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

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

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

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()

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())

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

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

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

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)

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.

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)

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.*

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: _plots_20_tnrs_names: changed to set of columns requested by Martha

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

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

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/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

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

schemas/public_.sql: added _plots_20_tnrs_input_names, _plots_21_tnrs_output_names

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

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

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

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()

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()

schemas/public_.sql: _km_to_m(): made it a wrapper around util._km_to_m() so this function is only in one place

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.

bugfix: inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13*: also need to include coordinate pairs which have one of their coordinates NULL, by using OR instead of AND

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

fix: schemas/vegbien.sql: public_validations schema comment: to remove a validations query so its columns can be changed: use rm_output_queries() rather than rm_query_view() because that also removes input queries

bugfix: schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: DISTINCT: added coordsaccuracy_m

bugfix: schemas/vegbien.sql: coordinates_unique: added coordsaccuracy_m

fix: schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: need to DISTINCT the values that are being counted, because the coordinates_unique unique constraint includes other columns as well, so there may be multiple instances of each lat/long

fix: schemas/vegbien.sql: specimens*_of_unique_verb_subsp_taxa_with_author: include only names with subspecies (filtering by taxonverbatim.subspecies rather than taxonlabel.taxonomicname)

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

fix: schemas/vegbien.sql: plots* with duplicated rows: removed duplicated rows

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

fix: schemas/vegbien.sql: _specimens_11_list_of_three_standard_political_divisions: use same column names as input query

schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: ran through pipeline

fix: schemas/vegbien.sql: _specimens_12_distinct_collector_name_collect_num_date_w_count: dateCollected: also need to convert to text in GROUP BY/ORDER BY

bugfix: schemas/vegbien.sql, inputs/NY/validations.sql, validation/aggregating/specimens/qualitative_validations_specimens.sql: _specimens_12_distinct_collector_name_collect_num_date_w_count: dateCollected: cast this to text rather than date because some values for this field are not valid dates and will throw an error if cast to date

schemas/vegbien.sql: _specimens_10_count_number_of_records_by_institution: ran through pipeline

bugfix: schemas/vegbien.sql, validation/aggregating/specimens/qualitative_validations_specimens.sql: _specimens_10_count_number_of_records_by_institution: need to dereference specimenreplicate.duplicate_institutions_sourcelist_id to the corresponding sourcelist.name

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: schema comment: documented how to run the validations. this information is also in the usage comment for public_validations.remake_diff_table(), but is copied here for easy reference.

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

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

fix: schemas/vegbien.sql: public_validations.rematerialize_out_view(text, regclass): run with join_collapse_limit = 1 to fix query planner issues. this option has been tested on the queries that do not yet use the standard join sequence (plots #11,12,13,14,16,17,18), and all of these queries also work fine with join_collapse_limit = 1. (the standard join sequence is used to ensure both correctness of the query and compatibility with join_collapse_limit = 1, but in some cases is not needed for join_collapse_limit.)

bugfix: schemas/vegbien.sql: schemas/vegbien.sql(): need to util.use_schema(schema_anchor) before initializing vars that use own-schema functions

schemas/vegbien.sql: updated _specimens_01_count_of_total_records_specimens_in_source_db

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: schema comment: changed "to sync the queries with schemas/vegbien.sql" to "to reset the queries to what's in schemas/vegbien.sql" for clarity

fix: schemas/vegbien.sql: schema comment: to reset the key and value columns for all validations queries: updated running of custom keys() functions to use keys() types instead

schemas/vegbien.sql: schema comment: to sync the queries with schemas/vegbien.sql: use new public_validations.rm_output_queries() instead of rm_all_queries() to leave the input queries in place

schemas/vegbien.sql: schema comment: documented how to reset the key and value columns for all validations queries

bugfix: schemas/vegbien.sql: rm_output_queries(): also need to include keys_* and values__* types, as these are also associated with the query

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

bugfix: schemas/vegbien.sql: public_validations.validation_views(): need to include views with letters after the query # (eg. _plots_06a_list_of_stems)

schemas/vegbien.sql: public_validations schema comment: added instructions to change the key and value columns for a validations query

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: public_validations: queries that use EXISTS: join locationevent.plot_id to plot.plot_id directly instead of going via location.plot_location_id

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: plot: removed explicit column lists added in the autorename of plot.location_id->plot_id

schemas/vegbien.sql: plot: renamed pkey to plot_id. note that the field is autorenamed in all validation views which use it.

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

bugfix: schemas/vegbien.sql: _plots_06_list_of_plots_with_stem_measurements: only include stemobservation records which have actual stem IDs, not merely stem-related measurements (DBH, etc.)

bugfix: schemas/vegbien.sql: _plots_06_list_of_plots_with_stem_measurements: LEFT JOIN to project instead of inner joining, to get Postgres to use the right query plan. this is the last change needed to make query #6 runnable.

bugfix: schemas/vegbien.sql: rematerialize_out_view(): run all queries with `SET enable_seqscan = off` to avoid slow query plans. this fixes _plots_06_list_of_plots_with_stem_measurements and significantly speeds up _plots_10_count_of_individuals_per_plot_in_each_project (and possibly others).

schemas/vegbien.sql: locationevent: documented `CREATE INDEX locationevent_place_visit_id` runtime (3 min)