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: 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
(geocoord, postgis.geometry): renamed to
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
(postgis.geography, postgis.geography): renamed to ~
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: 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/.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
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__*
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
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/
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
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
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
