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# Date Author Comment
13585 06/01/2014 05:00 AM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: tnrs__match_num__fill(): only fill if not set, to support case where tnrs is being restored from a .sql file (where match_num is already set)

13584 06/01/2014 04:36 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented runtime to add a constraint (3 min)

13583 06/01/2014 04:35 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: unique constraint on Name_submitted: added Name_matched to allow multiple matches per name, as is needed to implement #917

13582 06/01/2014 03:44 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented how to populate a new column

13581 06/01/2014 03:41 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: pkey: use match_num instead of Name_number to allow multiple matches per name, as is needed to implement #917

13580 05/31/2014 10:31 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs.match_num: made it NOT NULL now that it's populated

13579 05/31/2014 10:28 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: populate match_num

13578 05/31/2014 10:25 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: populate match_num

13577 05/31/2014 09:50 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented how to add and remove columns

13576 05/31/2014 08:58 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: made COMMENTs start on their own line, using the steps at wiki.vegpath.org/Postgres_queries#make-COMMENTs-start-on-their-own-line

13575 05/31/2014 08:58 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: made COMMENTs start on their own line, using the steps at wiki.vegpath.org/Postgres_queries#make-COMMENTs-start-on-their-own-line

13574 05/31/2014 08:11 PM Aaron Marcuse-Kubitza

inputs/test_taxonomic_names/_scrub/*: updated to TNRS schema

13573 05/31/2014 08:10 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: added match_num

13572 05/31/2014 08:06 PM Aaron Marcuse-Kubitza

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

13571 05/31/2014 08:03 PM Aaron Marcuse-Kubitza

schemas/Makefile: added back rename/%, which is used by `inputs/.TNRS/data.sql.run refresh`. updated it to use schema bundles.

13570 05/31/2014 06:44 PM Aaron Marcuse-Kubitza

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

13569 05/31/2014 06:29 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)

13568 05/31/2014 05:06 AM Aaron Marcuse-Kubitza

exports/2014-3-11.Jeff_Ott.climatic_range_determinants.csv.run: documented export_() runtime (11 min) and rowcount (11 million matching the filter criteria)

13567 05/30/2014 06:34 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)

13566 05/30/2014 06:22 PM Aaron Marcuse-Kubitza

schemas/util.sql: added seq__reset()

13565 05/30/2014 06:15 PM Aaron Marcuse-Kubitza

schemas/util.sql: added seq__create()

13564 05/30/2014 06:11 PM Aaron Marcuse-Kubitza

fix: schemas/util.sql: try_cast(), is_castable(): also catch invalid_schema_name, thrown by `'pg_temp.__'::regclass`

13563 05/30/2014 02:49 PM Aaron Marcuse-Kubitza

backups/TNRS.backup.md5: updated

13562 05/30/2014 07:50 AM Aaron Marcuse-Kubitza

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)

13561 05/30/2014 07:42 AM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: regenerated exports

13560 05/30/2014 07:39 AM Aaron Marcuse-Kubitza

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.

13559 05/30/2014 07:37 AM Aaron Marcuse-Kubitza

fix: lib/PostgreSQL-MySQL.csv: need to replace "double precision" with "double" to work with MySQL Workbench 5.2.47

13558 05/30/2014 06:58 AM Aaron Marcuse-Kubitza

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.

13557 05/30/2014 05:58 AM Aaron Marcuse-Kubitza

fix: schemas/vegbien.ERD.mwb: use schemas/vegbien.my.sql instead of schemas/vegbien.my.sql.changes.sql as the sync source

13556 05/30/2014 05:27 AM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: switched back to MySQL Workbench 6.1.6 version, which also works with MySQL Workbench 5.2.47

13555 05/30/2014 05:17 AM Aaron Marcuse-Kubitza

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

13554 05/30/2014 05:05 AM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: renamed to vegbien.ERD.MySQL_Workbench_6.1.6.mwb to differentiate the versions for different versions of MySQL Workbench

13553 05/30/2014 04:49 AM Aaron Marcuse-Kubitza

removed no longer used config/VirtualBox_VMs/VegCore ERD/. use the Ubuntu 14.04 VM instead, which now has the VegCore ERD setup.

13552 05/30/2014 04:48 AM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/Ubuntu 14.04/Ubuntu 14.04.vbox: added VegCore ERD setup

13551 05/30/2014 03:30 AM Aaron Marcuse-Kubitza

schemas/: svn:ignore *.changes.sql, needed for MySQL Workbench 6.1.6

13550 05/30/2014 03:30 AM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: updated

13549 05/30/2014 03:16 AM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: updated layout for MySQL Workbench 6.1.6, which uses a different line spacing

13548 05/29/2014 11:53 AM Aaron Marcuse-Kubitza

lib/tnrs.py: commented out the value of max_names that is not active, for clarity

13547 05/28/2014 03:54 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated: merged post-bootloader installation steps into one snapshot now that eth1 addition is successful

13546 05/28/2014 03:49 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated, which adds eth1

13545 05/28/2014 03:47 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/Ubuntu 12.04/Ubuntu 12.04.vbox: updated

13544 05/27/2014 11:12 PM Aaron Marcuse-Kubitza

lib/tnrs.py: sources: updated to list/sort order in issue #917

13543 05/27/2014 10:39 PM Aaron Marcuse-Kubitza

added exports/2014-3-11.Jeff_Ott.climatic_range_determinants.csv.run

13542 05/27/2014 10:38 PM Aaron Marcuse-Kubitza

schemas/public_.sql: added 2014-3-11.Jeff_Ott.climatic_range_determinants

13541 05/27/2014 10:17 PM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view: added scrubbed_taxon_name_with_author, needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)

13540 05/27/2014 10:13 PM Aaron Marcuse-Kubitza

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)

13539 05/27/2014 10:09 PM Aaron Marcuse-Kubitza

schemas/public_.sql: added scrubbed_specific_epithet, scrubbed_species_binomial, which are needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)

13538 05/27/2014 10:08 PM Aaron Marcuse-Kubitza

fix: schemas/public_.sql: sync_analytical_stem_to_view(): removed fkey to source.shortname because this prevents reloading individual datasources

13537 05/27/2014 09:19 PM Aaron Marcuse-Kubitza

added downloads/

13536 05/27/2014 03:27 AM Aaron Marcuse-Kubitza

schemas/public_.sql: added scrubbed_specific_epithet, scrubbed_species_binomial, which are needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)

13535 05/27/2014 03:21 AM Aaron Marcuse-Kubitza

fix: schemas/util.sql: mk_drop_from_create(): also support CREATE queries that include the SELECT statement on the same line as the CREATE

13534 05/27/2014 12:33 AM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view: scrubbed_morphospecies_binomial: use new taxon_scrub.scrubbed_morphospecies_binomial

13533 05/27/2014 12:28 AM Aaron Marcuse-Kubitza

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

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

13528 05/26/2014 11:20 PM Aaron Marcuse-Kubitza

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

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`

13523 05/23/2014 04:20 PM Aaron Marcuse-Kubitza

config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated

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

13521 05/23/2014 02:16 AM Aaron Marcuse-Kubitza

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

13520 05/22/2014 04:20 PM Aaron Marcuse-Kubitza

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

13519 05/22/2014 02:07 PM Aaron Marcuse-Kubitza

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

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()

13513 05/21/2014 05:58 PM Aaron Marcuse-Kubitza

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

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())

13500 05/21/2014 01:23 AM Aaron Marcuse-Kubitza

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

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)

13494 05/20/2014 02:39 PM Aaron Marcuse-Kubitza

/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

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()