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--
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-- PostgreSQL database dump
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--
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SET statement_timeout = 0;
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SET lock_timeout = 0;
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SET client_encoding = 'UTF8';
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SET standard_conforming_strings = on;
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SET check_function_bodies = false;
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SET client_min_messages = warning;
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--
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-- Name: TNRS; Type: SCHEMA; Schema: -; Owner: -
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--
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--CREATE SCHEMA "TNRS";
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--
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-- Name: SCHEMA "TNRS"; Type: COMMENT; Schema: -; Owner: -
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--
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COMMENT ON SCHEMA "TNRS" IS '
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IMPORTANT: when changing this schema, you must also make the same changes on vegbiendev:
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on vegbiendev:
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# back up existing TNRS schema (in case of an accidental incorrect change):
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$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")
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$ svn up
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$ svn di
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# make the changes shown in the diff
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## to change column types:
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SELECT util.set_col_types(''"TNRS".taxon_match'', ARRAY[
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(''col'', ''new_type'')
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]::util.col_cast[]); -- runtime: 9 min ("531282 ms")
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$ rm=1 inputs/.TNRS/schema.sql.run
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# repeat until `svn di` shows no diff
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# back up new TNRS schema:
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$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")
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';
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SET search_path = "TNRS", pg_catalog;
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--
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-- Name: batch__fill(); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION batch__fill() RETURNS trigger
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LANGUAGE plpgsql
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AS $$
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BEGIN
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new.id_by_time = new.time_submitted;
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new.id = COALESCE(new.id, new.id_by_time);
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RETURN new;
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END;
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$$;
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--
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-- Name: family_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION family_is_homonym(family text) RETURNS boolean
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LANGUAGE sql STABLE STRICT
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AS $_$
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SELECT EXISTS(SELECT * FROM "IRMNG".family_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
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$_$;
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--
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-- Name: genus_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION genus_is_homonym(genus text) RETURNS boolean
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LANGUAGE sql STABLE STRICT
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AS $_$
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SELECT EXISTS(SELECT * FROM "IRMNG".genus_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
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$_$;
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--
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-- Name: map_taxonomic_status(text, text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION map_taxonomic_status(taxonomic_status_verbatim text, accepted_taxon_name_no_author text) RETURNS text
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LANGUAGE sql IMMUTABLE
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AS $_$
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/* from http://wiki.vegpath.org/2013-11-14_conference_call#taxonomic-fields:
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"taxonomic_status should be accepted instead of synonym when an accepted name is
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available (this is not always the case when a name is marked as a synonym)" */
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SELECT CASE WHEN $2 IS NOT NULL THEN 'accepted' ELSE lower($1) END
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$_$;
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--
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-- Name: taxon_match__batch_begin(); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION taxon_match__batch_begin() RETURNS trigger
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LANGUAGE plpgsql
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AS $$
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BEGIN
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PERFORM util.seq__reset('pg_temp.taxon_match__match_num__seq', 0);
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RETURN NULL;
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END;
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$$;
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--
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-- Name: taxon_match__fill(); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION taxon_match__fill() RETURNS trigger
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LANGUAGE plpgsql
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AS $$
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BEGIN
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DECLARE
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"Specific_epithet_is_plant" boolean :=
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(CASE
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WHEN new."*Infraspecific_epithet_matched" IS NOT NULL
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OR new."*Infraspecific_epithet_2_matched" IS NOT NULL
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OR new."*Specific_epithet_score" >= 0.9 -- fuzzy match
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THEN true
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ELSE NULL -- ambiguous
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END);
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never_homonym boolean = COALESCE(new."*Author_score" >= 0.6, false);
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-- author disambiguates
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family_is_homonym boolean = NOT never_homonym
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AND "TNRS".family_is_homonym(new."*Family_matched");
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genus_is_homonym boolean = NOT never_homonym
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AND "TNRS".genus_is_homonym(new."*Genus_matched");
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BEGIN
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/* exclude homonyms because these are not valid matches (TNRS provides a
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name, but the name is not meaningful because it is not unambiguous) */
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new.is_valid_match = new."*Taxonomic_status" != 'Invalid'
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AND COALESCE(CASE
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WHEN new."*Family_score" = 1 AND NOT family_is_homonym -- exact match
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THEN true
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ELSE -- consider genus
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(CASE
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WHEN new."*Genus_score" = 1 -- exact match
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THEN
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(CASE
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WHEN NOT genus_is_homonym THEN true
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ELSE "Specific_epithet_is_plant"
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END)
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WHEN new."*Genus_score" >= 0.85 -- fuzzy match
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THEN "Specific_epithet_is_plant"
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ELSE NULL -- ambiguous
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END)
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END, false);
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END;
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DECLARE
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matched_taxon_name_with_author text = NULLIF(concat_ws(' '
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, NULLIF(NULLIF(new."*Name_matched_accepted_family", 'Unknown'),
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new."*Name_matched")
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, NULLIF(new."*Name_matched", 'No suitable matches found.')
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, new."*Name_matched_author"
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), '');
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accepted_taxon_name_with_author text = NULLIF(concat_ws(' '
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, NULLIF(NULLIF(new."*Accepted_name_family", 'Unknown'),
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new."*Accepted_name")
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, new."*Accepted_name"
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, new."*Accepted_name_author"
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), '');
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BEGIN
