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10778
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aaronmk
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--
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-- PostgreSQL database dump
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--
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10737
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aaronmk
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10778
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aaronmk
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SET statement_timeout = 0;
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11708
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aaronmk
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SET lock_timeout = 0;
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10778
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aaronmk
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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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10737
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aaronmk
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--
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10778
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aaronmk
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-- Name: TNRS; Type: SCHEMA; Schema: -; Owner: -
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--
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10737
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aaronmk
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10778
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aaronmk
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--CREATE SCHEMA "TNRS";
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10725
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aaronmk
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11614
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aaronmk
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--
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-- Name: SCHEMA "TNRS"; Type: COMMENT; Schema: -; Owner: -
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--
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13575
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aaronmk
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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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11617
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aaronmk
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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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11614
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aaronmk
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$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")
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11616
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aaronmk
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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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13861
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aaronmk
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SELECT util.set_col_types(''"TNRS".taxon_match'', ARRAY[
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11614
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aaronmk
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(''col'', ''new_type'')
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11616
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aaronmk
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]::util.col_cast[]); -- runtime: 9 min ("531282 ms")
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11617
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aaronmk
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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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13575
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aaronmk
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$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")
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';
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11614
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aaronmk
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10778
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aaronmk
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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 $$
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10728
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aaronmk
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BEGIN
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new.id_by_time = new.time_submitted;
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new.id = COALESCE(new.id, new.id_by_time);
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RETURN new;
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END;
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10778
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aaronmk
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$$;
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10728
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aaronmk
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--
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10778
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aaronmk
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-- Name: family_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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10728
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aaronmk
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10778
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aaronmk
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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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10736
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aaronmk
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10778
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aaronmk
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10736
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aaronmk
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--
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10778
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aaronmk
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-- Name: genus_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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10736
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aaronmk
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10778
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aaronmk
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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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7844
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aaronmk
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9985
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aaronmk
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10778
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aaronmk
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--
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11709
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aaronmk
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-- Name: map_taxonomic_status(text, text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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13503
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aaronmk
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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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11709
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aaronmk
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LANGUAGE sql IMMUTABLE
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AS $_$
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13503
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aaronmk
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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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11709
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aaronmk
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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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13868
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aaronmk
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-- Name: taxon_match__batch_begin(); Type: FUNCTION; Schema: TNRS; Owner: -
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13866
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aaronmk
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--
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13868
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aaronmk
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CREATE FUNCTION taxon_match__batch_begin() RETURNS trigger
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13866
|
aaronmk
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LANGUAGE plpgsql
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AS $$
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BEGIN
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13869
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aaronmk
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PERFORM util.seq__reset('pg_temp.taxon_match__match_num__seq', 0);
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13567
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aaronmk
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RETURN NULL;
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END;
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$$;
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--
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| 110 |
13868
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aaronmk
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-- Name: taxon_match__fill(); Type: FUNCTION; Schema: TNRS; Owner: -
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| 111 |
13578
|
aaronmk
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--
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| 112 |
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13868
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aaronmk
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CREATE FUNCTION taxon_match__fill() RETURNS trigger
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| 114 |
13578
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aaronmk
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LANGUAGE plpgsql
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AS $$
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| 116 |
11643
|
aaronmk
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BEGIN
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13871
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aaronmk
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DECLARE
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"Specific_epithet_is_plant" boolean :=
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11628
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aaronmk
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(CASE
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14111
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aaronmk
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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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13871
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aaronmk
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THEN true
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ELSE NULL -- ambiguous
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END);
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14111
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aaronmk
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never_homonym boolean = COALESCE(new."*Author_score" >= 0.6, false);
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13871
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aaronmk
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-- author disambiguates
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family_is_homonym boolean = NOT never_homonym
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14111
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aaronmk
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AND "TNRS".family_is_homonym(new."*Family_matched");
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13871
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aaronmk
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genus_is_homonym boolean = NOT never_homonym
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14111
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aaronmk
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AND "TNRS".genus_is_homonym(new."*Genus_matched");
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| 132 |
13871
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aaronmk
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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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14111
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aaronmk
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new.is_valid_match = new."*Taxonomic_status" != 'Invalid'
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13871
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aaronmk
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AND COALESCE(CASE
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| 137 |
14111
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aaronmk
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WHEN new."*Family_score" = 1 AND NOT family_is_homonym -- exact match
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13871
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aaronmk
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THEN true
