inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_best_match_jerry_lu index to facilitate finding names affected by the match-picking bug (#943)

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's and Martha's request (e-mails from Martha on 2014-8-12 at 17:37PT, and from Brian M on 2014-8-13 at 16:21PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: added view_full_occurrence_individual_*GBIF, analytical_stem_*GBIF requested by Mark. note that this change has already been made on vegbiendev.

schemas/public_.sql: view_full_occurrence_individual, analytical_stem: renamed columns to shortened names at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: analytical_stem_view: renamed to analytical_stem since this replaces the materialized analytical_stem table. note that this change has already been made on vegbiendev.

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: viewFullOccurrence_individual: re-ran viewFullOccurrence_individual_view_modify() to udpate this

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_name index

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_family index

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_species_binomial index

bugfix: schemas/public_.sql: *_view_modify(): need to set the search_path so that tables are created in the same schema as the function, rather than whichever schema happens to be at the beginning of the search_path

bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to support being used directly instead of via a materialized table

schemas/public_.sql: removed no longer used analytical_stem. use analytical_stem_view or viewFullOccurrence_individual instead.

fix: schemas/public_.sql: viewfulloccurrence_individual_view_modify(): fixed capitalization in function name (needs "" to preserve case)

schemas/public_.sql: other derived views: use viewFullOccurrence_individual instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)

schemas/public_.sql: validation views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)

schemas/public_.sql: derived views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)

schemas/public_.sql: removed no longer used threatened_taxonlabel_view. use iucn_red_list_view instead.

schemas/public_.sql: viewFullOccurrence_individual_view: documented materialize time (22 h)

inputs/.TNRS/schema.sql: taxon_match: removed no longer used scrubbed_unique_taxon_name. the scrubbed name ranks are now generated from the other TNRS columns instead.

schemas/public_.sql: viewFullOccurrence_*: documented materialize time

schemas/public_.sql: analytical_stem_view: use new materialized viewFullOccurrence_individual

schemas/public_.sql: added viewFullOccurrence_individual by running viewFullOccurrence_individual_view_modify()

schemas/public_.sql: added viewFullOccurrence_individual_view_modify(), analogous to analytical_stem_view_modify()

inputs/.TNRS/schema.sql: removed no longer used view ValidMatchedTaxon. use taxon_scrub instead.

inputs/.TNRS/schema.sql: removed no longer used view MatchedTaxon. use taxon_best_match instead.

inputs/.TNRS/schema.sql: removed no longer used taxon_scrub.scrubbed_unique_taxon_name.* . use taxon_scrub instead.

inputs/.TNRS/schema.sql: taxon_scrub: use taxon_match derived columns instead of the incorrect values in taxon_scrub.scrubbed_unique_taxon_name.* (which does not work with the multi-match strategy)

schemas/public_.sql: added viewFullOccurrence_{CVS,VegBank,NCU} for Bob

bugfix: inputs/.TNRS/schema.sql: removed no longer used derived column __accepted_infraspecific_label, which had a buggy formula that broke derived_cols_populate()

inputs/.TNRS/schema.sql: "[accepted_]genus__@DwC__@vegpath.org": don't need to use *Accepted_name anymore because _accepted{genus,specific_epithet,infra_{rank,epithet}} is now generated from *Accepted_name

inputs/.TNRS/schema.sql: taxon_match."__accepted_{genus,specific_epithet}": renamed to "__accepted_{genus,specific_epithet,infra_{rank,epithet}}" since this now includes these other ranks as well

bugfix: inputs/.TNRS/schema.sql: taxon_match: use "Accepted_species[_binomial]__@TNRS__@vegpath.org" instead of "*Accepted_name_species". this fixes a bug in __accepted_infraspecific_label where Accepted_name_species with trailing whitespace could not be prefix-removed from names that contained just a species binomial.

fix: inputs/.TNRS/schema.sql: taxon_match: added derived column "Accepted_species[_binomial]__@TNRS__@vegpath.org", which removes trailing whitespace

schemas/util.sql: remove_prefix(), remove_suffix(): support case-insensitive matching

schemas/public_.sql: *_view_modify(): added repopulate param, which is passed to rematerialize_view()

bugfix: inputs/.TNRS/schema.sql: taxon_match: use wrapper for util.remove_prefix() so CHECK constraints that use it don't get dropped when the util schema is reinstalled

schemas/public_.sql: *_view_modify(): use util.rematerialize_view(), which now supports table mods

schemas/public_.sql: analytical_stem_view: use viewFullOccurrence_individual_view to avoid duplicated code between the views. this moves the stem-related columns to the end of the view.