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new.scrubbed_unique_taxon_name = COALESCE(
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accepted_taxon_name_with_author, matched_taxon_name_with_author);
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END;
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RETURN new;
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END;
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$$;
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--
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-- Name: FUNCTION taxon_match__fill(); Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON FUNCTION taxon_match__fill() IS '
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IMPORTANT: when changing this function, you must regenerate the derived cols:
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UPDATE "TNRS".taxon_match SET "Name_submitted" = "Name_submitted"
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runtime: 30 min ("5564082 rows affected, 1918900 ms execution time")
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VACUUM ANALYZE "TNRS".taxon_match -- to remove previous rows
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runtime: 1.5 min ("92633 ms")
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';
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--
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-- Name: taxon_match__fill_derived(); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION taxon_match__fill_derived() RETURNS trigger
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LANGUAGE plpgsql
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AS $$
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BEGIN
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new."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT
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("*Genus_matched" || ' '::text) || "*Specific_epithet_matched"
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FROM (SELECT new.*) new);
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new."[matched_]scientificName[_with_author]__@DwC__@vegpath.org" = (SELECT
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"*Name_matched" || COALESCE((' '::text || "*Name_matched_author"), ''::text)
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FROM (SELECT new.*) new);
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new.matched_has_accepted = (SELECT
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"*Accepted_name" IS NOT NULL
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FROM (SELECT new.*) new);
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new."__accepted_{genus,specific_epithet}" = (SELECT
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regexp_split_to_array("*Accepted_name_species", ' '::text)
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FROM (SELECT new.*) new);
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new."[accepted_]genus__@DwC__@vegpath.org" = (SELECT
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"__accepted_{genus,specific_epithet}"[1]
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FROM (SELECT new.*) new);
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new."[accepted_]specificEpithet__@DwC__@vegpath.org" = (SELECT
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"__accepted_{genus,specific_epithet}"[2]
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FROM (SELECT new.*) new);
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new.__accepted_infraspecific_label = (SELECT
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ltrim(NULLIF(util.remove_prefix("*Accepted_name_species", "*Accepted_name", require := true), ''::text), ' '::text)
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FROM (SELECT new.*) new);
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new."__accepted_infraspecific_{rank,epithet}" = (SELECT
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regexp_split_to_array(__accepted_infraspecific_label, ' '::text)
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FROM (SELECT new.*) new);
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new."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" = (SELECT
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"__accepted_infraspecific_{rank,epithet}"[1]
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FROM (SELECT new.*) new);
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new."[accepted_]infraspecificEpithet__@DwC__@vegpath.org" = (SELECT
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"__accepted_infraspecific_{rank,epithet}"[2]
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FROM (SELECT new.*) new);
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new."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org" = (SELECT
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"*Accepted_name" || COALESCE((' '::text || "*Accepted_name_author"), ''::text)
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FROM (SELECT new.*) new);
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new."[scrubbed_]taxonRank__@DwC__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "*Accepted_name_rank"
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ELSE "*Name_matched_rank"
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END
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FROM (SELECT new.*) new);
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new."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "*Accepted_name_family"
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ELSE "*Name_matched_accepted_family"
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END
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FROM (SELECT new.*) new);
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new."[scrubbed_]genus__@DwC__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "[accepted_]genus__@DwC__@vegpath.org"
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ELSE "*Genus_matched"
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END
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FROM (SELECT new.*) new);
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new."[scrubbed_]specificEpithet__@DwC__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
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ELSE "*Specific_epithet_matched"
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END
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FROM (SELECT new.*) new);
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new."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "*Accepted_name_species"
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ELSE "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"
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END
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FROM (SELECT new.*) new);
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new."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"
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ELSE "*Infraspecific_rank"
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END
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FROM (SELECT new.*) new);
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new."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
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ELSE "*Infraspecific_epithet_matched"
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END
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FROM (SELECT new.*) new);
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new."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "*Accepted_name"
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ELSE "*Name_matched"
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END
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FROM (SELECT new.*) new);
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new."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "*Accepted_name_author"
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ELSE "*Name_matched_author"
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END
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FROM (SELECT new.*) new);
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new."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" = (SELECT
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CASE
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WHEN matched_has_accepted THEN "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"
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ELSE "[matched_]scientificName[_with_author]__@DwC__@vegpath.org"
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309
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END
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FROM (SELECT new.*) new);
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311
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312
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RETURN new;
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313
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END;
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314
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$$;
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315
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316
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317
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--
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318
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-- Name: FUNCTION taxon_match__fill_derived(); Type: COMMENT; Schema: TNRS; Owner: -
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319
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--
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320
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321
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COMMENT ON FUNCTION taxon_match__fill_derived() IS '
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322
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autogenerated, do not edit
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323
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324
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to regenerate:
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325
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SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
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';
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328
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--
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-- Name: taxon_match__match_num__fill(); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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332
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333
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CREATE FUNCTION taxon_match__match_num__fill() RETURNS trigger
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334
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LANGUAGE plpgsql