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ELSE -- consider genus
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| 140 |
11628
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aaronmk
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(CASE
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| 141 |
14111
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aaronmk
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WHEN new."*Genus_score" = 1 -- exact match
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13871
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aaronmk
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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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14111
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aaronmk
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WHEN new."*Genus_score" >= 0.85 -- fuzzy match
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13871
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aaronmk
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THEN "Specific_epithet_is_plant"
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ELSE NULL -- ambiguous
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| 150 |
11628
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aaronmk
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END)
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13871
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aaronmk
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END, false);
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END;
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| 153 |
11628
|
aaronmk
|
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| 154 |
13871
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aaronmk
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DECLARE
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matched_taxon_name_with_author text = NULLIF(concat_ws(' '
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| 156 |
14111
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aaronmk
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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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13871
|
aaronmk
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), '');
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accepted_taxon_name_with_author text = NULLIF(concat_ws(' '
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| 162 |
14111
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aaronmk
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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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| 166 |
13871
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aaronmk
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), '');
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BEGIN
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| 168 |
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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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| 171 |
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| 172 |
11628
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aaronmk
|
RETURN new;
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| 173 |
7134
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aaronmk
|
END;
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| 174 |
10778
|
aaronmk
|
$$;
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| 176 |
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| 177 |
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--
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| 178 |
13868
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aaronmk
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-- Name: FUNCTION taxon_match__fill(); Type: COMMENT; Schema: TNRS; Owner: -
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| 179 |
10778
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aaronmk
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--
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| 180 |
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| 181 |
13868
|
aaronmk
|
COMMENT ON FUNCTION taxon_match__fill() IS '
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| 182 |
13575
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aaronmk
|
IMPORTANT: when changing this function, you must regenerate the derived cols:
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| 183 |
13861
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aaronmk
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UPDATE "TNRS".taxon_match SET "Name_submitted" = "Name_submitted"
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| 184 |
11715
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aaronmk
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runtime: 30 min ("5564082 rows affected, 1918900 ms execution time")
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| 185 |
13861
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aaronmk
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VACUUM ANALYZE "TNRS".taxon_match -- to remove previous rows
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| 186 |
13575
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aaronmk
|
runtime: 1.5 min ("92633 ms")
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| 187 |
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';
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| 188 |
7134
|
aaronmk
|
|
| 189 |
7251
|
aaronmk
|
|
| 190 |
13631
|
aaronmk
|
--
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| 191 |
14122
|
aaronmk
|
-- Name: taxon_match__fill_derived(); Type: FUNCTION; Schema: TNRS; Owner: -
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| 192 |
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--
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| 193 |
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| 194 |
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CREATE FUNCTION taxon_match__fill_derived() RETURNS trigger
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| 195 |
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LANGUAGE plpgsql
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| 196 |
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AS $$
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| 197 |
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BEGIN
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| 198 |
14309
|
aaronmk
|
-- clear derived cols so old values won't be used in calculations
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| 199 |
14311
|
aaronmk
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new."[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org" = NULL;
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| 200 |
14309
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aaronmk
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new."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org" = NULL;
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| 201 |
14330
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aaronmk
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new."matched~Name[_no_author]___@TNRS__@vegpath.org" = NULL;
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| 202 |
14309
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aaronmk
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new."[matched_]scientificName[_with_author]__@DwC__@vegpath.org" = NULL;
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| 203 |
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new.matched_has_accepted = NULL;
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| 204 |
14318
|
aaronmk
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new."Accepted_family__@TNRS__@vegpath.org" = NULL;
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| 205 |
14309
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aaronmk
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new."__accepted_{genus,specific_epithet}" = NULL;
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| 206 |
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new."[accepted_]genus__@DwC__@vegpath.org" = NULL;
|
| 207 |
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new."[accepted_]specificEpithet__@DwC__@vegpath.org" = NULL;
|
| 208 |
14311
|
aaronmk
|
new."[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" = NULL;
|
| 209 |
14309
|
aaronmk
|
new.__accepted_infraspecific_label = NULL;
|
| 210 |
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new."__accepted_infraspecific_{rank,epithet}" = NULL;
|
| 211 |
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new."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" = NULL;
|
| 212 |
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new."[accepted_]infraspecificEpithet__@DwC__@vegpath.org" = NULL;
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| 213 |
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new."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org" = NULL;
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| 214 |
14328
|
aaronmk
|
new."[scrubbed_]taxonomicStatus__@DwC__@vegpath.org" = NULL;
|
| 215 |
14309
|
aaronmk
|
new."[scrubbed_]taxonRank__@DwC__@vegpath.org" = NULL;
|
| 216 |
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new."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" = NULL;
|
| 217 |
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new."[scrubbed_]genus__@DwC__@vegpath.org" = NULL;
|
| 218 |
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new."[scrubbed_]specificEpithet__@DwC__@vegpath.org" = NULL;
|
| 219 |
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new."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" = NULL;
|
| 220 |
14328
|
aaronmk
|
new."[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" = NULL;
|
| 221 |
14309
|
aaronmk
|
new."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" = NULL;
|
| 222 |
|
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new."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" = NULL;
|
| 223 |
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new."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" = NULL;
|
| 224 |
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new."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" = NULL;
|
| 225 |
|
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new."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" = NULL;
|
| 226 |
|
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|
| 227 |
|
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-- populate derived cols
|
| 228 |
14311
|
aaronmk
|
new."[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org" = (SELECT "*Unmatched_terms" FROM (SELECT new.*) new);
|
| 229 |
14308
|
aaronmk
|
new."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT ("*Genus_matched" || ' '::text) || "*Specific_epithet_matched" FROM (SELECT new.*) new);
|
| 230 |
14330
|
aaronmk
|
new."matched~Name[_no_author]___@TNRS__@vegpath.org" = (SELECT NULLIF("*Name_matched", 'No suitable matches found.'::text) FROM (SELECT new.*) new);
|
| 231 |
|
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new."[matched_]scientificName[_with_author]__@DwC__@vegpath.org" = (SELECT "matched~Name[_no_author]___@TNRS__@vegpath.org" || COALESCE((' '::text || "*Name_matched_author"), ''::text) FROM (SELECT new.*) new);
|
| 232 |
14308
|
aaronmk
|
new.matched_has_accepted = (SELECT "*Accepted_name" IS NOT NULL FROM (SELECT new.*) new);
|
| 233 |
14318
|
aaronmk
|
new."Accepted_family__@TNRS__@vegpath.org" = (SELECT COALESCE("*Accepted_name_family",
|
| 234 |
|
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CASE
|
| 235 |
|
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WHEN ("*Accepted_name_rank" = 'family'::text) THEN "*Accepted_name"
|
| 236 |
|
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ELSE NULL::text
|
| 237 |
|
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END) FROM (SELECT new.*) new);
|
| 238 |
14308
|
aaronmk
|
new."__accepted_{genus,specific_epithet}" = (SELECT regexp_split_to_array("*Accepted_name_species", ' '::text) FROM (SELECT new.*) new);
|
| 239 |
14325
|
aaronmk
|
new."[accepted_]genus__@DwC__@vegpath.org" = (SELECT COALESCE("__accepted_{genus,specific_epithet}"[1],
|
| 240 |
|
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CASE
|
| 241 |
|
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WHEN ("*Accepted_name_rank" = 'genus'::text) THEN "*Accepted_name"
|
| 242 |
|
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ELSE NULL::text
|
| 243 |
|
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END) FROM (SELECT new.*) new);
|
| 244 |
14308
|
aaronmk
|
new."[accepted_]specificEpithet__@DwC__@vegpath.org" = (SELECT "__accepted_{genus,specific_epithet}"[2] FROM (SELECT new.*) new);
|
| 245 |
14311
|
aaronmk
|
new."[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" = (SELECT CASE
|
| 246 |
14323
|
aaronmk
|
WHEN ("*Accepted_name_rank" = 'family'::text) THEN concat_ws(' '::text, "Accepted_family__@TNRS__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 247 |
14327
|
aaronmk
|
WHEN ("*Accepted_name_rank" = 'genus'::text) THEN concat_ws(' '::text, "[accepted_]genus__@DwC__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 248 |
14311
|
aaronmk
|
ELSE "*Accepted_name_species"
|
| 249 |
|
|
END FROM (SELECT new.*) new);
|
| 250 |
14308
|
aaronmk
|
new.__accepted_infraspecific_label = (SELECT ltrim(NULLIF(util.remove_prefix("*Accepted_name_species", "*Accepted_name", require := true), ''::text), ' '::text) FROM (SELECT new.*) new);
|
| 251 |
|
|
new."__accepted_infraspecific_{rank,epithet}" = (SELECT regexp_split_to_array(__accepted_infraspecific_label, ' '::text) FROM (SELECT new.*) new);
|
| 252 |
|
|
new."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" = (SELECT "__accepted_infraspecific_{rank,epithet}"[1] FROM (SELECT new.*) new);
|
| 253 |
|
|
new."[accepted_]infraspecificEpithet__@DwC__@vegpath.org" = (SELECT "__accepted_infraspecific_{rank,epithet}"[2] FROM (SELECT new.*) new);
|
| 254 |
|
|
new."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org" = (SELECT "*Accepted_name" || COALESCE((' '::text || "*Accepted_name_author"), ''::text) FROM (SELECT new.*) new);
|
| 255 |
14328
|
aaronmk
|
