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# Date Author Comment
13850 06/25/2014 03:33 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: renamed to tnrs_match to distinguish it from other TNRS-related tables

13849 06/25/2014 02:38 PM Aaron Marcuse-Kubitza

fix: lib/phpPgAdmin.login.php.diff: use relative file path rather than the path the file was at when the patch was created

13848 06/25/2014 02:34 PM Aaron Marcuse-Kubitza

/Makefile, lib/phpPgAdmin.login.php.diff: public_ user: added auto-filled password so that users would not be confused as to what to type in the password field

13847 06/25/2014 02:15 PM Aaron Marcuse-Kubitza

added schemas/VegCore/phpMyAdmin/libraries/plugins/auth/AuthenticationCookie.class.php.diff

13846 06/25/2014 10:39 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: `taxon_scrub.scrubbed_unique_taxon_name.*`: added to-modify instructions

13845 06/25/2014 10:36 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: *_modify(): merged these into the "to modify" instructions in the corresponding views, because there is no need to create a separate *_modify() function for every view now that their definitions are all the same

13844 06/25/2014 10:21 AM Aaron Marcuse-Kubitza

validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB

13843 06/25/2014 05:15 AM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view and related views: updated COMMENTs from data dictionary spreadsheet, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#copy-data-dictionary-definitions-to-database

13842 06/25/2014 04:11 AM Aaron Marcuse-Kubitza

schemas/public_.sql: ran analytical_stem_view_modify(), which transfers the column COMMENTs from analytical_stem_view to analytical_stem

13841 06/25/2014 04:04 AM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: view_def_to_orig(): need to handle cases when list of cols from the same table is not an expanded * expression

13840 06/25/2014 03:59 AM Aaron Marcuse-Kubitza

schemas/util.sql: added view_is_subset(view_def text)

13839 06/25/2014 03:58 AM Aaron Marcuse-Kubitza

schemas/util.sql: added view_is_automatically_updatable(view_def text)

13838 06/25/2014 03:23 AM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: show_create_view(): use the overridden version of pg_get_viewdef(), which supports expanded * expressions. this was possibly being used already whenever util happened to be in the search_path.

13837 06/24/2014 05:03 PM Aaron Marcuse-Kubitza

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

13836 06/24/2014 05:01 PM Aaron Marcuse-Kubitza

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

13835 06/24/2014 04:36 PM Aaron Marcuse-Kubitza

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

13834 06/24/2014 04:34 PM Aaron Marcuse-Kubitza

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

13833 06/24/2014 03:27 PM Aaron Marcuse-Kubitza

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

13832 06/20/2014 08:01 PM Aaron Marcuse-Kubitza

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

13831 06/19/2014 04:13 PM Aaron Marcuse-Kubitza

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

13830 06/19/2014 04:11 PM Aaron Marcuse-Kubitza

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

13829 06/19/2014 04:08 PM Aaron Marcuse-Kubitza

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

13828 06/19/2014 04:06 PM Aaron Marcuse-Kubitza

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

13827 06/19/2014 03:58 PM Aaron Marcuse-Kubitza

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

13826 06/19/2014 03:54 PM Aaron Marcuse-Kubitza

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

13825 06/19/2014 11:13 AM Aaron Marcuse-Kubitza

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

13824 06/19/2014 02:33 AM Aaron Marcuse-Kubitza

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"

13823 06/19/2014 02:27 AM Aaron Marcuse-Kubitza

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

13822 06/19/2014 02:24 AM Aaron Marcuse-Kubitza

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

13821 06/19/2014 01:57 AM Aaron Marcuse-Kubitza

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

13820 06/19/2014 01:45 AM Aaron Marcuse-Kubitza

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

13819 06/18/2014 08:56 PM Aaron Marcuse-Kubitza

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.

13818 06/18/2014 08:52 PM Aaron Marcuse-Kubitza

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

13817 06/18/2014 08:49 PM Aaron Marcuse-Kubitza

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()

13816 06/18/2014 08:44 PM Aaron Marcuse-Kubitza

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.

13815 06/18/2014 08:38 PM Aaron Marcuse-Kubitza

schemas/util.sql: added lat_long_in_new_world()

13814 06/18/2014 08:35 PM Aaron Marcuse-Kubitza

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).