schemas/public_.sql: added viewFullOccurrence_individual_view

bugfix: inputs/.TNRS/schema.sql: taxon_match: derived columns: use new "matched~Name[_no_author]___@TNRS__@vegpath.org" instead of "*Name_matched" so that "No suitable matches found." is removed before concatenating with other fields

inputs/.TNRS/schema.sql: taxon_match: added derived column "matched~Name[_no_author]___@TNRS__@vegpath.org", which removes the "No suitable matches found." string

inputs/.TNRS/schema.sql: reordered derived columns in dependency order

bugfix: inputs/.TNRS/schema.sql: "[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org": need to use "[accepted_]genus__@DwC__@vegpath.org" rather than "*Accepted_name" for this for rank = genus

inputs/.TNRS/schema.sql: taxon_match: added derived column "[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org"

bugfix: inputs/.TNRS/schema.sql: "[accepted_]genus__@DwC__@vegpath.org": need to populate this for rank = genus

inputs/.TNRS/schema.sql: taxon_match: added derived column "[scrubbed_]taxonomicStatus__@DwC__@vegpath.org"

bugfix: inputs/.TNRS/schema.sql: derived columns: use "Accepted_family__@TNRS__@vegpath.org" instead of "*Accepted_name_family" because "*Accepted_name_family" is sometimes missing

fix: inputs/.TNRS/schema.sql: taxon_match: added derived column "Accepted_family__@TNRS__@vegpath.org", which is needed because "*Accepted_name_family" isn't always populated

inputs/.TNRS/schema.sql: reordered derived columns in dependency order

inputs/.TNRS/schema.sql: taxon_match: added derived column "[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org"

inputs/.TNRS/schema.sql: taxon_match: added derived column "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org"

schemas/public_.sql: analytical_stem: synced to analytical_stem_view

inputs/.TNRS/schema.sql: taxon_match: added derived columns scrubbed_*

inputs/.TNRS/schema.sql: taxon_match: put matched-taxon derived columns before accepted-taxon derived columns

inputs/.TNRS/schema.sql: taxon_match: added derived column "[matched_]species[_binomial]~(Accepted_)__@TNRS__@vegpath.org"

inputs/.TNRS/schema.sql: _matched_has_accepted: renamed to matched_has_accepted because the leading _ did not create vertical alignment anyway, due to different quoting syntaxes

inputs/.TNRS/schema.sql: taxon_match: added derived column _matched_has_accepted

inputs/.TNRS/schema.sql: taxon_match: added derived columns "[matched_]scientificName[_with_author]__@DwC__@vegpath.org", "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"

inputs/.TNRS/schema.sql: taxon_match: added derived columns "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org", "[accepted_]infraspecificEpithet__@DwC__@vegpath.org"

inputs/.TNRS/schema.sql: taxon_match: added derived column "__accepted_infraspecific_{rank,epithet}"

inputs/.TNRS/schema.sql: taxon_match: added derived column __accepted_infraspecific_label

inputs/.TNRS/schema.sql: taxon_match: added derived columns "[accepted_]genus__@DwC__@vegpath.org", "[accepted_]specificEpithet__@DwC__@vegpath.org"

inputs/.TNRS/schema.sql: taxon_match: ran derived_cols_update()

fix: inputs/.TNRS/schema.sql: taxon_match: cluster the table so the rows are always exported in the same order, even when an UPDATE statement is used to run triggers

inputs/.TNRS/schema.sql: added _accepted{genus,specific_epithet} derived column, using the steps at wiki.vegpath.org/Postgres_queries#maintaining-derived-column-formulas-across-column-renames

fix: inputs/.TNRS/schema.sql: taxon_match: added back * prefixes on TNRS-namespace column names

schemas/public_.sql: removed no longer used threatened_taxonlabel. use iucn_red_list instead.

fix: schemas/public_.sql: analytical_stem_view: don't use threatened_taxonlabel, which was never populated correctly. instead, this can eventually be rewritten to use new iucn_red_list.

schemas/public_.sql: added iucn_red_list_view_modify() and use it in iucn_red_list_view's "after updating this" instructions

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

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

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

schemas/public_.sql: added in_iucn_red_list()

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

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: added iucn_red_list

schemas/public_.sql: added source__observation_type()

schemas/public_.sql: added subspecies() wrapper

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

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

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

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

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

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: added lat_long_in_new_world() wrapper around util.lat_long_in_new_world()