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335
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AS $$
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336
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BEGIN
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337
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IF new.match_num IS NULL THEN
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new.match_num = "TNRS".taxon_match__match_num__next();
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END IF;
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340
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RETURN new;
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341
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END;
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342
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$$;
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343
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344
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345
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--
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346
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-- Name: taxon_match__match_num__next(); Type: FUNCTION; Schema: TNRS; Owner: -
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347
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--
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348
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349
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CREATE FUNCTION taxon_match__match_num__next() RETURNS bigint
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350
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LANGUAGE sql
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351
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AS $$
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352
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SELECT nextval('pg_temp.taxon_match__match_num__seq');
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353
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$$;
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354
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355
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356
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--
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357
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-- Name: taxon_match_input__copy_to__insert(); Type: FUNCTION; Schema: TNRS; Owner: -
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358
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--
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359
|
|
|
360
|
CREATE FUNCTION taxon_match_input__copy_to__insert() RETURNS trigger
|
|
361
|
LANGUAGE plpgsql
|
|
362
|
AS $$
|
|
363
|
BEGIN
|
|
364
|
INSERT INTO "TNRS".taxon_match_input SELECT new.*;
|
|
365
|
RETURN NULL;
|
|
366
|
END;
|
|
367
|
$$;
|
|
368
|
|
|
369
|
|
|
370
|
--
|
|
371
|
-- Name: taxon_name_is_safe(text); Type: FUNCTION; Schema: TNRS; Owner: -
|
|
372
|
--
|
|
373
|
|
|
374
|
CREATE FUNCTION taxon_name_is_safe(taxon_name text) RETURNS boolean
|
|
375
|
LANGUAGE sql IMMUTABLE
|
|
376
|
AS $_$
|
|
377
|
SELECT NOT ($1 = ANY("TNRS".unsafe_taxon_names()))
|
|
378
|
$_$;
|
|
379
|
|
|
380
|
|
|
381
|
--
|
|
382
|
-- Name: unsafe_taxon_names(); Type: FUNCTION; Schema: TNRS; Owner: -
|
|
383
|
--
|
|
384
|
|
|
385
|
CREATE FUNCTION unsafe_taxon_names() RETURNS text[]
|
|
386
|
LANGUAGE sql IMMUTABLE
|
|
387
|
AS $$
|
|
388
|
SELECT ARRAY[
|
|
389
|
]::text[]
|
|
390
|
$$;
|
|
391
|
|
|
392
|
|
|
393
|
SET default_tablespace = '';
|
|
394
|
|
|
395
|
SET default_with_oids = false;
|
|
396
|
|
|
397
|
--
|
|
398
|
-- Name: taxon_match; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
|
399
|
--
|
|
400
|
|
|
401
|
CREATE TABLE taxon_match (
|
|
402
|
batch text DEFAULT now() NOT NULL,
|
|
403
|
match_num integer NOT NULL,
|
|
404
|
"*Name_number" integer NOT NULL,
|
|
405
|
"*Name_submitted" text NOT NULL,
|
|
406
|
"*Overall_score" double precision,
|
|
407
|
"*Name_matched" text,
|
|
408
|
"*Name_matched_rank" text,
|
|
409
|
"*Name_score" double precision,
|
|
410
|
"*Name_matched_author" text,
|
|
411
|
"*Name_matched_url" text,
|
|
412
|
"*Author_matched" text,
|
|
413
|
"*Author_score" double precision,
|
|
414
|
"*Family_matched" text,
|
|
415
|
"*Family_score" double precision,
|
|
416
|
"*Name_matched_accepted_family" text,
|
|
417
|
"*Genus_matched" text,
|
|
418
|
"*Genus_score" double precision,
|
|
419
|
"*Specific_epithet_matched" text,
|
|
420
|
"*Specific_epithet_score" double precision,
|
|
421
|
"*Infraspecific_rank" text,
|
|
422
|
"*Infraspecific_epithet_matched" text,
|
|
423
|
"*Infraspecific_epithet_score" double precision,
|
|
424
|
"*Infraspecific_rank_2" text,
|
|
425
|
"*Infraspecific_epithet_2_matched" text,
|
|
426
|
"*Infraspecific_epithet_2_score" double precision,
|
|
427
|
"*Annotations" text,
|
|
428
|
"*Unmatched_terms" text,
|
|
429
|
"*Taxonomic_status" text,
|
|
430
|
"*Accepted_name" text,
|
|
431
|
"*Accepted_name_author" text,
|
|
432
|
"*Accepted_name_rank" text,
|
|
433
|
"*Accepted_name_url" text,
|
|
434
|
"*Accepted_name_species" text,
|
|
435
|
"*Accepted_name_family" text,
|
|
436
|
"*Selected" text,
|
|
437
|
"*Source" text,
|
|
438
|
"*Warnings" text,
|
|
439
|
"*Accepted_name_lsid" text,
|
|
440
|
is_valid_match boolean NOT NULL,
|
|
441
|
scrubbed_unique_taxon_name text,
|
|
442
|
"[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
|
443
|
"[matched_]scientificName[_with_author]__@DwC__@vegpath.org" text,
|
|
444
|
matched_has_accepted boolean,
|
|
445
|
"__accepted_{genus,specific_epithet}" text[],
|
|
446
|
"[accepted_]genus__@DwC__@vegpath.org" text,
|
|
447
|
"[accepted_]specificEpithet__@DwC__@vegpath.org" text,
|
|
448
|
__accepted_infraspecific_label text,
|
|
449
|
"__accepted_infraspecific_{rank,epithet}" text[],
|
|
450
|
"[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" text,
|
|
451
|
"[accepted_]infraspecificEpithet__@DwC__@vegpath.org" text,
|
|
452
|
"[accepted_]scientificName[_with_author]__@DwC__@vegpath.org" text,
|
|
453
|
"[scrubbed_]taxonRank__@DwC__@vegpath.org" text,
|
|
454
|
"[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
|
455
|
"[scrubbed_]genus__@DwC__@vegpath.org" text,
|
|
456
|
"[scrubbed_]specificEpithet__@DwC__@vegpath.org" text,
|
|
457
|
"[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
|
458
|
"[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" text,
|
|
459
|
"[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" text,
|
|
460
|
"[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
|
461
|
"[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
|
462
|
"[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" text,
|
|
463
|
CONSTRAINT "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" CHECK ((NOT ("[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" IS DISTINCT FROM "__accepted_infraspecific_{rank,epithet}"[1]))),
|
|
464
|
CONSTRAINT "[accepted_]genus__@DwC__@vegpath.org" CHECK ((NOT ("[accepted_]genus__@DwC__@vegpath.org" IS DISTINCT FROM "__accepted_{genus,specific_epithet}"[1]))),
|
|
465
|
CONSTRAINT "[accepted_]infraspecificEpithet__@DwC__@vegpath.org" CHECK ((NOT ("[accepted_]infraspecificEpithet__@DwC__@vegpath.org" IS DISTINCT FROM "__accepted_infraspecific_{rank,epithet}"[2]))),
|
|
466
|
CONSTRAINT "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org" CHECK ((NOT ("[accepted_]scientificName[_with_author]__@DwC__@vegpath.org" IS DISTINCT FROM ("*Accepted_name" || COALESCE((' '::text || "*Accepted_name_author"), ''::text))))),
|
|
467
|
CONSTRAINT "[accepted_]specificEpithet__@DwC__@vegpath.org" CHECK ((NOT ("[accepted_]specificEpithet__@DwC__@vegpath.org" IS DISTINCT FROM "__accepted_{genus,specific_epithet}"[2]))),
|
|
468
|
CONSTRAINT "[matched_]scientificName[_with_author]__@DwC__@vegpath.org" CHECK ((NOT ("[matched_]scientificName[_with_author]__@DwC__@vegpath.org" IS DISTINCT FROM ("*Name_matched" || COALESCE((' '::text || "*Name_matched_author"), ''::text))))),
|
|
469
|
CONSTRAINT "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org" CHECK ((NOT ("[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org" IS DISTINCT FROM (("*Genus_matched" || ' '::text) || "*Specific_epithet_matched")))),
|
|
470
|
CONSTRAINT "[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" IS DISTINCT FROM
|
|
471
|
CASE
|
|
472
|
WHEN matched_has_accepted THEN "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"
|
|
473
|
ELSE "*Infraspecific_rank"
|
|
474
|
END))),
|
|
475
|
CONSTRAINT "[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" IS DISTINCT FROM
|
|
476
|
CASE
|
|
477
|
WHEN matched_has_accepted THEN "*Accepted_name_author"
|
|
478
|
ELSE "*Name_matched_author"
|
|
479
|
END))),
|
|
480
|
CONSTRAINT "[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" IS DISTINCT FROM
|
|
481
|
CASE
|
|
482
|
WHEN matched_has_accepted THEN "*Accepted_name_family"
|
|
483
|
ELSE "*Name_matched_accepted_family"
|
|
484
|
END))),
|
|
485
|
CONSTRAINT "[scrubbed_]genus__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]genus__@DwC__@vegpath.org" IS DISTINCT FROM
|
|
486
|
CASE
|
|
487
|
WHEN matched_has_accepted THEN "[accepted_]genus__@DwC__@vegpath.org"
|
|
488
|
ELSE "*Genus_matched"
|
|
489
|
END))),
|
|
490
|
CONSTRAINT "[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" IS DISTINCT FROM
|
|
491
|
CASE
|
|
492
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
|
493
|
ELSE "*Infraspecific_epithet_matched"
|
|
494
|
END))),
|
|
495
|
CONSTRAINT "[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" IS DISTINCT FROM
|
|
496
|
CASE
|
|
497
|
WHEN matched_has_accepted THEN "*Accepted_name"
|
|
498
|
ELSE "*Name_matched"
|
|
499
|
END))),
|
|
500
|
CONSTRAINT "[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" IS DISTINCT FROM
|
|
501
|
CASE
|
|
502
|
WHEN matched_has_accepted THEN "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"
|
|
503
|
ELSE "[matched_]scientificName[_with_author]__@DwC__@vegpath.org"
|
|
504
|
END))),
|
|
505
|
CONSTRAINT "[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" IS DISTINCT FROM
|
|
506
|
CASE
|
|
507
|
WHEN matched_has_accepted THEN "*Accepted_name_species"
|
|
508
|
ELSE "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"
|
|
509
|
END))),
|
|
510
|
CONSTRAINT "[scrubbed_]specificEpithet__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]specificEpithet__@DwC__@vegpath.org" IS DISTINCT FROM
|
|
511
|
CASE
|
|
512
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
|
513
|
ELSE "*Specific_epithet_matched"
|
|
514
|
END))),
|
|
515
|
CONSTRAINT "[scrubbed_]taxonRank__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]taxonRank__@DwC__@vegpath.org" IS DISTINCT FROM
|
|
516
|
CASE
|
|
517
|
WHEN matched_has_accepted THEN "*Accepted_name_rank"
|
|
518
|
ELSE "*Name_matched_rank"
|
|
519
|
END))),
|
|
520
|
CONSTRAINT __accepted_infraspecific_label CHECK ((NOT (__accepted_infraspecific_label IS DISTINCT FROM ltrim(NULLIF(util.remove_prefix("*Accepted_name_species", "*Accepted_name", require := true), ''::text), ' '::text)))),