new."[scrubbed_]taxonomicStatus__@DwC__@vegpath.org" = (SELECT "TNRS".map_taxonomic_status("*Taxonomic_status", "*Accepted_name") FROM (SELECT new.*) new);
|
| 256 |
14308
|
aaronmk
|
new."[scrubbed_]taxonRank__@DwC__@vegpath.org" = (SELECT CASE
|
| 257 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "*Accepted_name_rank"
|
| 258 |
|
|
ELSE "*Name_matched_rank"
|
| 259 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 260 |
|
|
new."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT CASE
|
| 261 |
14323
|
aaronmk
|
WHEN matched_has_accepted THEN "Accepted_family__@TNRS__@vegpath.org"
|
| 262 |
14282
|
aaronmk
|
ELSE "*Name_matched_accepted_family"
|
| 263 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 264 |
|
|
new."[scrubbed_]genus__@DwC__@vegpath.org" = (SELECT CASE
|
| 265 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]genus__@DwC__@vegpath.org"
|
| 266 |
|
|
ELSE "*Genus_matched"
|
| 267 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 268 |
|
|
new."[scrubbed_]specificEpithet__@DwC__@vegpath.org" = (SELECT CASE
|
| 269 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
| 270 |
|
|
ELSE "*Specific_epithet_matched"
|
| 271 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 272 |
|
|
new."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT CASE
|
| 273 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "*Accepted_name_species"
|
| 274 |
|
|
ELSE "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"
|
| 275 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 276 |
14328
|
aaronmk
|
new."[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" = (SELECT CASE
|
| 277 |
|
|
WHEN ("[scrubbed_]taxonRank__@DwC__@vegpath.org" = 'family'::text) THEN concat_ws(' '::text, "[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 278 |
|
|
WHEN ("[scrubbed_]taxonRank__@DwC__@vegpath.org" = 'genus'::text) THEN concat_ws(' '::text, "[scrubbed_]genus__@DwC__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 279 |
|
|
ELSE "[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org"
|
| 280 |
|
|
END FROM (SELECT new.*) new);
|
| 281 |
14308
|
aaronmk
|
new."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" = (SELECT CASE
|
| 282 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"
|
| 283 |
|
|
ELSE "*Infraspecific_rank"
|
| 284 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 285 |
|
|
new."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" = (SELECT CASE
|
| 286 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
| 287 |
|
|
ELSE "*Infraspecific_epithet_matched"
|
| 288 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 289 |
|
|
new."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT CASE
|
| 290 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "*Accepted_name"
|
| 291 |
14330
|
aaronmk
|
ELSE "matched~Name[_no_author]___@TNRS__@vegpath.org"
|
| 292 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 293 |
|
|
new."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" = (SELECT CASE
|
| 294 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "*Accepted_name_author"
|
| 295 |
|
|
ELSE "*Name_matched_author"
|
| 296 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 297 |
|
|
new."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" = (SELECT CASE
|
| 298 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"
|
| 299 |
|
|
ELSE "[matched_]scientificName[_with_author]__@DwC__@vegpath.org"
|
| 300 |
14308
|
aaronmk
|
END FROM (SELECT new.*) new);
|
| 301 |
14304
|
aaronmk
|
|
| 302 |
14122
|
aaronmk
|
RETURN new;
|
| 303 |
|
|
END;
|
| 304 |
|
|
$$;
|
| 305 |
|
|
|
| 306 |
|
|
|
| 307 |
|
|
--
|
| 308 |
14254
|
aaronmk
|
-- Name: FUNCTION taxon_match__fill_derived(); Type: COMMENT; Schema: TNRS; Owner: -
|
| 309 |
|
|
--
|
| 310 |
|
|
|
| 311 |
|
|
COMMENT ON FUNCTION taxon_match__fill_derived() IS '
|
| 312 |
|
|
autogenerated, do not edit
|
| 313 |
|
|
|
| 314 |
|
|
to regenerate:
|
| 315 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 316 |
|
|
';
|
| 317 |
|
|
|
| 318 |
|
|
|
| 319 |
|
|
--
|
| 320 |
13868
|
aaronmk
|
-- Name: taxon_match__match_num__fill(); Type: FUNCTION; Schema: TNRS; Owner: -
|
| 321 |
|
|
--
|
| 322 |
|
|
|
| 323 |
|
|
CREATE FUNCTION taxon_match__match_num__fill() RETURNS trigger
|
| 324 |
|
|
LANGUAGE plpgsql
|
| 325 |
|
|
AS $$
|
| 326 |
|
|
BEGIN
|
| 327 |
|
|
IF new.match_num IS NULL THEN
|
| 328 |
13869
|
aaronmk
|
new.match_num = "TNRS".taxon_match__match_num__next();
|
| 329 |
13868
|
aaronmk
|
END IF;
|
| 330 |
|
|
RETURN new;
|
| 331 |
|
|
END;
|
| 332 |
|
|
$$;
|
| 333 |
|
|
|
| 334 |
|
|
|
| 335 |
|
|
--
|
| 336 |
13869
|
aaronmk
|
-- Name: taxon_match__match_num__next(); Type: FUNCTION; Schema: TNRS; Owner: -
|
| 337 |
|
|
--
|
| 338 |
|
|
|
| 339 |
|
|
CREATE FUNCTION taxon_match__match_num__next() RETURNS bigint
|
| 340 |
|
|
LANGUAGE sql
|
| 341 |
|
|
AS $$
|
| 342 |
|
|
SELECT nextval('pg_temp.taxon_match__match_num__seq');
|
| 343 |
|
|
$$;
|
| 344 |
|
|
|
| 345 |
|
|
|
| 346 |
|
|
--
|
| 347 |
13868
|
aaronmk
|
-- Name: taxon_match_input__copy_to__insert(); Type: FUNCTION; Schema: TNRS; Owner: -
|
| 348 |
|
|
--
|
| 349 |
|
|
|
| 350 |
|
|
CREATE FUNCTION taxon_match_input__copy_to__insert() RETURNS trigger
|
| 351 |
|
|
LANGUAGE plpgsql
|
| 352 |
|
|
AS $$
|
| 353 |
|
|
BEGIN
|
| 354 |
|
|
INSERT INTO "TNRS".taxon_match_input SELECT new.*;
|
| 355 |
|
|
RETURN NULL;
|
| 356 |
|
|
END;
|
| 357 |
|
|
$$;
|
| 358 |
|
|
|
| 359 |
|
|
|
| 360 |
|
|
--
|
| 361 |
|
|
-- Name: taxon_name_is_safe(text); Type: FUNCTION; Schema: TNRS; Owner: -
|
| 362 |
|
|
--
|
| 363 |
|
|
|
| 364 |
|
|
CREATE FUNCTION taxon_name_is_safe(taxon_name text) RETURNS boolean
|
| 365 |
|
|
LANGUAGE sql IMMUTABLE
|
| 366 |
|
|
AS $_$
|
| 367 |
|
|
SELECT NOT ($1 = ANY("TNRS".unsafe_taxon_names()))
|
| 368 |
|
|
$_$;
|
| 369 |
|
|
|
| 370 |
|
|
|
| 371 |
|
|
--
|
| 372 |
13631
|
aaronmk
|
-- Name: unsafe_taxon_names(); Type: FUNCTION; Schema: TNRS; Owner: -
|
| 373 |
|
|
--
|
| 374 |
|
|
|
| 375 |
|
|
CREATE FUNCTION unsafe_taxon_names() RETURNS text[]
|
| 376 |
|
|
LANGUAGE sql IMMUTABLE
|
| 377 |
|
|
AS $$
|
| 378 |
|
|
SELECT ARRAY[
|
| 379 |
13686
|
aaronmk
|
]::text[]
|
| 380 |
13631
|
aaronmk
|
$$;
|
| 381 |
|
|
|
| 382 |
|
|
|
| 383 |
10778
|
aaronmk
|
SET default_tablespace = '';
|
| 384 |
|
|
|
| 385 |
|
|
SET default_with_oids = false;
|
| 386 |
|
|
|
| 387 |
10728
|
aaronmk
|
--
|
| 388 |
13861
|
aaronmk
|
-- Name: taxon_match; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 389 |
10778
|
aaronmk
|
--
|
| 390 |
7251
|
aaronmk
|
|
| 391 |
13861
|
aaronmk
|
CREATE TABLE taxon_match (
|
| 392 |
10778
|
aaronmk
|
batch text DEFAULT now() NOT NULL,
|
| 393 |
13580
|
aaronmk
|
match_num integer NOT NULL,
|
| 394 |
14111
|
aaronmk
|
"*Name_number" integer NOT NULL,
|
| 395 |
|
|
"*Name_submitted" text NOT NULL,
|
| 396 |
|
|
"*Overall_score" double precision,
|
| 397 |
|
|
"*Name_matched" text,
|
| 398 |
|
|
"*Name_matched_rank" text,
|
| 399 |
|
|
"*Name_score" double precision,
|
| 400 |
|
|
"*Name_matched_author" text,
|
| 401 |
|
|
"*Name_matched_url" text,
|
| 402 |
|
|
"*Author_matched" text,
|
| 403 |
|
|
"*Author_score" double precision,
|
| 404 |
|
|
"*Family_matched" text,
|
| 405 |
|
|
"*Family_score" double precision,
|
| 406 |
|
|
"*Name_matched_accepted_family" text,
|
| 407 |
|
|
"*Genus_matched" text,
|
| 408 |
|
|
"*Genus_score" double precision,
|
| 409 |
|
|
"*Specific_epithet_matched" text,
|
| 410 |
|
|
"*Specific_epithet_score" double precision,
|
| 411 |
|
|
"*Infraspecific_rank" text,
|
| 412 |
|
|
"*Infraspecific_epithet_matched" text,
|
| 413 |
|
|
"*Infraspecific_epithet_score" double precision,
|
| 414 |
|
|
"*Infraspecific_rank_2" text,
|
| 415 |
|
|
"*Infraspecific_epithet_2_matched" text,
|
| 416 |
|
|
"*Infraspecific_epithet_2_score" double precision,
|
| 417 |
|
|
"*Annotations" text,
|
| 418 |
|
|
"*Unmatched_terms" text,
|
| 419 |
|
|
"*Taxonomic_status" text,
|
| 420 |
|
|
"*Accepted_name" text,
|
| 421 |
|
|
"*Accepted_name_author" text,
|
| 422 |
|
|
"*Accepted_name_rank" text,
|
| 423 |
|
|
"*Accepted_name_url" text,
|
| 424 |
|
|
"*Accepted_name_species" text,
|
| 425 |
|
|
"*Accepted_name_family" text,
|
| 426 |
|
|
"*Selected" text,
|
| 427 |
|
|
"*Source" text,
|
| 428 |
|
|
"*Warnings" text,
|
| 429 |
|
|
"*Accepted_name_lsid" text,
|
| 430 |
11628
|
aaronmk
|
is_valid_match boolean NOT NULL,
|
| 431 |
14122
|
aaronmk
|
scrubbed_unique_taxon_name text,
|
| 432 |
14310
|
aaronmk
|
"[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org" text,
|
| 433 |
14279
|
aaronmk
|
"[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
| 434 |
14329
|
aaronmk
|
"matched~Name[_no_author]___@TNRS__@vegpath.org" text,
|
| 435 |
14279
|
aaronmk
|
"[matched_]scientificName[_with_author]__@DwC__@vegpath.org" text,
|
| 436 |
|
|
matched_has_accepted boolean,
|
| 437 |
14318
|
aaronmk
|
"Accepted_family__@TNRS__@vegpath.org" text,
|
| 438 |
14122
|
aaronmk
|
"__accepted_{genus,specific_epithet}" text[],
|
| 439 |
14257
|
aaronmk
|
"[accepted_]genus__@DwC__@vegpath.org" text,
|
| 440 |
|
|
"[accepted_]specificEpithet__@DwC__@vegpath.org" text,
|
| 441 |
14310
|
aaronmk
|
"[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" text,
|
| 442 |
14264
|
aaronmk
|
__accepted_infraspecific_label text,
|
| 443 |
14265
|
aaronmk
|
"__accepted_infraspecific_{rank,epithet}" text[],
|
| 444 |
14266
|
aaronmk
|
"[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" text,
|
| 445 |
|
|
"[accepted_]infraspecificEpithet__@DwC__@vegpath.org" text,
|
| 446 |
14267
|
aaronmk
|
"[accepted_]scientificName[_with_author]__@DwC__@vegpath.org" text,
|
| 447 |
14328
|
aaronmk
|
"[scrubbed_]taxonomicStatus__@DwC__@vegpath.org" text,
|
| 448 |
14281
|
aaronmk
|
"[scrubbed_]taxonRank__@DwC__@vegpath.org" text,
|
| 449 |
|
|
"[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
| 450 |
|
|
"[scrubbed_]genus__@DwC__@vegpath.org" text,
|
| 451 |
|
|
"[scrubbed_]specificEpithet__@DwC__@vegpath.org" text,
|
| 452 |
|
|
"[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
| 453 |
14328
|
aaronmk
|
"[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" text,
|
| 454 |
14281
|
aaronmk
|
"[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" text,
|
| 455 |
|
|
"[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" text,
|
| 456 |
|
|
"[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
| 457 |
|
|
"[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" text,
|
| 458 |
|
|
"[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" text,
|
| 459 |
14318
|
aaronmk
|
CONSTRAINT "Accepted_family__@TNRS__@vegpath.org" CHECK ((NOT ("Accepted_family__@TNRS__@vegpath.org" IS DISTINCT FROM COALESCE("*Accepted_name_family",
|
| 460 |
|
|
CASE
|
| 461 |
|
|
WHEN ("*Accepted_name_rank" = 'family'::text) THEN "*Accepted_name"
|
| 462 |
|
|
ELSE NULL::text
|
| 463 |
|
|
END)))),
|
| 464 |
14266
|
aaronmk
|
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]))),
|
| 465 |
14325
|
aaronmk
|
CONSTRAINT "[accepted_]genus__@DwC__@vegpath.org" CHECK ((NOT ("[accepted_]genus__@DwC__@vegpath.org" IS DISTINCT FROM COALESCE("__accepted_{genus,specific_epithet}"[1],
|
| 466 |
|
|
CASE
|
| 467 |
|
|
WHEN ("*Accepted_name_rank" = 'genus'::text) THEN "*Accepted_name"
|
| 468 |
|
|
ELSE NULL::text
|
| 469 |
|
|
END)))),
|
| 470 |
14266
|
aaronmk
|
CONSTRAINT "[accepted_]infraspecificEpithet__@DwC__@vegpath.org" CHECK ((NOT ("[accepted_]infraspecificEpithet__@DwC__@vegpath.org" IS DISTINCT FROM "__accepted_infraspecific_{rank,epithet}"[2]))),
|
| 471 |
14304
|
aaronmk
|
CONSTRAINT "[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" CHECK ((NOT ("[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" IS DISTINCT FROM
|
| 472 |
|
|
CASE
|
| 473 |
14323
|
aaronmk
|
WHEN ("*Accepted_name_rank" = 'family'::text) THEN concat_ws(' '::text, "Accepted_family__@TNRS__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 474 |
14327
|
aaronmk
|
WHEN ("*Accepted_name_rank" = 'genus'::text) THEN concat_ws(' '::text, "[accepted_]genus__@DwC__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 475 |
14304
|
aaronmk
|
ELSE "*Accepted_name_species"
|
| 476 |
|
|
END))),
|
| 477 |
14267
|
aaronmk
|
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))))),
|
| 478 |
14257
|
aaronmk
|
CONSTRAINT "[accepted_]specificEpithet__@DwC__@vegpath.org" CHECK ((NOT ("[accepted_]specificEpithet__@DwC__@vegpath.org" IS DISTINCT FROM "__accepted_{genus,specific_epithet}"[2]))),
|
| 479 |
14330
|
aaronmk
|
CONSTRAINT "[matched_]scientificName[_with_author]__@DwC__@vegpath.org" CHECK ((NOT ("[matched_]scientificName[_with_author]__@DwC__@vegpath.org" IS DISTINCT FROM ("matched~Name[_no_author]___@TNRS__@vegpath.org" || COALESCE((' '::text || "*Name_matched_author"), ''::text))))),
|
| 480 |
14278
|
aaronmk
|
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")))),
|
| 481 |
14303
|
aaronmk
|
CONSTRAINT "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org" CHECK ((NOT ("[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org" IS DISTINCT FROM "*Unmatched_terms"))),
|
| 482 |
14281
|
aaronmk
|
CONSTRAINT "[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" IS DISTINCT FROM
|
| 483 |
|
|
CASE
|
| 484 |
|
|
WHEN matched_has_accepted THEN "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"
|
| 485 |
|
|
ELSE "*Infraspecific_rank"
|
| 486 |
|
|
END))),
|
| 487 |
|
|
CONSTRAINT "[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" IS DISTINCT FROM
|
| 488 |
|
|
CASE
|
| 489 |
|
|
WHEN matched_has_accepted THEN "*Accepted_name_author"
|
| 490 |
|
|
ELSE "*Name_matched_author"
|
| 491 |
|
|
END))),
|
| 492 |
|
|
CONSTRAINT "[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" IS DISTINCT FROM
|
| 493 |
|
|
CASE
|
| 494 |
14323
|
aaronmk
|
WHEN matched_has_accepted THEN "Accepted_family__@TNRS__@vegpath.org"
|
| 495 |
14281
|
aaronmk
|
ELSE "*Name_matched_accepted_family"
|
| 496 |
|
|
END))),
|
| 497 |
|
|
CONSTRAINT "[scrubbed_]genus__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]genus__@DwC__@vegpath.org" IS DISTINCT FROM
|
| 498 |
|
|
CASE
|
| 499 |
|
|
WHEN matched_has_accepted THEN "[accepted_]genus__@DwC__@vegpath.org"
|
| 500 |
|
|
ELSE "*Genus_matched"
|
| 501 |
|
|
END))),
|
| 502 |
|
|
CONSTRAINT "[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" IS DISTINCT FROM
|
| 503 |
|
|
CASE
|
| 504 |
|
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
| 505 |
|
|
ELSE "*Infraspecific_epithet_matched"
|
| 506 |
|
|
END))),
|
| 507 |
14326
|
aaronmk
|
CONSTRAINT "[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" CHECK ((NOT ("[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" IS DISTINCT FROM
|
| 508 |
|
|
CASE
|
| 509 |
|
|
