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/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
