removed no longer needed inputs/.TNRS/grants.sql, since the grants in schema.sql are now being run

bugfix: inputs/input.Makefile: sql/install: schema.sql should not be passed through pg_dump_limit because it contains GRANT statements that need to be run

schemas/public_.sql: iucn_red_list_view: documented how to regenerate iucn_red_list from this

exports/2014-6-4.Iara_Lacher.reserve_prioritization.csv.run: documented runtime (7.5 min) and rowcount (3.5 million)

bugfix: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: fixed slowdown in materializing the view, which was caused by source__observation_type(), by replacing this with a LEFT JOIN as was done for is_threatened_iucn

schemas/util.sql: in_south_america(): optimized by using BETWEEN instead of util.contained_within__no_dateline(). this reduces the filter time for 2014-6-4.Iara_Lacher.reserve_prioritization by about 10%.

fix: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: is_threatened_iucn: generate this much faster by doing a LEFT JOIN, which can reuse the same in-memory hash index for every row

bugfix: schemas/public_.sql: wrapper functions can't use util-schema types because these will cause the wrapper function to be cascadingly dropped when the util schema is reinstalled

bugfix: in_south_america(): must use util.contained_within__no_dateline() instead of util.contained_within_approx() to ensure that the more accurate geometry logic is used

bugfix: schemas/public_.sql: source__observation_type(): don't display NOTICEs about the search_path, because this function will be called millions of times

bugfix: schemas/public_.sql: in_iucn_red_list(): don't display NOTICEs about the search_path, because this function will be called millions of times

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

schemas/public_.sql: added in_iucn_red_list()

schemas/public_.sql: added iucn_red_list, materialized from iucn_red_list_view

bugfix: schemas/vegbien.sql: iucn_red_list_view: need to include only names with an accepted name, and distinctify on the accepted names

schemas/public_.sql: added iucn_red_list

schemas/util.sql: materialize_view(): use util.copy() instead of util.materialize_query() so that all view metadata is transferred

schemas/public_.sql: iucn_red_list: renamed to iucn_red_list_view since this will be materialized

schemas/public_.sql: added iucn_red_list

schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added collection_type (using source__observation_type())

schemas/public_.sql: added source__observation_type()

schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added accepted_subspecies, and removed accepted_taxon_name_with_author which had been substituting for it

schemas/public_.sql: added subspecies() wrapper

schemas/util.sql: added subspecies()

schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: include only coordinates in South America

schemas/util.sql: added south_america(), in_south_america()

fix: schemas/util.sql: OPERATOR ~(geocoord, postgis.geometry): renamed to because this is not an approximate comparison for geometry

fix: schemas/util.sql: contained_within_approx(geocoord, postgis.geometry): renamed to contained_within__no_dateline(__) because this is not an approximate comparison for geometry

schemas/util.sql: lat_long_in_new_world(): renamed to just in_new_world() because the lat/long is implied by the param type

schemas/util.sql: lat_long_in_new_world(): take a geocoord param instead of separate lat/long params

backups/TNRS.backup.md5: updated

schemas/util.sql: added contained_within_approx(geocoord, geometry) and corresponding OPERATOR ~@(geocoord, geometry)

schemas/util.sql: added OPERATOR ~@(geocoord, geography)

schemas/util.sql: lat_long_in_new_world(): use new contained_within_approx(geocoord, geography)

schemas/util.sql: added contained_within_approx(geocoord, postgis.geography), which enables specifying just `(lat, long)` without the ::util.geocoord type specifier

schemas/util.sql: OPERATOR (postgis.geography, postgis.geography): renamed to ~ because it's approximate

schemas/util.sql: contained_within(): renamed to contained_within_approx() because the latitude lines of geography type bounding boxes bulge outward, creating false positives above and below the bounding box

schemas/util.sql: added contained_within__no_dateline(geometry, geometry) and corresponding operator @

