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

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

schemas/util.sql: added recreate_view(), a special case of util.recreate()

fix: schemas/util.sql: recreate(): usage: use `schema` instead of `schemas`

config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated

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

config/VirtualBox_VMs/Ubuntu */*.vbox: updated

bugfix: config/VirtualBox_VMs/: switched from symlinks to hard links, because svn does not follow symlinks

added config/VirtualBox_VMs/, containing the .vbox settings and password.txt (a non-empty password is needed for some system commands)

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

schemas/util.sql: recreate(): perform the correct DROP VIEW in the function itself so that the caller does not have to worry about forming it properly

bugfix: schemas/util.sql: mk_drop_from_create(): added `DROP`

schemas/util.sql: added mk_drop_from_create()

schemas/util.sql: added regexp_match()

planning/meetings/BIEN conference call availability.xlsx: updated

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()

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())

fix: lib/PostgreSQL-MySQL.csv: also remove left-behind lines such as `$$);`

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)

/README.TXT: to back up the vegbiendev databases: added step to review diff before performing backup, in case the backup scripts break and try to synchronize things incorrectly

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: lib/runscripts/util.run: $is_runscript: unexport so don't pass it to invoked scripts

backups/pg_snapshot: documented runtime for initial backup (4 h)

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()

/README.TXT: Maintenance: added steps to back up the vegbiendev databases

bugfix: lib/runscripts/util.run: run_args_cmd(): don't prepend main to args if no args, because for a non-runscript, all args will be passed to main(), leading `main` to be doubled

lib/tnrs.py: use the TNRS dev server (with private URL in tnrs.url) instead of the live server, since that contains datasources that we need

lib/streams.py: added file_get_contents()

lib/tnrs.py: configure the server separately from the base URL

lib/: svn:ignore tnrs.url so the TNRS dev server URL does not become public

bugfix: web/.phpPgAdmin/.htaccess: only append subject if non-empty, to avoid confusing redirect.php

bugfix: web/.phpPgAdmin/.htaccess: custom pages: need to handle in query string because .php filename would be treated as path element

web/.phpPgAdmin/.htaccess: support custom .php pages

planning/meetings/BIEN conference call availability.xlsx: updated

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

bugfix: inputs/.TNRS/grants.sql: added GRANT statements from schema.sql because these aren't run by `make inputs/.TNRS/reinstall`

lib/tnrs.py: retrieval_request_template: taxonomic_constraint, source_sorting: documented their meaning and why they need to be on/off

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

validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB

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

/README.TXT: Full database import: for test import, turn off DB backup: added () after after_import to show that it's a function

/README.TXT: Full database import: refer to the shell instead of screen because it's also possible to use a nested shell for this