bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to new analytical_stem_view column names

fix: schemas/public_.sql: analytical_stem_view derived and related views: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database but with the current columns of analytical_stem as the left-hand column

bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to new analytical_stem_view column names

schemas/public_.sql: analytical_stem_view: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database

lib/tnrs.py: source_sorting (Constrain by Source): documented the different behavior for this in each match mode (all-matches and best-match)

schemas/public_.sql: added 2014-6-4.Iara_Lacher.reserve_prioritization

bugfix: web/.phpPgAdmin/.htaccess: : handlers: use `chain` to only run them when the RewriteRule they apply to is run

web/.phpPgAdmin/.htaccess: schema : handler: removed `env=subject:schema` because that has already been set

web/.phpPgAdmin/.htaccess: tables: added : suffix handler

bugfix: web/.phpPgAdmin/.htaccess: view : match: moved to right after `view=` because it only applies to views, not functions

web/.phpPgAdmin/.htaccess: schema: page: indicate by prefixing with : to avoid needing to explicitly list all possible pages

web/.phpPgAdmin/.htaccess: table: action: indicate by prefixing with : to avoid needing to explicitly list all possible actions

exports/2014-6-12.Jeff_Ott.climatic_range_determinants.csv.run: updated export_() runtime (35 min) and rowcount (23 million)

fix: /README.TXT: Full database import: disk space: removed instructions to rerun the import if the disk space gets used up, because this is actually a bug and is not generally "fixed just by rerunning the import"

schemas/util.sql: lat_long_in_new_world(): use function rather than operator+search_path to allow inlining, which enables util.new_world() to only be evaluated once

bugfix: schemas/util.sql: operator @(postgis.geography, postgis.geography): must use wrapper function because st_coveredby() needs postgis to be in the search_path

fix: lib/runscripts/extract.run: export_(): explicitly prevent files from becoming web-accessible, to protect against an incorrect umask in the calling process

fix: schemas/util.sql: point(): hide benign "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" notices

schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: also include New World occurrences by coordinates, using new lat_long_in_new_world(). this modification (as requested by Jeff) will help reduce the false negatives filtered out by including only data with placenames.

schemas/public_.sql: added lat_long_in_new_world() wrapper around util.lat_long_in_new_world()

schemas/util.sql: lat_long_in_new_world(): documented that this includes false positives above and below the New World bounding box, as described in util.bounding_box()

schemas/util.sql: bounding_box(): documented that the geography type stores all edges as arcs of great circles, resulting in the latitude lines bulging outward from the true bounding box. this will create false positives above and below the bounding box.

schemas/util.sql: added lat_long_in_new_world()

schemas/util.sql: added operator @(postgis.geography, postgis.geography). can't use && for this because it only compares 2D bounding boxes (which are geometry objects that do not support geocoordinate wraparound).

schemas/util.sql: added point()

schemas/util.sql: new_world(): removed no longer needed cast to postgis.geography

bugfix: schemas/util.sql: bounding_box(): must use postgis.geography (instead of postgis.geometry) because that handles geocoordinate wraparound correctly

bugfix: schemas/util.sql: bounding_box(): need to explicitly set SRID to make sure the correct value is used

bugfix: schemas/util.sql: bounding_box(): use st_makeenvelope() instead of st_makebox2d() because st_makebox2d() doesn't support geocoordinate wraparound (it is not SRID-aware)

schemas/util.sql: new_world(): removed no longer needed cast to postgis.geometry

schemas/util.sql: bounding_box(): return postgis.geometry instead of postgis.box2d because box2d is not directly used in postgis functions

bugfix: /Makefile: mk_db: plpython3u: use CREATE EXTENSION instead of createlang so that the plpython3u extension is created in addition to the plpython3u language (as it is on Linux)

schemas/util.sql: added new_world()

bugfix: schemas/util.sql: bounding_box(): use util.range instead of numrange to support wraparound ranges for geocoordinates

schemas/util.sql: range(numeric, numeric): use util.range instead of numrange to support wraparound ranges (which use a modulus system such as geocoordinates)

schemas/util.sql: added `range` type (and cast to numrange), which allows wraparound ranges such as for geocoordinates

schemas/util.sql: bounding_box(): documented usage

schemas/public_.sql, inputs/.TNRS/schema.sql: upgraded to Postgres 9.3.4 format, which removes trailing " "

schemas/util.sql: added bounding_box()

bugfix: /Makefile: postgis schema: also need to make it accessible to non-superusers

