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()

schemas/util.sql: show_create_view(): use new mk_set_relation_metadata()

schemas/util.sql: added mk_set_relation_metadata()

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

inputs/.TNRS/schema.sql: MatchedTaxon: documented how to modify it (using util.force_recreate())

schemas/util.sql: force_recreate(): documented usage, which is somewhat complex and has several important parts

inputs/.TNRS/schema.sql: MatchedTaxon, etc.: added accepted_morphospecies_binomial derived field

bugfix: schemas/util.sql: restore_views(): need to specify view name for a manual existence check, in case the view definition becomes invalid, which would produce a nonstandard (uncatchable) exception

bugfix: schemas/util.sql: explain(): don't display any log messages printed by IMMUTABLE functions in the query, which EXPLAIN apparently runs

schemas/util.sql: create_if_not_exists(): added relation param, which can be used to ensure that a standard exception is always generated if the relation exists, even if the table definition would be invalid (which generates a variety of exceptions)

bugfix: schemas/util.sql: try_cast(), is_castable(): also need to handle syntax_error_or_access_rule_violation, which is thrown by ::regclass

schemas/util.sql: added relation_exists()

schemas/util.sql: save_drop_views()/restore_views(): store the view path in addition to the definition so it can be used in restoring

bugfix: schemas/util.sql: in_reverse(): can't use `SELECT *` for composite types because this expands them

bugfix: schemas/util.sql: array_reverse(): can't use `SELECT *` for composite types because this expands them

schemas/util.sql: save_drop_views()/restore_views(): use opaque return type so it can be changed without changing the local var type in functions that use this

schemas/util.sql: force_recreate(): recreate_users_cmds: renamed to restore_views_info since this is now whatever is needed by util.restore_views()

schemas/util.sql: added restore_views() and use it in force_recreate()

bugfix: schemas/util.sql: save_drop_views(): views must be dropped in reverse dependency order, but returned in forward dependency order

bugfix: schemas/util.sql: force_recreate(): dependent views need to be re-created in forward dependency order. this is done by reversing the dependencies only for save_drop_views().

bugfix: schemas/util.sql: mk_set_comment(): need to use VIEW instead of TABLE for views

bugfix: schemas/util.sql: show_create_view(): also need to include view comment

fix: schemas/util.sql: mk_set_comment(): added ;

fix: schemas/util.sql: show_set_comment(): don't display a COMMENT ON statement if no comment, because this will be appended to table defs, etc. and would create clutter

bugfix: schemas/util.sql: mk_set_comment(): need to handle NULL comment properly

schemas/util.sql: added show_set_comment(regclass)

schemas/util.sql: set_comment(): use util.mk_set_comment()

schemas/Makefile: added vegbien/install, vegbien/uninstall which also handle TNRS

fix: schemas/Makefile: vegbien.sql: also remake inputs/.TNRS/schema.sql since its contents change along with vegbien.sql

schemas/util.sql: added mk_set_comment()

bugfix: schemas/util.sql: force_recreate(): recreate_users_cmds: use create_if_not_exists() rather than eval(), because cmd might manually re-create a deleted dependent view, causing it to already exist

bugfix: schemas/util.sql: save_drop_view(): util.show_create_view(): don't include `OR REPLACE` because that causes nonuniform errors (eg. invalid_table_definition), instead of the standard duplicate_table exception caught by util.create_if_not_exists()

fix: schemas/util.sql: show_create_view(): removed extra trailing ; because pg_get_viewdef() now includes one

schemas/util.sql: show_create_view(): made inclusion of `OR REPLACE` configurable

schemas/util.sql: save_drop_view(): use util.drop_view()

schemas/util.sql: save_drop_views(): return text[] instead of concatenated text so that the queries will be run individually and be easier to debug

schemas/util.sql: added eval(queries text[])

bugfix: schemas/util.sql: force_recreate(): need to drop users in reverse to avoid dependencies that block the drop

schemas/util.sql: added array_reverse()

schemas/util.sql: added in_reverse()

bugfix: schemas/util.sql: force_recreate(): need to use :lower:, not [:lower:]

schemas/util.sql: force_recreate(): debug-print PG_EXCEPTION_DETAIL, users to assist in debugging

fix: schemas/util.sql: debug_print_value(): added trailing newline to visually distinguish the printed value

schemas/util.sql: added debug_print_var()

schemas/util.sql: debug_print_return_value(): use new util.debug_print_value()

schemas/util.sql: added debug_print_value()

fix: schemas/util.sql: util.force_recreate(): also support dropping things besides tables

inputs/.TNRS/schema.sql: MatchedTaxon.Accepted_name_species: mapped to accepted_species_binomial

fix: inputs/.TNRS/schema.sql: COMMENTs: always include newline before and after

bugfix: schemas/public_.sql: plots_20_tnrs_names: tnrs_accepted*: use new accepted_*, not scrubbed_*, as scrubbed_* does not contain only the accepted name (as implied by the tnrs_accepted_* column name)

bugfix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: undid rename of accepted name columns to scrubbed_* (r13435), because these are actually not the same (scrubbed_* is the combination of accepted and no-opinion names). the accepted name columns will now be named accepted_*, following the standard naming scheme.

