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/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/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: include only coordinates in South America
schemas/util.sql: added south_america(), in_south_america()
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
schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: include only georeferenced occurrences (lat/long NOT NULL)
schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added functional traits that we have 1st-class columns for (dbh_cm, height_m)
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
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
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
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
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
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: `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
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/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
schemas/public_.sql: added 2014-6-4.Iara_Lacher.reserve_prioritization
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/public_.sql, inputs/.TNRS/schema.sql: upgraded to Postgres 9.3.4 format, which removes trailing " "
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
schemas/vegbien.sql: added 2014-6-12.Jeff_Ott.climatic_range_determinants (wiki.vegpath.org/Data_requests)
schemas/public_.sql: analytical_stem_view: example terms from each source: added location in the VegBIEN core DB
schemas/public_.sql: analytical_stem_view: terms in normalized schemas: put the source name right next to the term name (instead of after the table name) so it's easy to find
schemas/public_.sql: analytical_stem_view: VegX terms: populated definitions
schemas/public_.sql: analytical_stem_view: VegX terms: referenced to the specific table/subpath that they are in
bugfix: schemas/public_.sql: analytical_stem_view: locationName: re-sourced to VegX because this is actually not a DwC term
schemas/public_.sql: analytical_stem_view: populated definitions of linked DwC terms from DwC data dictionary
schemas/public_.sql: analytical_stem_view: renamed terms to link URLs, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#data-dictionary-rename-terms-to-link-URLs
inputs/.TNRS/schema.sql: unsafe_taxon_names(): removed the name with "spp." now that this TNRS bug (https://pods.iplantcollaborative.org/jira/browse/TNRS-193) has been fixed
schemas/public_.sql: analytical_stem_view: populated links from unrenamed term names, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#data-dictionary-populate-links-from-unrenamed-term-names
fix: schemas/public_.sql: analytical_stem_view: links: removed = before them because the link is in fact one member in a list of definitions (the = would apply to all definitions, not just the link, and since it apply to all definitions, it's redundant because of course the comment is what the column equals)
fix: schemas/public_.sql: analytical_stem_view: vegpath.org links: use ; instead of : between link and definition, because it makes more grammatical sense
schemas/public_.sql: analytical_stem_view: vegpath.org links: removed no longer needed // suffix
schemas/public_.sql: analytical_stem_view: added links and definitions for half a dozen of the terms from various sources
schemas/public_.sql: analytical_stem_view: indicated provenance of the rest of the terms
schemas/public_.sql: analytical_stem_view: flagged the DwC terms
schemas/public_.sql: added plot.**.modify()
inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()
fix: schemas/public_.sql: tnrs_input_name: added ORDER BY to ensure a stable sort order. this also creates better query plans by enabling merge joins.
bugfix: schemas/public_.sql: tnrs_input_name: need to exclude unsafe taxon names as a workaround to #935 (TNRS crashes when scrubbing names with two infraspecific epithets)
schemas/public_.sql: taxonlabel: added index on taxonomicname to facilitate retrieving rows from tnrs_input_name
inputs/.TNRS/schema.sql: added taxon_name_is_safe()
inputs/.TNRS/schema.sql: added unsafe_taxon_names()
schemas/public_.sql: sync_*(): renamed to *_modify() to facilitate finding these functions when modifying the corresponding view (using the new naming convention for a view's on-modify function)
bugfix: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): updated to include taxon_scrub derived fields
inputs/.TNRS/schema.sql: *_modify(): allow running without a view_query, as recreate_view() now supports this
fix: schemas/public_.sql: sync_*(): use util.copy() instead of CREATE TABLE AS so that table and column comments are also copied. this avoids the need to separately add the same comments to the view and its materialized table.
bugfix: schemas/public_.sql: sync_geoscrub_input_to_view(): `CREATE TABLE geoscrub_input AS __`: needs `LIMIT 0`
schemas/public_.sql: sync_analytical_stem_to_view(): removed DROP TABLE IF EXISTS because this is now done automatically by util.recreate()
fix: inputs/.TNRS/schema.sql: added back index on Name_submitted, which is needed for tnrs_input_name to work properly (now that there is no automatic index created by a unique constraint)
schemas/vegbien.sql: tnrs_input_name: don't scrub accepted names, as using multiple matches per name no longer provides a single accepted name to scrub. instead, the Accepted_* fields can be whitespace-split to generate the same columns that would have been generated by the scrubbing (and without the overhead of the extra TNRS call).
fix: inputs/.TNRS/schema.sql: tnrs: removed unique constraint on Name_submitted, Name_matched because there can be more than one match with the same Name_matched (but different accepted names, etc.)
fix: inputs/.TNRS/schema.sql: tnrs.tnrs__valid_match index: made it non-unique to allow multiple matches per name, as is needed to implement #917
bugfix: inputs/.TNRS/schema.sql: tnrs__match_num__fill(): only fill if not set, to support case where tnrs is being restored from a .sql file (where match_num is already set)
inputs/.TNRS/schema.sql: tnrs: documented runtime to add a constraint (3 min)
inputs/.TNRS/schema.sql: unique constraint on Name_submitted: added Name_matched to allow multiple matches per name, as is needed to implement #917
inputs/.TNRS/schema.sql: tnrs: documented how to populate a new column
inputs/.TNRS/schema.sql: tnrs: pkey: use match_num instead of Name_number to allow multiple matches per name, as is needed to implement #917
inputs/.TNRS/schema.sql: tnrs.match_num: made it NOT NULL now that it's populated
inputs/.TNRS/schema.sql: tnrs: populate match_num
inputs/.TNRS/schema.sql: tnrs: documented how to add and remove columns
inputs/.TNRS/schema.sql: made COMMENTs start on their own line, using the steps at wiki.vegpath.org/Postgres_queries#make-COMMENTs-start-on-their-own-line
inputs/.TNRS/schema.sql: tnrs: added match_num
inputs/.TNRS/schema.sql: added tnrs__match_num__next()
inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)
schemas/public_.sql: added 2014-3-11.Jeff_Ott.climatic_range_determinants
schemas/public_.sql: analytical_stem_view: added scrubbed_taxon_name_with_author, needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
inputs/.TNRS/schema.sql: taxon_scrub.scrubbed_unique_taxon_name.*: added scrubbed_taxon_name_with_author, needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
schemas/public_.sql: added scrubbed_specific_epithet, scrubbed_species_binomial, which are needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
fix: schemas/public_.sql: sync_analytical_stem_to_view(): removed fkey to source.shortname because this prevents reloading individual datasources
schemas/public_.sql: analytical_stem_view: scrubbed_morphospecies_binomial: use new taxon_scrub.scrubbed_morphospecies_binomial
