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# Date Author Comment
13532 05/27/2014 12:13 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*

13531 05/26/2014 11:54 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_scrub: documented how to modify it

13530 05/26/2014 11:51 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added taxon_scrub_modify()

13529 05/26/2014 11:41 PM Aaron Marcuse-Kubitza

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

13527 05/23/2014 06:17 PM Aaron Marcuse-Kubitza

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

13526 05/23/2014 06:15 PM Aaron Marcuse-Kubitza

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

13525 05/23/2014 06:09 PM Aaron Marcuse-Kubitza

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

13524 05/23/2014 04:24 PM Aaron Marcuse-Kubitza

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

13522 05/23/2014 03:57 PM Aaron Marcuse-Kubitza

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

13518 05/21/2014 07:30 PM Aaron Marcuse-Kubitza

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

13517 05/21/2014 07:30 PM Aaron Marcuse-Kubitza

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

13516 05/21/2014 07:19 PM Aaron Marcuse-Kubitza

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

13515 05/21/2014 07:18 PM Aaron Marcuse-Kubitza

schemas/util.sql: added mk_drop_from_create()

13514 05/21/2014 06:52 PM Aaron Marcuse-Kubitza

schemas/util.sql: added regexp_match()

13512 05/21/2014 05:50 PM Aaron Marcuse-Kubitza

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

13511 05/21/2014 05:49 PM Aaron Marcuse-Kubitza

fix: schemas/public_.sql: _plots_20_tnrs_names: fixed order of tnrs_taxonomic_status, tnrs_accepted_name_family

13510 05/21/2014 04:45 PM Aaron Marcuse-Kubitza

schemas/public_.sql: _plots_20_tnrs_names: added tnrs_taxonomic_status, as requested in issue #915

13509 05/21/2014 04:34 PM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view: taxonomic_status: don't filter with map_taxonomic_status() anymore since this is now done by "TNRS"."MatchedTaxon"

13508 05/21/2014 04:25 PM Aaron Marcuse-Kubitza

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

13507 05/21/2014 04:05 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon: to modify: use new MatchedTaxon_modify(), which eliminates the work of putting together the dependent views

13506 05/21/2014 03:53 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added MatchedTaxon_modify()

13505 05/21/2014 03:44 PM Aaron Marcuse-Kubitza

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

13504 05/21/2014 03:41 PM Aaron Marcuse-Kubitza

schemas/util.sql: added mk_set_relation_metadata()

13503 05/21/2014 04:13 AM Aaron Marcuse-Kubitza

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.

13502 05/21/2014 01:50 AM Aaron Marcuse-Kubitza

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

13501 05/21/2014 01:27 AM Aaron Marcuse-Kubitza

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

13499 05/21/2014 12:59 AM Aaron Marcuse-Kubitza

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

13498 05/20/2014 05:46 PM Aaron Marcuse-Kubitza

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

13497 05/20/2014 05:40 PM Aaron Marcuse-Kubitza

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

13496 05/20/2014 05:33 PM Aaron Marcuse-Kubitza

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

13495 05/20/2014 05:21 PM Aaron Marcuse-Kubitza

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)

13493 05/19/2014 09:08 PM Aaron Marcuse-Kubitza

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

13492 05/19/2014 08:52 PM Aaron Marcuse-Kubitza

schemas/util.sql: added relation_exists()

13491 05/19/2014 08:27 PM Aaron Marcuse-Kubitza

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

13490 05/19/2014 08:24 PM Aaron Marcuse-Kubitza

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

13489 05/19/2014 08:21 PM Aaron Marcuse-Kubitza

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

13488 05/19/2014 07:50 PM Aaron Marcuse-Kubitza

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

13487 05/19/2014 07:22 PM Aaron Marcuse-Kubitza

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

13486 05/19/2014 07:16 PM Aaron Marcuse-Kubitza

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

13485 05/19/2014 02:07 AM Aaron Marcuse-Kubitza

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

13484 05/19/2014 01:36 AM Aaron Marcuse-Kubitza

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().

13483 05/19/2014 12:48 AM Aaron Marcuse-Kubitza

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

13482 05/19/2014 12:29 AM Aaron Marcuse-Kubitza

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

13481 05/19/2014 12:24 AM Aaron Marcuse-Kubitza

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

13480 05/19/2014 12:20 AM Aaron Marcuse-Kubitza

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

13479 05/19/2014 12:16 AM Aaron Marcuse-Kubitza

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

13478 05/19/2014 12:06 AM Aaron Marcuse-Kubitza

schemas/util.sql: added show_set_comment(regclass)

