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From 10/17/2014 to 11/15/2014

11/03/2014

07:05 AM Revision 14940: fix: /README.TXT: Full database import: Check # observations: updated to use view_full_occurrence_individual instead of analytical_stem
Aaron Marcuse-Kubitza
06:56 AM Revision 14939: fix: /README.TXT: Full database import: Check that source contains the right datasources: use explicit list instead of checking just the count of datasources
Aaron Marcuse-Kubitza

10/31/2014

04:02 PM Revision 14938: schemas/public_.sql: taxon_trait_view: added geospatial columns
Aaron Marcuse-Kubitza
01:47 PM Revision 14937: exports/2014-10-18.Juergen_Dengler.sPlot.csv.run: documented total runtime (55 min)
Aaron Marcuse-Kubitza
01:46 PM Revision 14936: exports/2014-10-18.Juergen_Dengler.sPlot.csv.run: export_only(): documented runtime (45 min)
Aaron Marcuse-Kubitza
01:39 PM Revision 14935: bugfix: schemas/public_.sql: analytical_stem_CVS: need to reset columns list to *
Aaron Marcuse-Kubitza
01:31 PM Revision 14934: bugfix: exports/analytical_stem_CVS.run needs .csv extension
Aaron Marcuse-Kubitza
01:29 PM Revision 14933: added exports/analytical_stem_CVS.run
Aaron Marcuse-Kubitza
01:28 PM Revision 14932: schemas/public_.sql: added analytical_stem_CVS view
Aaron Marcuse-Kubitza
10:16 AM Revision 14931: added exports/2014-10-18.Juergen_Dengler.sPlot.csv.run
Aaron Marcuse-Kubitza
10:03 AM Revision 14930: schemas/public_.sql: added 2014-10-18.Juergen_Dengler.sPlot view
Aaron Marcuse-Kubitza
09:49 AM Revision 14929: schemas/public_.sql: added public_datasources()
Aaron Marcuse-Kubitza
09:32 AM Revision 14928: removed no longer used inputs/datasource_release_status.xlsx. instead, use inputs/public datasources.xlsx.
Aaron Marcuse-Kubitza
09:29 AM Revision 14927: inputs/publishable datasources.xlsx: updated: changed "publishable" to shorter "public" (and also in filename)
Aaron Marcuse-Kubitza
07:08 AM Revision 14926: added backups/vegbien.r14827.backup.md5
Aaron Marcuse-Kubitza
07:07 AM Revision 14925: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
06:51 AM Revision 14924: bugfix: /README.TXT: to back up the local machine's settings: backing up / to vegbiendev: also need standard excludes from "to back up the local machine's hard drive"
Aaron Marcuse-Kubitza
06:50 AM Revision 14923: /README.TXT: to back up the local machine's settings: also back up / to vegbiendev
Aaron Marcuse-Kubitza
06:49 AM Revision 14922: /README.TXT: `sudo find / -name .DS_Store -print -delete`: documented runtime (23 min)
Aaron Marcuse-Kubitza

10/30/2014

10:02 PM Revision 14921: web/links/index.htm: updated to Firefox bookmarks: Ubuntu: added VNC server links
Aaron Marcuse-Kubitza
08:43 PM Revision 14920: bugfix: /README.TXT: to back up the local machine's hard drive: need to turn off Time Machine to prevent Time Machine from running when the backup is booted, which messes up the Time Machine backup because the partition UUID is different
Aaron Marcuse-Kubitza
08:33 PM Revision 14919: fix: /README.TXT: to back up the local machine's hard drive: don't need to pause Dropbox, since it will be reinitialized for the new partition UUID anyway
Aaron Marcuse-Kubitza
07:57 PM Revision 14918: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza
12:06 PM Revision 14917: bugfix: /README.TXT: to back up the local machine's hard drive: first need to resize the BIEN3.**SAVE** partition so there is enough space
Aaron Marcuse-Kubitza
11:52 AM Revision 14916: bugfix: /README.TXT: to backup files not in Time Machine: need to use `brew services __ postgresql` instead of `launchctl __ ~/Library/LaunchAgents/homebrew.mxcl.postgresql.plist`
Aaron Marcuse-Kubitza
11:51 AM Revision 14915: bugfix: /README.TXT: to back up the local machine's hard drive: need to use `brew services __ postgresql` instead of `launchctl __ ~/Library/LaunchAgents/homebrew.mxcl.postgresql.plist`
Aaron Marcuse-Kubitza
06:41 AM Revision 14914: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to retrieve the contents of the VM: can't use inplace=1 optimization because this messes up the shared hardlinks used by ~/Documents/BIEN/vegbiendev/
Aaron Marcuse-Kubitza
06:40 AM Revision 14913: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to retrieve the contents of the VM: don't need to boot the VM because those snapshots are already booted
Aaron Marcuse-Kubitza
06:05 AM Revision 14912: bugfix: /README.TXT: to back up vegbiendev: can't use inplace=1 optimization because this messes up the shared hardlinks used by ~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT*/
Aaron Marcuse-Kubitza
04:26 AM Revision 14911: bugfix: /README.TXT: to back up vegbiendev: also need to lock hardlinked files at end
Aaron Marcuse-Kubitza

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
03:29 PM Bug #966 (New): figure out why some rows are not getting geoscrubbed
affected rows:
|*country*|*stateProvince*|*county*|*decimalLatitude*|*decimalLongitude*|
|Argentina|Neuquen|Los L...
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

06:27 PM Bug #965 (Resolved): some VegBank plots are missing the plot name
Aaron Marcuse-Kubitza
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

04:35 PM Bug #965 (Resolved): some VegBank plots are missing the plot name
h3. problem
this applies to 358 @location@ rows:...
Aaron Marcuse-Kubitza
03:26 PM Bug #945 (New): incorrect synonym being selected in TNRS
Aaron Marcuse-Kubitza
03:17 PM Bug #945 (Resolved): incorrect synonym being selected in TNRS
Aaron Marcuse-Kubitza
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
11:26 AM Bug #950 (Resolved): fix view_full_occurrence_individual_view rows with is_geovalid NULL
Aaron Marcuse-Kubitza
 

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