WHEN ("[scrubbed_]taxonRank__@DwC__@vegpath.org" = 'family'::text) THEN concat_ws(' '::text, "[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 510 |
|
|
WHEN ("[scrubbed_]taxonRank__@DwC__@vegpath.org" = 'genus'::text) THEN concat_ws(' '::text, "[scrubbed_]genus__@DwC__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 511 |
|
|
ELSE "[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org"
|
| 512 |
|
|
END))),
|
| 513 |
14281
|
aaronmk
|
CONSTRAINT "[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" IS DISTINCT FROM
|
| 514 |
|
|
CASE
|
| 515 |
|
|
WHEN matched_has_accepted THEN "*Accepted_name"
|
| 516 |
14330
|
aaronmk
|
ELSE "matched~Name[_no_author]___@TNRS__@vegpath.org"
|
| 517 |
14281
|
aaronmk
|
END))),
|
| 518 |
|
|
CONSTRAINT "[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" IS DISTINCT FROM
|
| 519 |
|
|
CASE
|
| 520 |
|
|
WHEN matched_has_accepted THEN "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"
|
| 521 |
|
|
ELSE "[matched_]scientificName[_with_author]__@DwC__@vegpath.org"
|
| 522 |
|
|
END))),
|
| 523 |
|
|
CONSTRAINT "[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" CHECK ((NOT ("[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" IS DISTINCT FROM
|
| 524 |
|
|
CASE
|
| 525 |
|
|
WHEN matched_has_accepted THEN "*Accepted_name_species"
|
| 526 |
|
|
ELSE "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"
|
| 527 |
|
|
END))),
|
| 528 |
|
|
CONSTRAINT "[scrubbed_]specificEpithet__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]specificEpithet__@DwC__@vegpath.org" IS DISTINCT FROM
|
| 529 |
|
|
CASE
|
| 530 |
|
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
| 531 |
|
|
ELSE "*Specific_epithet_matched"
|
| 532 |
|
|
END))),
|
| 533 |
|
|
CONSTRAINT "[scrubbed_]taxonRank__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]taxonRank__@DwC__@vegpath.org" IS DISTINCT FROM
|
| 534 |
|
|
CASE
|
| 535 |
|
|
WHEN matched_has_accepted THEN "*Accepted_name_rank"
|
| 536 |
|
|
ELSE "*Name_matched_rank"
|
| 537 |
|
|
END))),
|
| 538 |
14324
|
aaronmk
|
CONSTRAINT "[scrubbed_]taxonomicStatus__@DwC__@vegpath.org" CHECK ((NOT ("[scrubbed_]taxonomicStatus__@DwC__@vegpath.org" IS DISTINCT FROM map_taxonomic_status("*Taxonomic_status", "*Accepted_name")))),
|
| 539 |
14264
|
aaronmk
|
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)))),
|
| 540 |
14265
|
aaronmk
|
CONSTRAINT "__accepted_infraspecific_{rank,epithet}" CHECK ((NOT ("__accepted_infraspecific_{rank,epithet}" IS DISTINCT FROM regexp_split_to_array(__accepted_infraspecific_label, ' '::text)))),
|
| 541 |
14269
|
aaronmk
|
CONSTRAINT "__accepted_{genus,specific_epithet}" CHECK ((NOT ("__accepted_{genus,specific_epithet}" IS DISTINCT FROM regexp_split_to_array("*Accepted_name_species", ' '::text)))),
|
| 542 |
14329
|
aaronmk
|
CONSTRAINT matched_has_accepted CHECK ((NOT (matched_has_accepted IS DISTINCT FROM ("*Accepted_name" IS NOT NULL)))),
|
| 543 |
|
|
CONSTRAINT "matched~Name[_no_author]___@TNRS__@vegpath.org" CHECK ((NOT ("matched~Name[_no_author]___@TNRS__@vegpath.org" IS DISTINCT FROM NULLIF("*Name_matched", 'No suitable matches found.'::text))))
|
| 544 |
10778
|
aaronmk
|
);
|
| 545 |
7823
|
aaronmk
|
|
| 546 |
9759
|
aaronmk
|
|
| 547 |
10778
|
aaronmk
|
--
|
| 548 |
13861
|
aaronmk
|
-- Name: TABLE taxon_match; Type: COMMENT; Schema: TNRS; Owner: -
|
| 549 |
10778
|
aaronmk
|
--
|
| 550 |
7823
|
aaronmk
|
|
| 551 |
13861
|
aaronmk
|
COMMENT ON TABLE taxon_match IS '
|
| 552 |
14161
|
aaronmk
|
whenever columns are renamed:
|
| 553 |
14312
|
aaronmk
|
SELECT util.derived_cols_update(''"TNRS".taxon_match'');
|
| 554 |
14161
|
aaronmk
|
|
| 555 |
14332
|
aaronmk
|
to port derived column changes to vegbiendev:
|
| 556 |
|
|
SELECT util.derived_cols_export(''"TNRS".taxon_match'');
|
| 557 |
|
|
# run the returned SQL on vegbiendev
|
| 558 |
|
|
|
| 559 |
13577
|
aaronmk
|
to remove columns or add columns at the end:
|
| 560 |
|
|
$ rm=1 inputs/.TNRS/data.sql.run
|
| 561 |
|
|
$ make schemas/remake
|
| 562 |
|
|
|
| 563 |
|
|
to add columns in the middle:
|
| 564 |
|
|
make the changes in inputs/.TNRS/schema.sql
|
| 565 |
|
|
$ inputs/.TNRS/data.sql.run refresh # re-run TNRS
|
| 566 |
14313
|
aaronmk
|
SELECT util.derived_cols_update(''"TNRS".taxon_match'');
|
| 567 |
14317
|
aaronmk
|
SELECT util.derived_cols_repopulate(''"TNRS".taxon_match'');
|
| 568 |
13577
|
aaronmk
|
$ make schemas/remake
|
| 569 |
13582
|
aaronmk
|
|
| 570 |
|
|
to populate a new column:
|
| 571 |
13868
|
aaronmk
|
ALTER TABLE "TNRS".taxon_match DISABLE TRIGGER taxon_match__fill; --speeds up update
|
| 572 |
13861
|
aaronmk
|
UPDATE "TNRS".taxon_match SET "col" = value;
|
| 573 |
13582
|
aaronmk
|
-- runtime: 30 min ("5564201 rows affected, 1624829 ms execution time")
|
| 574 |
14132
|
aaronmk
|
CLUSTER "TNRS".taxon_match; -- ensure rows are exported in sorted order
|
| 575 |
13868
|
aaronmk
|
ALTER TABLE "TNRS".taxon_match ENABLE TRIGGER taxon_match__fill;
|
| 576 |
13861
|
aaronmk
|
VACUUM ANALYZE "TNRS".taxon_match --remove previous rows; runtime: 1.5 min ("92633 ms")
|
| 577 |
13584
|
aaronmk
|
|
| 578 |
|
|
to add a constraint: runtime: 3 min ("173620 ms")
|
| 579 |
13575
|
aaronmk
|
';
|
| 580 |
10778
|
aaronmk
|
|
| 581 |
|
|
|
| 582 |
|
|
--
|
| 583 |
14311
|
aaronmk
|
-- Name: COLUMN taxon_match."[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 584 |
|
|
--
|
| 585 |
|
|
|
| 586 |
|
|
COMMENT ON COLUMN taxon_match."[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org" IS '
|
| 587 |
|
|
= "*Unmatched_terms"
|
| 588 |
|
|
|
| 589 |
|
|
derived column
|
| 590 |
|
|
|
| 591 |
|
|
to modify expr:
|
| 592 |
|
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org'')::util.col, $$"*Unmatched_terms"$$)::util.derived_col_def);
|
| 593 |
|
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 594 |
|
|
|
| 595 |
|
|
to rename:
|
| 596 |
|
|
# rename column
|
| 597 |
|
|
# rename CHECK constraint
|
| 598 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 599 |
|
|
';
|
| 600 |
|
|
|
| 601 |
|
|
|
| 602 |
|
|
--
|
| 603 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 604 |
14254
|
aaronmk
|
--
|
| 605 |
|
|
|
| 606 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
| 607 |
14283
|
aaronmk
|
= ("*Genus_matched" || '' ''::text) || "*Specific_epithet_matched"
|
| 608 |
14254
|
aaronmk
|
|
| 609 |
14283
|
aaronmk
|
derived column
|
| 610 |
|
|
|
| 611 |
14275
|
aaronmk
|
to modify expr:
|
| 612 |
14282
|
aaronmk
|
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);
|
| 613 |
14258
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 614 |
14275
|
aaronmk
|
|
| 615 |
|
|
to rename:
|
| 616 |
|
|
# rename column
|
| 617 |
|
|
# rename CHECK constraint
|
| 618 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 619 |
14254
|
aaronmk
|
';
|
| 620 |
|
|
|
| 621 |
|
|
|
| 622 |
|
|
--
|
| 623 |
14329
|
aaronmk
|
-- Name: COLUMN taxon_match."matched~Name[_no_author]___@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 624 |
|
|
--
|
| 625 |
|
|
|
| 626 |
|
|
COMMENT ON COLUMN taxon_match."matched~Name[_no_author]___@TNRS__@vegpath.org" IS '
|
| 627 |
|
|
= NULLIF("*Name_matched", ''No suitable matches found.''::text)
|
| 628 |
|
|
|
| 629 |
|
|
derived column
|
| 630 |
|
|
|
| 631 |
|
|
to modify expr:
|
| 632 |
|
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''matched~Name[_no_author]___@TNRS__@vegpath.org'')::util.col, $$NULLIF("*Name_matched", ''No suitable matches found.''::text)$$)::util.derived_col_def);
|
| 633 |
|
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 634 |
|
|
|
| 635 |
|
|
to rename:
|
| 636 |
|
|
# rename column
|
| 637 |
|
|
# rename CHECK constraint
|
| 638 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 639 |
|
|
';
|
| 640 |
|
|
|
| 641 |
|
|
|
| 642 |
|
|
--
|
| 643 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match."[matched_]scientificName[_with_author]__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 644 |
14257
|
aaronmk
|
--
|
| 645 |
|
|
|
| 646 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match."[matched_]scientificName[_with_author]__@DwC__@vegpath.org" IS '
|
| 647 |
14330
|
aaronmk
|
= "matched~Name[_no_author]___@TNRS__@vegpath.org" || COALESCE(('' ''::text || "*Name_matched_author"), ''''::text)
|
| 648 |
14257
|
aaronmk
|
|
| 649 |
14283
|
aaronmk
|
derived column
|
| 650 |
|
|
|
| 651 |
14275
|
aaronmk
|
to modify expr:
|
| 652 |
14330
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[matched_]scientificName[_with_author]__@DwC__@vegpath.org'')::util.col, $$"matched~Name[_no_author]___@TNRS__@vegpath.org" || COALESCE(('' ''::text || "*Name_matched_author"), ''''::text)$$)::util.derived_col_def);
|
| 653 |
14258
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 654 |
14275
|
aaronmk
|
|
| 655 |
|
|
to rename:
|
| 656 |
|
|
# rename column
|
| 657 |
|
|
# rename CHECK constraint
|
| 658 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 659 |
14257
|
aaronmk
|
';
|
| 660 |
|
|
|
| 661 |
|
|
|
| 662 |
|
|
--
|
| 663 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match.matched_has_accepted; Type: COMMENT; Schema: TNRS; Owner: -
|
| 664 |
14257
|
aaronmk
|
--
|
| 665 |
|
|
|
| 666 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match.matched_has_accepted IS '
|
| 667 |
14283
|
aaronmk
|
= "*Accepted_name" IS NOT NULL
|
| 668 |
14257
|
aaronmk
|
|
| 669 |
14283
|
aaronmk
|
derived column
|
| 670 |
|
|
|
| 671 |
14275
|
aaronmk
|
to modify expr:
|
| 672 |
14279
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''matched_has_accepted'')::util.col, $$"*Accepted_name" IS NOT NULL$$)::util.derived_col_def);
|
| 673 |
14258
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 674 |
14275
|
aaronmk
|
|
| 675 |
|
|
to rename:
|
| 676 |
|
|
# rename column
|
| 677 |
|
|
# rename CHECK constraint
|
| 678 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 679 |
14257
|
aaronmk
|
';
|
| 680 |
|
|
|
| 681 |
|
|
|
| 682 |
|
|
--
|
| 683 |
14318
|
aaronmk
|
-- Name: COLUMN taxon_match."Accepted_family__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 684 |
|
|
--
|
| 685 |
|
|
|
| 686 |
|
|
COMMENT ON COLUMN taxon_match."Accepted_family__@TNRS__@vegpath.org" IS '
|
| 687 |
|
|
= COALESCE("*Accepted_name_family",
|
| 688 |
|
|
CASE
|
| 689 |
|
|
WHEN ("*Accepted_name_rank" = ''family''::text) THEN "*Accepted_name"
|
| 690 |
|
|
ELSE NULL::text
|
| 691 |
|
|
END)
|
| 692 |
|
|
|
| 693 |
|
|
derived column
|
| 694 |
|
|
|
| 695 |
|
|
to modify expr:
|
| 696 |
|
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''Accepted_family__@TNRS__@vegpath.org'')::util.col, $$COALESCE("*Accepted_name_family",
|
| 697 |
|
|
CASE
|
| 698 |
|
|
WHEN ("*Accepted_name_rank" = ''family''::text) THEN "*Accepted_name"
|
| 699 |
|
|
ELSE NULL::text
|
| 700 |
|
|
END)$$)::util.derived_col_def);
|
| 701 |
|
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 702 |
|
|
|
| 703 |
|
|
to rename:
|
| 704 |
|
|
# rename column
|
| 705 |
|
|
# rename CHECK constraint
|
| 706 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 707 |
|
|
';
|
| 708 |
|
|
|
| 709 |
|
|
|
| 710 |
|
|
--
|
| 711 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match."__accepted_{genus,specific_epithet}"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 712 |
14264
|
aaronmk
|
--
|
| 713 |
|
|
|
| 714 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match."__accepted_{genus,specific_epithet}" IS '
|
| 715 |
14283
|
aaronmk
|
= regexp_split_to_array("*Accepted_name_species", '' ''::text)
|
| 716 |
14264
|
aaronmk
|
|
| 717 |
14283
|
aaronmk
|
derived column
|
| 718 |
|
|
|
| 719 |
14275
|
aaronmk
|
to modify expr:
|
| 720 |
14279
|
aaronmk
|
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);
|
| 721 |
14264
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 722 |
14275
|
aaronmk
|
|
| 723 |
|
|
to rename:
|
| 724 |
|
|
# rename column
|
| 725 |
|
|
# rename CHECK constraint
|
| 726 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 727 |
14264
|
aaronmk
|
';
|
| 728 |
|
|
|
| 729 |
|
|
|
| 730 |
|
|
--
|
| 731 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match."[accepted_]genus__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 732 |
14265
|
aaronmk
|
--
|
| 733 |
|
|
|
| 734 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match."[accepted_]genus__@DwC__@vegpath.org" IS '
|
| 735 |
14325
|
aaronmk
|
= COALESCE("__accepted_{genus,specific_epithet}"[1],
|
| 736 |
|
|
CASE
|
| 737 |
|
|
WHEN ("*Accepted_name_rank" = ''genus''::text) THEN "*Accepted_name"
|
| 738 |
|
|
ELSE NULL::text
|
| 739 |
|
|
END)
|
| 740 |
14265
|
aaronmk
|
|
| 741 |
14283
|
aaronmk
|
derived column
|
| 742 |
|
|
|
| 743 |
14275
|
aaronmk
|
to modify expr:
|
| 744 |
14325
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[accepted_]genus__@DwC__@vegpath.org'')::util.col, $$COALESCE("__accepted_{genus,specific_epithet}"[1],
|
| 745 |
|
|
CASE
|
| 746 |
|
|
WHEN ("*Accepted_name_rank" = ''genus''::text) THEN "*Accepted_name"
|
| 747 |
|
|
ELSE NULL::text
|
| 748 |
|
|
END)$$)::util.derived_col_def);
|
| 749 |
14265
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 750 |
14275
|
aaronmk
|
|
| 751 |
|
|
to rename:
|
| 752 |
|
|
# rename column
|
| 753 |
|
|
# rename CHECK constraint
|
| 754 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 755 |
14265
|
aaronmk
|
';
|
| 756 |
|
|
|
| 757 |
|
|
|
| 758 |
|
|
--
|
| 759 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match."[accepted_]specificEpithet__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 760 |
14266
|
aaronmk
|
--
|
| 761 |
|
|
|
| 762 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match."[accepted_]specificEpithet__@DwC__@vegpath.org" IS '
|
| 763 |
14283
|
aaronmk
|
= "__accepted_{genus,specific_epithet}"[2]
|
| 764 |
14266
|
aaronmk
|
|
| 765 |
14283
|
aaronmk
|
derived column
|
| 766 |
|
|
|
| 767 |
14275
|
aaronmk
|
to modify expr:
|
| 768 |
14279
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[accepted_]specificEpithet__@DwC__@vegpath.org'')::util.col, $$"__accepted_{genus,specific_epithet}"[2]$$)::util.derived_col_def);
|
| 769 |
14266
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 770 |
14275
|
aaronmk
|
|
| 771 |
|
|
to rename:
|
| 772 |
|
|
# rename column
|
| 773 |
|
|
# rename CHECK constraint
|
| 774 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 775 |
14266
|
aaronmk
|
';
|
| 776 |
|
|
|
| 777 |
|
|
|
| 778 |
|
|
--
|
| 779 |
14311
|
aaronmk
|
-- Name: COLUMN taxon_match."[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 780 |
|
|
--
|
| 781 |
|
|
|
| 782 |
|
|
COMMENT ON COLUMN taxon_match."[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" IS '
|
| 783 |