schemas/util.sql: contained_within(): renamed to contained_within_approx() because the latitude lines of geography type bounding boxes bulge outward, creating false positives above and below the bounding box

schemas/util.sql: geometry(geocoord): documented that it is not possible to create a cast for this, as a bug in pg_dump prevents the cast from being exported, even when no export filters are applied

schemas/util.sql: point(geocoord): renamed to geometry(geocoord) since this is now a cast

schemas/util.sql: point(): return geometry instead of geography to support using points with geometry arithmetic

schemas/util.sql: point(): take a single util.geocoord param instead of separate lat/long

schemas/util.sql: added geocoord type

schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: include only georeferenced occurrences (lat/long NOT NULL)

schemas/util.sql: bounding_box(): use bounding_box__no_dateline() to construct the postgis.geometry object

schemas/util.sql: added bounding_box__no_dateline(), which is more accurate than util.bounding_box() (latitude lines will be straight), but geocoordinate wraparound is not supported

schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added functional traits that we have 1st-class columns for (dbh_cm, height_m)

added exports/2014-6-4.Iara_Lacher.reserve_prioritization.csv.run

inputs/publishable datasources.xlsx: updated

inputs/publishable datasources.xlsx: updated

inputs/.TNRS/schema.sql: matchedFamily: just use Name_matched_accepted_family, because TNRS has now been reloaded so that the names that were missing this have it populated

planning/meetings/BIEN conference call availability.xlsx: updated

inputs/.TNRS/schema.sql: taxon_match: taxon_match__valid_match: replaced with taxon_best_match__valid_match, which also applies taxon_best_match's filters, since taxon_match is now accessed through taxon_best_match

fix: inputs/.TNRS/schema.sql: MatchedTaxon: use taxon_best_match instead of taxon_match because this should provide only one match per taxon

bugfix: /README.TXT: Mac settings backup: backup to jupiter: need to exclude ~/software/**/.svn/ because these are different on jupiter

/README.TXT: Mac settings backup: backup to jupiter: removed no longer applicable exclude of /VirtualBox VMs/Ubuntu/Ubuntu.vdi

inputs/.TNRS/schema.sql: added taxon_best_match view

inputs/.TNRS/schema.sql: taxon_match: added taxon_match__one_selected_match unique index

backups/TNRS.backup.md5: updated

planning/meetings/BIEN conference call availability.xlsx: updated

inputs/.TNRS/schema.sql: taxon_match__fill(): split into separate DECLARE blocks for each field for clarity

inputs/.TNRS/data.sql: refreshed

fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*

fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*

inputs/.TNRS/data.sql: refreshed

inputs/.TNRS/schema.sql: taxon_match: insert names via taxon_match_input auto-updatable view instead of directly into taxon_match, to allow the taxon_match columns to be renamed while still supporting inserts using the TNRS column names

fix: schemas/Makefile: vegbien.sql: also need to update inputs/.TNRS/data.sql, since its contents change along with this

inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name

inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name

inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name

inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name

lib/tnrs.py: dirty: documented that this actually used to be on in the web app (see r9910, 2013-6-18), but does not appear to be needed (the source_sorting bug alluded to in r9910 is not fixed by enabling the dirty setting)

lib/tnrs.py: requests: also debug-print request URL

lib/tnrs.py: Download: include the same debug info as do_request()

lib/tnrs.py: do_request(): also debug-print request headers

lib/tnrs.py: download_request_template: dirty: documented why this must be off

bugfix: lib/tnrs.py: download_request_template: fixed bug where multiple names were being marked as Selected, because dirty was incorrectly set to true unlike in the web app

added derived/TNRS/web_app/protocol/

inputs/.TNRS/data.sql: refreshed

bugfix: inputs/.TNRS/schema.sql: taxon_name_is_safe(): need to use `NOT (_ = ANY()) instead of ` != ANY`, because the != operator is applied to each element

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

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

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

/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

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

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

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

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

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

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

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

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

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

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.

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)