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__*

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

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

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: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database

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: 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()

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: added scrubbed_specific_epithet, scrubbed_species_binomial, which are needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)

schemas/public_.sql: analytical_stem_view: scrubbed_morphospecies_binomial: use new taxon_scrub.scrubbed_morphospecies_binomial

inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*

inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*

inputs/.TNRS/schema.sql: taxon_scrub: documented how to modify it

inputs/.TNRS/schema.sql: added taxon_scrub_modify()

inputs/.TNRS/schema.sql: MatchedTaxon_modify(): use simpler util.recreate_view()

inputs/.TNRS/schema.sql: MatchedTaxon_modify(): documented usage

bugfix: schemas/public_.sql: _plots_20_tnrs_names: verbatim_name_with_author: use taxonverbatim.taxonomicname rather than taxonlabel.taxonomicname

inputs/.TNRS/schema.sql: MatchedTaxon_modify(): removed no longer needed DROP VIEW statement

fix: schemas/util.sql: force_recreate(): renamed to just recreate(), because "force" normally implies that things will be deleted, which this function does not do

fix: schemas/public_.sql: _plots_20_tnrs_names: fixed order of tnrs_taxonomic_status, tnrs_accepted_name_family

schemas/public_.sql: _plots_20_tnrs_names: added tnrs_taxonomic_status, as requested in issue #915

schemas/public_.sql: analytical_stem_view: taxonomic_status: don't filter with map_taxonomic_status() anymore since this is now done by "TNRS"."MatchedTaxon"

fix: inputs/.TNRS/schema.sql: MatchedTaxon.taxonomicStatus: filter using map_taxonomic_status() so that the corrected value is available in the normalized DB, not just analytical_stem

inputs/.TNRS/schema.sql: MatchedTaxon: to modify: use new MatchedTaxon_modify(), which eliminates the work of putting together the dependent views

inputs/.TNRS/schema.sql: added MatchedTaxon_modify()

bugfix: inputs/.TNRS/schema.sql: map_taxonomic_status(): need to use accepted name instead of scrubbed name (which also includes no-opinion names), as described at http://wiki.vegpath.org/2013-11-14_conference_call#taxonomic-fields. this used to be the accepted name, but got switched when the concatenated name was also used to store the matched name for no-opinion names.

schemas/public_.sql: _plots_20_tnrs_names: use accepted_morphospecies_binomial, which is now available directly in the TNRS results, instead of just the morphospecies_suffix, as requested in issue #915