|
|
= CASE
|
| 784 |
14323
|
aaronmk
|
WHEN ("*Accepted_name_rank" = ''family''::text) THEN concat_ws('' ''::text, "Accepted_family__@TNRS__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 785 |
14327
|
aaronmk
|
WHEN ("*Accepted_name_rank" = ''genus''::text) THEN concat_ws('' ''::text, "[accepted_]genus__@DwC__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 786 |
14311
|
aaronmk
|
ELSE "*Accepted_name_species"
|
| 787 |
|
|
END
|
| 788 |
|
|
|
| 789 |
|
|
derived column
|
| 790 |
|
|
|
| 791 |
|
|
to modify expr:
|
| 792 |
|
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org'')::util.col, $$CASE
|
| 793 |
14323
|
aaronmk
|
WHEN ("*Accepted_name_rank" = ''family''::text) THEN concat_ws('' ''::text, "Accepted_family__@TNRS__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 794 |
14327
|
aaronmk
|
WHEN ("*Accepted_name_rank" = ''genus''::text) THEN concat_ws('' ''::text, "[accepted_]genus__@DwC__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 795 |
14311
|
aaronmk
|
ELSE "*Accepted_name_species"
|
| 796 |
|
|
END$$)::util.derived_col_def);
|
| 797 |
|
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 798 |
|
|
|
| 799 |
|
|
to rename:
|
| 800 |
|
|
# rename column
|
| 801 |
|
|
# rename CHECK constraint
|
| 802 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 803 |
|
|
';
|
| 804 |
|
|
|
| 805 |
|
|
|
| 806 |
|
|
--
|
| 807 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match.__accepted_infraspecific_label; Type: COMMENT; Schema: TNRS; Owner: -
|
| 808 |
14266
|
aaronmk
|
--
|
| 809 |
|
|
|
| 810 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match.__accepted_infraspecific_label IS '
|
| 811 |
14283
|
aaronmk
|
= ltrim(NULLIF(util.remove_prefix("*Accepted_name_species", "*Accepted_name", require := true), ''''::text), '' ''::text)
|
| 812 |
14266
|
aaronmk
|
|
| 813 |
14283
|
aaronmk
|
derived column
|
| 814 |
|
|
|
| 815 |
14275
|
aaronmk
|
to modify expr:
|
| 816 |
14279
|
aaronmk
|
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);
|
| 817 |
14266
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 818 |
14275
|
aaronmk
|
|
| 819 |
|
|
to rename:
|
| 820 |
|
|
# rename column
|
| 821 |
|
|
# rename CHECK constraint
|
| 822 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 823 |
14266
|
aaronmk
|
';
|
| 824 |
|
|
|
| 825 |
|
|
|
| 826 |
|
|
--
|
| 827 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match."__accepted_infraspecific_{rank,epithet}"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 828 |
14267
|
aaronmk
|
--
|
| 829 |
|
|
|
| 830 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match."__accepted_infraspecific_{rank,epithet}" IS '
|
| 831 |
14283
|
aaronmk
|
= regexp_split_to_array(__accepted_infraspecific_label, '' ''::text)
|
| 832 |
14267
|
aaronmk
|
|
| 833 |
14283
|
aaronmk
|
derived column
|
| 834 |
|
|
|
| 835 |
14275
|
aaronmk
|
to modify expr:
|
| 836 |
14279
|
aaronmk
|
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);
|
| 837 |
14267
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 838 |
14275
|
aaronmk
|
|
| 839 |
|
|
to rename:
|
| 840 |
|
|
# rename column
|
| 841 |
|
|
# rename CHECK constraint
|
| 842 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 843 |
14267
|
aaronmk
|
';
|
| 844 |
|
|
|
| 845 |
|
|
|
| 846 |
|
|
--
|
| 847 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 848 |
14267
|
aaronmk
|
--
|
| 849 |
|
|
|
| 850 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" IS '
|
| 851 |
14283
|
aaronmk
|
= "__accepted_infraspecific_{rank,epithet}"[1]
|
| 852 |
14267
|
aaronmk
|
|
| 853 |
14283
|
aaronmk
|
derived column
|
| 854 |
|
|
|
| 855 |
14275
|
aaronmk
|
to modify expr:
|
| 856 |
14279
|
aaronmk
|
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);
|
| 857 |
14267
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 858 |
14275
|
aaronmk
|
|
| 859 |
|
|
to rename:
|
| 860 |
|
|
# rename column
|
| 861 |
|
|
# rename CHECK constraint
|
| 862 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 863 |
14267
|
aaronmk
|
';
|
| 864 |
|
|
|
| 865 |
|
|
|
| 866 |
|
|
--
|
| 867 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match."[accepted_]infraspecificEpithet__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 868 |
14269
|
aaronmk
|
--
|
| 869 |
|
|
|
| 870 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match."[accepted_]infraspecificEpithet__@DwC__@vegpath.org" IS '
|
| 871 |
14283
|
aaronmk
|
= "__accepted_infraspecific_{rank,epithet}"[2]
|
| 872 |
14269
|
aaronmk
|
|
| 873 |
14283
|
aaronmk
|
derived column
|
| 874 |
|
|
|
| 875 |
14275
|
aaronmk
|
to modify expr:
|
| 876 |
14279
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[accepted_]infraspecificEpithet__@DwC__@vegpath.org'')::util.col, $$"__accepted_infraspecific_{rank,epithet}"[2]$$)::util.derived_col_def);
|
| 877 |
14269
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 878 |
14275
|
aaronmk
|
|
| 879 |
|
|
to rename:
|
| 880 |
|
|
# rename column
|
| 881 |
|
|
# rename CHECK constraint
|
| 882 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 883 |
14269
|
aaronmk
|
';
|
| 884 |
|
|
|
| 885 |
|
|
|
| 886 |
|
|
--
|
| 887 |
14279
|
aaronmk
|
-- Name: COLUMN taxon_match."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 888 |
14278
|
aaronmk
|
--
|
| 889 |
|
|
|
| 890 |
14279
|
aaronmk
|
COMMENT ON COLUMN taxon_match."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org" IS '
|
| 891 |
14283
|
aaronmk
|
= "*Accepted_name" || COALESCE(('' ''::text || "*Accepted_name_author"), ''''::text)
|
| 892 |
14278
|
aaronmk
|
|
| 893 |
14283
|
aaronmk
|
derived column
|
| 894 |
|
|
|
| 895 |
14278
|
aaronmk
|
to modify expr:
|
| 896 |
14279
|
aaronmk
|
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);
|
| 897 |
14278
|
aaronmk
|
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 |
14328
|
aaronmk
|
-- Name: COLUMN taxon_match."[scrubbed_]taxonomicStatus__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 908 |
|
|
--
|
| 909 |
|
|
|
| 910 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]taxonomicStatus__@DwC__@vegpath.org" IS '
|
| 911 |
|
|
= "TNRS".map_taxonomic_status("*Taxonomic_status", "*Accepted_name")
|
| 912 |
|
|
|
| 913 |
|
|
derived column
|
| 914 |
|
|
|
| 915 |
|
|
to modify expr:
|
| 916 |
|
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]taxonomicStatus__@DwC__@vegpath.org'')::util.col, $$"TNRS".map_taxonomic_status("*Taxonomic_status", "*Accepted_name")$$)::util.derived_col_def);
|
| 917 |
|
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 918 |
|
|
|
| 919 |
|
|
to rename:
|
| 920 |
|
|
# rename column
|
| 921 |
|
|
# rename CHECK constraint
|
| 922 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 923 |
|
|
';
|
| 924 |
|
|
|
| 925 |
|
|
|
| 926 |
|
|
--
|
| 927 |
14281
|
aaronmk
|
-- Name: COLUMN taxon_match."[scrubbed_]taxonRank__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 928 |
|
|
--
|
| 929 |
|
|
|
| 930 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]taxonRank__@DwC__@vegpath.org" IS '
|
| 931 |
14283
|
aaronmk
|
= CASE
|
| 932 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "*Accepted_name_rank"
|
| 933 |
|
|
ELSE "*Name_matched_rank"
|
| 934 |
|
|
END
|
| 935 |
14281
|
aaronmk
|
|
| 936 |
14283
|
aaronmk
|
derived column
|
| 937 |
|
|
|
| 938 |
14281
|
aaronmk
|
to modify expr:
|
| 939 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]taxonRank__@DwC__@vegpath.org'')::util.col, $$CASE
|
| 940 |
|
|
WHEN matched_has_accepted THEN "*Accepted_name_rank"
|
| 941 |
|
|
ELSE "*Name_matched_rank"
|
| 942 |
|
|
END$$)::util.derived_col_def);
|
| 943 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 944 |
|
|
|
| 945 |
|
|
to rename:
|
| 946 |
|
|
# rename column
|
| 947 |
|
|
# rename CHECK constraint
|
| 948 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 949 |
|
|
';
|
| 950 |
|
|
|
| 951 |
|
|
|
| 952 |
|
|
--
|
| 953 |
|
|
-- Name: COLUMN taxon_match."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 954 |
|
|
--
|
| 955 |
|
|
|
| 956 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
| 957 |
14283
|
aaronmk
|
= CASE
|
| 958 |
14323
|
aaronmk
|
WHEN matched_has_accepted THEN "Accepted_family__@TNRS__@vegpath.org"
|
| 959 |
14282
|
aaronmk
|
ELSE "*Name_matched_accepted_family"
|
| 960 |
|
|
END
|
| 961 |
14281
|
aaronmk
|
|
| 962 |
14283
|
aaronmk
|
derived column
|
| 963 |
|
|
|
| 964 |
14281
|
aaronmk
|
to modify expr:
|
| 965 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org'')::util.col, $$CASE
|
| 966 |
14323
|
aaronmk
|
WHEN matched_has_accepted THEN "Accepted_family__@TNRS__@vegpath.org"
|
| 967 |
14282
|
aaronmk
|
ELSE "*Name_matched_accepted_family"
|
| 968 |
|
|
END$$)::util.derived_col_def);
|
| 969 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 970 |
|
|
|
| 971 |
|
|
to rename:
|
| 972 |
|
|
# rename column
|
| 973 |
|
|
# rename CHECK constraint
|
| 974 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 975 |
|
|
';
|
| 976 |
|
|
|
| 977 |
|
|
|
| 978 |
|
|
--
|
| 979 |
|
|
-- Name: COLUMN taxon_match."[scrubbed_]genus__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 980 |
|
|
--
|
| 981 |
|
|
|
| 982 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]genus__@DwC__@vegpath.org" IS '
|
| 983 |
14283
|
aaronmk
|
= CASE
|
| 984 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]genus__@DwC__@vegpath.org"
|
| 985 |
|
|
ELSE "*Genus_matched"
|
| 986 |
|
|
END
|
| 987 |
14281
|
aaronmk
|
|
| 988 |
14283
|
aaronmk
|
derived column
|
| 989 |
|
|
|
| 990 |
14281
|
aaronmk
|
to modify expr:
|
| 991 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]genus__@DwC__@vegpath.org'')::util.col, $$CASE
|
| 992 |
|
|
WHEN matched_has_accepted THEN "[accepted_]genus__@DwC__@vegpath.org"
|
| 993 |
|
|
ELSE "*Genus_matched"
|
| 994 |
|
|
END$$)::util.derived_col_def);
|
| 995 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 996 |
|
|
|
| 997 |
|
|
to rename:
|
| 998 |
|
|
# rename column
|
| 999 |
|
|
# rename CHECK constraint
|
| 1000 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 1001 |
|
|
';
|
| 1002 |
|
|
|
| 1003 |
|
|
|
| 1004 |
|
|
--
|
| 1005 |
|
|
-- Name: COLUMN taxon_match."[scrubbed_]specificEpithet__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1006 |
|
|
--
|
| 1007 |
|
|
|
| 1008 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]specificEpithet__@DwC__@vegpath.org" IS '
|
| 1009 |
14283
|
aaronmk
|
= CASE
|
| 1010 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
| 1011 |
|
|
ELSE "*Specific_epithet_matched"
|
| 1012 |
|
|
END
|
| 1013 |
14281
|
aaronmk
|
|
| 1014 |
14283
|
aaronmk
|
derived column
|
| 1015 |
|
|
|
| 1016 |
14281
|
aaronmk
|
to modify expr:
|
| 1017 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]specificEpithet__@DwC__@vegpath.org'')::util.col, $$CASE
|
| 1018 |
|
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
| 1019 |
|
|
ELSE "*Specific_epithet_matched"
|
| 1020 |
|
|
END$$)::util.derived_col_def);
|
| 1021 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 1022 |
|
|
|
| 1023 |
|
|
to rename:
|
| 1024 |
|
|
# rename column
|
| 1025 |
|
|
# rename CHECK constraint
|
| 1026 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 1027 |
|
|
';
|
| 1028 |
|
|
|
| 1029 |
|
|
|
| 1030 |
|
|
--
|
| 1031 |
|
|
-- Name: COLUMN taxon_match."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1032 |
|
|
--
|
| 1033 |
|
|
|
| 1034 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
| 1035 |
14283
|
aaronmk
|
= CASE
|
| 1036 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "*Accepted_name_species"
|
| 1037 |
|
|
ELSE "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"
|
| 1038 |
|
|
END
|
| 1039 |
14281
|
aaronmk
|
|
| 1040 |
14283
|
aaronmk
|
derived column
|
| 1041 |
|
|
|
| 1042 |
14281
|
aaronmk
|
to modify expr:
|
| 1043 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org'')::util.col, $$CASE
|
| 1044 |
|
|
WHEN matched_has_accepted THEN "*Accepted_name_species"
|
| 1045 |
|
|
ELSE "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"
|
| 1046 |
|
|
END$$)::util.derived_col_def);
|
| 1047 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 1048 |
|
|
|
| 1049 |
|
|
to rename:
|
| 1050 |
|
|
# rename column
|
| 1051 |
|
|
# rename CHECK constraint
|
| 1052 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 1053 |
|
|
';
|
| 1054 |
|
|
|
| 1055 |
|
|
|
| 1056 |
|
|
--
|
| 1057 |
14328
|
aaronmk
|
-- Name: COLUMN taxon_match."[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1058 |
|
|
--
|
| 1059 |
|
|
|
| 1060 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org" IS '
|
| 1061 |
|
|
= CASE
|
| 1062 |
|
|
WHEN ("[scrubbed_]taxonRank__@DwC__@vegpath.org" = ''family''::text) THEN concat_ws('' ''::text, "[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 1063 |
|
|
WHEN ("[scrubbed_]taxonRank__@DwC__@vegpath.org" = ''genus''::text) THEN concat_ws('' ''::text, "[scrubbed_]genus__@DwC__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 1064 |
|
|
ELSE "[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org"
|
| 1065 |
|
|
END
|
| 1066 |
|
|
|
| 1067 |
|
|
derived column
|
| 1068 |
|
|
|
| 1069 |
|
|
to modify expr:
|
| 1070 |
|
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org'')::util.col, $$CASE
|
| 1071 |
|
|
WHEN ("[scrubbed_]taxonRank__@DwC__@vegpath.org" = ''family''::text) THEN concat_ws('' ''::text, "[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 1072 |
|
|
WHEN ("[scrubbed_]taxonRank__@DwC__@vegpath.org" = ''genus''::text) THEN concat_ws('' ''::text, "[scrubbed_]genus__@DwC__@vegpath.org", "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org")
|
| 1073 |
|
|
ELSE "[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org"
|
| 1074 |
|
|
END$$)::util.derived_col_def);
|
| 1075 |
|
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 1076 |
|
|
|
| 1077 |
|
|
to rename:
|
| 1078 |
|
|
# rename column
|
| 1079 |
|
|
# rename CHECK constraint
|
| 1080 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 1081 |
|
|
';
|
| 1082 |
|
|
|
| 1083 |
|
|
|
| 1084 |
|
|
--
|
| 1085 |
14281
|
aaronmk
|
-- Name: COLUMN taxon_match."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1086 |
|
|
--
|
| 1087 |
|
|
|
| 1088 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org" IS '
|
| 1089 |
14283
|
aaronmk
|
= CASE
|
| 1090 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"
|
| 1091 |
|
|
ELSE "*Infraspecific_rank"
|
| 1092 |
|
|
END
|
| 1093 |
14281
|
aaronmk
|
|
| 1094 |
14283
|
aaronmk
|
derived column
|
| 1095 |
|
|
|
| 1096 |
14281
|
aaronmk
|
to modify expr:
|
| 1097 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org'')::util.col, $$CASE
|
| 1098 |
|
|
