lib/common.Makefile: added $(wildcard+suffix), needed because on Linux, builtin $(wildcard) doesn't handle suffixes that don't exist
inputs/Makefile: install: support $(all) mode like for download
inputs/Makefile: download: don't download log files, to speed up installation on a new machine
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.
bugfix: /README.TXT: Full database import: need to unlock hardlinked files
/README.TXT: back up Postgres: backups/pg_snapshot: documented runtime when queries have been run (1 h)
fix: /README.TXT: Full database import: also need to run `unset TMOUT` in the outer `screen` shell
fix: /README.TXT: back up Postgres: needs to be run in `screen`
/README.TXT: to synchronize vegbiendev, jupiter, and your local machine: update mtimes in Dropbox: preserve uncommitted changes
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
fix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: TWiki: need to fix_perms after running this to reset perms on hardlinks
/README.TXT: syncing: use del instead of overwrite where possible, to avoid overwriting newer files
/README.TXT: Full database import: should also snapshot Postgres before starting import
bugfix: inputs/import.stats.xls: need to exclude postprocessing from the ms/row and Change formulas, also for the "<2014-2-2" tab
inputs/import.stats.xls: updated import times
/README.TXT: record the import times: documented how to update the Postprocessing times
bugfix: /README.TXT: globs that list all the datasources: this was incorrectly excluding U, so fixed to match bin/with_all $hidden_srcs
fix: inputs/VegBank/project/: added _no_import because this is imported as part of taxon_observation.**
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.
bugfix: inputs/import.stats.xls: restored missing formatting for multi-day times. prepped tabs to have new import stats data added.
fix: /README.TXT: record the import times: need to first click the "current" tab
/README.TXT: To re-run geoscrubbing: updated runtimes and revision #s
bugfix: /README.TXT: To re-run geoscrubbing: don't close subshell because it closes automatically (this would instead exit `screen`)
/README.TXT: To re-run geoscrubbing: updated runtimes
_license/VegBank_schema/applies_to.txt: added exports/sPlot/BIEN-sPLot-Skype-finalNotes.docx
added exports/sPlot/BIEN-sPLot-Skype-finalNotes.docx from Bob
bugfix: /README.TXT: To re-run geoscrubbing: "press Enter" and `unset TMOUT` steps are reversed
bugfix: schemas/public_.sql: geoscrub_input_new: need to join on the ARRAY[] of each column, to compare NULLs properly
bugfix: lib/sh/util.sh: become_sudo don't continue running function after self_sudo finishes
/README.TXT: datasource removal: linked to runtimes on the wiki
bugfix: inputs/input.Makefile: %/map.csv: need to save it if errors occur in unmapped_terms.csv, new_terms.csv
fix: inputs/FIA/PLOT/map.csv: added plotArea_ha, requested by Brian McGill
added backups/old_backups.txt
added backups/TNRS.2014-6-2.backup.md5
_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
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
inputs/Cyrille_traits/trait_observation/postprocess.sql: accessRights index: added vegbiendev runtime
fix: inputs/Cyrille_traits/trait_observation/postprocess.sql: need to remove private data, as clarified by Cyrille
inputs/publishable datasources.xlsx: updated: Cyrille traits: updated with Cyrille's clarifications on publishability
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.
lib/sh/util.sh: become_sudo: documented that this is for funcs that run multiple sudo commands
lib/sh/util.sh: $sudo_cmd_wrapper: use esc() so this does not need to be embedded with [@] array notation
bugfix: lib/runscripts/util.run: $wrap_fn: this always needs to contain `is_runscript=1` because $is_runscript is not (and cannot be) exported
bugfix: lib/sh/util.sh: sudo(): when don't need sudo: do need `command` to have effects of invoking external command
fix: lib/sh/db.sh: pg_snapshot(): first need to run pg_stop_backup() in case a backup was not stopped cleanly
fix: lib/sh/db.sh: pg_stop_backup(): ignore benign "a backup is not in progress" error
lib/sh/util.sh: sudo(): only run sudo if needed
lib/sh/util.sh: sudo(): factored PATH-preserving code out into separate wrapper var that can also be used separately, eg. with `sudo -u`
lib/sh/util.sh: sudo(): moved addition of -E (which should always happen) to separate, overridden sudo() function
lib/sh/util.sh: moved -E to is_callable section because it just applies to that
fix: inputs/input.Makefile: $(svnFilesGlob): only svn:ignore *.log in the top-level dir
added inputs/XAL/Specimen/data.csv (empty template)
fix: inputs/input.Makefile: add!: verify/: also svn:ignore .zip
lib/sh/util.sh: added become_sudo alias
lib/sh/util.sh: added $is_root
inputs/publishable datasources.xlsx: updated: replaced BIEN2 traits with Cyrille traits
exports/view_full_occurrence_CVS.csv.run: documented runtime (2 min for 5000 rows)
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
inputs/publishable datasources.xlsx: updated
inputs/publishable datasources.xlsx: updated: conditions of use: indicated which datasources have no restrictions
web/BIEN3/Redmine/issues/.htaccess: dest: decoded chars that don't need to be escaped, for clarity
bugfix: web/BIEN3/Redmine/issues/.htaccess: need to store dest in separate var because % is treated specially in the replacement str
inputs/CVS/^taxon_observation.**.sample/test.xml.ref: updated
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
web/BIEN3/Redmine/issues/.htaccess: main page: sort by priority
planning/meetings/BIEN conference call availability.xlsx: updated
planning/meetings/BIEN conference call availability.xlsx: updated: added and populated fall 2014 tab
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 format: this would attempt to run an existing postprocess.sql, out of order, instead of starting with no postprocess.sql as we usually do....
lib/sql_io.py: cleanup_table(): trim(): documented that this also converts character varying fields to text
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.
/README.TXT: To re-run geoscrubbing: re-create public-schema views that were cascadingly deleted: listed which views these currently are
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.
lib/sql_io.py: cleanup_table(): debug-print null_strs
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)
inputs/Cyrille_traits/Makefile: set custom $(null_strs) which handles "NA"
inputs/input.Makefile: pass make var $(null_strs) to invoked commands so it can be used by lib/sql_io.py
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.
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.
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
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)
added inputs/CVS/_src/cvs-eep-archive-2014-10-07-correctedCVSData.{data,schema}.sql.ini
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.
added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.{data,schema}.sql.ini
added inputs/CVS/_src/{data,schema}.sql.ini
added backups/vegbien.r14673.backup.md5
inputs/publishable datasources.xlsx: updated: use white text on dark backgrounds for better visibility, and to create more visual contrast for the unredistributable indicators
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.
added inputs/CVS/verify/Review of CVS data in BIEN3-RKP2014Sept7-Revised.docx from Bob
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)
/README.TXT: To re-run geoscrubbing: also need to `unset TMOUT` because TMOUT causes shell to exit even with background processes
config/dev_machine/com.apple.PowerManagement.plist: UPSShutdownAtLevel: decreased to 5% to allow working longer on UPS power
config/dev_machine/com.apple.PowerManagement.plist: UPSShutdownAtMinutesLeft: decreased to 3 min to allow working longer on UPS power