13813 06/18/2014 08:06 PM Aaron Marcuse-Kubitza

schemas/util.sql: added point()

13812 06/18/2014 08:00 PM Aaron Marcuse-Kubitza

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

13811 06/18/2014 07:59 PM Aaron Marcuse-Kubitza

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

13810 06/18/2014 07:52 PM Aaron Marcuse-Kubitza

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

13809 06/18/2014 07:39 PM Aaron Marcuse-Kubitza

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)

13808 06/18/2014 07:32 PM Aaron Marcuse-Kubitza

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

13807 06/18/2014 07:31 PM Aaron Marcuse-Kubitza

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

13806 06/18/2014 07:12 PM Aaron Marcuse-Kubitza

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)

13805 06/18/2014 04:43 PM Aaron Marcuse-Kubitza

schemas/util.sql: added new_world()

13804 06/18/2014 04:30 PM Aaron Marcuse-Kubitza

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

13803 06/18/2014 04:26 PM Aaron Marcuse-Kubitza

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

13802 06/18/2014 04:20 PM Aaron Marcuse-Kubitza

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

13801 06/18/2014 03:56 PM Aaron Marcuse-Kubitza

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

13800 06/18/2014 03:53 PM Aaron Marcuse-Kubitza

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

13799 06/18/2014 03:52 PM Aaron Marcuse-Kubitza

schemas/util.sql: added bounding_box()

13798 06/18/2014 03:41 PM Aaron Marcuse-Kubitza

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

13797 06/18/2014 03:12 PM Aaron Marcuse-Kubitza

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

13796 06/18/2014 01:40 PM Aaron Marcuse-Kubitza

backups/TNRS.backup.md5: updated

13795 06/17/2014 04:48 PM Aaron Marcuse-Kubitza

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

13794 06/17/2014 04:39 PM Aaron Marcuse-Kubitza

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

13793 06/17/2014 04:26 PM Aaron Marcuse-Kubitza

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

13792 06/17/2014 04:22 PM Aaron Marcuse-Kubitza

/Makefile: removed no longer used nonApacheOnPort80 code

13791 06/17/2014 04:13 PM Aaron Marcuse-Kubitza

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

13790 06/16/2014 06:50 PM Aaron Marcuse-Kubitza

schemas/util.sql: added ~ operator for ranges

13789 06/16/2014 04:35 PM Aaron Marcuse-Kubitza

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

13788 06/16/2014 04:34 PM Aaron Marcuse-Kubitza

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

13787 06/16/2014 03:52 PM Aaron Marcuse-Kubitza

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

13786 06/16/2014 03:50 PM Aaron Marcuse-Kubitza

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

13785 06/16/2014 02:13 PM Aaron Marcuse-Kubitza

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

13784 06/16/2014 02:03 PM Aaron Marcuse-Kubitza

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

13783 06/13/2014 08:34 PM Aaron Marcuse-Kubitza

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

13782 06/13/2014 08:24 PM Aaron Marcuse-Kubitza

web/index.php: Brad: added attribution/

13781 06/13/2014 08:22 PM Aaron Marcuse-Kubitza

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

13780 06/13/2014 08:21 PM Aaron Marcuse-Kubitza

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

13779 06/13/2014 08:11 PM Aaron Marcuse-Kubitza

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

13778 06/13/2014 08:11 PM Aaron Marcuse-Kubitza

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

13777 06/13/2014 08:08 PM Aaron Marcuse-Kubitza

added web/people/Brad_Boyle/identifiers

13776 06/13/2014 08:07 PM Aaron Marcuse-Kubitza

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

13775 06/13/2014 07:58 PM Aaron Marcuse-Kubitza

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

13774 06/13/2014 07:57 PM Aaron Marcuse-Kubitza

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

13773 06/13/2014 07:56 PM Aaron Marcuse-Kubitza

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

13772 06/13/2014 07:43 PM Aaron Marcuse-Kubitza

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

13771 06/13/2014 07:08 PM Aaron Marcuse-Kubitza

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

13770 06/13/2014 07:06 PM Aaron Marcuse-Kubitza

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

13769 06/13/2014 07:02 PM Aaron Marcuse-Kubitza

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

13768 06/13/2014 07:01 PM Aaron Marcuse-Kubitza

web/main.conf: updated paths

13767 06/13/2014 06:34 PM Aaron Marcuse-Kubitza

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

13766 06/13/2014 06:20 PM Aaron Marcuse-Kubitza

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

13765 06/13/2014 06:07 PM Aaron Marcuse-Kubitza

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

13764 06/13/2014 05:51 PM Aaron Marcuse-Kubitza

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

13763 06/13/2014 05:49 PM Aaron Marcuse-Kubitza

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

13762 06/13/2014 05:15 PM Aaron Marcuse-Kubitza

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

13761 06/13/2014 04:29 PM Aaron Marcuse-Kubitza

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

13760 06/13/2014 04:11 PM Aaron Marcuse-Kubitza

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

13759 06/13/2014 04:09 PM Aaron Marcuse-Kubitza

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

13758 06/13/2014 04:07 PM Aaron Marcuse-Kubitza

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

13757 06/13/2014 04:02 PM Aaron Marcuse-Kubitza

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

13756 06/13/2014 04:01 PM Aaron Marcuse-Kubitza

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

13755 06/13/2014 03:58 PM Aaron Marcuse-Kubitza

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

13754 06/13/2014 03:40 PM Aaron Marcuse-Kubitza

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

13753 06/13/2014 03:26 PM Aaron Marcuse-Kubitza

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

13752 06/13/2014 02:20 PM Aaron Marcuse-Kubitza

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

13751 06/13/2014 02:20 PM Aaron Marcuse-Kubitza

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