|
|
521
|
CONSTRAINT "__accepted_infraspecific_{rank,epithet}" CHECK ((NOT ("__accepted_infraspecific_{rank,epithet}" IS DISTINCT FROM regexp_split_to_array(__accepted_infraspecific_label, ' '::text)))),
|
|
522
|
CONSTRAINT "__accepted_{genus,specific_epithet}" CHECK ((NOT ("__accepted_{genus,specific_epithet}" IS DISTINCT FROM regexp_split_to_array("*Accepted_name_species", ' '::text)))),
|
|
523
|
CONSTRAINT matched_has_accepted CHECK ((NOT (matched_has_accepted IS DISTINCT FROM ("*Accepted_name" IS NOT NULL))))
|
|
524
|
);
|
|
525
|
|
|
526
|
|
|
527
|
--
|
|
528
|
-- Name: TABLE taxon_match; Type: COMMENT; Schema: TNRS; Owner: -
|
|
529
|
--
|
|
530
|
|
|
531
|
COMMENT ON TABLE taxon_match IS '
|
|
532
|
whenever columns are renamed:
|
|
533
|
SELECT util.derived_cols_sync(''"TNRS".taxon_match'');
|
|
534
|
|
|
535
|
to remove columns or add columns at the end:
|
|
536
|
$ rm=1 inputs/.TNRS/data.sql.run
|
|
537
|
$ make schemas/remake
|
|
538
|
|
|
539
|
to add columns in the middle:
|
|
540
|
make the changes in inputs/.TNRS/schema.sql
|
|
541
|
$ inputs/.TNRS/data.sql.run refresh # re-run TNRS
|
|
542
|
$ make schemas/remake
|
|
543
|
|
|
544
|
to populate a new column:
|
|
545
|
ALTER TABLE "TNRS".taxon_match DISABLE TRIGGER taxon_match__fill; --speeds up update
|
|
546
|
UPDATE "TNRS".taxon_match SET "col" = value;
|
|
547
|
-- runtime: 30 min ("5564201 rows affected, 1624829 ms execution time")
|
|
548
|
CLUSTER "TNRS".taxon_match; -- ensure rows are exported in sorted order
|
|
549
|
ALTER TABLE "TNRS".taxon_match ENABLE TRIGGER taxon_match__fill;
|
|
550
|
VACUUM ANALYZE "TNRS".taxon_match --remove previous rows; runtime: 1.5 min ("92633 ms")
|
|
551
|
|
|
552
|
to add a constraint: runtime: 3 min ("173620 ms")
|
|
553
|
';
|
|
554
|
|
|
555
|
|
|
556
|
--
|
|
557
|
-- Name: COLUMN taxon_match."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
558
|
--
|
|
559
|
|
|
560
|
COMMENT ON COLUMN taxon_match."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
|
561
|
= ("*Genus_matched" || '' ''::text) || "*Specific_epithet_matched"
|
|
562
|
|
|
563
|
derived column
|
|
564
|
|
|
565
|
to modify expr:
|
|
566
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org'')::util.col, $$("*Genus_matched" || '' ''::text) || "*Specific_epithet_matched"$$)::util.derived_col_def);
|
|
567
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
568
|
|
|
569
|
to rename:
|
|
570
|
# rename column
|
|
571
|
# rename CHECK constraint
|
|
572
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
573
|
';
|
|
574
|
|
|
575
|
|
|
576
|
--
|
|
577
|
-- Name: COLUMN taxon_match."[matched_]scientificName[_with_author]__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
578
|
--
|
|
579
|
|
|
580
|
COMMENT ON COLUMN taxon_match."[matched_]scientificName[_with_author]__@DwC__@vegpath.org" IS '
|
|
581
|
= "*Name_matched" || COALESCE(('' ''::text || "*Name_matched_author"), ''''::text)
|
|
582
|
|
|
583
|
derived column
|
|
584
|
|
|
585
|
to modify expr:
|
|
586
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[matched_]scientificName[_with_author]__@DwC__@vegpath.org'')::util.col, $$"*Name_matched" || COALESCE(('' ''::text || "*Name_matched_author"), ''''::text)$$)::util.derived_col_def);
|
|
587
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
588
|
|
|
589
|
to rename:
|
|
590
|
# rename column
|
|
591
|
# rename CHECK constraint
|
|
592
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
593
|
';
|
|
594
|
|
|
595
|
|
|
596
|
--
|
|
597
|
-- Name: COLUMN taxon_match.matched_has_accepted; Type: COMMENT; Schema: TNRS; Owner: -
|
|
598
|
--
|
|
599
|
|
|
600
|
COMMENT ON COLUMN taxon_match.matched_has_accepted IS '
|
|
601
|
= "*Accepted_name" IS NOT NULL
|
|
602
|
|
|
603
|
derived column
|
|
604
|
|
|
605
|
to modify expr:
|
|
606
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''matched_has_accepted'')::util.col, $$"*Accepted_name" IS NOT NULL$$)::util.derived_col_def);
|
|
607
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
608
|
|
|
609
|
to rename:
|
|
610
|
# rename column
|
|
611
|
# rename CHECK constraint
|
|
612
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
613
|
';
|
|
614
|
|
|
615
|
|
|
616
|
--
|
|
617
|
-- Name: COLUMN taxon_match."__accepted_{genus,specific_epithet}"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
618
|
--
|
|
619
|
|
|
620
|
COMMENT ON COLUMN taxon_match."__accepted_{genus,specific_epithet}" IS '
|
|
621
|
= regexp_split_to_array("*Accepted_name_species", '' ''::text)
|
|
622
|
|
|
623
|
derived column
|
|
624
|
|
|
625
|
to modify expr:
|
|
626
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''__accepted_{genus,specific_epithet}'')::util.col, $$regexp_split_to_array("*Accepted_name_species", '' ''::text)$$)::util.derived_col_def);
|
|
627
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
628
|
|
|
629
|
to rename:
|
|
630
|
# rename column
|
|
631
|
# rename CHECK constraint
|
|
632
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
633
|
';
|
|
634
|
|
|
635
|
|
|
636
|
--
|
|
637
|
-- Name: COLUMN taxon_match."[accepted_]genus__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
638
|
--
|
|
639
|
|
|
640
|
COMMENT ON COLUMN taxon_match."[accepted_]genus__@DwC__@vegpath.org" IS '
|
|
641
|
= "__accepted_{genus,specific_epithet}"[1]
|
|
642
|
|
|
643
|
derived column
|
|
644
|
|
|
645
|
to modify expr:
|
|
646
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[accepted_]genus__@DwC__@vegpath.org'')::util.col, $$"__accepted_{genus,specific_epithet}"[1]$$)::util.derived_col_def);
|
|
647
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
648
|
|
|
649
|
to rename:
|
|
650
|
# rename column
|
|
651
|
# rename CHECK constraint
|
|
652
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
653
|
';
|
|
654
|
|
|
655
|
|
|
656
|
--
|
|
657
|
-- Name: COLUMN taxon_match."[accepted_]specificEpithet__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
658
|
--
|
|
659
|
|
|
660
|
COMMENT ON COLUMN taxon_match."[accepted_]specificEpithet__@DwC__@vegpath.org" IS '
|
|
661
|
= "__accepted_{genus,specific_epithet}"[2]
|
|
662
|
|
|
663
|
derived column
|
|
664
|
|
|
665
|
to modify expr:
|
|
666
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[accepted_]specificEpithet__@DwC__@vegpath.org'')::util.col, $$"__accepted_{genus,specific_epithet}"[2]$$)::util.derived_col_def);
|
|
667
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
668
|
|
|
669
|
to rename:
|
|
670
|
# rename column
|
|
671
|
# rename CHECK constraint
|
|
672
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
673
|
';
|
|
674
|
|
|
675
|
|
|
676
|
--
|
|
677
|
-- Name: COLUMN taxon_match.__accepted_infraspecific_label; Type: COMMENT; Schema: TNRS; Owner: -
|
|
678
|
--
|
|
679
|
|
|
680
|
COMMENT ON COLUMN taxon_match.__accepted_infraspecific_label IS '
|
|
681
|
= ltrim(NULLIF(util.remove_prefix("*Accepted_name_species", "*Accepted_name", require := true), ''''::text), '' ''::text)
|
|
682
|
|
|
683
|
derived column
|
|
684
|
|
|
685
|
to modify expr:
|
|
686
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''__accepted_infraspecific_label'')::util.col, $$ltrim(NULLIF(util.remove_prefix("*Accepted_name_species", "*Accepted_name", require := true), ''''::text), '' ''::text)$$)::util.derived_col_def);
|
|
687
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
688
|
|
|
689
|
to rename:
|
|
690
|
# rename column
|
|
691
|
# rename CHECK constraint
|
|
692
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
693
|
';
|
|
694
|
|
|
695
|
|
|
696
|
--
|
|
697
|
-- Name: COLUMN taxon_match."__accepted_infraspecific_{rank,epithet}"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
698
|
--
|
|
699
|
|
|
700
|
COMMENT ON COLUMN taxon_match."__accepted_infraspecific_{rank,epithet}" IS '
|
|
701
|
= regexp_split_to_array(__accepted_infraspecific_label, '' ''::text)
|
|
702
|
|
|
703
|
derived column
|
|
704
|
|
|
705
|
to modify expr:
|
|
706
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''__accepted_infraspecific_{rank,epithet}'')::util.col, $$regexp_split_to_array(__accepted_infraspecific_label, '' ''::text)$$)::util.derived_col_def);
|
|
707
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
708
|
|
|
709
|
to rename:
|
|
710
|
# rename column
|
|
711
|
# rename CHECK constraint
|
|
712
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
713
|
';
|
|
714
|
|
|
715
|
|
|
716
|
--
|
|
717
|
-- Name: COLUMN taxon_match."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
718
|
--
|
|
719
|
|
|
720
|
COMMENT ON COLUMN taxon_match."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" IS '
|
|
721
|
= "__accepted_infraspecific_{rank,epithet}"[1]
|
|
722
|
|
|
723
|
derived column
|
|
724
|
|
|
725
|
to modify expr:
|
|
726
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org'')::util.col, $$"__accepted_infraspecific_{rank,epithet}"[1]$$)::util.derived_col_def);
|
|
727
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
728
|
|
|
729
|
to rename:
|
|
730
|
# rename column
|
|
731
|
# rename CHECK constraint
|
|
732
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
733
|
';
|
|
734
|
|
|
735
|
|
|
736
|
--
|
|
737
|
-- Name: COLUMN taxon_match."[accepted_]infraspecificEpithet__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
738
|
--
|
|
739
|
|
|
740
|
COMMENT ON COLUMN taxon_match."[accepted_]infraspecificEpithet__@DwC__@vegpath.org" IS '
|
|
741
|
= "__accepted_infraspecific_{rank,epithet}"[2]
|
|
742
|
|
|
743
|
derived column
|
|
744
|
|
|
745
|
to modify expr:
|
|
746
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[accepted_]infraspecificEpithet__@DwC__@vegpath.org'')::util.col, $$"__accepted_infraspecific_{rank,epithet}"[2]$$)::util.derived_col_def);
|
|
747
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
748
|
|
|
749
|
to rename:
|
|
750
|
# rename column
|
|
751
|
# rename CHECK constraint
|
|
752
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
753
|
';
|
|
754
|
|
|
755
|
|
|
756
|
--
|
|
757
|
-- Name: COLUMN taxon_match."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
758
|
--
|
|
759
|
|
|
760
|
COMMENT ON COLUMN taxon_match."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org" IS '
|
|
761
|
= "*Accepted_name" || COALESCE(('' ''::text || "*Accepted_name_author"), ''''::text)
|
|
762
|
|
|
763
|
derived column
|
|
764
|
|
|
765
|
to modify expr:
|
|
766
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[accepted_]scientificName[_with_author]__@DwC__@vegpath.org'')::util.col, $$"*Accepted_name" || COALESCE(('' ''::text || "*Accepted_name_author"), ''''::text)$$)::util.derived_col_def);
|
|
767
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
768
|
|
|
769
|
to rename:
|
|
770
|
# rename column
|
|
771
|
# rename CHECK constraint
|
|
772
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
773
|
';
|
|
774
|
|
|
775
|
|
|
776
|
--
|
|
777
|
-- Name: COLUMN taxon_match."[scrubbed_]taxonRank__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
778
|
--
|
|
779
|
|
|
780
|
COMMENT ON COLUMN taxon_match."[scrubbed_]taxonRank__@DwC__@vegpath.org" IS '
|
|
781
|
= CASE
|
|
782
|
WHEN matched_has_accepted THEN "*Accepted_name_rank"
