lib/tnrs.py: single_tnrs_request(): use_tnrs_export=False: need to obtain export columns

lib/csvs.py: added header(stream)

fix: lib/tnrs.py: single_tnrs_request(): need to `assert name_ct >= 1`, because with no names, TNRS hangs indefinitely

bin/tnrs_client: added env var to configure use_tnrs_export

/README.TXT: to back up vegbiendev: use inplace=1 to speed stopping and resuming transfer

fix: /README.TXT: to back up the local machine's hard drive: removed --extended-attributes (after initial sync) because rsync apparently has to visit every file for this

fix: /README.TXT: to back up the local machine's hard drive: also need --extended-attributes

/README.TXT: to back up the local machine's hard drive: removed --delete-before now that that partition has been expanded

fix: /README.TXT: to back up vegbiendev: exclude /var/lib/mysql.bak,postgresql.bak because the local machine doesn't need 2 copies of this information

/README.TXT: to back up vegbiendev: removed no longer needed exclude of Dropbox subdir backup

fix: /README.TXT: to back up vegbiendev: also need to do steps under Maintenance > "to synchronize vegbiendev, jupiter, and your local machine" because /home/aaronmk/bien is not synced here

bugfix: /README.TXT: to back up vegbiendev: need `overwrite=1`

/README.TXT: to back up vegbiendev: removed no longer needed exclude of Dropbox subdir backup

/README.TXT: to back up the version history: don't also need this on vegbiendev because it's already on jupiter and the local machine

bugfix: /README.TXT: to back up vegbiendev: need to include Postgres config files

/README.TXT: to back up the local machine's hard drive: don't back up temp files: added /.fseventsd/

fix: /README.TXT: to back up the local machine's hard drive: initial runtime: use range instead because some of the later runtime might have been from the same files

/README.TXT: to back up the local machine's hard drive: updated initial runtime to include additional transferred files (17 h)

fix: /README.TXT: to back up the local machine's hard drive: need to use --delete-before because the backup partition is near capacity

/README.TXT: to back up the local machine's hard drive: don't back up temp files such as /private/var/vm/*

fix: /README.TXT: to back up the local machine's hard drive: back up most Dropbox/Postgres files before stopping processes, to minimize downtime

bugfix: /README.TXT: to back up the local machine's hard drive: can't use ~ with --exclude

fix: inputs/.geoscrub/geoscrub_output/postprocess.sql: map_geovalidity(): unscrubbable names should actually be geo*in*valid, not geovalid=NULL, according to Brad

/README.TXT: to back up the local machine's hard drive: back up the non-Dropbox, non-Postgres files separately to minimize the Dropbox and Postgres downtime

/README.TXT: to back up the vegbiendev databases: don't need to review diff for these as it's always unidirectional

/README.TXT: added instructions to back up vegbiendev

fix: /README.TXT: to back up the local machine's hard drive: also need to repeat backup command until only minimal changes

/README.TXT: to back up the local machine's hard drive: added step to stop Postgres

bugfix: /README.TXT: to back up the local machine's hard drive: also need to stop Dropbox

/README.TXT: to back up the local machine's settings: added step to remove .DS_Store

fix: /README.TXT: to back up the local machine's settings: Dropbox: shoudl not run with `del=`, because the backup should be an exact replica

backups/TNRS.*: removed no longer needed old TNRS backups, which are part of the respective full-database backups in any case

added config/phpMyAdmin/ symlink to schemas/VegCore/phpMyAdmin/

bugfix: lib/sh/archives.sh: compress(): don't include dir prefix in zip archive

lib/sh/util.sh: cd(): use echo_run instead of a manual echo_cmd call

fix: lib/sh/util.sh: cd(): indent after running cd rather than before

lib/sh/util.sh: cd(): support rebasing path vars for the new dir

bugfix: lib/sh/archives.sh: compress(): need to use zip's path syntax to avoid the file in the archive being named "-"

lib/tnrs.py: added option to avoid using TNRS's TSV export feature, which currently returns incorrect selected matches (vegpath.org/issues/943). this has been implemented up through the GWT/JSON decoding.

lib/tnrs.py: added gwt_decode()

lib/strings.py: added unesc_quotes() and helper functions

lib/strings.py: added json_decode()

/README.TXT: To re-run geoscrubbing: updated runtimes

exports/*_GBIF.csv.run: documented compress_() runtime (20 min-1 h)

lib/runscripts/extract.run: export_(): also compress created file

lib/sh/archives.sh: added compress(), expand(), which handle compression of individual files

bugfix: inputs/input.Makefile: sql/install: ";" for commands inside $(if) blocks need to be inside the $(if) block, too, because otherwise there will be dangling ";" without a statement (bash does not support empty statements containing just ";")

/README.TXT: Full database import: converted database commands to command-line commands to make them easier to run

