schemas/vegbien.sql: taxon_scrub: documented steps to merge synonymous columns

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

inputs/.TNRS/schema.sql: ValidMatchedTaxon: use taxon_best_match now that it's equivalent to MatchedTaxon

bugfix: schemas/public_.sql: tnrs_input_name: use taxon_match instead of taxon_best_match because there is no index on taxon_match that includes just the filters used by taxon_best_match

schemas/public_.sql: tnrs_input_name: use taxon_best_match now that it's equivalent to MatchedTaxon

backups/TNRS.backup.md5: updated

fix: inputs/.TNRS/schema.sql: MatchedTaxon: merged synonymous columns

fix: schemas/util.sql: view_is_subset_or_renaming(): views with CASE statements are also not subsets/renamings

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)

inputs/.TNRS/schema.sql: MatchedTaxon: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.

inputs/.TNRS/schema.sql: taxon_scrub: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.

added exports/viewFullOccurrence_{CVS,VegBank,NCU}.csv.run

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

bugfix: schemas/util.sql: added GRANT USAGE for bien_read, public_ so that util schema functions can be called by other users

inputs/.TNRS/schema.sql: taxon_match: to port derived column changes to vegbiendev: derived_cols_export() code: documented runtime (6 h)

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

bugfix: schemas/util.sql: drop_derived_col(): also need to run util.derived_cols_trigger_update()

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

fix: inputs/.TNRS/schema.sql: taxon_match: to remove a column: updated instructions

bugfix: lib/sh/util.sh: str2varname(): need to lowercase str because on case-insensitive filesystems, paths sometimes canonicalize to a different capitalization than the original

lib/sh/util.sh: added lowercase()

bugfix: lib/sh/util.sh: die(): need stub since this is invoked before it's defined

bugfix: lib/sh/util.sh: setup_log_fd(): don't change $log_fd to stdlog until stdlog is set up, to avoid "Bad file descriptor" errors

**: updated to use the local machine's new hostname, frenzy

lib/sh/util.sh: func_override(), copy_func(): added echo_func to facilitate debugging

bugfix: lib/sh/util.sh: stubs: log++ alias also needs to be moved to stub section

bugfix: lib/Firefox_bookmarks.reformat.csv: URLs: match only the uppercase tags used by Firefox, not any lowercase tags added by the user

fix: lib/Firefox_bookmarks.reformat.csv: page's self-description: updated comment to match regexp

bugfix: lib/Firefox_bookmarks.reformat.csv: page's self-description: updated "page's self-description: " prefix to remove

web/links/index.htm: updated to Firefox bookmarks: added links for SSD vs. HDD reliability

/README.TXT: added steps to restore from Time Machine

/README.TXT: added steps to back up the local machine's hard drive

/README.TXT: to synchronize a Mac's settings with my testing machine's: renamed to "to back up the local machine's settings"

/README.TXT: to synchronize a Mac's settings with my testing machine's: removed download section because we don't use this

added backups/vegbien.r14089.backup.md5

backups/TNRS.backup.md5: updated

bin/after_import: use new bin/make_backups

bugfix: bin/make_backups: need to `popd` when done

bugfix: bin/make_backups: need to `set +x` when done

bin/make_backups: run with initial "." so background processes will be owned by the invoking shell

added bin/make_backups

web/links/index.htm: updated to Firefox bookmarks: VirtualBox: performance: added that context-switching also imposes an overhead, in addition to sandboxing.

web/links/index.htm: updated to Firefox bookmarks: BIEN: added list of machines this has been tested on. VirtualBox: added links to performance considerations of running in a VM.

inputs/.TNRS/schema.sql: added new derived columns to derived views

fix: schemas/util.sql: view_def_to_orig(): need to support aliased columns (produced when a column is renamed)

schemas/util.sql: added aliased_col_re()

schemas/util.sql: added alias_re()

fix: schemas/util.sql: view_is_subset(): renamed to view_is_subset_or_renaming() because this also supports views that just rename columns, which should not be .*-ed by view_def_to_orig()

fix: schemas/util.sql: view_def_to_orig(): can't use FROM to alias util.col_re() because that prevents inlining the function

fix: schemas/util.sql: view_def_to_orig(): can't use FROM to alias util.col_re() because that prevents inlining the function

schemas/util.sql: view_def_to_orig(): use util.col_re() for clarity

schemas/util.sql: added col_re()

fix: schemas/util.sql: derived_col_update(): also need steps to drop column, because DROP __ CASCADE doesn't work when there are dependent views

inputs/.TNRS/schema.sql: _accepted_infraspecific{rank,epithet}: use array slice of new _accepted{genus,specific_epithet,infra_{rank,epithet}}, which is simpler than using remove_prefix() in __accepted_infraspecific_label