|
|
783
|
ELSE "*Name_matched_rank"
|
|
784
|
END
|
|
785
|
|
|
786
|
derived column
|
|
787
|
|
|
788
|
to modify expr:
|
|
789
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]taxonRank__@DwC__@vegpath.org'')::util.col, $$CASE
|
|
790
|
WHEN matched_has_accepted THEN "*Accepted_name_rank"
|
|
791
|
ELSE "*Name_matched_rank"
|
|
792
|
END$$)::util.derived_col_def);
|
|
793
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
794
|
|
|
795
|
to rename:
|
|
796
|
# rename column
|
|
797
|
# rename CHECK constraint
|
|
798
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
799
|
';
|
|
800
|
|
|
801
|
|
|
802
|
--
|
|
803
|
-- Name: COLUMN taxon_match."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
804
|
--
|
|
805
|
|
|
806
|
COMMENT ON COLUMN taxon_match."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
|
807
|
= CASE
|
|
808
|
WHEN matched_has_accepted THEN "*Accepted_name_family"
|
|
809
|
ELSE "*Name_matched_accepted_family"
|
|
810
|
END
|
|
811
|
|
|
812
|
derived column
|
|
813
|
|
|
814
|
to modify expr:
|
|
815
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org'')::util.col, $$CASE
|
|
816
|
WHEN matched_has_accepted THEN "*Accepted_name_family"
|
|
817
|
ELSE "*Name_matched_accepted_family"
|
|
818
|
END$$)::util.derived_col_def);
|
|
819
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
820
|
|
|
821
|
to rename:
|
|
822
|
# rename column
|
|
823
|
# rename CHECK constraint
|
|
824
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
825
|
';
|
|
826
|
|
|
827
|
|
|
828
|
--
|
|
829
|
-- Name: COLUMN taxon_match."[scrubbed_]genus__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
830
|
--
|
|
831
|
|
|
832
|
COMMENT ON COLUMN taxon_match."[scrubbed_]genus__@DwC__@vegpath.org" IS '
|
|
833
|
= CASE
|
|
834
|
WHEN matched_has_accepted THEN "[accepted_]genus__@DwC__@vegpath.org"
|
|
835
|
ELSE "*Genus_matched"
|
|
836
|
END
|
|
837
|
|
|
838
|
derived column
|
|
839
|
|
|
840
|
to modify expr:
|
|
841
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]genus__@DwC__@vegpath.org'')::util.col, $$CASE
|
|
842
|
WHEN matched_has_accepted THEN "[accepted_]genus__@DwC__@vegpath.org"
|
|
843
|
ELSE "*Genus_matched"
|
|
844
|
END$$)::util.derived_col_def);
|
|
845
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
846
|
|
|
847
|
to rename:
|
|
848
|
# rename column
|
|
849
|
# rename CHECK constraint
|
|
850
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
851
|
';
|
|
852
|
|
|
853
|
|
|
854
|
--
|
|
855
|
-- Name: COLUMN taxon_match."[scrubbed_]specificEpithet__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
856
|
--
|
|
857
|
|
|
858
|
COMMENT ON COLUMN taxon_match."[scrubbed_]specificEpithet__@DwC__@vegpath.org" IS '
|
|
859
|
= CASE
|
|
860
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
|
861
|
ELSE "*Specific_epithet_matched"
|
|
862
|
END
|
|
863
|
|
|
864
|
derived column
|
|
865
|
|
|
866
|
to modify expr:
|
|
867
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]specificEpithet__@DwC__@vegpath.org'')::util.col, $$CASE
|
|
868
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
|
869
|
ELSE "*Specific_epithet_matched"
|
|
870
|
END$$)::util.derived_col_def);
|
|
871
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
872
|
|
|
873
|
to rename:
|
|
874
|
# rename column
|
|
875
|
# rename CHECK constraint
|
|
876
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
877
|
';
|
|
878
|
|
|
879
|
|
|
880
|
--
|
|
881
|
-- Name: COLUMN taxon_match."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
882
|
--
|
|
883
|
|
|
884
|
COMMENT ON COLUMN taxon_match."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
|
885
|
= CASE
|
|
886
|
WHEN matched_has_accepted THEN "*Accepted_name_species"
|
|
887
|
ELSE "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"
|
|
888
|
END
|
|
889
|
|
|
890
|
derived column
|
|
891
|
|
|
892
|
to modify expr:
|
|
893
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org'')::util.col, $$CASE
|
|
894
|
WHEN matched_has_accepted THEN "*Accepted_name_species"
|
|
895
|
ELSE "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"
|
|
896
|
END$$)::util.derived_col_def);
|
|
897
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
898
|
|
|
899
|
to rename:
|
|
900
|
# rename column
|
|
901
|
# rename CHECK constraint
|
|
902
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
903
|
';
|
|
904
|
|
|
905
|
|
|
906
|
--
|
|
907
|
-- Name: COLUMN taxon_match."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
908
|
--
|
|
909
|
|
|
910
|
COMMENT ON COLUMN taxon_match."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" IS '
|
|
911
|
= CASE
|
|
912
|
WHEN matched_has_accepted THEN "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"
|
|
913
|
ELSE "*Infraspecific_rank"
|
|
914
|
END
|
|
915
|
|
|
916
|
derived column
|
|
917
|
|
|
918
|
to modify expr:
|
|
919
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org'')::util.col, $$CASE
|
|
920
|
WHEN matched_has_accepted THEN "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"
|
|
921
|
ELSE "*Infraspecific_rank"
|
|
922
|
END$$)::util.derived_col_def);
|
|
923
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
924
|
|
|
925
|
to rename:
|
|
926
|
# rename column
|
|
927
|
# rename CHECK constraint
|
|
928
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
929
|
';
|
|
930
|
|
|
931
|
|
|
932
|
--
|
|
933
|
-- Name: COLUMN taxon_match."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
934
|
--
|
|
935
|
|
|
936
|
COMMENT ON COLUMN taxon_match."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" IS '
|
|
937
|
= CASE
|
|
938
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
|
939
|
ELSE "*Infraspecific_epithet_matched"
|
|
940
|
END
|
|
941
|
|
|
942
|
derived column
|
|
943
|
|
|
944
|
to modify expr:
|
|
945
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org'')::util.col, $$CASE
|
|
946
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
|
947
|
ELSE "*Infraspecific_epithet_matched"
|
|
948
|
END$$)::util.derived_col_def);
|
|
949
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
950
|
|
|
951
|
to rename:
|
|
952
|
# rename column
|
|
953
|
# rename CHECK constraint
|
|
954
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
955
|
';
|
|
956
|
|
|
957
|
|
|
958
|
--
|
|
959
|
-- Name: COLUMN taxon_match."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
960
|
--
|
|
961
|
|
|
962
|
COMMENT ON COLUMN taxon_match."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
|
963
|
= CASE
|
|
964
|
WHEN matched_has_accepted THEN "*Accepted_name"
|
|
965
|
ELSE "*Name_matched"
|
|
966
|
END
|
|
967
|
|
|
968
|
derived column
|
|
969
|
|
|
970
|
to modify expr:
|
|
971
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org'')::util.col, $$CASE
|
|
972
|
WHEN matched_has_accepted THEN "*Accepted_name"
|
|
973
|
ELSE "*Name_matched"
|
|
974
|
END$$)::util.derived_col_def);
|
|
975
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
976
|
|
|
977
|
to rename:
|
|
978
|
# rename column
|
|
979
|
# rename CHECK constraint
|
|
980
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
981
|
';
|
|
982
|
|
|
983
|
|
|
984
|
--
|
|
985
|
-- Name: COLUMN taxon_match."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
986
|
--
|
|
987
|
|
|
988
|
COMMENT ON COLUMN taxon_match."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
|
989
|
= CASE
|
|
990
|
WHEN matched_has_accepted THEN "*Accepted_name_author"
|
|
991
|
ELSE "*Name_matched_author"
|
|
992
|
END
|
|
993
|
|
|
994
|
derived column
|
|
995
|
|
|
996
|
to modify expr:
|
|
997
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org'')::util.col, $$CASE
|
|
998
|
WHEN matched_has_accepted THEN "*Accepted_name_author"
|
|
999
|
ELSE "*Name_matched_author"
|
|
1000
|
END$$)::util.derived_col_def);
|
|
1001
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
1002
|
|
|
1003
|
to rename:
|
|
1004
|
# rename column
|
|
1005
|
# rename CHECK constraint
|
|
1006
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
1007
|
';
|
|
1008
|
|
|
1009
|
|
|
1010
|
--
|
|
1011
|
-- Name: COLUMN taxon_match."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1012
|
--
|
|
1013
|
|
|
1014
|
COMMENT ON COLUMN taxon_match."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" IS '
|
|
1015
|
= CASE
|
|
1016
|
WHEN matched_has_accepted THEN "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"
|
|
1017
|
ELSE "[matched_]scientificName[_with_author]__@DwC__@vegpath.org"
|
|
1018
|
END
|
|
1019
|
|
|
1020
|
derived column
|
|
1021
|
|
|
1022
|
to modify expr:
|
|
1023
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org'')::util.col, $$CASE
|
|
1024
|
WHEN matched_has_accepted THEN "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"
|
|
1025
|
ELSE "[matched_]scientificName[_with_author]__@DwC__@vegpath.org"
|
|
1026
|
END$$)::util.derived_col_def);
|
|
1027
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
|
1028
|
|
|
1029
|
to rename:
|
|
1030
|
# rename column
|
|
1031
|
# rename CHECK constraint
|
|
1032
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
|
1033
|
';
|
|
1034
|
|
|
1035
|
|
|
1036
|
--
|
|
1037
|
-- Name: taxon_best_match; Type: VIEW; Schema: TNRS; Owner: -
|
|
1038
|
--
|
|
1039
|
|
|
1040
|
CREATE VIEW taxon_best_match AS
|
|
1041
|
SELECT taxon_match.batch,
|
|
1042
|
taxon_match.match_num,
|
|
1043
|
taxon_match."*Name_number",
|
|
1044
|
taxon_match."*Name_submitted",
|
|
1045
|
taxon_match."*Overall_score",
|
|
1046
|
taxon_match."*Name_matched",
|
|
1047
|
taxon_match."*Name_matched_rank",
|
|
1048
|
taxon_match."*Name_score",
|
|
1049
|
taxon_match."*Name_matched_author",
|
|
1050
|
taxon_match."*Name_matched_url",
|
|
1051
|
taxon_match."*Author_matched",
|
|
1052
|
taxon_match."*Author_score",
|
|
1053
|
taxon_match."*Family_matched",
|
|
1054
|
taxon_match."*Family_score",
|
|
1055
|
taxon_match."*Name_matched_accepted_family",
|
|
1056
|
taxon_match."*Genus_matched",
|
|
1057
|
taxon_match."*Genus_score",
|
|
1058
|
taxon_match."*Specific_epithet_matched",
|
|
1059
|
taxon_match."*Specific_epithet_score",
|
|
1060
|
taxon_match."*Infraspecific_rank",
|
|
1061
|
taxon_match."*Infraspecific_epithet_matched",
|
|
1062
|
taxon_match."*Infraspecific_epithet_score",
|
|
1063
|
taxon_match."*Infraspecific_rank_2",
|
|
1064
|
taxon_match."*Infraspecific_epithet_2_matched",
|
|
1065
|
taxon_match."*Infraspecific_epithet_2_score",
|
|
1066
|
taxon_match."*Annotations",
|
|
1067
|
taxon_match."*Unmatched_terms",
|
|
1068
|
taxon_match."*Taxonomic_status",
|
|
1069
|
taxon_match."*Accepted_name",
|
|
1070
|
taxon_match."*Accepted_name_author",
|
|
1071
|
taxon_match."*Accepted_name_rank",
|
|
1072
|
taxon_match."*Accepted_name_url",
|
|
1073
|
taxon_match."*Accepted_name_species",
|
|
1074
|
taxon_match."*Accepted_name_family",
|
|
1075
|
taxon_match."*Selected",
|
|
1076
|
taxon_match."*Source",
|
|
1077
|
taxon_match."*Warnings",
|
|
1078
|
taxon_match."*Accepted_name_lsid",
|
|
1079
|
taxon_match.is_valid_match,
|
|
1080
|
taxon_match.scrubbed_unique_taxon_name,
|
|
1081
|
taxon_match."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1082
|
taxon_match."[matched_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1083
|