13477 05/18/2014 11:57 PM Aaron Marcuse-Kubitza

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

13476 05/18/2014 11:48 PM Aaron Marcuse-Kubitza

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

13475 05/17/2014 06:26 PM Aaron Marcuse-Kubitza

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

13474 05/17/2014 06:22 PM Aaron Marcuse-Kubitza

schemas/util.sql: added mk_set_comment()

13471 05/17/2014 05:36 PM Aaron Marcuse-Kubitza

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

13470 05/17/2014 05:27 PM Aaron Marcuse-Kubitza

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()

13469 05/17/2014 05:25 PM Aaron Marcuse-Kubitza

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

13468 05/17/2014 05:24 PM Aaron Marcuse-Kubitza

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

13467 05/17/2014 05:10 PM Aaron Marcuse-Kubitza

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

13456 05/13/2014 11:19 AM Aaron Marcuse-Kubitza

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

13455 05/13/2014 11:00 AM Aaron Marcuse-Kubitza

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

13454 05/13/2014 09:43 AM Aaron Marcuse-Kubitza

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

13453 05/13/2014 09:25 AM Aaron Marcuse-Kubitza

schemas/util.sql: added array_reverse()

13452 05/13/2014 09:25 AM Aaron Marcuse-Kubitza

schemas/util.sql: added in_reverse()

13451 05/13/2014 08:39 AM Aaron Marcuse-Kubitza

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

13450 05/13/2014 08:34 AM Aaron Marcuse-Kubitza

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

13449 05/13/2014 08:33 AM Aaron Marcuse-Kubitza

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

13448 05/13/2014 08:27 AM Aaron Marcuse-Kubitza

schemas/util.sql: added debug_print_var()

13447 05/13/2014 07:06 AM Aaron Marcuse-Kubitza

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

13446 05/13/2014 06:59 AM Aaron Marcuse-Kubitza

schemas/util.sql: added debug_print_value()

13445 05/13/2014 05:45 AM Aaron Marcuse-Kubitza

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

13444 05/13/2014 04:50 AM Aaron Marcuse-Kubitza

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

13443 05/13/2014 04:09 AM Aaron Marcuse-Kubitza

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

13442 05/13/2014 03:50 AM Aaron Marcuse-Kubitza

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)

13441 05/13/2014 03:46 AM Aaron Marcuse-Kubitza

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.

13440 05/13/2014 03:28 AM Aaron Marcuse-Kubitza

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)

13439 05/13/2014 03:13 AM Aaron Marcuse-Kubitza

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.*

13438 05/13/2014 02:53 AM Aaron Marcuse-Kubitza

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

13435 05/12/2014 04:28 PM Aaron Marcuse-Kubitza

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

13433 05/10/2014 09:17 PM Aaron Marcuse-Kubitza

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

13432 05/10/2014 09:13 PM Aaron Marcuse-Kubitza

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

13431 05/10/2014 08:49 PM Aaron Marcuse-Kubitza

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

13430 05/10/2014 08:10 PM Aaron Marcuse-Kubitza

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

13420 05/09/2014 01:35 AM Aaron Marcuse-Kubitza

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

13403 05/03/2014 03:10 PM Aaron Marcuse-Kubitza

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

13398 05/03/2014 01:37 AM Aaron Marcuse-Kubitza

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

13397 05/03/2014 01:28 AM Aaron Marcuse-Kubitza

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

13394 05/02/2014 11:34 PM Aaron Marcuse-Kubitza

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

13390 05/02/2014 10:01 PM Aaron Marcuse-Kubitza

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

13389 05/02/2014 09:54 PM Aaron Marcuse-Kubitza

schemas/public_.sql: added _plots_20_tnrs_input_names, _plots_21_tnrs_output_names

13388 05/02/2014 06:17 PM Aaron Marcuse-Kubitza

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

13387 05/02/2014 04:53 PM Aaron Marcuse-Kubitza

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

13386 05/02/2014 04:50 PM Aaron Marcuse-Kubitza

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

13385 05/02/2014 04:14 PM Aaron Marcuse-Kubitza

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

13384 05/02/2014 03:53 PM Aaron Marcuse-Kubitza

schemas/util.sql: added loop_ignore_errors()

13383 05/01/2014 10:38 PM Aaron Marcuse-Kubitza

schemas/public_.sql: added output_queries(prefix)

13382 05/01/2014 10:27 PM Aaron Marcuse-Kubitza

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

13381 05/01/2014 10:13 PM Aaron Marcuse-Kubitza

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

13380 05/01/2014 10:05 PM Aaron Marcuse-Kubitza

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

13379 05/01/2014 10:03 PM Aaron Marcuse-Kubitza

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

13378 05/01/2014 08:55 PM Aaron Marcuse-Kubitza

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

13377 05/01/2014 08:42 PM Aaron Marcuse-Kubitza

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

13376 05/01/2014 08:06 PM Aaron Marcuse-Kubitza

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()