WHEN matched_has_accepted THEN "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org"
|
| 1099 |
|
|
ELSE "*Infraspecific_rank"
|
| 1100 |
|
|
END$$)::util.derived_col_def);
|
| 1101 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 1102 |
|
|
|
| 1103 |
|
|
to rename:
|
| 1104 |
|
|
# rename column
|
| 1105 |
|
|
# rename CHECK constraint
|
| 1106 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 1107 |
|
|
';
|
| 1108 |
|
|
|
| 1109 |
|
|
|
| 1110 |
|
|
--
|
| 1111 |
|
|
-- Name: COLUMN taxon_match."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1112 |
|
|
--
|
| 1113 |
|
|
|
| 1114 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org" IS '
|
| 1115 |
14283
|
aaronmk
|
= CASE
|
| 1116 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
| 1117 |
|
|
ELSE "*Infraspecific_epithet_matched"
|
| 1118 |
|
|
END
|
| 1119 |
14281
|
aaronmk
|
|
| 1120 |
14283
|
aaronmk
|
derived column
|
| 1121 |
|
|
|
| 1122 |
14281
|
aaronmk
|
to modify expr:
|
| 1123 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org'')::util.col, $$CASE
|
| 1124 |
|
|
WHEN matched_has_accepted THEN "[accepted_]specificEpithet__@DwC__@vegpath.org"
|
| 1125 |
|
|
ELSE "*Infraspecific_epithet_matched"
|
| 1126 |
|
|
END$$)::util.derived_col_def);
|
| 1127 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 1128 |
|
|
|
| 1129 |
|
|
to rename:
|
| 1130 |
|
|
# rename column
|
| 1131 |
|
|
# rename CHECK constraint
|
| 1132 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 1133 |
|
|
';
|
| 1134 |
|
|
|
| 1135 |
|
|
|
| 1136 |
|
|
--
|
| 1137 |
|
|
-- Name: COLUMN taxon_match."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1138 |
|
|
--
|
| 1139 |
|
|
|
| 1140 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
| 1141 |
14283
|
aaronmk
|
= CASE
|
| 1142 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "*Accepted_name"
|
| 1143 |
14330
|
aaronmk
|
ELSE "matched~Name[_no_author]___@TNRS__@vegpath.org"
|
| 1144 |
14282
|
aaronmk
|
END
|
| 1145 |
14281
|
aaronmk
|
|
| 1146 |
14283
|
aaronmk
|
derived column
|
| 1147 |
|
|
|
| 1148 |
14281
|
aaronmk
|
to modify expr:
|
| 1149 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org'')::util.col, $$CASE
|
| 1150 |
|
|
WHEN matched_has_accepted THEN "*Accepted_name"
|
| 1151 |
14330
|
aaronmk
|
ELSE "matched~Name[_no_author]___@TNRS__@vegpath.org"
|
| 1152 |
14282
|
aaronmk
|
END$$)::util.derived_col_def);
|
| 1153 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 1154 |
|
|
|
| 1155 |
|
|
to rename:
|
| 1156 |
|
|
# rename column
|
| 1157 |
|
|
# rename CHECK constraint
|
| 1158 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 1159 |
|
|
';
|
| 1160 |
|
|
|
| 1161 |
|
|
|
| 1162 |
|
|
--
|
| 1163 |
|
|
-- Name: COLUMN taxon_match."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1164 |
|
|
--
|
| 1165 |
|
|
|
| 1166 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org" IS '
|
| 1167 |
14283
|
aaronmk
|
= CASE
|
| 1168 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "*Accepted_name_author"
|
| 1169 |
|
|
ELSE "*Name_matched_author"
|
| 1170 |
|
|
END
|
| 1171 |
14281
|
aaronmk
|
|
| 1172 |
14283
|
aaronmk
|
derived column
|
| 1173 |
|
|
|
| 1174 |
14281
|
aaronmk
|
to modify expr:
|
| 1175 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org'')::util.col, $$CASE
|
| 1176 |
|
|
WHEN matched_has_accepted THEN "*Accepted_name_author"
|
| 1177 |
|
|
ELSE "*Name_matched_author"
|
| 1178 |
|
|
END$$)::util.derived_col_def);
|
| 1179 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 1180 |
|
|
|
| 1181 |
|
|
to rename:
|
| 1182 |
|
|
# rename column
|
| 1183 |
|
|
# rename CHECK constraint
|
| 1184 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 1185 |
|
|
';
|
| 1186 |
|
|
|
| 1187 |
|
|
|
| 1188 |
|
|
--
|
| 1189 |
|
|
-- Name: COLUMN taxon_match."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1190 |
|
|
--
|
| 1191 |
|
|
|
| 1192 |
|
|
COMMENT ON COLUMN taxon_match."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org" IS '
|
| 1193 |
14283
|
aaronmk
|
= CASE
|
| 1194 |
14282
|
aaronmk
|
WHEN matched_has_accepted THEN "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"
|
| 1195 |
|
|
ELSE "[matched_]scientificName[_with_author]__@DwC__@vegpath.org"
|
| 1196 |
|
|
END
|
| 1197 |
14281
|
aaronmk
|
|
| 1198 |
14283
|
aaronmk
|
derived column
|
| 1199 |
|
|
|
| 1200 |
14281
|
aaronmk
|
to modify expr:
|
| 1201 |
14282
|
aaronmk
|
SELECT util.derived_col_update(((''"TNRS".taxon_match'', ''[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org'')::util.col, $$CASE
|
| 1202 |
|
|
WHEN matched_has_accepted THEN "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"
|
| 1203 |
|
|
ELSE "[matched_]scientificName[_with_author]__@DwC__@vegpath.org"
|
| 1204 |
|
|
END$$)::util.derived_col_def);
|
| 1205 |
14281
|
aaronmk
|
SELECT util.derived_cols_populate(''"TNRS".taxon_match''::regclass);
|
| 1206 |
|
|
|
| 1207 |
|
|
to rename:
|
| 1208 |
|
|
# rename column
|
| 1209 |
|
|
# rename CHECK constraint
|
| 1210 |
|
|
SELECT util.derived_cols_update(''"TNRS".taxon_match''::regclass);
|
| 1211 |
|
|
';
|
| 1212 |
|
|
|
| 1213 |
|
|
|
| 1214 |
|
|
--
|
| 1215 |
13878
|
aaronmk
|
-- Name: taxon_best_match; Type: VIEW; Schema: TNRS; Owner: -
|
| 1216 |
|
|
--
|
| 1217 |
|
|
|
| 1218 |
|
|
CREATE VIEW taxon_best_match AS
|
| 1219 |
|
|
SELECT taxon_match.batch,
|
| 1220 |
|
|
taxon_match.match_num,
|
| 1221 |
14111
|
aaronmk
|
taxon_match."*Name_number",
|
| 1222 |
|
|
taxon_match."*Name_submitted",
|
| 1223 |
|
|
taxon_match."*Overall_score",
|
| 1224 |
|
|
taxon_match."*Name_matched",
|
| 1225 |
|
|
taxon_match."*Name_matched_rank",
|
| 1226 |
|
|
taxon_match."*Name_score",
|
| 1227 |
|
|
taxon_match."*Name_matched_author",
|
| 1228 |
|
|
taxon_match."*Name_matched_url",
|
| 1229 |
|
|
taxon_match."*Author_matched",
|
| 1230 |
|
|
taxon_match."*Author_score",
|
| 1231 |
|
|
taxon_match."*Family_matched",
|
| 1232 |
|
|
taxon_match."*Family_score",
|
| 1233 |
|
|
taxon_match."*Name_matched_accepted_family",
|
| 1234 |
|
|
taxon_match."*Genus_matched",
|
| 1235 |
|
|
taxon_match."*Genus_score",
|
| 1236 |
|
|
taxon_match."*Specific_epithet_matched",
|
| 1237 |
|
|
taxon_match."*Specific_epithet_score",
|
| 1238 |
|
|
taxon_match."*Infraspecific_rank",
|
| 1239 |
|
|
taxon_match."*Infraspecific_epithet_matched",
|
| 1240 |
|
|
taxon_match."*Infraspecific_epithet_score",
|
| 1241 |
|
|
taxon_match."*Infraspecific_rank_2",
|
| 1242 |
|
|
taxon_match."*Infraspecific_epithet_2_matched",
|
| 1243 |
|
|
taxon_match."*Infraspecific_epithet_2_score",
|
| 1244 |
|
|
taxon_match."*Annotations",
|
| 1245 |
|
|
taxon_match."*Unmatched_terms",
|
| 1246 |
|
|
taxon_match."*Taxonomic_status",
|
| 1247 |
|
|
taxon_match."*Accepted_name",
|
| 1248 |
|
|
taxon_match."*Accepted_name_author",
|
| 1249 |
|
|
taxon_match."*Accepted_name_rank",
|
| 1250 |
|
|
taxon_match."*Accepted_name_url",
|
| 1251 |
|
|
taxon_match."*Accepted_name_species",
|
| 1252 |
|
|
taxon_match."*Accepted_name_family",
|
| 1253 |
|
|
taxon_match."*Selected",
|
| 1254 |
|
|
taxon_match."*Source",
|
| 1255 |
|
|
taxon_match."*Warnings",
|
| 1256 |
|
|
taxon_match."*Accepted_name_lsid",
|
| 1257 |
13878
|
aaronmk
|
taxon_match.is_valid_match,
|
| 1258 |
14268
|
aaronmk
|
taxon_match.scrubbed_unique_taxon_name,
|
| 1259 |
14284
|
aaronmk
|
taxon_match."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1260 |
|
|
taxon_match."[matched_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1261 |
|
|
taxon_match.matched_has_accepted,
|
| 1262 |
14268
|
aaronmk
|
taxon_match."__accepted_{genus,specific_epithet}",
|
| 1263 |
|
|
taxon_match."[accepted_]genus__@DwC__@vegpath.org",
|
| 1264 |
|
|
taxon_match."[accepted_]specificEpithet__@DwC__@vegpath.org",
|
| 1265 |
|
|
taxon_match.__accepted_infraspecific_label,
|
| 1266 |
|
|
taxon_match."__accepted_infraspecific_{rank,epithet}",
|
| 1267 |
|
|
taxon_match."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
| 1268 |
|
|
taxon_match."[accepted_]infraspecificEpithet__@DwC__@vegpath.org",
|
| 1269 |
14284
|
aaronmk
|
taxon_match."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1270 |
|
|
taxon_match."[scrubbed_]taxonRank__@DwC__@vegpath.org",
|
| 1271 |
|
|
taxon_match."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1272 |
|
|
taxon_match."[scrubbed_]genus__@DwC__@vegpath.org",
|
| 1273 |
|
|
taxon_match."[scrubbed_]specificEpithet__@DwC__@vegpath.org",
|
| 1274 |
|
|
taxon_match."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1275 |
|
|
taxon_match."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
| 1276 |
|
|
taxon_match."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org",
|
| 1277 |
|
|
taxon_match."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1278 |
|
|
taxon_match."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1279 |
|
|
taxon_match."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org"
|
| 1280 |
13878
|
aaronmk
|
FROM taxon_match
|
| 1281 |
14111
|
aaronmk
|
WHERE (taxon_match."*Selected" = 'true'::text);
|
| 1282 |
13878
|
aaronmk
|
|
| 1283 |
|
|
|
| 1284 |
|
|
--
|
| 1285 |
|
|
-- Name: VIEW taxon_best_match; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1286 |
|
|
--
|
| 1287 |
|
|
|
| 1288 |
|
|
COMMENT ON VIEW taxon_best_match IS '
|
| 1289 |
|
|
to modify:
|
| 1290 |
|
|
SELECT util.recreate_view(''"TNRS"."taxon_best_match"'', $$
|
| 1291 |
|
|
SELECT __
|
| 1292 |
|
|
$$);
|
| 1293 |
|
|
';
|
| 1294 |
|
|
|
| 1295 |
|
|
|
| 1296 |
|
|
--
|
| 1297 |
10778
|
aaronmk
|
-- Name: MatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
|
| 1298 |
|
|
--
|
| 1299 |
|
|
|
| 1300 |
|
|
CREATE VIEW "MatchedTaxon" AS
|
| 1301 |
14110
|
aaronmk
|
SELECT taxon_best_match.batch,
|
| 1302 |
|
|
taxon_best_match.match_num,
|
| 1303 |
14111
|
aaronmk
|
taxon_best_match."*Name_number",
|
| 1304 |
|
|
taxon_best_match."*Name_submitted",
|
| 1305 |
|
|
taxon_best_match."*Overall_score",
|
| 1306 |
|
|
taxon_best_match."*Name_matched",
|
| 1307 |
|
|
taxon_best_match."*Name_matched_rank",
|
| 1308 |
|
|
taxon_best_match."*Name_score",
|
| 1309 |
|
|
taxon_best_match."*Name_matched_author",
|
| 1310 |
|
|
taxon_best_match."*Name_matched_url",
|
| 1311 |
|
|
taxon_best_match."*Author_matched",
|
| 1312 |
|
|
taxon_best_match."*Author_score",
|
| 1313 |
|
|
taxon_best_match."*Family_matched",
|
| 1314 |
|
|
taxon_best_match."*Family_score",
|
| 1315 |
|
|
taxon_best_match."*Name_matched_accepted_family",
|
| 1316 |
|
|
taxon_best_match."*Genus_matched",
|
| 1317 |
|
|
taxon_best_match."*Genus_score",
|
| 1318 |
|
|
taxon_best_match."*Specific_epithet_matched",
|
| 1319 |
|
|
taxon_best_match."*Specific_epithet_score",
|
| 1320 |
|
|
taxon_best_match."*Infraspecific_rank",
|
| 1321 |
|
|
taxon_best_match."*Infraspecific_epithet_matched",
|
| 1322 |
|
|
taxon_best_match."*Infraspecific_epithet_score",
|
| 1323 |
|
|
taxon_best_match."*Infraspecific_rank_2",
|
| 1324 |
|
|
taxon_best_match."*Infraspecific_epithet_2_matched",
|
| 1325 |
|
|
taxon_best_match."*Infraspecific_epithet_2_score",
|
| 1326 |
|
|
taxon_best_match."*Annotations",
|
| 1327 |
|
|
taxon_best_match."*Unmatched_terms",
|
| 1328 |
|
|
taxon_best_match."*Taxonomic_status",
|
| 1329 |
|
|
taxon_best_match."*Accepted_name",
|
| 1330 |
|
|
taxon_best_match."*Accepted_name_author",
|
| 1331 |
|
|
taxon_best_match."*Accepted_name_rank",
|
| 1332 |
|
|
taxon_best_match."*Accepted_name_url",
|
| 1333 |
|
|
taxon_best_match."*Accepted_name_species",
|
| 1334 |
|
|
taxon_best_match."*Accepted_name_family",
|
| 1335 |
|
|
taxon_best_match."*Selected",
|
| 1336 |
|
|
taxon_best_match."*Source",
|
| 1337 |
|
|
taxon_best_match."*Warnings",
|
| 1338 |
|
|
taxon_best_match."*Accepted_name_lsid",
|
| 1339 |
14110
|
aaronmk
|
taxon_best_match.is_valid_match,
|
| 1340 |
|
|
taxon_best_match.scrubbed_unique_taxon_name,
|
| 1341 |
14284
|
aaronmk
|
taxon_best_match."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1342 |
|
|
taxon_best_match."[matched_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1343 |
|
|
taxon_best_match.matched_has_accepted,
|
| 1344 |
14268
|
aaronmk
|
taxon_best_match."__accepted_{genus,specific_epithet}",
|
| 1345 |
|
|
taxon_best_match."[accepted_]genus__@DwC__@vegpath.org",
|
| 1346 |
|
|
taxon_best_match."[accepted_]specificEpithet__@DwC__@vegpath.org",
|
| 1347 |
|
|
taxon_best_match.__accepted_infraspecific_label,
|
| 1348 |
|
|
taxon_best_match."__accepted_infraspecific_{rank,epithet}",
|
| 1349 |
|
|
taxon_best_match."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
| 1350 |
|
|
taxon_best_match."[accepted_]infraspecificEpithet__@DwC__@vegpath.org",
|
| 1351 |
|
|
taxon_best_match."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1352 |
14284
|
aaronmk
|
taxon_best_match."[scrubbed_]taxonRank__@DwC__@vegpath.org",
|
| 1353 |
|
|
taxon_best_match."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1354 |
|
|
taxon_best_match."[scrubbed_]genus__@DwC__@vegpath.org",
|
| 1355 |
|
|
taxon_best_match."[scrubbed_]specificEpithet__@DwC__@vegpath.org",
|
| 1356 |
|
|
taxon_best_match."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1357 |
|
|
taxon_best_match."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
| 1358 |
|
|
taxon_best_match."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org",
|
| 1359 |
|
|
taxon_best_match."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1360 |
|
|
taxon_best_match."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1361 |
|
|
taxon_best_match."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1362 |
14111
|
aaronmk
|
map_taxonomic_status(taxon_best_match."*Taxonomic_status", taxon_best_match."*Accepted_name") AS "taxonomicStatus",
|
| 1363 |
13498
|
aaronmk
|
CASE
|
| 1364 |
14111
|
aaronmk
|
WHEN (taxon_best_match."*Accepted_name_rank" = 'family'::text) THEN concat_ws(' '::text, taxon_best_match."*Accepted_name_family", taxon_best_match."*Unmatched_terms")
|
| 1365 |
|
|
WHEN (taxon_best_match."*Accepted_name_rank" = 'genus'::text) THEN concat_ws(' '::text, taxon_best_match."*Accepted_name", taxon_best_match."*Unmatched_terms")
|
| 1366 |
|
|
ELSE taxon_best_match."*Accepted_name_species"
|
| 1367 |
13498
|
aaronmk
|
END AS accepted_morphospecies_binomial
|
| 1368 |
14110
|
aaronmk
|
FROM taxon_best_match;
|
| 1369 |
10778
|
aaronmk
|
|
| 1370 |
|
|
|
| 1371 |
|
|
--
|
| 1372 |
13498
|
aaronmk
|
-- Name: VIEW "MatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1373 |
|
|
--
|
| 1374 |
|
|
|
| 1375 |
|
|
COMMENT ON VIEW "MatchedTaxon" IS '
|
| 1376 |
13501
|
aaronmk
|
to modify:
|
| 1377 |
13845
|
aaronmk
|
SELECT util.recreate_view(''"TNRS"."MatchedTaxon"'', $$
|
| 1378 |
13647
|
aaronmk
|
SELECT __
|
