron Marcuse-Kubitza
06:23 AM Revision 14810: added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.{data,schema}.sql.ini
Aaron Marcuse-Kubitza
06:17 AM Revision 14809: added inputs/CVS/_src/{data,schema}.sql.ini
Aaron Marcuse-Kubitza
05:25 AM Revision 14808: added backups/vegbien.r14673.backup.md5
Aaron Marcuse-Kubitza
04:45 AM Revision 14807: /README.TXT: To re-run geoscrubbing: updated runtimes
Aaron Marcuse-Kubitza

10/12/2014

03:58 PM Revision 14806: inputs/publishable datasources.xlsx: updated: use white text on dark backgrounds for better visibility, and to create more visual contrast for the unredistributable indicators
Aaron Marcuse-Kubitza
03:52 PM Revision 14805: inputs/publishable datasources.xlsx: updated: consolidated Brian E's new columns into a single "conditions?" column. fix: "what is needed to publish it": renamed to "conditions of use/remaining tasks". "conditions of use": changed color scheme to match "publishable?" columns.
Aaron Marcuse-Kubitza

10/09/2014

12:34 AM Revision 14804: added inputs/CVS/verify/Review of CVS data in BIEN3-RKP2014Sept7-Revised.docx from Bob
Aaron Marcuse-Kubitza

10/07/2014

12:01 AM Revision 14803: bugfix: lib/tnrs.py: encode_map: also need to encode + because TNRS removes it from the morphospecies (vegpath.org/wiki/CVS_validation#Bobs-revised-document > issue #4)
Aaron Marcuse-Kubitza

10/06/2014

11:35 PM Revision 14802: /README.TXT: To re-run geoscrubbing: also need to `unset TMOUT` because TMOUT causes shell to exit even with background processes
Aaron Marcuse-Kubitza

10/03/2014

05:56 PM Revision 14801: config/dev_machine/com.apple.PowerManagement.plist: UPSShutdownAtLevel: decreased to 5% to allow working longer on UPS power
Aaron Marcuse-Kubitza
05:53 PM Revision 14800: config/dev_machine/com.apple.PowerManagement.plist: UPSShutdownAtMinutesLeft: decreased to 3 min to allow working longer on UPS power
Aaron Marcuse-Kubitza
05:36 PM Revision 14799: bugfix: inputs/CVS/plot_/postprocess.sql: locality: site_name should come before directions_to_place because it is at a higher level of granularity
Aaron Marcuse-Kubitza
05:08 PM Revision 14798: /README.TXT: To re-run geoscrubbing: `rm=1 inputs/.geoscrub/run`: should just need to reinstall the geoscrub_output table
Aaron Marcuse-Kubitza
05:06 PM Revision 14797: schemas/public_.sql: geoscrub_input_view_modify(): add unique constraint on the same columns as geoscrub.geoscrub_output, as a sanity check to assist future debugging
Aaron Marcuse-Kubitza
04:57 PM Revision 14796: bugfix: schemas/postgresql.conf: need to set extra_float_digits = 3 (the maximum) to enable verbatim export. this should fix issue #955.
Aaron Marcuse-Kubitza
12:37 PM Revision 14795: added inputs/CVS/verify/Review of CVS data in BIEN3-RKP2014Sept7.docx from Bob
Aaron Marcuse-Kubitza
08:18 AM Revision 14794: added config/dev_machine/com.apple.PowerManagement.plist from /Library/Preferences/SystemConfiguration/com.apple.PowerManagement.plist , so that this file can be easily restored when the system spuriously resets settings in it
Aaron Marcuse-Kubitza

10/02/2014

09:42 PM Revision 14793: /README.TXT: To re-run geoscrubbing: updated runtimes. note that these are faster on the new hardware.
Aaron Marcuse-Kubitza

10/01/2014

09:51 PM Revision 14792: 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
Aaron Marcuse-Kubitza
09:39 PM Revision 14791: fix: /README.TXT: Single datasource refresh: also back up DB after this
Aaron Marcuse-Kubitza
09:38 PM Revision 14790: /README.TXT: datasource removal: documented bien2_traits runtime
Aaron Marcuse-Kubitza
09:35 PM Revision 14789: added inputs/bien2_traits/_no_import since bien2_traits has been replaced by Cyrille_traits
Aaron Marcuse-Kubitza
09:32 PM Revision 14788: /README.TXT: added datasource removal instructions
Aaron Marcuse-Kubitza
09:22 PM Revision 14787: fix: /README.TXT: Single datasource refresh: place updated extract: generalized datasrc name
Aaron Marcuse-Kubitza

09/30/2014

07:45 AM Revision 14786: added inputs/Cyrille_traits/
Aaron Marcuse-Kubitza
07:36 AM Revision 14785: lib/sql_io.py: null_strs: added N/A and NA (this will remove a common abbr for North America, but we don't use the continent, so this is OK)
Aaron Marcuse-Kubitza
05:04 AM Revision 14784: mappings/VegCore.htm: regenerated from wiki. made verbatimLocality a synonym of locality since they are used to store the same data.
Aaron Marcuse-Kubitza
03:25 AM Revision 14783: bugfix: schemas/util.sql: col_rename(): also need to run util.name_truncate() on the names used in the "don't try to rename to itself" comparison
Aaron Marcuse-Kubitza
01:54 AM Revision 14782: fix: schemas/util.sql: col_rename(): don't try to rename a column to itself (this will cause an error)
Aaron Marcuse-Kubitza
01:22 AM Revision 14781: schemas/util.sql: set_col_names(): use util.col_rename() so that all renames uses this function
Aaron Marcuse-Kubitza
12:54 AM Revision 14780: schemas/util.sql: added col_rename()
Aaron Marcuse-Kubitza
12:02 AM Revision 14779: schemas/util.sql: added quote_ident() wrapper
Aaron Marcuse-Kubitza
12:01 AM Revision 14778: schemas/util.sql: added name_truncate()
Aaron Marcuse-Kubitza
 

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