/README.TXT: Full database import: converted database commands to command-line commands to make them easier to run

web/links/index.htm: updated to Firefox bookmarks: added instructions for how to enable automatic restart on power loss for the UPS (which isn't accessible in the GUI)

fix: schemas/util.sql: contained_within_approx(point geocoord, region postgis.geography): use util.geography() instead of implicit cast to suppress "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" NOTICEs

schemas/util.sql: added geography(util.geocoord), which suppresses "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" NOTICEs

exports/native_status_resolver.csv.run: updated export_() runtime (5 min, now that we're using the narrower New World criterion)

fix: schemas/public_.sql: native_status_resolver: don't include rows with New World coordinates that don't also have New World country names, since the NSR only uses the country name

schemas/public_.sql: native_status_resolver: removed rows with is_geovalid NULL, at Brad's request. note that this removes valid rows with standardized country names.

exports/native_status_resolver.csv.run: updated export_() runtime (30 min)

fix: schemas/public_.sql: native_status_resolver: added country IS NOT NULL filter requested by Brad

fix: schemas/public_.sql: native_status_resolver: remove the id because this prevents SELECT DISTINCT from having the desired effect. instead, the results will be joined back using the other columns.

exports/native_status_resolver.csv.run: upload_(): documented runtime (2.5 min)

bugfix: exports/native_status_resolver.csv.run: upload_(): $live must be exported

exports/native_status_resolver.csv.run: upload_(): use `live=1` instead for consistency with other invocations of put

fix: exports/native_status_resolver.csv.run: upload_(): need `l=1`

exports/native_status_resolver.csv.run: documented export_() runtime (45 min)

exports/native_status_resolver.csv.run: added upload_() to get the file onto nimoy

added exports/native_status_resolver.csv.run

schemas/public_.sql: added native_status_resolver view, requested by Brad (wiki.vegpath.org/Data_requests)

inputs/publishable datasources.xlsx: udpated

lib/tnrs.py: documentation about output of the retrieve step: added that this is also unusable because the array does not contain all the columns and contains no column names

removed no longer used web/BIEN3/Redmine/main/. use Redmine/!__ instead.

web/BIEN3/Redmine/issues/.htaccess: perform .. redirects using new ! prefix

web/BIEN3/Redmine/.htaccess: enable redirects that avoid using a subdir's .htaccess

web/BIEN3/Redmine/wiki/.htaccess: removed no longer needed ignore_fs, since the .htaccess does not have RewriteRules that would need this in a RewriteCond

web/BIEN3/Redmine/issues/.htaccess: main issues page: added default filter conditions

bugfix: web/BIEN3/Redmine/issues/.htaccess: need to redirect to separate URL for individual issues, because they are not located under the issues/ subdir in Redmine

added web/.issues symlink and dest dir (needed because Apache does not support dangling symlinks)

web/BIEN3/Redmine/wiki/.htaccess: documented that this dir is needed because Apache does not support dangling symlinks

bugfix: web/.htaccess: need to expand top-level symlinks to avoid RewriteBase issues

web/main.conf: added RewriteMap for readlink

added web/readlink

web/links/index.htm: updated to Firefox bookmarks: updated favicons

web/links/index.htm: updated to Firefox bookmarks: updated favicons

web/BIEN3/Redmine/wiki/.htaccess: just use this dir as symlink dest, since the dir name is the same as the URL path within Redmine

web/.htaccess: don't rewrite existing files/dirs: allow forcing rewrite of existing things with %{ENV:ignore_fs}

web/BIEN3/Redmine/svn-web/.htaccess: use Redmine/ instead of main/ subdir

web/BIEN3/Redmine/.htaccess: point this to the Redmine root instead of to the wiki, to avoid the need to append /main

backups/vegbien.r14089.backup.md5: updated

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_best_match_jerry_lu index to facilitate finding names affected by the match-picking bug (#943)

backups/TNRS.backup.md5: updated

fix: inputs/HVAA/Specimen/postprocess.sql, map.csv: monthCollected/dayCollected: fix indefinite dates (which aren't supported by Postgres), as decided by Bob (https://docs.google.com/spreadsheets/d/1PI8n0CRttN7ttsXs5qfh5OFFzSoAfJj0gSbylgX6vj4/edit#gid=0)

schemas/util.sql: added date_part_fix()

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's and Martha's request (e-mails from Martha on 2014-8-12 at 17:37PT, and from Brian M on 2014-8-13 at 16:21PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: added view_full_occurrence_individual_*GBIF, analytical_stem_*GBIF requested by Mark. note that this change has already been made on vegbiendev.

schemas/VegBIEN/data_dictionary/VegBIEN data dictionary.xlsx: updated

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: view_full_occurrence_individual, analytical_stem: renamed columns to shortened names at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: analytical_stem_view: renamed to analytical_stem since this replaces the materialized analytical_stem table. note that this change has already been made on vegbiendev.

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: viewFullOccurrence_individual: re-ran viewFullOccurrence_individual_view_modify() to udpate this

bugfix: schemas/util.sql: copy_struct(): also need to util.copy_comment() because CREATE TABLE __ INCLUDING ALL is missing this

schemas/util.sql: added copy_comment(regclass, regclass)