/Makefile, /README.TXT: PostgreSQL: Mac OS X: switched to using homebrew, which supports PostGIS

backups/TNRS.backup.md5: updated

schemas/util.sql: range(numeric, numeric): use simpler numrange() constructor instead of text input syntax

schemas/util.sql: operator functions: renamed to plain-text names to follow the Postgres convention of making the function name be the human-readable name of the operator

fix: bin/in_place: usage: removed duplicate copy of [preserve_mtime=1]

/Makefile: removed no longer used nonApacheOnPort80 code

bugfix: /Makefile: phppgadmin-Linux: don't change the Apache port if something "else" is running on port 80, because this feature was only needed when tomcat was running on that port, but is now buggy

schemas/util.sql: added ~ operator for ranges

/Makefile: mk_db: added PostGIS so it can be used by our functions

bugfix: /Makefile: postgres-Linux: postgis: updated apt-get target names for Ubuntu 14.04

*/LICENSE.TXT: use lowercase when there is a single set of *__

/LICENSE.TXT: refers to: removed trunk/ because of course it also applies to the branches/ and tags/ subdirs

schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: allow geovalid_bien = NULL to enable filtering New World status by coordinates rather than country

schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: added geovalid_bien

web/util.js: removed no longer used parse_dot_path(), etc. this is handled by web/.htaccess instead.

web/index.php: Brad: added attribution/

web/index.php: removed no longer used PHP redirects. these are now handled by Apache .htaccess files instead.

web/index.php: removed no longer used PHP redirects. these are now handled by Apache .htaccess files instead.

web/people/Brad_Boyle/data_provenance: abbreviated to provenance to enable shorter URLs

web/people/Brad_Boyle/data_provenance: abbreviated to provenance to enable shorter URLs

added web/people/Brad_Boyle/identifiers

bugfix: web/index.php: Brad: updated resource names to match filesystem

bugfix: web/index.php: Brad: fixed URL base

web/index.php: sources: reordered/recategorized to match the subdirs and wiki.vegpath.org/VegCore

schemas/VegCore/.htaccess: RewriteBase: use full path

merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema

schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/

added web/people/Brad_Boyle/identifier_examples, which is used by the VegBIEN data dictionary

placed web/BIEN3/TWiki/lib/LocalSite.cfg under version control because it contains absolute paths that need to be maintained

web/main.conf: updated paths

web/people/Brad_Boyle/*/.htaccess: set the destination filename using RewriteRule env, to allow escaping " " with "\ " instead of the difficult-to-read "\%20"

web/people/Brad_Boyle/*/.htaccess: use relative paths to new symlinks to avoid hardcoding paths

web/BIEN3/TWiki/twiki.conf: updated paths

bugfix: /README.TXT: Installation: Check out svn: need to use trunk instead of root

*: use vegbiendev:/home/bien instead of /home/bien/svn

web/people/Brad_Boyle/: added symlinks to Brad's files that are used in the data dictionaries

schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/

schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database

web/BIEN3/Redmine/svn/.htaccess: removed unneeded RewriteBase because this does not use a relative redirect with ../

schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database

schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database

schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database

merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema

web/BIEN3: link to Redmine instead of directly to the wiki, since the Redmine/ dir should manage where BIEN3 default-redirects to

schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/

merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema

merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema

schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/

schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/

added schemas/VegBIEN/data_dictionary/create_bien3_viewFullOccurrence.txt from Brad

schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/

added schemas/VegBIEN/data_dictionary/schema_docum.pptx from Brian McGill

merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema

removed no longer needed inputs/VegBIEN/fs symlink. use web/.fs instead.

web/.fs: changed to point directly to the svn root, so that the VegBIEN dir does not contain any recursive symlinks

/README.TXT: Mac settings backup: to Dropbox: stop Dropbox beforehand to prevent Dropbox from trying to capture filesystem events while syncing

/README.TXT: Mac settings backup: exclude ~/Library/Thunderbird/Profiles/9oo8rcyn.default/global-messages-db.sqlite because this file does not sync (issue #907)

web/links/index.htm: updated to Firefox bookmarks: oXygen XML editor: added download link for the version (13.2) that works with NCEAS's license. bash: added fix to enable Ctrl+Arrow to work. GVFS: added links for file permissions bug. iPlant: added Atmosphere/Data Store links. Quick links: updated vegpath.org link to `vegpath.org.`.

web/username_prefix.php: username/password prompt message: added instructions to always append "." when visiting the homepage of the site ("vegpath.org.")

schemas/VegBIEN/VegBIEN data dictionary.xlsx: moved to schemas/VegBIEN/data_dictionary/