fix: inputs/.TNRS/schema.sql: taxon_match: to populate a new column: also need to recluster table so rows are exported in sorted order

fix: inputs/.TNRS/schema.sql: taxon_match: cluster the table so the rows are always exported in the same order, even when an UPDATE statement is used to run triggers

inputs/.TNRS/schema.sql: added _accepted{genus,specific_epithet} derived column, using the steps at wiki.vegpath.org/Postgres_queries#maintaining-derived-column-formulas-across-column-renames

fix: inputs/.TNRS/schema.sql: taxon_match: added back * prefixes on TNRS-namespace column names

inputs/.TNRS/schema.sql: MatchedTaxon: taxon_best_match: don't alias to `s` since this is no longer a nested select

inputs/.TNRS/schema.sql: MatchedTaxon: nested select: use just taxon_best_match since this no longer performs renamings

inputs/.TNRS/schema.sql: MatchedTaxon: renamed output columns to match input columns, so that the nested select would not be performing any renamings

fix: inputs/.TNRS/schema.sql: MatchedTaxon: added all columns from taxon_match (some of them apparently hadn't been included in MatchedTaxon)

fix: inputs/.TNRS/schema.sql: reordered columns to match taxon_match

fix: inputs/.TNRS/schema.sql: MatchedTaxon: added all columns from taxon_match (some of them apparently hadn't been included in MatchedTaxon)

fix: inputs/.TNRS/schema.sql: added back Family_matched, which had gotten merged with Name_matched_accepted_family when TNRS temporarily stopped populating Name_matched_accepted_family

inputs/.TNRS/schema.sql: MatchedTaxon: taxonomicStatus: moved outside the inner SELECT so that the inner SELECT would consist solely of renamings

inputs/.TNRS/schema.sql: MatchedTaxon: removed unneeded "Name_matched." prefix on source-specific names (only the * is needed because there is only one table)

inputs/.TNRS/schema.sql: matchedFamily: just use Name_matched_accepted_family, because TNRS has now been reloaded so that the names that were missing this have it populated

inputs/.TNRS/schema.sql: taxon_match: taxon_match__valid_match: replaced with taxon_best_match__valid_match, which also applies taxon_best_match's filters, since taxon_match is now accessed through taxon_best_match

fix: inputs/.TNRS/schema.sql: MatchedTaxon: use taxon_best_match instead of taxon_match because this should provide only one match per taxon

inputs/.TNRS/schema.sql: added taxon_best_match view

inputs/.TNRS/schema.sql: taxon_match: added taxon_match__one_selected_match unique index

inputs/.TNRS/schema.sql: taxon_match__fill(): split into separate DECLARE blocks for each field for clarity

fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*

fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*

inputs/.TNRS/schema.sql: taxon_match: insert names via taxon_match_input auto-updatable view instead of directly into taxon_match, to allow the taxon_match columns to be renamed while still supporting inserts using the TNRS column names

inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name

bugfix: inputs/.TNRS/schema.sql: taxon_name_is_safe(): need to use `NOT (_ = ANY()) instead of ` != ANY`, because the != operator is applied to each element

inputs/.TNRS/schema.sql: tnrs: renamed to tnrs_match to distinguish it from other TNRS-related tables

inputs/.TNRS/schema.sql: `taxon_scrub.scrubbed_unique_taxon_name.*`: added to-modify instructions

inputs/.TNRS/schema.sql: *_modify(): merged these into the "to modify" instructions in the corresponding views, because there is no need to create a separate *_modify() function for every view now that their definitions are all the same

schemas/public_.sql, inputs/.TNRS/schema.sql: upgraded to Postgres 9.3.4 format, which removes trailing " "

inputs/.TNRS/schema.sql: unsafe_taxon_names(): removed the name with "spp." now that this TNRS bug (https://pods.iplantcollaborative.org/jira/browse/TNRS-193) has been fixed

inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()

inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()

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

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

bugfix: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): updated to include taxon_scrub derived fields

inputs/.TNRS/schema.sql: *_modify(): allow running without a view_query, as recreate_view() now supports this

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.)

fix: inputs/.TNRS/schema.sql: tnrs.tnrs__valid_match index: made it non-unique to allow multiple matches per name, as is needed to implement #917

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)

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

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: documented how to populate a new column

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: documented how to add and remove columns

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

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)

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)

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

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()

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

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

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: 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.

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: 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.