bugfix: schemas/public_.sql: _plots_20_tnrs_names: morphospeciesSuffix must still be called morphospecies_suffix, not taxon_morphospecies, because that column has not been updated to the taxon_morphospecies yet (fixes r13435)

fix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: scrubbed_*: use columns from MatchedTaxon whenever possible, to as much as possible avoid the need to join to taxon_scrub.scrubbed_unique_taxon_name.*

schemas/Makefile: vegbien.sql: exclude the same set of Source tables excluded by inputs/.TNRS/schema.sql, so that reinstalling TNRS doesn't change the contents of this file

schemas/public_.sql: _plots_20_tnrs_names: changed to set of columns requested by Martha

schemas/public_.sql: _plots_20_tnrs_names: added morphospecies suffix in order to also validate it

schemas/public_.sql: _plots_20_tnrs_names: added verbatim name in order to also validate the formation of the concatenated name

schemas/public_.sql: merged _plots_20_tnrs_input_names, _plots_21_tnrs_output_names into _plots_20_tnrs_names so the input and output names can be compared side-by-side

schemas/vegbien.sql: synced to DB, which adds Source.errors table indexes added in the import

bugfix: schemas/Makefile: `%/install: public_.sql`: also need to replace `public` when preceded by ( , as it is in the validations queries

bugfix: schemas/util.sql: explain2notice_msg_if_can(): don't use util.is_explainable() because the list provided by Postgres (http://www.postgresql.org/docs/9.3/static/sql-explain.html#AEN77691) excludes some query types that are in fact EXPLAIN-able

schemas/public_.sql: _plots_20_tnrs_input_names, _plots_21_tnrs_output_names: added Brad's comments

bugfix: schemas/util.sql: materialize_query(): contents generated from: need to include search_path so query is runnable

schemas/vegbien.sql: _plots_21_tnrs_output_names: use scrubbed_unique_taxon_name (concatenated output name) because this is more similar to the concatenated name used in _plots_20_tnrs_input_names

bugfix: schemas/public_.sql: _plots_21_tnrs_output_names: need to use TNRS output rather than input name

schemas/public_.sql: added _plots_20_tnrs_input_names, _plots_21_tnrs_output_names

schemas/public_.sql: public_validations: schema comment: documented how to run just the output queries on a particular datasource

fix: schemas/public_.sql: rm_all_queries(): also remove output-only result tables

schemas/public_.sql: query_view_regexp(): also match auxiliary tables

schemas/public_.sql: added remake_output_tables(datasource_schema, prefix)

schemas/util.sql: added loop_ignore_errors()

schemas/public_.sql: added output_queries(prefix)

schemas/public_.sql: validation_views(): added prefix param, which can be used for additional subsetting

schemas/public_.sql: query_relations(): removed no longer used max_prefix_len default param

schemas/public_.sql: query_relations(): use new public_validations.truncated_prefixed_name_regexp(), which does not require passing in a max_prefix_len

schemas/vegbien.sql: added public_validations.truncated_prefixed_name_regexp(), which does not require passing in a max_prefix_len

schemas/public_.sql: rm_output_queries(), validation_views(): use public_validations.query_view_regexp()

schemas/public_.sql: added public_validations.query_view_regexp()

bugfix: schemas/public_.sql: public_validations.rm_output_queries(): default regexp needs to be anchored at beginning of string, and should match the regexp in public_validations.validation_views()

schemas/public_.sql: _km_to_m(): made it a wrapper around util._km_to_m() so this function is only in one place

schemas/util.sql: added _km_to_m() for use when public._km_to_m() is not defined yet

schemas/postgresql.conf: wal_level: set to hot_standby to enable online backup with pg_start_backup()

schemas/vegbien.ERD.mwb: regenerated exports

fix: lib/PostgreSQL-MySQL.csv: preserve schema assignments by translating `SET search_path` to `USE`

schemas/vegbien.ERD.mwb: regenerated exports

schemas/vegbien.ERD.mwb: added geoscrub, TNRS tables, as requested in the 2014-04-10 conference call (wiki.vegpath.org/2014-04-10_conference_call#VegBIEN-schema)

schemas/Makefile: vegbien.sql: also include geoscrub, TNRS schemas, as requested in the 2014-04-10 conference call (wiki.vegpath.org/2014-04-10_conference_call#VegBIEN-schema). this involves having a separate public_.sql file for restoring the public schema.

schemas/vegbien.ERD.mwb: regenerated exports

bugfix: inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13*: also need to include coordinate pairs which have one of their coordinates NULL, by using OR instead of AND

inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: added breakdowns _specimens_13a_list_of_all_verbatim_lat_long, _specimens_13b_list_of_all_decimal_lat_long to help troubleshoot the diff

fix: inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: count lat/longs together instead of separately, because the DISTINCT is by coordinate pair, not individual coordinate value (which wouldn't make much sense)

bugfix: schemas/vegbien.sql: rm_output_queries(): need to account for the fact that util.truncated_prefixed_name_regexp() returns a whole-string regexp. this drops support for removing output queries with a particular group prefix, which we no longer use.

bugfix: schemas/vegbien.sql: rm_output_queries(): need to include relations whose names were truncated, as well

fix: schemas/vegbien.sql: public_validations schema comment: to remove a validations query so its columns can be changed: use rm_output_queries() rather than rm_query_view() because that also removes input queries

bugfix: schemas/util.sql: is_castable(): need to pass NULL through, for proper NULL propagation

schemas/util.sql: added is_castable()