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."__accepted_{genus,specific_epithet}": use "*Accepted_name" instead of "Accepted_species[_binomial]__@TNRS__@vegpath.org" (from "*Accepted_name_species") because Accepted_name_species apparently sometimes does not match the Accepted_name and uses malformed Unicode characters

backups/README.TXT: added backup retention policy

bugfix: schemas/util.sql: derived_cols_export(): also need to first run util.derived_cols_remove() if changing the derived column order

schemas/util.sql: added derived_cols_remove(), which allows derived columns to be re-created in a different order

schemas/util.sql: added drop_derived_col(), which ensures that drop_column() only cascades to views

fix: schemas/util.sql: drop_column(): also need to recreate dependent views

schemas/util.sql: added drop_constraint()

inputs/.TNRS/schema.sql: taxon_match: `inputs/.TNRS/data.sql.run refresh`: documented runtime (1 min)

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

inputs/.TNRS/schema.sql: added steps to remove a column and to add a non-derived column

inputs/.TNRS/schema.sql: taxon_match: to remove columns or add columns at the end: merged into "to add a new derived column"

inputs/.TNRS/schema.sql: to add columns in the middle: renamed to "to move a column to the middle" for clarity

inputs/.TNRS/schema.sql: to populate a new column: updated to use util.derived_col_update()

fix: inputs/.TNRS/schema.sql: taxon_match: to remove columns or add columns: also need to run util.recreate_view()

inputs/.TNRS/schema.sql: taxon_match: to remove columns or add columns at the end: don't need to run `rm=1 inputs/.TNRS/data.sql.run` because this is now run by `make schemas/remake`

inputs/.TNRS/schema.sql: added new derived columns to derived views

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

bugfix: inputs/.TNRS/schema.sql: taxon_match.__accepted_infraspecific_label: need to use case-insensitive matching of the removed prefix because TNRS lowercases part of the Accepted_name

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

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

schemas/util.sql: added case-sensitive-optional versions of starts_with(), ends_with()

schemas/util.sql: added canon_case(str text, case_sensitive boolean)

schemas/util.sql: check_constraint_disable(): documented that we can't use ADD CONSTRAINT NOT VALID for this because it does not disable the constraint completely, but instead causes new rows to be validated against it. the ADD CONSTRAINT NOT VALID behavior does not work for the derived columns use case of this function.

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

schemas/util.sql: rematerialize_view(): support updating just the table's schema, without populating it

schemas/util.sql: rematerialize_view(): don't need extra eval() around table_mod_sql because recreate() performs eval()

lib/sh/sync.sh: db_snapshot(): before backing up, trim bloated temp files (eg. from rolled back changes)

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/util.sql: rematerialize_view(): added support for table mods to run after creating table

bugfix: schemas/util.sql: rematerialize_view(): don't populate unless recreate() can successfully recreate the dependent views, to avoid populating the entire table (which for some views can take hours) only to have the changes rolled back by a failing dependent view

schemas/util.sql: removed no longer used materialize_view(). use util.copy() instead.

schemas/util.sql: rematerialize_view(): call util.copy() directly instead of via util.materialize_view()

schemas/util.sql: removed no longer used copy_types_and_data(). use util.materialize_view() instead.

schemas/util.sql: to_freq(): use util.copy() instead of util.copy_types_and_data() to avoid a dependency on util.copy_types_and_data()

fix: schemas/util.sql: copy_data(): also need to ANALYZE table after loading data into it

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

web/username_prefix.php: substitutions: also support "" because Postgres doubles " to escape them

web/username_prefix.php: added support for substitutions ( x."_y@url -> x.x_y@url ), which can be used when a table name is repeated in a column name

backups/TNRS.backup.md5: updated

schemas/util.sql: derived_col_constraint_initially_enabled(): clarified that this is always based on whether the existing constraint is enabled