| 1379 |
13501
|
aaronmk
|
$$);
|
| 1380 |
13498
|
aaronmk
|
';
|
| 1381 |
|
|
|
| 1382 |
|
|
|
| 1383 |
|
|
--
|
| 1384 |
10778
|
aaronmk
|
-- Name: ValidMatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
|
| 1385 |
|
|
--
|
| 1386 |
|
|
|
| 1387 |
|
|
CREATE VIEW "ValidMatchedTaxon" AS
|
| 1388 |
14108
|
aaronmk
|
SELECT "MatchedTaxon".batch,
|
| 1389 |
14105
|
aaronmk
|
"MatchedTaxon".match_num,
|
| 1390 |
14111
|
aaronmk
|
"MatchedTaxon"."*Name_number",
|
| 1391 |
|
|
"MatchedTaxon"."*Name_submitted",
|
| 1392 |
|
|
"MatchedTaxon"."*Overall_score",
|
| 1393 |
|
|
"MatchedTaxon"."*Name_matched",
|
| 1394 |
|
|
"MatchedTaxon"."*Name_matched_rank",
|
| 1395 |
|
|
"MatchedTaxon"."*Name_score",
|
| 1396 |
|
|
"MatchedTaxon"."*Name_matched_author",
|
| 1397 |
|
|
"MatchedTaxon"."*Name_matched_url",
|
| 1398 |
|
|
"MatchedTaxon"."*Author_matched",
|
| 1399 |
|
|
"MatchedTaxon"."*Author_score",
|
| 1400 |
|
|
"MatchedTaxon"."*Family_matched",
|
| 1401 |
|
|
"MatchedTaxon"."*Family_score",
|
| 1402 |
|
|
"MatchedTaxon"."*Name_matched_accepted_family",
|
| 1403 |
|
|
"MatchedTaxon"."*Genus_matched",
|
| 1404 |
|
|
"MatchedTaxon"."*Genus_score",
|
| 1405 |
|
|
"MatchedTaxon"."*Specific_epithet_matched",
|
| 1406 |
|
|
"MatchedTaxon"."*Specific_epithet_score",
|
| 1407 |
|
|
"MatchedTaxon"."*Infraspecific_rank",
|
| 1408 |
|
|
"MatchedTaxon"."*Infraspecific_epithet_matched",
|
| 1409 |
|
|
"MatchedTaxon"."*Infraspecific_epithet_score",
|
| 1410 |
|
|
"MatchedTaxon"."*Infraspecific_rank_2",
|
| 1411 |
|
|
"MatchedTaxon"."*Infraspecific_epithet_2_matched",
|
| 1412 |
|
|
"MatchedTaxon"."*Infraspecific_epithet_2_score",
|
| 1413 |
|
|
"MatchedTaxon"."*Annotations",
|
| 1414 |
|
|
"MatchedTaxon"."*Unmatched_terms",
|
| 1415 |
|
|
"MatchedTaxon"."*Taxonomic_status",
|
| 1416 |
|
|
"MatchedTaxon"."*Accepted_name",
|
| 1417 |
|
|
"MatchedTaxon"."*Accepted_name_author",
|
| 1418 |
|
|
"MatchedTaxon"."*Accepted_name_rank",
|
| 1419 |
|
|
"MatchedTaxon"."*Accepted_name_url",
|
| 1420 |
|
|
"MatchedTaxon"."*Accepted_name_species",
|
| 1421 |
|
|
"MatchedTaxon"."*Accepted_name_family",
|
| 1422 |
|
|
"MatchedTaxon"."*Selected",
|
| 1423 |
|
|
"MatchedTaxon"."*Source",
|
| 1424 |
|
|
"MatchedTaxon"."*Warnings",
|
| 1425 |
|
|
"MatchedTaxon"."*Accepted_name_lsid",
|
| 1426 |
14108
|
aaronmk
|
"MatchedTaxon".is_valid_match,
|
| 1427 |
13800
|
aaronmk
|
"MatchedTaxon".scrubbed_unique_taxon_name,
|
| 1428 |
14284
|
aaronmk
|
"MatchedTaxon"."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1429 |
|
|
"MatchedTaxon"."[matched_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1430 |
|
|
"MatchedTaxon".matched_has_accepted,
|
| 1431 |
14268
|
aaronmk
|
"MatchedTaxon"."__accepted_{genus,specific_epithet}",
|
| 1432 |
|
|
"MatchedTaxon"."[accepted_]genus__@DwC__@vegpath.org",
|
| 1433 |
|
|
"MatchedTaxon"."[accepted_]specificEpithet__@DwC__@vegpath.org",
|
| 1434 |
|
|
"MatchedTaxon".__accepted_infraspecific_label,
|
| 1435 |
|
|
"MatchedTaxon"."__accepted_infraspecific_{rank,epithet}",
|
| 1436 |
|
|
"MatchedTaxon"."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
| 1437 |
|
|
"MatchedTaxon"."[accepted_]infraspecificEpithet__@DwC__@vegpath.org",
|
| 1438 |
|
|
"MatchedTaxon"."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1439 |
14284
|
aaronmk
|
"MatchedTaxon"."[scrubbed_]taxonRank__@DwC__@vegpath.org",
|
| 1440 |
|
|
"MatchedTaxon"."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1441 |
|
|
"MatchedTaxon"."[scrubbed_]genus__@DwC__@vegpath.org",
|
| 1442 |
|
|
"MatchedTaxon"."[scrubbed_]specificEpithet__@DwC__@vegpath.org",
|
| 1443 |
|
|
"MatchedTaxon"."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1444 |
|
|
"MatchedTaxon"."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
| 1445 |
|
|
"MatchedTaxon"."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org",
|
| 1446 |
|
|
"MatchedTaxon"."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1447 |
|
|
"MatchedTaxon"."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1448 |
|
|
"MatchedTaxon"."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1449 |
14103
|
aaronmk
|
"MatchedTaxon"."taxonomicStatus",
|
| 1450 |
13498
|
aaronmk
|
"MatchedTaxon".accepted_morphospecies_binomial
|
| 1451 |
11708
|
aaronmk
|
FROM "MatchedTaxon"
|
| 1452 |
14108
|
aaronmk
|
WHERE "MatchedTaxon".is_valid_match;
|
| 1453 |
10778
|
aaronmk
|
|
| 1454 |
|
|
|
| 1455 |
|
|
--
|
| 1456 |
|
|
-- Name: VIEW "ValidMatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1457 |
|
|
--
|
| 1458 |
|
|
|
| 1459 |
13443
|
aaronmk
|
COMMENT ON VIEW "ValidMatchedTaxon" IS '
|
| 1460 |
|
|
to update, use * as the column list
|
| 1461 |
|
|
';
|
| 1462 |
10778
|
aaronmk
|
|
| 1463 |
|
|
|
| 1464 |
|
|
--
|
| 1465 |
|
|
-- Name: batch; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 1466 |
|
|
--
|
| 1467 |
|
|
|
| 1468 |
|
|
CREATE TABLE batch (
|
| 1469 |
|
|
id text NOT NULL,
|
| 1470 |
|
|
id_by_time text,
|
| 1471 |
|
|
time_submitted timestamp with time zone DEFAULT now(),
|
| 1472 |
|
|
client_version text
|
| 1473 |
|
|
);
|
| 1474 |
|
|
|
| 1475 |
|
|
|
| 1476 |
|
|
--
|
| 1477 |
|
|
-- Name: batch_download_settings; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 1478 |
|
|
--
|
| 1479 |
|
|
|
| 1480 |
|
|
CREATE TABLE batch_download_settings (
|
| 1481 |
|
|
id text NOT NULL,
|
| 1482 |
|
|
"E-mail" text,
|
| 1483 |
|
|
"Id" text,
|
| 1484 |
|
|
"Job type" text,
|
| 1485 |
|
|
"Contains Id" boolean,
|
| 1486 |
|
|
"Start time" text,
|
| 1487 |
|
|
"Finish time" text,
|
| 1488 |
|
|
"TNRS version" text,
|
| 1489 |
|
|
"Sources selected" text,
|
| 1490 |
|
|
"Match threshold" double precision,
|
| 1491 |
|
|
"Classification" text,
|
| 1492 |
|
|
"Allow partial matches?" boolean,
|
| 1493 |
|
|
"Sort by source" boolean,
|
| 1494 |
|
|
"Constrain by higher taxonomy" boolean
|
| 1495 |
|
|
);
|
| 1496 |
|
|
|
| 1497 |
|
|
|
| 1498 |
|
|
--
|
| 1499 |
|
|
-- Name: TABLE batch_download_settings; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1500 |
|
|
--
|
| 1501 |
|
|
|
| 1502 |
13575
|
aaronmk
|
COMMENT ON TABLE batch_download_settings IS '
|
| 1503 |
|
|
stores data from http://tnrs.iplantcollaborative.org/TNRSapp.html > Submit List > results section > Download settings > settings.txt
|
| 1504 |
|
|
';
|
| 1505 |
10778
|
aaronmk
|
|
| 1506 |
|
|
|
| 1507 |
|
|
--
|
| 1508 |
|
|
-- Name: client_version; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 1509 |
|
|
--
|
| 1510 |
|
|
|
| 1511 |
|
|
CREATE TABLE client_version (
|
| 1512 |
|
|
id text NOT NULL,
|
| 1513 |
|
|
global_rev integer NOT NULL,
|
| 1514 |
|
|
"/lib/tnrs.py rev" integer,
|
| 1515 |
|
|
"/bin/tnrs_db rev" integer
|
| 1516 |
|
|
);
|
| 1517 |
|
|
|
| 1518 |
|
|
|
| 1519 |
|
|
--
|
| 1520 |
|
|
-- Name: TABLE client_version; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1521 |
|
|
--
|
| 1522 |
|
|
|
| 1523 |
13575
|
aaronmk
|
COMMENT ON TABLE client_version IS '
|
| 1524 |
|
|
contains svn revisions
|
| 1525 |
|
|
';
|
| 1526 |
10778
|
aaronmk
|
|
| 1527 |
|
|
|
| 1528 |
|
|
--
|
| 1529 |
|
|
-- Name: COLUMN client_version.global_rev; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1530 |
|
|
--
|
| 1531 |
|
|
|
| 1532 |
13575
|
aaronmk
|
COMMENT ON COLUMN client_version.global_rev IS '
|
| 1533 |
|
|
from `svn info .` > Last Changed Rev
|
| 1534 |
|
|
';
|
| 1535 |
10778
|
aaronmk
|
|
| 1536 |
|
|
|
| 1537 |
|
|
--
|
| 1538 |
|
|
-- Name: COLUMN client_version."/lib/tnrs.py rev"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1539 |
|
|
--
|
| 1540 |
|
|
|
| 1541 |
13575
|
aaronmk
|
COMMENT ON COLUMN client_version."/lib/tnrs.py rev" IS '
|
| 1542 |
|
|
from `svn info lib/tnrs.py` > Last Changed Rev
|
| 1543 |
|
|
';
|
| 1544 |
10778
|
aaronmk
|
|
| 1545 |
|
|
|
| 1546 |
|
|
--
|
| 1547 |
|
|
-- Name: COLUMN client_version."/bin/tnrs_db rev"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1548 |
|
|
--
|
| 1549 |
|
|
|
| 1550 |
13575
|
aaronmk
|
COMMENT ON COLUMN client_version."/bin/tnrs_db rev" IS '
|
| 1551 |
|
|
from `svn info bin/tnrs_db` > Last Changed Rev
|
| 1552 |
|
|
';
|
| 1553 |
10778
|
aaronmk
|
|
| 1554 |
|
|
|
| 1555 |
|
|
--
|
| 1556 |
13866
|
aaronmk
|
-- Name: taxon_match_input; Type: VIEW; Schema: TNRS; Owner: -
|
| 1557 |
|
|
--
|
| 1558 |
|
|
|
| 1559 |
|
|
CREATE VIEW taxon_match_input AS
|
| 1560 |
14111
|
aaronmk
|
SELECT taxon_match."*Name_number" AS "Name_number",
|
| 1561 |
|
|
taxon_match."*Name_submitted" AS "Name_submitted",
|
| 1562 |
|
|
taxon_match."*Overall_score" AS "Overall_score",
|
| 1563 |
|
|
taxon_match."*Name_matched" AS "Name_matched",
|
| 1564 |
|
|
taxon_match."*Name_matched_rank" AS "Name_matched_rank",
|
| 1565 |
|
|
taxon_match."*Name_score" AS "Name_score",
|
| 1566 |
|
|
taxon_match."*Name_matched_author" AS "Name_matched_author",
|
| 1567 |
|
|
taxon_match."*Name_matched_url" AS "Name_matched_url",
|
| 1568 |
|
|
taxon_match."*Author_matched" AS "Author_matched",
|
| 1569 |
|
|
taxon_match."*Author_score" AS "Author_score",
|
| 1570 |
|
|
taxon_match."*Family_matched" AS "Family_matched",
|
| 1571 |
|
|
taxon_match."*Family_score" AS "Family_score",
|
| 1572 |
|
|
taxon_match."*Name_matched_accepted_family" AS "Name_matched_accepted_family",
|
| 1573 |
|
|
taxon_match."*Genus_matched" AS "Genus_matched",
|
| 1574 |
|
|
taxon_match."*Genus_score" AS "Genus_score",
|
| 1575 |
|
|
taxon_match."*Specific_epithet_matched" AS "Specific_epithet_matched",
|
| 1576 |
|
|
taxon_match."*Specific_epithet_score" AS "Specific_epithet_score",
|
| 1577 |
|
|
taxon_match."*Infraspecific_rank" AS "Infraspecific_rank",
|
| 1578 |
|
|
taxon_match."*Infraspecific_epithet_matched" AS "Infraspecific_epithet_matched",
|
| 1579 |
|
|
taxon_match."*Infraspecific_epithet_score" AS "Infraspecific_epithet_score",
|
| 1580 |
|
|
taxon_match."*Infraspecific_rank_2" AS "Infraspecific_rank_2",
|
| 1581 |
|
|
taxon_match."*Infraspecific_epithet_2_matched" AS "Infraspecific_epithet_2_matched",
|
| 1582 |
|
|
taxon_match."*Infraspecific_epithet_2_score" AS "Infraspecific_epithet_2_score",
|
| 1583 |
|
|
taxon_match."*Annotations" AS "Annotations",
|
| 1584 |
|
|
taxon_match."*Unmatched_terms" AS "Unmatched_terms",
|
| 1585 |
|
|
taxon_match."*Taxonomic_status" AS "Taxonomic_status",
|
| 1586 |
|
|
taxon_match."*Accepted_name" AS "Accepted_name",
|
| 1587 |
|
|
taxon_match."*Accepted_name_author" AS "Accepted_name_author",
|
| 1588 |
|
|
taxon_match."*Accepted_name_rank" AS "Accepted_name_rank",
|
| 1589 |
|
|
taxon_match."*Accepted_name_url" AS "Accepted_name_url",
|
| 1590 |
|
|
taxon_match."*Accepted_name_species" AS "Accepted_name_species",
|
| 1591 |
|
|
taxon_match."*Accepted_name_family" AS "Accepted_name_family",
|
| 1592 |
|
|
taxon_match."*Selected" AS "Selected",
|
| 1593 |
|
|
taxon_match."*Source" AS "Source",
|
| 1594 |
|
|
taxon_match."*Warnings" AS "Warnings",
|
| 1595 |
|
|
taxon_match."*Accepted_name_lsid" AS "Accepted_name_lsid"
|
| 1596 |
13866
|
aaronmk
|
FROM taxon_match;
|
| 1597 |
|
|
|
| 1598 |
|
|
|
| 1599 |
|
|
--
|
| 1600 |
|
|
-- Name: taxon_match_input__copy_to; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 1601 |
|
|
--
|
| 1602 |
|
|
|
| 1603 |
|
|
CREATE TABLE taxon_match_input__copy_to (
|
| 1604 |
|
|
"Name_number" integer,
|
| 1605 |
|
|
"Name_submitted" text,
|
| 1606 |
|
|
"Overall_score" double precision,
|
| 1607 |
|
|
"Name_matched" text,
|
| 1608 |
|
|
"Name_matched_rank" text,
|
| 1609 |
|
|
"Name_score" double precision,
|
| 1610 |
|
|
"Name_matched_author" text,
|
| 1611 |
|
|
"Name_matched_url" text,
|
| 1612 |
|
|
"Author_matched" text,
|
| 1613 |
|
|
"Author_score" double precision,
|
| 1614 |
|
|
"Family_matched" text,
|
| 1615 |
|
|
"Family_score" double precision,
|
| 1616 |
|
|
"Name_matched_accepted_family" text,
|
| 1617 |
|
|
"Genus_matched" text,
|
| 1618 |
|
|
"Genus_score" double precision,
|
| 1619 |
|
|
"Specific_epithet_matched" text,
|
| 1620 |
|
|
"Specific_epithet_score" double precision,
|
| 1621 |
|
|
"Infraspecific_rank" text,
|
| 1622 |
|
|
"Infraspecific_epithet_matched" text,
|
| 1623 |
|
|
"Infraspecific_epithet_score" double precision,
|
| 1624 |
|
|
"Infraspecific_rank_2" text,
|
| 1625 |
|
|
"Infraspecific_epithet_2_matched" text,
|
| 1626 |
|
|
"Infraspecific_epithet_2_score" double precision,
|
| 1627 |
|
|
"Annotations" text,
|
| 1628 |
|
|
"Unmatched_terms" text,
|
| 1629 |
|
|
"Taxonomic_status" text,
|
| 1630 |
|
|
"Accepted_name" text,
|
| 1631 |
|
|
"Accepted_name_author" text,
|
| 1632 |
|
|
"Accepted_name_rank" text,
|
| 1633 |
|
|
"Accepted_name_url" text,
|
| 1634 |
|
|
"Accepted_name_species" text,
|
| 1635 |
|
|
"Accepted_name_family" text,
|
| 1636 |
|
|
"Selected" text,
|
| 1637 |
|
|
"Source" text,
|
| 1638 |
|
|
"Warnings" text,
|
| 1639 |
|
|
"Accepted_name_lsid" text
|
| 1640 |
|
|
);
|
| 1641 |
|
|
|
| 1642 |
|
|
|
| 1643 |
|
|
--
|
| 1644 |
11964
|
aaronmk
|
-- Name: taxon_scrub.scrubbed_unique_taxon_name.*; Type: VIEW; Schema: TNRS; Owner: -
|
| 1645 |
|
|
--
|
| 1646 |
|
|
|
| 1647 |
|
|
CREATE VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" AS
|
| 1648 |
14111
|
aaronmk
|
SELECT taxon_match."*Name_submitted" AS scrubbed_unique_taxon_name,
|
| 1649 |
|
|
taxon_match."*Name_matched_rank" AS scrubbed_taxon_rank,
|
| 1650 |
|
|
COALESCE(taxon_match."*Name_matched_accepted_family", taxon_match."*Family_matched") AS scrubbed_family,
|
| 1651 |
|
|
taxon_match."*Genus_matched" AS scrubbed_genus,
|
| 1652 |
|
|
taxon_match."*Specific_epithet_matched" AS scrubbed_specific_epithet,
|
| 1653 |
|
|
taxon_match."*Infraspecific_rank" AS scrubbed_infraspecific_rank,
|
| 1654 |
|
|
taxon_match."*Infraspecific_epithet_matched" AS scrubbed_infraspecific_epithet,
|
| 1655 |
|
|
taxon_match."*Name_matched_author" AS scrubbed_author,
|
| 1656 |
|
|
taxon_match."*Name_matched" AS scrubbed_taxon_name_no_author,
|
| 1657 |
|
|
(taxon_match."*Name_matched" || COALESCE((' '::text || taxon_match."*Name_matched_author"), ''::text)) AS scrubbed_taxon_name_with_author
|
| 1658 |
13861
|
aaronmk
|
FROM taxon_match;
|
| 1659 |
11964
|
aaronmk
|
|
| 1660 |
|
|
|
| 1661 |
|
|
--
|
| 1662 |
11965
|
aaronmk
|
-- Name: VIEW "taxon_scrub.scrubbed_unique_taxon_name.*"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1663 |
|
|
--
|
| 1664 |
|
|
|
| 1665 |
13575
|
aaronmk
|
COMMENT ON VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" IS '
|
| 1666 |
13846
|
aaronmk
|
to modify:
|
| 1667 |
|
|
SELECT util.recreate_view(''"TNRS"."taxon_scrub.scrubbed_unique_taxon_name.*"'', $$
|
| 1668 |
|
|
SELECT __
|
| 1669 |
|
|
$$);
|
| 1670 |
|
|
|
| 1671 |
13575
|
aaronmk
|
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.