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.*

moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).

bugfix: inputs/.TNRS/schema.sql: scrubbed_family: Name_matched_accepted_family was missing from the TNRS results at one point, so we are now using Family_matched as a workaround to populate this. the workaround is for accepted names only, as no opinion names do not have an Accepted_name_family to prepend to the scrubbed name to parse.

inputs/.TNRS/schema.sql: reexported from live DB, which changes the element order

bugfix: inputs/.TNRS/schema.sql: granted bien_read SELECT access to derived views as well as the core tnrs table

inputs/.TNRS/schema.sql: updated runtime (30 min) and rowcount (+2 million)

fix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): is_valid_match: set this to false if Taxonomic_status is Invalid

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

inputs/.TNRS/schema.sql, data.sql: updated for PostgreSQL 9.3

inputs/.TNRS/schema.sql: tnrs_populate_fields(): regenerate the derived cols: updated runtime (40 min)

inputs/.TNRS/schema.sql: tnrs: removed no longer used Accepted_scientific_name. use scrubbed_unique_taxon_name instead.

inputs/.TNRS/schema.sql: MatchedTaxon, etc.: removed no longer used acceptedScientificName (from tnrs.Accepted_scientific_name). use scrubbed_unique_taxon_name instead.

inputs/.TNRS/schema.sql: removed no longer used AcceptedTaxon. use taxon_scrub.scrubbed_unique_taxon_name.* instead.

inputs/.TNRS/schema.sql: removed no longer used ScrubbedTaxon. use taxon_scrub instead.

inputs/.TNRS/schema.sql: added taxon_scrub, which combines ValidMatchedTaxon with scrubbed_unique_taxon_name.* instead of AcceptedTaxon

inputs/.TNRS/schema.sql: ValidMatchedTaxon: synced to MatchedTaxon

fix: inputs/.TNRS/schema.sql: scrubbed_taxon_name_with_author: renamed to scrubbed_unique_taxon_name because this also contains the family, and is therefore different from just the taxon name with author

inputs/.TNRS/schema.sql: MatchedTaxon: added scrubbed_taxon_name_with_author

inputs/.TNRS/schema.sql: tnrs: removed Is_homonym, since this did not take into account the never_homonym status (when the author disambiguates) or the ability of a non-homonym at a lower rank to override a homonym at a higher rank. taking these into account just produces the value of is_valid_match.

inputs/.TNRS/schema.sql: tnrs: removed Is_plant, since this functionality is now provided by is_valid_match. note that whether a name is a plant is not meaningful for TNRS, because it can match only plant names (thus a "non-plant" is actually a non-match).

inputs/.TNRS/schema.sql: tnrs: added scrubbed_taxon_name_with_author derived column, which uses the matched name when an accepted name is not available

inputs/.TNRS/schema.sql: tnrs: removed no longer used Max_score. use is_valid_match to determine validity instead.

bugfix: lib/runscripts/file.pg.sql.run: export_(): exclude Source and related tables so that these will be re-created by the staging tables installation instead, ensuring that they are always in sync with the Source/ subdir

inputs/.TNRS/schema.sql: removed no longer used score_ok(). use tnrs.Is_plant instead. (the threshold is still documented in tnrs_populate_fields().)

inputs/.TNRS/schema.sql: tnrs_populate_fields(): is_valid_match: don't consider Max_score because Is_plant will always be false when the Max_score is insufficient (<0.8)

inputs/.TNRS/schema.sql: schema comment: added steps to remake schema.sql and back up the new TNRS schema. documented that these steps should be run on vegbiendev.

inputs/.TNRS/schema.sql: schema comment: added steps to determine what changes need to be made on vegbiendev

inputs/.TNRS/schema.sql: tnrs_populate_fields(): regenerate the derived cols: updated runtimes (~same)

inputs/.TNRS/schema.sql: tnrs: moved instructions to apply schema changes on vegbiendev to the TNRS schema, because this applies to all elements in the TNRS schema, not just the tnrs table

inputs/.TNRS/schema.sql: score_ok(): don't make it STRICT because this prevents it from being inlined

inputs/.TNRS/schema.sql: tnrs: removed no longer used tnrs_score_ok index. use tnrs__valid_match instead.

bugfix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): is_valid_match: documented that this excludes homonyms because these are not valid matches (i.e. TNRS provides a name, but the name is not meaningful because it is not unambiguous)