taxon_match.matched_has_accepted,
|
|
1084
|
taxon_match."__accepted_{genus,specific_epithet}",
|
|
1085
|
taxon_match."[accepted_]genus__@DwC__@vegpath.org",
|
|
1086
|
taxon_match."[accepted_]specificEpithet__@DwC__@vegpath.org",
|
|
1087
|
taxon_match.__accepted_infraspecific_label,
|
|
1088
|
taxon_match."__accepted_infraspecific_{rank,epithet}",
|
|
1089
|
taxon_match."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
|
1090
|
taxon_match."[accepted_]infraspecificEpithet__@DwC__@vegpath.org",
|
|
1091
|
taxon_match."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1092
|
taxon_match."[scrubbed_]taxonRank__@DwC__@vegpath.org",
|
|
1093
|
taxon_match."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1094
|
taxon_match."[scrubbed_]genus__@DwC__@vegpath.org",
|
|
1095
|
taxon_match."[scrubbed_]specificEpithet__@DwC__@vegpath.org",
|
|
1096
|
taxon_match."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1097
|
taxon_match."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
|
1098
|
taxon_match."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org",
|
|
1099
|
taxon_match."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1100
|
taxon_match."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1101
|
taxon_match."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org"
|
|
1102
|
FROM taxon_match
|
|
1103
|
WHERE (taxon_match."*Selected" = 'true'::text);
|
|
1104
|
|
|
1105
|
|
|
1106
|
--
|
|
1107
|
-- Name: VIEW taxon_best_match; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1108
|
--
|
|
1109
|
|
|
1110
|
COMMENT ON VIEW taxon_best_match IS '
|
|
1111
|
to modify:
|
|
1112
|
SELECT util.recreate_view(''"TNRS"."taxon_best_match"'', $$
|
|
1113
|
SELECT __
|
|
1114
|
$$);
|
|
1115
|
';
|
|
1116
|
|
|
1117
|
|
|
1118
|
--
|
|
1119
|
-- Name: MatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
|
|
1120
|
--
|
|
1121
|
|
|
1122
|
CREATE VIEW "MatchedTaxon" AS
|
|
1123
|
SELECT taxon_best_match.batch,
|
|
1124
|
taxon_best_match.match_num,
|
|
1125
|
taxon_best_match."*Name_number",
|
|
1126
|
taxon_best_match."*Name_submitted",
|
|
1127
|
taxon_best_match."*Overall_score",
|
|
1128
|
taxon_best_match."*Name_matched",
|
|
1129
|
taxon_best_match."*Name_matched_rank",
|
|
1130
|
taxon_best_match."*Name_score",
|
|
1131
|
taxon_best_match."*Name_matched_author",
|
|
1132
|
taxon_best_match."*Name_matched_url",
|
|
1133
|
taxon_best_match."*Author_matched",
|
|
1134
|
taxon_best_match."*Author_score",
|
|
1135
|
taxon_best_match."*Family_matched",
|
|
1136
|
taxon_best_match."*Family_score",
|
|
1137
|
taxon_best_match."*Name_matched_accepted_family",
|
|
1138
|
taxon_best_match."*Genus_matched",
|
|
1139
|
taxon_best_match."*Genus_score",
|
|
1140
|
taxon_best_match."*Specific_epithet_matched",
|
|
1141
|
taxon_best_match."*Specific_epithet_score",
|
|
1142
|
taxon_best_match."*Infraspecific_rank",
|
|
1143
|
taxon_best_match."*Infraspecific_epithet_matched",
|
|
1144
|
taxon_best_match."*Infraspecific_epithet_score",
|
|
1145
|
taxon_best_match."*Infraspecific_rank_2",
|
|
1146
|
taxon_best_match."*Infraspecific_epithet_2_matched",
|
|
1147
|
taxon_best_match."*Infraspecific_epithet_2_score",
|
|
1148
|
taxon_best_match."*Annotations",
|
|
1149
|
taxon_best_match."*Unmatched_terms",
|
|
1150
|
taxon_best_match."*Taxonomic_status",
|
|
1151
|
taxon_best_match."*Accepted_name",
|
|
1152
|
taxon_best_match."*Accepted_name_author",
|
|
1153
|
taxon_best_match."*Accepted_name_rank",
|
|
1154
|
taxon_best_match."*Accepted_name_url",
|
|
1155
|
taxon_best_match."*Accepted_name_species",
|
|
1156
|
taxon_best_match."*Accepted_name_family",
|
|
1157
|
taxon_best_match."*Selected",
|
|
1158
|
taxon_best_match."*Source",
|
|
1159
|
taxon_best_match."*Warnings",
|
|
1160
|
taxon_best_match."*Accepted_name_lsid",
|
|
1161
|
taxon_best_match.is_valid_match,
|
|
1162
|
taxon_best_match.scrubbed_unique_taxon_name,
|
|
1163
|
taxon_best_match."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1164
|
taxon_best_match."[matched_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1165
|
taxon_best_match.matched_has_accepted,
|
|
1166
|
taxon_best_match."__accepted_{genus,specific_epithet}",
|
|
1167
|
taxon_best_match."[accepted_]genus__@DwC__@vegpath.org",
|
|
1168
|
taxon_best_match."[accepted_]specificEpithet__@DwC__@vegpath.org",
|
|
1169
|
taxon_best_match.__accepted_infraspecific_label,
|
|
1170
|
taxon_best_match."__accepted_infraspecific_{rank,epithet}",
|
|
1171
|
taxon_best_match."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
|
1172
|
taxon_best_match."[accepted_]infraspecificEpithet__@DwC__@vegpath.org",
|
|
1173
|
taxon_best_match."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1174
|
taxon_best_match."[scrubbed_]taxonRank__@DwC__@vegpath.org",
|
|
1175
|
taxon_best_match."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1176
|
taxon_best_match."[scrubbed_]genus__@DwC__@vegpath.org",
|
|
1177
|
taxon_best_match."[scrubbed_]specificEpithet__@DwC__@vegpath.org",
|
|
1178
|
taxon_best_match."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1179
|
taxon_best_match."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
|
1180
|
taxon_best_match."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org",
|
|
1181
|
taxon_best_match."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1182
|
taxon_best_match."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1183
|
taxon_best_match."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1184
|
map_taxonomic_status(taxon_best_match."*Taxonomic_status", taxon_best_match."*Accepted_name") AS "taxonomicStatus",
|
|
1185
|
CASE
|
|
1186
|
WHEN (taxon_best_match."*Accepted_name_rank" = 'family'::text) THEN concat_ws(' '::text, taxon_best_match."*Accepted_name_family", taxon_best_match."*Unmatched_terms")
|
|
1187
|
WHEN (taxon_best_match."*Accepted_name_rank" = 'genus'::text) THEN concat_ws(' '::text, taxon_best_match."*Accepted_name", taxon_best_match."*Unmatched_terms")
|
|
1188
|
ELSE taxon_best_match."*Accepted_name_species"
|
|
1189
|
END AS accepted_morphospecies_binomial
|
|
1190
|
FROM taxon_best_match;
|
|
1191
|
|
|
1192
|
|
|
1193
|
--
|
|
1194
|
-- Name: VIEW "MatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1195
|
--
|
|
1196
|
|
|
1197
|
COMMENT ON VIEW "MatchedTaxon" IS '
|
|
1198
|
to modify:
|
|
1199
|
SELECT util.recreate_view(''"TNRS"."MatchedTaxon"'', $$
|
|
1200
|
SELECT __
|
|
1201
|
$$);
|
|
1202
|
';
|
|
1203
|
|
|
1204
|
|
|
1205
|
--
|
|
1206
|
-- Name: ValidMatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
|
|
1207
|
--
|
|
1208
|
|
|
1209
|
CREATE VIEW "ValidMatchedTaxon" AS
|
|
1210
|
SELECT "MatchedTaxon".batch,
|
|
1211
|
"MatchedTaxon".match_num,
|
|
1212
|
"MatchedTaxon"."*Name_number",
|
|
1213
|
"MatchedTaxon"."*Name_submitted",
|
|
1214
|
"MatchedTaxon"."*Overall_score",
|
|
1215
|
"MatchedTaxon"."*Name_matched",
|
|
1216
|
"MatchedTaxon"."*Name_matched_rank",
|
|
1217
|
"MatchedTaxon"."*Name_score",
|
|
1218
|
"MatchedTaxon"."*Name_matched_author",
|
|
1219
|
"MatchedTaxon"."*Name_matched_url",
|
|
1220
|
"MatchedTaxon"."*Author_matched",
|
|
1221
|
"MatchedTaxon"."*Author_score",
|
|
1222
|
"MatchedTaxon"."*Family_matched",
|
|
1223
|
"MatchedTaxon"."*Family_score",
|
|
1224
|
"MatchedTaxon"."*Name_matched_accepted_family",
|
|
1225
|
"MatchedTaxon"."*Genus_matched",
|
|
1226
|
"MatchedTaxon"."*Genus_score",
|
|
1227
|
"MatchedTaxon"."*Specific_epithet_matched",
|
|
1228
|
"MatchedTaxon"."*Specific_epithet_score",
|
|
1229
|
"MatchedTaxon"."*Infraspecific_rank",
|
|
1230
|
"MatchedTaxon"."*Infraspecific_epithet_matched",
|
|
1231
|
"MatchedTaxon"."*Infraspecific_epithet_score",
|
|
1232
|
"MatchedTaxon"."*Infraspecific_rank_2",
|
|
1233
|
"MatchedTaxon"."*Infraspecific_epithet_2_matched",
|
|
1234
|
"MatchedTaxon"."*Infraspecific_epithet_2_score",
|
|
1235
|
"MatchedTaxon"."*Annotations",
|
|
1236
|
"MatchedTaxon"."*Unmatched_terms",
|
|
1237
|
"MatchedTaxon"."*Taxonomic_status",
|
|
1238
|
"MatchedTaxon"."*Accepted_name",
|
|
1239
|
"MatchedTaxon"."*Accepted_name_author",
|
|
1240
|
"MatchedTaxon"."*Accepted_name_rank",
|
|
1241
|
"MatchedTaxon"."*Accepted_name_url",
|
|
1242
|
"MatchedTaxon"."*Accepted_name_species",
|
|
1243
|
"MatchedTaxon"."*Accepted_name_family",
|
|
1244
|
"MatchedTaxon"."*Selected",
|
|
1245
|
"MatchedTaxon"."*Source",
|
|
1246
|
"MatchedTaxon"."*Warnings",
|
|
1247
|
"MatchedTaxon"."*Accepted_name_lsid",
|
|
1248
|
"MatchedTaxon".is_valid_match,
|
|
1249
|
"MatchedTaxon".scrubbed_unique_taxon_name,
|
|
1250
|
"MatchedTaxon"."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1251
|
"MatchedTaxon"."[matched_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1252
|
"MatchedTaxon".matched_has_accepted,
|
|
1253
|
"MatchedTaxon"."__accepted_{genus,specific_epithet}",
|
|
1254
|
"MatchedTaxon"."[accepted_]genus__@DwC__@vegpath.org",
|
|
1255
|
"MatchedTaxon"."[accepted_]specificEpithet__@DwC__@vegpath.org",
|
|
1256
|
"MatchedTaxon".__accepted_infraspecific_label,
|
|
1257
|
"MatchedTaxon"."__accepted_infraspecific_{rank,epithet}",
|
|
1258
|
"MatchedTaxon"."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
|
1259
|
"MatchedTaxon"."[accepted_]infraspecificEpithet__@DwC__@vegpath.org",
|
|
1260
|
"MatchedTaxon"."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1261
|
"MatchedTaxon"."[scrubbed_]taxonRank__@DwC__@vegpath.org",
|
|
1262
|
"MatchedTaxon"."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1263
|
"MatchedTaxon"."[scrubbed_]genus__@DwC__@vegpath.org",
|
|
1264
|
"MatchedTaxon"."[scrubbed_]specificEpithet__@DwC__@vegpath.org",
|
|
1265
|
"MatchedTaxon"."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1266
|
"MatchedTaxon"."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
|
1267
|
"MatchedTaxon"."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org",
|
|
1268
|
"MatchedTaxon"."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1269
|
"MatchedTaxon"."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1270
|
"MatchedTaxon"."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1271
|
"MatchedTaxon"."taxonomicStatus",
|
|
1272
|
"MatchedTaxon".accepted_morphospecies_binomial
|
|
1273
|
FROM "MatchedTaxon"
|
|
1274
|
WHERE "MatchedTaxon".is_valid_match;
|
|
1275
|
|
|
1276
|
|
|
1277
|
--
|
|
1278
|
-- Name: VIEW "ValidMatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1279
|
--
|
|
1280
|
|
|
1281
|
COMMENT ON VIEW "ValidMatchedTaxon" IS '
|
|
1282
|
to update, use * as the column list
|
|
1283
|
';
|
|
1284
|
|
|
1285
|
|
|
1286
|
--
|
|
1287
|
-- Name: batch; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
|
1288
|
--
|
|
1289
|
|
|
1290
|
CREATE TABLE batch (
|
|
1291
|
id text NOT NULL,
|
|
1292
|
id_by_time text,
|
|
1293
|
time_submitted timestamp with time zone DEFAULT now(),
|
|
1294
|
client_version text
|
|
1295
|
);
|
|
1296
|
|
|
1297
|
|
|
1298
|
--
|
|
1299
|
-- Name: batch_download_settings; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
|
1300
|
--
|
|
1301
|
|
|
1302
|
CREATE TABLE batch_download_settings (
|
|
1303
|
id text NOT NULL,
|
|
1304
|
"E-mail" text,
|
|
1305
|
"Id" text,
|
|
1306
|
"Job type" text,
|
|
1307
|
"Contains Id" boolean,
|
|
1308
|
"Start time" text,
|
|