|
| 1672 |
|
|
';
|
| 1673 |
11965
|
aaronmk
|
|
| 1674 |
|
|
|
| 1675 |
|
|
--
|
| 1676 |
11964
|
aaronmk
|
-- Name: taxon_scrub; Type: VIEW; Schema: TNRS; Owner: -
|
| 1677 |
|
|
--
|
| 1678 |
|
|
|
| 1679 |
|
|
CREATE VIEW taxon_scrub AS
|
| 1680 |
13800
|
aaronmk
|
SELECT "ValidMatchedTaxon".scrubbed_unique_taxon_name,
|
| 1681 |
14108
|
aaronmk
|
"ValidMatchedTaxon".batch,
|
| 1682 |
14105
|
aaronmk
|
"ValidMatchedTaxon".match_num,
|
| 1683 |
14111
|
aaronmk
|
"ValidMatchedTaxon"."*Name_number",
|
| 1684 |
|
|
"ValidMatchedTaxon"."*Name_submitted",
|
| 1685 |
|
|
"ValidMatchedTaxon"."*Overall_score",
|
| 1686 |
|
|
"ValidMatchedTaxon"."*Name_matched",
|
| 1687 |
|
|
"ValidMatchedTaxon"."*Name_matched_rank",
|
| 1688 |
|
|
"ValidMatchedTaxon"."*Name_score",
|
| 1689 |
|
|
"ValidMatchedTaxon"."*Name_matched_author",
|
| 1690 |
|
|
"ValidMatchedTaxon"."*Name_matched_url",
|
| 1691 |
|
|
"ValidMatchedTaxon"."*Author_matched",
|
| 1692 |
|
|
"ValidMatchedTaxon"."*Author_score",
|
| 1693 |
|
|
"ValidMatchedTaxon"."*Family_matched",
|
| 1694 |
|
|
"ValidMatchedTaxon"."*Family_score",
|
| 1695 |
|
|
"ValidMatchedTaxon"."*Name_matched_accepted_family",
|
| 1696 |
|
|
"ValidMatchedTaxon"."*Genus_matched",
|
| 1697 |
|
|
"ValidMatchedTaxon"."*Genus_score",
|
| 1698 |
|
|
"ValidMatchedTaxon"."*Specific_epithet_matched",
|
| 1699 |
|
|
"ValidMatchedTaxon"."*Specific_epithet_score",
|
| 1700 |
|
|
"ValidMatchedTaxon"."*Infraspecific_rank",
|
| 1701 |
|
|
"ValidMatchedTaxon"."*Infraspecific_epithet_matched",
|
| 1702 |
|
|
"ValidMatchedTaxon"."*Infraspecific_epithet_score",
|
| 1703 |
|
|
"ValidMatchedTaxon"."*Infraspecific_rank_2",
|
| 1704 |
|
|
"ValidMatchedTaxon"."*Infraspecific_epithet_2_matched",
|
| 1705 |
|
|
"ValidMatchedTaxon"."*Infraspecific_epithet_2_score",
|
| 1706 |
|
|
"ValidMatchedTaxon"."*Annotations",
|
| 1707 |
|
|
"ValidMatchedTaxon"."*Unmatched_terms",
|
| 1708 |
|
|
"ValidMatchedTaxon"."*Taxonomic_status",
|
| 1709 |
|
|
"ValidMatchedTaxon"."*Accepted_name",
|
| 1710 |
|
|
"ValidMatchedTaxon"."*Accepted_name_author",
|
| 1711 |
|
|
"ValidMatchedTaxon"."*Accepted_name_rank",
|
| 1712 |
|
|
"ValidMatchedTaxon"."*Accepted_name_url",
|
| 1713 |
|
|
"ValidMatchedTaxon"."*Accepted_name_species",
|
| 1714 |
|
|
"ValidMatchedTaxon"."*Accepted_name_family",
|
| 1715 |
|
|
"ValidMatchedTaxon"."*Selected",
|
| 1716 |
|
|
"ValidMatchedTaxon"."*Source",
|
| 1717 |
|
|
"ValidMatchedTaxon"."*Warnings",
|
| 1718 |
|
|
"ValidMatchedTaxon"."*Accepted_name_lsid",
|
| 1719 |
14108
|
aaronmk
|
"ValidMatchedTaxon".is_valid_match,
|
| 1720 |
14284
|
aaronmk
|
"ValidMatchedTaxon"."[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1721 |
|
|
"ValidMatchedTaxon"."[matched_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1722 |
|
|
"ValidMatchedTaxon".matched_has_accepted,
|
| 1723 |
14268
|
aaronmk
|
"ValidMatchedTaxon"."__accepted_{genus,specific_epithet}",
|
| 1724 |
|
|
"ValidMatchedTaxon"."[accepted_]genus__@DwC__@vegpath.org",
|
| 1725 |
|
|
"ValidMatchedTaxon"."[accepted_]specificEpithet__@DwC__@vegpath.org",
|
| 1726 |
|
|
"ValidMatchedTaxon".__accepted_infraspecific_label,
|
| 1727 |
|
|
"ValidMatchedTaxon"."__accepted_infraspecific_{rank,epithet}",
|
| 1728 |
|
|
"ValidMatchedTaxon"."[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
| 1729 |
|
|
"ValidMatchedTaxon"."[accepted_]infraspecificEpithet__@DwC__@vegpath.org",
|
| 1730 |
|
|
"ValidMatchedTaxon"."[accepted_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1731 |
14284
|
aaronmk
|
"ValidMatchedTaxon"."[scrubbed_]taxonRank__@DwC__@vegpath.org",
|
| 1732 |
|
|
"ValidMatchedTaxon"."[scrubbed_]family~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1733 |
|
|
"ValidMatchedTaxon"."[scrubbed_]genus__@DwC__@vegpath.org",
|
| 1734 |
|
|
"ValidMatchedTaxon"."[scrubbed_]specificEpithet__@DwC__@vegpath.org",
|
| 1735 |
|
|
"ValidMatchedTaxon"."[scrubbed_]species[_binom]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1736 |
|
|
"ValidMatchedTaxon"."[scrubbed_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org",
|
| 1737 |
|
|
"ValidMatchedTaxon"."[scrubbed_]infraspecificEpithet__@DwC__@vegpath.org",
|
| 1738 |
|
|
"ValidMatchedTaxon"."[scrubbed_]name[_no_author]~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1739 |
|
|
"ValidMatchedTaxon"."[scrubbed_]author~(-Accepted_-)__@TNRS__@vegpath.org",
|
| 1740 |
|
|
"ValidMatchedTaxon"."[scrubbed_]scientificName[_with_author]__@DwC__@vegpath.org",
|
| 1741 |
14103
|
aaronmk
|
"ValidMatchedTaxon"."taxonomicStatus",
|
| 1742 |
13800
|
aaronmk
|
"ValidMatchedTaxon".accepted_morphospecies_binomial,
|
| 1743 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_rank,
|
| 1744 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_family,
|
| 1745 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus,
|
| 1746 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet,
|
| 1747 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_rank,
|
| 1748 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_epithet,
|
| 1749 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_author,
|
| 1750 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_no_author,
|
| 1751 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_with_author,
|
| 1752 |
13532
|
aaronmk
|
CASE
|
| 1753 |
14111
|
aaronmk
|
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")
|
| 1754 |
|
|
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")
|
| 1755 |
13532
|
aaronmk
|
ELSE (("taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus || ' '::text) || "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet)
|
| 1756 |
|
|
END AS scrubbed_morphospecies_binomial
|
| 1757 |
11964
|
aaronmk
|
FROM ("ValidMatchedTaxon"
|
| 1758 |
|
|
LEFT JOIN "taxon_scrub.scrubbed_unique_taxon_name.*" USING (scrubbed_unique_taxon_name));
|
| 1759 |
|
|
|
| 1760 |
|
|
|
| 1761 |
|
|
--
|
| 1762 |
|
|
-- Name: VIEW taxon_scrub; Type: COMMENT; Schema: TNRS; Owner: -
|
| 1763 |
|
|
--
|
| 1764 |
|
|
|
| 1765 |
13443
|
aaronmk
|
COMMENT ON VIEW taxon_scrub IS '
|
| 1766 |
13531
|
aaronmk
|
to modify:
|
| 1767 |
13845
|
aaronmk
|
SELECT util.recreate_view(''"TNRS".taxon_scrub'', $$
|
| 1768 |
13647
|
aaronmk
|
SELECT __
|
| 1769 |
13531
|
aaronmk
|
$$);
|
| 1770 |
13443
|
aaronmk
|
';
|
| 1771 |
11964
|
aaronmk
|
|
| 1772 |
|
|
|
| 1773 |
|
|
--
|
| 1774 |
10778
|
aaronmk
|
-- Name: batch_download_settings_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 1775 |
|
|
--
|
| 1776 |
|
|
|
| 1777 |
|
|
ALTER TABLE ONLY batch_download_settings
|
| 1778 |
|
|
ADD CONSTRAINT batch_download_settings_pkey PRIMARY KEY (id);
|
| 1779 |
|
|
|
| 1780 |
|
|
|
| 1781 |
|
|
--
|
| 1782 |
|
|
-- Name: batch_id_by_time_key; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 1783 |
|
|
--
|
| 1784 |
|
|
|
| 1785 |
|
|
ALTER TABLE ONLY batch
|
| 1786 |
|
|
ADD CONSTRAINT batch_id_by_time_key UNIQUE (id_by_time);
|
| 1787 |
|
|
|
| 1788 |
|
|
|
| 1789 |
|
|
--
|
| 1790 |
|
|
-- Name: batch_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 1791 |
|
|
--
|
| 1792 |
|
|
|
| 1793 |
|
|
ALTER TABLE ONLY batch
|
| 1794 |
|
|
ADD CONSTRAINT batch_pkey PRIMARY KEY (id);
|
| 1795 |
|
|
|
| 1796 |
|
|
|
| 1797 |
|
|
--
|
| 1798 |
|
|
-- Name: client_version_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 1799 |
|
|
--
|
| 1800 |
|
|
|
| 1801 |
|
|
ALTER TABLE ONLY client_version
|
| 1802 |
|
|
ADD CONSTRAINT client_version_pkey PRIMARY KEY (id);
|
| 1803 |
|
|
|
| 1804 |
|
|
|
| 1805 |
|
|
--
|
| 1806 |
13868
|
aaronmk
|
-- Name: taxon_match_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 1807 |
10778
|
aaronmk
|
--
|
| 1808 |
|
|
|
| 1809 |
13861
|
aaronmk
|
ALTER TABLE ONLY taxon_match
|
| 1810 |
13868
|
aaronmk
|
ADD CONSTRAINT taxon_match_pkey PRIMARY KEY (batch, match_num);
|
| 1811 |
10778
|
aaronmk
|
|
| 1812 |
14125
|
aaronmk
|
ALTER TABLE taxon_match CLUSTER ON taxon_match_pkey;
|
| 1813 |
10778
|
aaronmk
|
|
| 1814 |
14125
|
aaronmk
|
|
| 1815 |
10778
|
aaronmk
|
--
|
| 1816 |
10793
|
aaronmk
|
-- Name: batch_client_version_idx; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 1817 |
|
|
--
|
| 1818 |
|
|
|
| 1819 |
|
|
CREATE INDEX batch_client_version_idx ON batch USING btree (client_version);
|
| 1820 |
|
|
|
| 1821 |
|
|
|
| 1822 |
|
|
--
|
| 1823 |
13879
|
aaronmk
|
-- Name: taxon_best_match__valid_match; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 1824 |
13589
|
aaronmk
|
--
|
| 1825 |
|
|
|
| 1826 |
14111
|
aaronmk
|
CREATE INDEX taxon_best_match__valid_match ON taxon_match USING btree ("*Name_submitted") WHERE (("*Selected" = 'true'::text) AND is_valid_match);
|
| 1827 |
13589
|
aaronmk
|
|
| 1828 |
|
|
|
| 1829 |
|
|
--
|
| 1830 |
13879
|
aaronmk
|
-- Name: taxon_match_Name_submitted_idx; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 1831 |
13874
|
aaronmk
|
--
|
| 1832 |
|
|
|
| 1833 |
14111
|
aaronmk
|
CREATE INDEX "taxon_match_Name_submitted_idx" ON taxon_match USING btree ("*Name_submitted");
|
| 1834 |
13874
|
aaronmk
|
|
| 1835 |
|
|
|
| 1836 |
|
|
--
|
| 1837 |
13879
|
aaronmk
|
-- Name: taxon_match__one_selected_match; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 1838 |
11607
|
aaronmk
|
--
|
| 1839 |
|
|
|
| 1840 |
14111
|
aaronmk
|
CREATE UNIQUE INDEX taxon_match__one_selected_match ON taxon_match USING btree (batch, "*Name_number") WHERE ("*Selected" = 'true'::text);
|
| 1841 |
11607
|
aaronmk
|
|
| 1842 |
|
|
|
| 1843 |
|
|
--
|
| 1844 |
10778
|
aaronmk
|
-- Name: batch__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 1845 |
|
|
--
|
| 1846 |
|
|
|
| 1847 |
|
|
CREATE TRIGGER batch__fill BEFORE INSERT OR UPDATE ON batch FOR EACH ROW EXECUTE PROCEDURE batch__fill();
|
| 1848 |
|
|
|
| 1849 |
|
|
|
| 1850 |
|
|
--
|
| 1851 |
13868
|
aaronmk
|
-- Name: taxon_match__batch_begin; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 1852 |
13866
|
aaronmk
|
--
|
| 1853 |
|
|
|
| 1854 |
13868
|
aaronmk
|
CREATE TRIGGER taxon_match__batch_begin BEFORE INSERT ON taxon_match_input__copy_to FOR EACH STATEMENT EXECUTE PROCEDURE taxon_match__batch_begin();
|
| 1855 |
13866
|
aaronmk
|
|
| 1856 |
|
|
|
| 1857 |
|
|
--
|
| 1858 |
13868
|
aaronmk
|
-- Name: taxon_match__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 1859 |
13567
|
aaronmk
|
--
|
| 1860 |
|
|
|
| 1861 |
13868
|
aaronmk
|
CREATE TRIGGER taxon_match__fill BEFORE INSERT OR UPDATE ON taxon_match FOR EACH ROW EXECUTE PROCEDURE taxon_match__fill();
|
| 1862 |
13567
|
aaronmk
|
|
| 1863 |
|
|
|
| 1864 |
|
|
--
|
| 1865 |
14122
|
aaronmk
|
-- Name: taxon_match__fill_derived; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 1866 |
|
|
--
|
| 1867 |
|
|
|
| 1868 |
|
|
CREATE TRIGGER taxon_match__fill_derived BEFORE INSERT OR UPDATE ON taxon_match FOR EACH ROW EXECUTE PROCEDURE taxon_match__fill_derived();
|
| 1869 |
|
|
|
| 1870 |
|
|
|
| 1871 |
|
|
--
|
| 1872 |
13868
|
aaronmk
|
-- Name: taxon_match__match_num__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 1873 |
13578
|
aaronmk
|
--
|
| 1874 |
|
|
|
| 1875 |
13868
|
aaronmk
|
CREATE TRIGGER taxon_match__match_num__fill BEFORE INSERT ON taxon_match FOR EACH ROW EXECUTE PROCEDURE taxon_match__match_num__fill();
|
| 1876 |
13578
|
aaronmk
|
|
| 1877 |
|
|
|
| 1878 |
|
|
--
|
| 1879 |
13868
|
aaronmk
|
-- Name: taxon_match_input__copy_to__insert; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 1880 |
10778
|
aaronmk
|
--
|
| 1881 |
|
|
|
| 1882 |
13868
|
aaronmk
|
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();
|
| 1883 |
10778
|
aaronmk
|
|
| 1884 |
|
|
|
| 1885 |
|
|
--
|
| 1886 |
|
|
-- Name: batch_client_version_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
| 1887 |
|
|
--
|
| 1888 |
|
|
|
| 1889 |
|
|
ALTER TABLE ONLY batch
|
| 1890 |
|
|
ADD CONSTRAINT batch_client_version_fkey FOREIGN KEY (client_version) REFERENCES client_version(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 1891 |
|
|
|
| 1892 |
|
|
|
| 1893 |
|
|
--
|
| 1894 |
|
|
-- Name: batch_download_settings_id_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
| 1895 |
|
|
--
|
| 1896 |
|
|
|
| 1897 |
|
|
ALTER TABLE ONLY batch_download_settings
|
| 1898 |
|
|
ADD CONSTRAINT batch_download_settings_id_fkey FOREIGN KEY (id) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 1899 |
|
|
|
| 1900 |
|
|
|
| 1901 |
|
|
--
|
| 1902 |
13868
|
aaronmk
|
-- Name: taxon_match_batch_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
| 1903 |
10778
|
aaronmk
|
--
|
| 1904 |
|
|
|
| 1905 |
13861
|
aaronmk
|
ALTER TABLE ONLY taxon_match
|
| 1906 |
13868
|
aaronmk
|
ADD CONSTRAINT taxon_match_batch_fkey FOREIGN KEY (batch) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 1907 |
10778
|
aaronmk
|
|
| 1908 |
|
|
|
| 1909 |
|
|
--
|
| 1910 |
|
|
-- Name: TNRS; Type: ACL; Schema: -; Owner: -
|
| 1911 |
|
|
--
|
| 1912 |
|
|
|
| 1913 |
|
|
REVOKE ALL ON SCHEMA "TNRS" FROM PUBLIC;
|
| 1914 |
|
|
REVOKE ALL ON SCHEMA "TNRS" FROM bien;
|
| 1915 |
|
|
GRANT ALL ON SCHEMA "TNRS" TO bien;
|
| 1916 |
|
|
GRANT USAGE ON SCHEMA "TNRS" TO bien_read;
|
| 1917 |
|
|
|
| 1918 |
|
|
|
| 1919 |
|
|
--
|
| 1920 |
13861
|
aaronmk
|
-- Name: taxon_match; Type: ACL; