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/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 ../
web/BIEN3: link to Redmine instead of directly to the wiki, since the Redmine/ dir should manage where BIEN3 default-redirects to
schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/
added schemas/VegBIEN/data_dictionary/create_bien3_viewFullOccurrence.txt from Brad
added schemas/VegBIEN/data_dictionary/schema_docum.pptx from Brian McGill
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/
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: analytical_stem_view: approved by/to discuss: renamed to * (removing "approved by") because the participants in today's conference call indicated that they were happy with the definitions, and the issues raised before the call had been addressed
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added all tables used to create analytical_stem_view, not just those that Brian M listed. (Brian M generated his tables list from the analytical_stem_view columns rather than the joins, and renamed plot.** to plot, which is why his list ended up missing tables and in the wrong order.)
added exports/2014-6-12.Jeff_Ott.climatic_range_determinants.csv.run
schemas/vegbien.sql: added 2014-6-12.Jeff_Ott.climatic_range_determinants (wiki.vegpath.org/Data_requests)
web/username_prefix.php: deletion comments: require ... strikethrough on both () to avoid ambiguity when the deleted part starts or ends with -
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: resized columns to fit laptop screen
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added my and Brian McGill's notes from the data dictionary conference call
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added analytical_stem_view table definitions
removed schemas/vegbien.ERD.MySQL_Workbench_6.1.6.mwb, because vegbien.ERD.mwb is now targeted to the correct version of MySQL Workbench (and is more up-to-date)
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
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added "to discuss" column requested by Martha. resized columns to avoid truncating the viewFullOccurrence term names.
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating definitions of terms
web/username_prefix.php: deletion comments: also support strikethrough syntax for clarity: (c_)x@url -> c_x@url
added schemas/DwC/hist symlink to history/ to help fit URLs in the 63-char limit
web/username_prefix.php: insertion comments: documented that the semantic meaning of the [] portion also applies, even though it's not included in the linked term name
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating viewFullOccurrence->analytical_stem_view and analytical_stem_view->viewFullOccurrence mappings
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: use new deletion comments (with () ) to indicate portions of external terms whose semantic meaning does not apply to our usage
web/username_prefix.php: added support for deletion comments of the form (c_)x(_d)@url -> c_x_d@url . deletion indicates that the semantic meaning of the () portion does not apply, even though it's included in the linked term name.
web/username_prefix.php: comments: use [] instead of () because in writing, [] denotes insertion, while () (as an editing mark) denotes something to remove
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: removed extra rows and columns so that they aren't included when copying and pasting
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added tab to store viewFullOccurrence->analytical_stem_view mapping
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added viewFullOccurrence column