1309
|
"Finish time" text,
|
|
1310
|
"TNRS version" text,
|
|
1311
|
"Sources selected" text,
|
|
1312
|
"Match threshold" double precision,
|
|
1313
|
"Classification" text,
|
|
1314
|
"Allow partial matches?" boolean,
|
|
1315
|
"Sort by source" boolean,
|
|
1316
|
"Constrain by higher taxonomy" boolean
|
|
1317
|
);
|
|
1318
|
|
|
1319
|
|
|
1320
|
--
|
|
1321
|
-- Name: TABLE batch_download_settings; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1322
|
--
|
|
1323
|
|
|
1324
|
COMMENT ON TABLE batch_download_settings IS '
|
|
1325
|
stores data from http://tnrs.iplantcollaborative.org/TNRSapp.html > Submit List > results section > Download settings > settings.txt
|
|
1326
|
';
|
|
1327
|
|
|
1328
|
|
|
1329
|
--
|
|
1330
|
-- Name: client_version; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
|
1331
|
--
|
|
1332
|
|
|
1333
|
CREATE TABLE client_version (
|
|
1334
|
id text NOT NULL,
|
|
1335
|
global_rev integer NOT NULL,
|
|
1336
|
"/lib/tnrs.py rev" integer,
|
|
1337
|
"/bin/tnrs_db rev" integer
|
|
1338
|
);
|
|
1339
|
|
|
1340
|
|
|
1341
|
--
|
|
1342
|
-- Name: TABLE client_version; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1343
|
--
|
|
1344
|
|
|
1345
|
COMMENT ON TABLE client_version IS '
|
|
1346
|
contains svn revisions
|
|
1347
|
';
|
|
1348
|
|
|
1349
|
|
|
1350
|
--
|
|
1351
|
-- Name: COLUMN client_version.global_rev; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1352
|
--
|
|
1353
|
|
|
1354
|
COMMENT ON COLUMN client_version.global_rev IS '
|
|
1355
|
from `svn info .` > Last Changed Rev
|
|
1356
|
';
|
|
1357
|
|
|
1358
|
|
|
1359
|
--
|
|
1360
|
-- Name: COLUMN client_version."/lib/tnrs.py rev"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1361
|
--
|
|
1362
|
|
|
1363
|
COMMENT ON COLUMN client_version."/lib/tnrs.py rev" IS '
|
|
1364
|
from `svn info lib/tnrs.py` > Last Changed Rev
|
|
1365
|
';
|
|
1366
|
|
|
1367
|
|
|
1368
|
--
|
|
1369
|
-- Name: COLUMN client_version."/bin/tnrs_db rev"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1370
|
--
|
|
1371
|
|
|
1372
|
COMMENT ON COLUMN client_version."/bin/tnrs_db rev" IS '
|
|
1373
|
from `svn info bin/tnrs_db` > Last Changed Rev
|
|
1374
|
';
|
|
1375
|
|
|
1376
|
|
|
1377
|
--
|
|
1378
|
-- Name: taxon_match_input; Type: VIEW; Schema: TNRS; Owner: -
|
|
1379
|
--
|
|
1380
|
|
|
1381
|
CREATE VIEW taxon_match_input AS
|
|
1382
|
SELECT taxon_match."*Name_number" AS "Name_number",
|
|
1383
|
taxon_match."*Name_submitted" AS "Name_submitted",
|
|
1384
|
taxon_match."*Overall_score" AS "Overall_score",
|
|
1385
|
taxon_match."*Name_matched" AS "Name_matched",
|
|
1386
|
taxon_match."*Name_matched_rank" AS "Name_matched_rank",
|
|
1387
|
taxon_match."*Name_score" AS "Name_score",
|
|
1388
|
taxon_match."*Name_matched_author" AS "Name_matched_author",
|
|
1389
|
taxon_match."*Name_matched_url" AS "Name_matched_url",
|
|
1390
|
taxon_match."*Author_matched" AS "Author_matched",
|
|
1391
|
taxon_match."*Author_score" AS "Author_score",
|
|
1392
|
taxon_match."*Family_matched" AS "Family_matched",
|
|
1393
|
taxon_match."*Family_score" AS "Family_score",
|
|
1394
|
taxon_match."*Name_matched_accepted_family" AS "Name_matched_accepted_family",
|
|
1395
|
taxon_match."*Genus_matched" AS "Genus_matched",
|
|
1396
|
taxon_match."*Genus_score" AS "Genus_score",
|
|
1397
|
taxon_match."*Specific_epithet_matched" AS "Specific_epithet_matched",
|
|
1398
|
taxon_match."*Specific_epithet_score" AS "Specific_epithet_score",
|
|
1399
|
taxon_match."*Infraspecific_rank" AS "Infraspecific_rank",
|
|
1400
|
taxon_match."*Infraspecific_epithet_matched" AS "Infraspecific_epithet_matched",
|
|
1401
|
taxon_match."*Infraspecific_epithet_score" AS "Infraspecific_epithet_score",
|
|
1402
|
taxon_match."*Infraspecific_rank_2" AS "Infraspecific_rank_2",
|
|
1403
|
taxon_match."*Infraspecific_epithet_2_matched" AS "Infraspecific_epithet_2_matched",
|
|
1404
|
taxon_match."*Infraspecific_epithet_2_score" AS "Infraspecific_epithet_2_score",
|
|
1405
|
taxon_match."*Annotations" AS "Annotations",
|
|
1406
|
taxon_match."*Unmatched_terms" AS "Unmatched_terms",
|
|
1407
|
taxon_match."*Taxonomic_status" AS "Taxonomic_status",
|
|
1408
|
taxon_match."*Accepted_name" AS "Accepted_name",
|
|
1409
|
taxon_match."*Accepted_name_author" AS "Accepted_name_author",
|
|
1410
|
taxon_match."*Accepted_name_rank" AS "Accepted_name_rank",
|
|
1411
|
taxon_match."*Accepted_name_url" AS "Accepted_name_url",
|
|
1412
|
taxon_match."*Accepted_name_species" AS "Accepted_name_species",
|
|
1413
|
taxon_match."*Accepted_name_family" AS "Accepted_name_family",
|
|
1414
|
taxon_match."*Selected" AS "Selected",
|
|
1415
|
taxon_match."*Source" AS "Source",
|
|
1416
|
taxon_match."*Warnings" AS "Warnings",
|
|
1417
|
taxon_match."*Accepted_name_lsid" AS "Accepted_name_lsid"
|
|
1418
|
FROM taxon_match;
|
|
1419
|
|
|
1420
|
|
|
1421
|
--
|
|
1422
|
-- Name: taxon_match_input__copy_to; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
|
1423
|
--
|
|
1424
|
|
|
1425
|
CREATE TABLE taxon_match_input__copy_to (
|
|
1426
|
"Name_number" integer,
|
|
1427
|
"Name_submitted" text,
|
|
1428
|
"Overall_score" double precision,
|
|
1429
|
"Name_matched" text,
|
|
1430
|
"Name_matched_rank" text,
|
|
1431
|
"Name_score" double precision,
|
|
1432
|
"Name_matched_author" text,
|
|
1433
|
"Name_matched_url" text,
|
|
1434
|
"Author_matched" text,
|
|
1435
|
"Author_score" double precision,
|
|
1436
|
"Family_matched" text,
|
|
1437
|
"Family_score" double precision,
|
|
1438
|
"Name_matched_accepted_family" text,
|
|
1439
|
"Genus_matched" text,
|
|
1440
|
"Genus_score" double precision,
|
|
1441
|
"Specific_epithet_matched" text,
|
|
1442
|
"Specific_epithet_score" double precision,
|
|
1443
|
"Infraspecific_rank" text,
|
|
1444
|
"Infraspecific_epithet_matched" text,
|
|
1445
|
"Infraspecific_epithet_score" double precision,
|
|
1446
|
"Infraspecific_rank_2" text,
|
|
1447
|
"Infraspecific_epithet_2_matched" text,
|
|
1448
|
"Infraspecific_epithet_2_score" double precision,
|
|
1449
|
"Annotations" text,
|
|
1450
|
"Unmatched_terms" text,
|
|
1451
|
"Taxonomic_status" text,
|
|
1452
|
"Accepted_name" text,
|
|
1453
|
"Accepted_name_author" text,
|
|
1454
|
"Accepted_name_rank" text,
|
|
1455
|
"Accepted_name_url" text,
|
|
1456
|
"Accepted_name_species" text,
|
|
1457
|
"Accepted_name_family" text,
|
|
1458
|
"Selected" text,
|
|
1459
|
"Source" text,
|
|
1460
|
"Warnings" text,
|
|
1461
|
"Accepted_name_lsid" text
|
|
1462
|
);
|
|
1463
|
|
|
1464
|
|
|
1465
|
--
|
|
1466
|
-- Name: taxon_scrub.scrubbed_unique_taxon_name.*; Type: VIEW; Schema: TNRS; Owner: -
|
|
1467
|
--
|
|
1468
|
|
|
1469
|
CREATE VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" AS
|
|
1470
|
SELECT taxon_match."*Name_submitted" AS scrubbed_unique_taxon_name,
|
|
1471
|
taxon_match."*Name_matched_rank" AS scrubbed_taxon_rank,
|
|
1472
|
COALESCE(taxon_match."*Name_matched_accepted_family", taxon_match."*Family_matched") AS scrubbed_family,
|
|
1473
|
taxon_match."*Genus_matched" AS scrubbed_genus,
|
|
1474
|
taxon_match."*Specific_epithet_matched" AS scrubbed_specific_epithet,
|
|
1475
|
taxon_match."*Infraspecific_rank" AS scrubbed_infraspecific_rank,
|
|
1476
|
taxon_match."*Infraspecific_epithet_matched" AS scrubbed_infraspecific_epithet,
|
|
1477
|
taxon_match."*Name_matched_author" AS scrubbed_author,
|
|
1478
|
taxon_match."*Name_matched" AS scrubbed_taxon_name_no_author,
|
|
1479
|
(taxon_match."*Name_matched" || COALESCE((' '::text || taxon_match."*Name_matched_author"), ''::text)) AS scrubbed_taxon_name_with_author
|
|
1480
|
FROM taxon_match;
|
|
1481
|
|
|
1482
|
|
|
1483
|
--
|
|
1484
|
-- Name: VIEW "taxon_scrub.scrubbed_unique_taxon_name.*"; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1485
|
--
|
|
1486
|
|
|
1487
|
COMMENT ON VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" IS '
|
|
1488
|
to modify:
|
|
1489
|
SELECT util.recreate_view(''"TNRS"."taxon_scrub.scrubbed_unique_taxon_name.*"'', $$
|
|
1490
|
SELECT __
|
|
1491
|
$$);
|
|
1492
|
|
|
1493
|
scrubbed_family: Name_matched_accepted_family was missing from the TNRS results at one point, so Family_matched is used 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.
|
|
1494
|
';
|
|
1495
|
|
|
1496
|
|
|
1497
|
--
|
|
1498
|
-- Name: taxon_scrub; Type: VIEW; Schema: TNRS; Owner: -
|
|
1499
|
--
|
|
1500
|
|
|
1501
|
CREATE VIEW taxon_scrub AS
|
|
1502
|
SELECT "ValidMatchedTaxon".scrubbed_unique_taxon_name,
|
|
1503
|
"ValidMatchedTaxon".batch,
|
|
1504
|
"ValidMatchedTaxon".match_num,
|
|
1505
|
"ValidMatchedTaxon"."*Name_number",
|
|
1506
|
"ValidMatchedTaxon"."*Name_submitted",
|
|
1507
|
"ValidMatchedTaxon"."*Overall_score",
|
|
1508
|
"ValidMatchedTaxon"."*Name_matched",
|
|
1509
|
"ValidMatchedTaxon"."*Name_matched_rank",
|
|
1510
|
"ValidMatchedTaxon"."*Name_score",
|
|
1511
|
"ValidMatchedTaxon"."*Name_matched_author",
|
|
1512
|
"ValidMatchedTaxon"."*Name_matched_url",
|
|
1513
|
"ValidMatchedTaxon"."*Author_matched",
|
|
1514
|
"ValidMatchedTaxon"."*Author_score",
|
|
1515
|
"ValidMatchedTaxon"."*Family_matched",
|
|
1516
|
"ValidMatchedTaxon"."*Family_score",
|
|
1517
|
"ValidMatchedTaxon"."*Name_matched_accepted_family",
|
|
1518
|
"ValidMatchedTaxon"."*Genus_matched",
|
|
1519
|
"ValidMatchedTaxon"."*Genus_score",
|
|
1520
|
"ValidMatchedTaxon"."*Specific_epithet_matched",
|
|
1521
|
"ValidMatchedTaxon"."*Specific_epithet_score",
|
|
1522
|
"ValidMatchedTaxon"."*Infraspecific_rank",
|
|
1523
|
"ValidMatchedTaxon"."*Infraspecific_epithet_matched",
|
|
1524
|
"ValidMatchedTaxon"."*Infraspecific_epithet_score",
|
|
1525
|
"ValidMatchedTaxon"."*Infraspecific_rank_2",
|
|
1526
|
"ValidMatchedTaxon"."*Infraspecific_epithet_2_matched",
|
|
1527
|
"ValidMatchedTaxon"."*Infraspecific_epithet_2_score",
|
|
1528
|
"ValidMatchedTaxon"."*Annotations",
|
|
1529
|
"ValidMatchedTaxon"."*Unmatched_terms",
|
|
1530
|
"ValidMatchedTaxon"."*Taxonomic_status",
|
|
1531
|
"ValidMatchedTaxon"."*Accepted_name",
|
|
1532
|
"ValidMatchedTaxon"."*Accepted_name_author",
|
|
1533
|
"ValidMatchedTaxon"."*Accepted_name_rank",
|
|
1534
|
"ValidMatchedTaxon"."*Accepted_name_url",
|
|
1535
|
"ValidMatchedTaxon"."*Accepted_name_species",
|
|
1536
|
"ValidMatchedTaxon"."*Accepted_name_family",
|
|
1537
|
"ValidMatchedTaxon"."*Selected",
|
|
1538
|
"ValidMatchedTaxon"."*Source",
|
|
1539
|
"ValidMatchedTaxon"."*Warnings",
|
|
1540
|
"ValidMatchedTaxon"."*Accepted_name_lsid",
|
|
1541
|
"ValidMatchedTaxon".is_valid_match,
|
|
1542
|
"ValidMatchedTaxon"."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1543
|
"ValidMatchedTaxon"."[matched_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1544
|
"ValidMatchedTaxon".matched_has_accepted,
|
|
1545
|
"ValidMatchedTaxon"."__accepted_{genus,specific_epithet}",
|
|
1546
|
"ValidMatchedTaxon"."[accepted_]genus__@DwC__@vegpath.org",
|
|
1547
|
"ValidMatchedTaxon"."[accepted_]specificEpithet__@DwC__@vegpath.org",
|
|
1548
|
"ValidMatchedTaxon".__accepted_infraspecific_label,
|
|
1549
|
"ValidMatchedTaxon"."__accepted_infraspecific_{rank,epithet}",
|
|
1550
|
"ValidMatchedTaxon"."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
|
1551
|
