schemas/public_.sql: analytical_stem_view: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database

schemas/public_.sql: analytical_stem_view: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database

schemas/public_.sql: analytical_stem_view: terms in normalized schemas: put the source name right next to the term name (instead of after the table name) so it's easy to find

schemas/public_.sql: analytical_stem_view: VegX terms: populated definitions

schemas/public_.sql: analytical_stem_view: VegX terms: referenced to the specific table/subpath that they are in

schemas/public_.sql: analytical_stem_view: populated definitions of linked DwC terms from DwC data dictionary

schemas/public_.sql: analytical_stem_view: renamed terms to link URLs, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#data-dictionary-rename-terms-to-link-URLs

schemas/public_.sql: analytical_stem_view: indicated provenance of the rest of the terms

schemas/public_.sql: analytical_stem_view: flagged the DwC terms

schemas/public_.sql: added plot.**.modify()

schemas/public_.sql: taxonlabel: added index on taxonomicname to facilitate retrieving rows from tnrs_input_name

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

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

schemas/public_.sql: sync_*(): renamed to *_modify() to facilitate finding these functions when modifying the corresponding view (using the new naming convention for a view's on-modify function)

fix: inputs/.TNRS/schema.sql: added back index on Name_submitted, which is needed for tnrs_input_name to work properly (now that there is no automatic index created by a unique constraint)

fix: inputs/.TNRS/schema.sql: tnrs: removed unique constraint on Name_submitted, Name_matched because there can be more than one match with the same Name_matched (but different accepted names, etc.)

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

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

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

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

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

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

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

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

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)

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

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

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

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()

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

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

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

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

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

schemas/public_.sql: added _plots_20_tnrs_input_names, _plots_21_tnrs_output_names

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

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

schemas/public_.sql: added output_queries(prefix)

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

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

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

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

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

fix: lib/PostgreSQL-MySQL.csv: preserve schema assignments by translating `SET search_path` to `USE`

schemas/Makefile: vegbien.sql: also include geoscrub, TNRS schemas, as requested in the 2014-04-10 conference call (wiki.vegpath.org/2014-04-10_conference_call#VegBIEN-schema). this involves having a separate public_.sql file for restoring the public schema.

inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: added breakdowns _specimens_13a_list_of_all_verbatim_lat_long, _specimens_13b_list_of_all_decimal_lat_long to help troubleshoot the diff

fix: inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: count lat/longs together instead of separately, because the DISTINCT is by coordinate pair, not individual coordinate value (which wouldn't make much sense)

bugfix: schemas/vegbien.sql: rm_output_queries(): need to account for the fact that util.truncated_prefixed_name_regexp() returns a whole-string regexp. this drops support for removing output queries with a particular group prefix, which we no longer use.

bugfix: schemas/vegbien.sql: rm_output_queries(): need to include relations whose names were truncated, as well

schemas/vegbien.sql: taxonverbatim: added subspecies, as decided in the conference call (wiki.vegpath.org/2014-04-10_conference_call#VegBIEN-schema-2)

schemas/vegbien.sql: specimens*: ran through pipeline

schemas/vegbien.sql: _specimens_16_list_distinct_specimen_descriptions: re-ran through pipeline after removing duplicated rows

schemas/vegbien.sql: rm_output_queries(): also support removing just a particular output query

schemas/vegbien.sql: _specimens_11_list_of_three_standard_political_divisions: ran through pipeline

schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: ran through pipeline

schemas/vegbien.sql: _specimens_10_count_number_of_records_by_institution: ran through pipeline

schemas/vegbien.sql: public_validations._specimens_*: added comments from validation/aggregating/specimens/qualitative_validations_specimens.sql

schemas/vegbien.sql: remake_diff_tables(schema text): removed bien2_traits runtime because this applies only to one datasource. the bien2_traits runtime is now documented in inputs/bien2_traits/run.

schemas/vegbien.sql: public_validations: specimens queries: added autogenerated ~type tables

schemas/vegbien.sql: public_validations: added specimens queries to pipeline

schemas/vegbien.sql: public_validations: added _specimens_01_count_of_total_records_specimens_in_source_db

schemas/vegbien.sql: specimenreplicate.institution_id: renamed to duplicate_institutions_sourcelist_id, as decided in the conference calls (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2)

schemas/vegbien.sql: _plots_08_list_of_plots_which_use_percent_cover, _plots_15_pct_cover_of_each_verb_taxon_in_each_plot_in_each_pro: reran with fixes, which removes the incorrectly auto-added copies columns. (they were only able to be auto-added because the tables had no rows.)

