inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)
schemas/util.sql: added seq__reset()
schemas/util.sql: added seq__create()
fix: schemas/util.sql: try_cast(), is_castable(): also catch invalid_schema_name, thrown by `'pg_temp.__'::regclass`
backups/TNRS.backup.md5: updated
lib/tnrs.py: max_names: increased to 100000 because the dev server can handle more names (no simultaneous users), as decided in the conference call (wiki.vegpath.org/2014-05-29_conference_call#TNRS)
schemas/vegbien.ERD.mwb: regenerated exports
schemas/vegbien.ERD.mwb: re-updated to schemas/vegbien.my.sql, which now recognizes the broken tables. fixed sync issues. vegbien.ERD.mwb is now fully in sync with vegbien.my.sql.
fix: lib/PostgreSQL-MySQL.csv: need to replace "double precision" with "double" to work with MySQL Workbench 5.2.47
schemas/vegbien.ERD.mwb: updated to schemas/vegbien.my.sql. some tables weren't recognized (likely due to bugs in MySQL Workbench 5.2.47), and have been left as-is (unsynced). note that downgrading to 5.2.35 is not an option, because that is fatally broken by a system upgrade.
fix: schemas/vegbien.ERD.mwb: use schemas/vegbien.my.sql instead of schemas/vegbien.my.sql.changes.sql as the sync source
schemas/vegbien.ERD.mwb: switched back to MySQL Workbench 6.1.6 version, which also works with MySQL Workbench 5.2.47
schemas/vegbien.ERD.mwb: restored version for MySQL Workbench 5.2.35 (undid r13549), as 6.1.6 has bugs in the DDL file sync
schemas/vegbien.ERD.mwb: renamed to vegbien.ERD.MySQL_Workbench_6.1.6.mwb to differentiate the versions for different versions of MySQL Workbench
removed no longer used config/VirtualBox_VMs/VegCore ERD/. use the Ubuntu 14.04 VM instead, which now has the VegCore ERD setup.
config/VirtualBox_VMs/Ubuntu 14.04/Ubuntu 14.04.vbox: added VegCore ERD setup
schemas/: svn:ignore *.changes.sql, needed for MySQL Workbench 6.1.6
schemas/vegbien.ERD.mwb: updated
schemas/vegbien.ERD.mwb: updated layout for MySQL Workbench 6.1.6, which uses a different line spacing
lib/tnrs.py: commented out the value of max_names that is not active, for clarity
config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated: merged post-bootloader installation steps into one snapshot now that eth1 addition is successful
config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated, which adds eth1
config/VirtualBox_VMs/Ubuntu 12.04/Ubuntu 12.04.vbox: updated
lib/tnrs.py: sources: updated to list/sort order in issue #917
added exports/2014-3-11.Jeff_Ott.climatic_range_determinants.csv.run
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
added downloads/
fix: schemas/util.sql: mk_drop_from_create(): also support CREATE queries that include the SELECT statement on the same line as the CREATE
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: documented how to modify it
inputs/.TNRS/schema.sql: added taxon_scrub_modify()
schemas/util.sql: create_if_not_exists(): print message if already exists, so the function doesn't inexplicably appear not to have run at all
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