"ValidMatchedTaxon"."[accepted_]infraspecificEpithet__@DwC__@vegpath.org",
|
|
1552
|
"ValidMatchedTaxon"."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1553
|
"ValidMatchedTaxon"."[scrubbed_]taxonRank__@DwC__@vegpath.org",
|
|
1554
|
"ValidMatchedTaxon"."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1555
|
"ValidMatchedTaxon"."[scrubbed_]genus__@DwC__@vegpath.org",
|
|
1556
|
"ValidMatchedTaxon"."[scrubbed_]specificEpithet__@DwC__@vegpath.org",
|
|
1557
|
"ValidMatchedTaxon"."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1558
|
"ValidMatchedTaxon"."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
|
1559
|
"ValidMatchedTaxon"."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org",
|
|
1560
|
"ValidMatchedTaxon"."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1561
|
"ValidMatchedTaxon"."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org",
|
|
1562
|
"ValidMatchedTaxon"."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org",
|
|
1563
|
"ValidMatchedTaxon"."taxonomicStatus",
|
|
1564
|
"ValidMatchedTaxon".accepted_morphospecies_binomial,
|
|
1565
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_rank,
|
|
1566
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_family,
|
|
1567
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus,
|
|
1568
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet,
|
|
1569
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_rank,
|
|
1570
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_epithet,
|
|
1571
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_author,
|
|
1572
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_no_author,
|
|
1573
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_with_author,
|
|
1574
|
CASE
|
|
1575
|
WHEN ("taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_rank = 'family'::text) THEN concat_ws(' '::text, "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_family, "ValidMatchedTaxon"."*Unmatched_terms")
|
|
1576
|
WHEN ("taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_rank = 'genus'::text) THEN concat_ws(' '::text, "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_no_author, "ValidMatchedTaxon"."*Unmatched_terms")
|
|
1577
|
ELSE (("taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus || ' '::text) || "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet)
|
|
1578
|
END AS scrubbed_morphospecies_binomial
|
|
1579
|
FROM ("ValidMatchedTaxon"
|
|
1580
|
LEFT JOIN "taxon_scrub.scrubbed_unique_taxon_name.*" USING (scrubbed_unique_taxon_name));
|
|
1581
|
|
|
1582
|
|
|
1583
|
--
|
|
1584
|
-- Name: VIEW taxon_scrub; Type: COMMENT; Schema: TNRS; Owner: -
|
|
1585
|
--
|
|
1586
|
|
|
1587
|
COMMENT ON VIEW taxon_scrub IS '
|
|
1588
|
to modify:
|
|
1589
|
SELECT util.recreate_view(''"TNRS".taxon_scrub'', $$
|
|
1590
|
SELECT __
|
|
1591
|
$$);
|
|
1592
|
';
|
|
1593
|
|
|
1594
|
|
|
1595
|
--
|
|
1596
|
-- Name: batch_download_settings_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
|
1597
|
--
|
|
1598
|
|
|
1599
|
ALTER TABLE ONLY batch_download_settings
|
|
1600
|
ADD CONSTRAINT batch_download_settings_pkey PRIMARY KEY (id);
|
|
1601
|
|
|
1602
|
|
|
1603
|
--
|
|
1604
|
-- Name: batch_id_by_time_key; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
|
1605
|
--
|
|
1606
|
|
|
1607
|
ALTER TABLE ONLY batch
|
|
1608
|
ADD CONSTRAINT batch_id_by_time_key UNIQUE (id_by_time);
|
|
1609
|
|
|
1610
|
|
|
1611
|
--
|
|
1612
|
-- Name: batch_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
|
1613
|
--
|
|
1614
|
|
|
1615
|
ALTER TABLE ONLY batch
|
|
1616
|
ADD CONSTRAINT batch_pkey PRIMARY KEY (id);
|
|
1617
|
|
|
1618
|
|
|
1619
|
--
|
|
1620
|
-- Name: client_version_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
|
1621
|
--
|
|
1622
|
|
|
1623
|
ALTER TABLE ONLY client_version
|
|
1624
|
ADD CONSTRAINT client_version_pkey PRIMARY KEY (id);
|
|
1625
|
|
|
1626
|
|
|
1627
|
--
|
|
1628
|
-- Name: taxon_match_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
|
1629
|
--
|
|
1630
|
|
|
1631
|
ALTER TABLE ONLY taxon_match
|
|
1632
|
ADD CONSTRAINT taxon_match_pkey PRIMARY KEY (batch, match_num);
|
|
1633
|
|
|
1634
|
ALTER TABLE taxon_match CLUSTER ON taxon_match_pkey;
|
|
1635
|
|
|
1636
|
|
|
1637
|
--
|
|
1638
|
-- Name: batch_client_version_idx; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
|
1639
|
--
|
|
1640
|
|
|
1641
|
CREATE INDEX batch_client_version_idx ON batch USING btree (client_version);
|
|
1642
|
|
|
1643
|
|
|
1644
|
--
|
|
1645
|
-- Name: taxon_best_match__valid_match; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
|
1646
|
--
|
|
1647
|
|
|
1648
|
CREATE INDEX taxon_best_match__valid_match ON taxon_match USING btree ("*Name_submitted") WHERE (("*Selected" = 'true'::text) AND is_valid_match);
|
|
1649
|
|
|
1650
|
|
|
1651
|
--
|
|
1652
|
-- Name: taxon_match_Name_submitted_idx; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
|
1653
|
--
|
|
1654
|
|
|
1655
|
CREATE INDEX "taxon_match_Name_submitted_idx" ON taxon_match USING btree ("*Name_submitted");
|
|
1656
|
|
|
1657
|
|
|
1658
|
--
|
|
1659
|
-- Name: taxon_match__one_selected_match; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
|
1660
|
--
|
|
1661
|
|
|
1662
|
CREATE UNIQUE INDEX taxon_match__one_selected_match ON taxon_match USING btree (batch, "*Name_number") WHERE ("*Selected" = 'true'::text);
|
|
1663
|
|
|
1664
|
|
|
1665
|
--
|
|
1666
|
-- Name: batch__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
|
1667
|
--
|
|
1668
|
|
|
1669
|
CREATE TRIGGER batch__fill BEFORE INSERT OR UPDATE ON batch FOR EACH ROW EXECUTE PROCEDURE batch__fill();
|
|
1670
|
|
|
1671
|
|
|
1672
|
--
|
|
1673
|
-- Name: taxon_match__batch_begin; Type: TRIGGER; Schema: TNRS; Owner: -
|
|
1674
|
--
|
|
1675
|
|
|
1676
|
CREATE TRIGGER taxon_match__batch_begin BEFORE INSERT ON taxon_match_input__copy_to FOR EACH STATEMENT EXECUTE PROCEDURE taxon_match__batch_begin();
|
|
1677
|
|
|
1678
|
|
|
1679
|
--
|
|
1680
|
-- Name: taxon_match__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
|
1681
|
--
|
|
1682
|
|
|
1683
|
CREATE TRIGGER taxon_match__fill BEFORE INSERT OR UPDATE ON taxon_match FOR EACH ROW EXECUTE PROCEDURE taxon_match__fill();
|
|
1684
|
|
|
1685
|
|
|
1686
|
--
|
|
1687
|
-- Name: taxon_match__fill_derived; Type: TRIGGER; Schema: TNRS; Owner: -
|
|
1688
|
--
|
|
1689
|
|
|
1690
|
CREATE TRIGGER taxon_match__fill_derived BEFORE INSERT OR UPDATE ON taxon_match FOR EACH ROW EXECUTE PROCEDURE taxon_match__fill_derived();
|
|
1691
|
|
|
1692
|
|
|
1693
|
--
|
|
1694
|
-- Name: taxon_match__match_num__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
|
1695
|
--
|
|
1696
|
|
|
1697
|
CREATE TRIGGER taxon_match__match_num__fill BEFORE INSERT ON taxon_match FOR EACH ROW EXECUTE PROCEDURE taxon_match__match_num__fill();
|
|
1698
|
|
|
1699
|
|
|
1700
|
--
|
|
1701
|
-- Name: taxon_match_input__copy_to__insert; Type: TRIGGER; Schema: TNRS; Owner: -
|
|
1702
|
--
|
|
1703
|
|
|
1704
|
CREATE TRIGGER taxon_match_input__copy_to__insert BEFORE INSERT ON taxon_match_input__copy_to FOR EACH ROW EXECUTE PROCEDURE taxon_match_input__copy_to__insert();
|
|
1705
|
|
|
1706
|
|
|
1707
|
--
|
|
1708
|
-- Name: batch_client_version_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
|
1709
|
--
|
|
1710
|
|
|
1711
|
ALTER TABLE ONLY batch
|
|
1712
|
ADD CONSTRAINT batch_client_version_fkey FOREIGN KEY (client_version) REFERENCES client_version(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
1713
|
|
|
1714
|
|
|
1715
|
--
|
|
1716
|
-- Name: batch_download_settings_id_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
|
1717
|
--
|
|
1718
|
|
|
1719
|
ALTER TABLE ONLY batch_download_settings
|
|
1720
|
ADD CONSTRAINT batch_download_settings_id_fkey FOREIGN KEY (id) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
1721
|
|
|
1722
|
|
|
1723
|
--
|
|
1724
|
-- Name: taxon_match_batch_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
|
1725
|
--
|
|
1726
|
|
|
1727
|
ALTER TABLE ONLY taxon_match
|
|
1728
|
ADD CONSTRAINT taxon_match_batch_fkey FOREIGN KEY (batch) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
1729
|
|
|
1730
|
|
|
1731
|
--
|
|
1732
|
-- Name: TNRS; Type: ACL; Schema: -; Owner: -
|
|
1733
|
--
|
|
1734
|
|
|
1735
|
REVOKE ALL ON SCHEMA "TNRS" FROM PUBLIC;
|
|
1736
|
REVOKE ALL ON SCHEMA "TNRS" FROM bien;
|
|
1737
|
GRANT ALL ON SCHEMA "TNRS" TO bien;
|
|
1738
|
GRANT USAGE ON SCHEMA "TNRS" TO bien_read;
|
|
1739
|
|
|
1740
|
|
|
1741
|
--
|
|
1742
|
-- Name: taxon_match; Type: ACL; Schema: TNRS; Owner: -
|
|
1743
|
--
|
|
1744
|
|
|
1745
|
REVOKE ALL ON TABLE taxon_match FROM PUBLIC;
|
|
1746
|
REVOKE ALL ON TABLE taxon_match FROM bien;
|
|
1747
|
GRANT ALL ON TABLE taxon_match TO bien;
|
|
1748
|
GRANT SELECT ON TABLE taxon_match TO bien_read;
|
|
1749
|
|
|
1750
|
|
|
1751
|
--
|
|
1752
|
-- Name: taxon_best_match; Type: ACL; Schema: TNRS; Owner: -
|
|
1753
|
--
|
|
1754
|
|
|
1755
|
REVOKE ALL ON TABLE taxon_best_match FROM PUBLIC;
|
|
1756
|
REVOKE ALL ON TABLE taxon_best_match FROM bien;
|
|
1757
|
GRANT ALL ON TABLE taxon_best_match TO bien;
|
|
1758
|
GRANT SELECT ON TABLE taxon_best_match TO bien_read;
|
|
1759
|
|
|
1760
|
|
|
1761
|
--
|
|
1762
|
-- Name: MatchedTaxon; Type: ACL; Schema: TNRS; Owner: -
|
|
1763
|
--
|
|
1764
|
|
|
1765
|
REVOKE ALL ON TABLE "MatchedTaxon" FROM PUBLIC;
|
|
1766
|
REVOKE ALL ON TABLE "MatchedTaxon" FROM bien;
|
|
1767
|
GRANT ALL ON TABLE "MatchedTaxon" TO bien;
|
|
1768
|
GRANT SELECT ON TABLE "MatchedTaxon" TO bien_read;
|
|
1769
|
|
|
1770
|
|
|
1771
|
--
|
|
1772
|
-- Name: ValidMatchedTaxon; Type: ACL; Schema: TNRS; Owner: -
|
|
1773
|
--
|
|
1774
|
|
|
1775
|
REVOKE ALL ON TABLE "ValidMatchedTaxon" FROM PUBLIC;
|
|
1776
|
REVOKE ALL ON TABLE "ValidMatchedTaxon" FROM bien;
|
|
1777
|
GRANT ALL ON TABLE "ValidMatchedTaxon" TO bien;
|
|
1778
|
GRANT SELECT ON TABLE "ValidMatchedTaxon" TO bien_read;
|
|
1779
|
|
|
1780
|
|
|
1781
|
--
|
|
1782
|
-- Name: taxon_match_input; Type: ACL; Schema: TNRS; Owner: -
|
|
1783
|
--
|
|
1784
|
|
|
1785
|
REVOKE ALL ON TABLE taxon_match_input FROM PUBLIC;
|
|
1786
|
REVOKE ALL ON TABLE taxon_match_input FROM bien;
|
|
1787
|
GRANT ALL ON TABLE taxon_match_input TO bien;
|
|
1788
|
GRANT SELECT ON TABLE taxon_match_input TO bien_read;
|
|
1789
|
|
|
1790
|
|
|
1791
|
--
|
|
1792
|
-- Name: taxon_scrub.scrubbed_unique_taxon_name.*; Type: ACL; Schema: TNRS; Owner: -
|
|
1793
|
--
|
|
1794
|
|
|
1795
|
REVOKE ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" FROM PUBLIC;
|
|
1796
|
REVOKE ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" FROM bien;
|
|
1797
|
GRANT ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" TO bien;
|
|
1798
|
GRANT SELECT ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" TO bien_read;
|
|
1799
|
|
|
1800
|
|
|
1801
|
--
|
|
1802
|
-- Name: taxon_scrub; Type: ACL; Schema: TNRS; Owner: -
|
|
1803
|
--
|
|
1804
|
|
|
1805
|
REVOKE ALL ON TABLE taxon_scrub FROM PUBLIC;
|
|
1806
|
REVOKE ALL ON TABLE taxon_scrub FROM bien;
|
|
1807
|
GRANT ALL ON TABLE taxon_scrub TO bien;
|
|
1808
|
GRANT SELECT ON TABLE taxon_scrub TO bien_read;
|
|
1809
|
|
|
1810
|
|
|
1811
|
--
|
|
1812
|
-- PostgreSQL database dump complete
|
|
1813
|
--
|
|
1814
|
|