schemas/vegbien.sql: implemented _plots_19_count_of_censuses_per_plot_in_each_project

schemas/vegbien.sql: public_validations: regenerated ~type tables, which adds `copies` columns for queries with a mismatch in the # of occurrences of each row

schemas/vegbien.sql: implemented _plots_16_intercepts_for_each_verb_taxon_in_each_plot_each_proj

schemas/vegbien.sql: implemented _plots_09_list_of_plots_which_use_line_intercept

schemas/vegbien.sql: implemented _plots_08_list_of_plots_which_use_percent_cover

schemas/vegbien.sql: implemented _plots_07_list_of_plots_which_use_counts_of_indiv_per_species

schemas/vegbien.sql, inputs/SALVIAS/validations.sql: added _plots_06a_list_of_stems, for use in figuring out the diff in _plots_06_list_of_plots_with_stem_measurements

schemas/vegbien.sql: locationevent: added autopopulated plot_id column which points to the outermost plot of the locationevent's location

bugfix: schemas/vegbien.sql: locationevent: added missing fkey on place_visit_id

fix: schemas/vegbien.sql: locationevent: added locationevent_place_visit_id index to facilitate joins to place_visit_id in the validations queries

fix: schemas/vegbien.sql: location: added plot_source_id index to provide the equivalent of the location.source_id index for outer plots. this will help Postgres choose the right query plans in queries involving outer plots.

schemas/vegbien.sql: _plots_18_list_of_subplots_codes_for_each_plot_for_each_project: added ~type table

schemas/vegbien.sql: _plots_15_pct_cover_of_each_verb_taxon_in_each_plot_in_each_pro: added ~type table

schemas/vegbien.sql, inputs/SALVIAS/validations.sql: added _plots_10a_aggregate_observation_individual_counts, for use in debugging diffs in _plots_10_count_of_individuals_per_plot_in_each_proj

schemas/vegbien.sql: added place_visit view, analogous to plot but for top-level locationevents. this is needed by the SALVIAS validation queries.

schemas/vegbien.sql: locationevent: added locationevent_set_place_visit_id() trigger, analogous to location_set_plot_location_id() but for the locationevent nesting hierarchy. this is needed by the SALVIAS validation queries.

fix: schemas/vegbien.sql: location_set_plot_location_id(): removed incorrect comment that this is a pull-forward trigger

schemas/vegbien.sql: public_validations: re-auto-added keys(), values_() functions for all queries

schemas/vegbien.sql: public_validations: re-auto-added keys(), values_() functions for all queries

schemas/vegbien.sql: public_validations: auto-added values_() functions for all queries

schemas/vegbien.sql: public_validations: auto-added keys() functions for all queries

schemas/vegbien.sql: synced with DB, which reorders ~type tables

bugfix: schemas/vegbien.sql: added back keys() matchup functions, which get cascadingly deleted when the queries are re-created to change column names, etc. note that this causes the associated ~type tables to sort before them.

schemas/vegbien.sql: added new ~type tables

schemas/vegbien.sql: rm_query_group(): support removing all validations as well as just those with a particular group prefix (and renamed to rm_output_queries())

schemas/vegbien.sql: synced with DB, which reorders ~type tables

fix: schemas/vegbien.sql: added back traits* ~type tables

fix: schemas/vegbien.sql: plots* validation queries: renamed plot_code columns (with names plotcode, plotCode, SiteCode) to match the input queries (plot_code)

schemas/vegbien.sql: top_plot view: renamed to plot, as requested by Brad (wiki.vegpath.org/2014-02-27_conference_call#schema-changes)

schemas/vegbien.sql: location.top_plot: renamed to plot_location_id, as requested by Brad (wiki.vegpath.org/2014-02-27_conference_call#schema-changes)

bugfix: *.sql: public.source_by_shortname(): need to wrap it in a nested SELECT because Postgres incorrectly does not constant-fold (inline) it, leading to a slowdown when it is therefore run many times. this is done using the steps at wiki.vegpath.org/Postgres_queries#wrap-function-call-in-nested-SELECT .

schemas/vegbien.sql: source_by_shortname(): documented that it must be run as a nested SELECT, because otherwise Postgres will not inline it. not inlining causes the query to be run for each row in a table of potentially millions, and creates a significant slowdown (eg. >1.5 hours for SALVIAS._plots_06_list_of_plots_with_stem_measurements)

fix: schemas/vegbien.sql: location: added index on top_plot

fix: schemas/vegbien.sql: _plots_06_list_of_plots_with_stem_measurements: changed columns to match input query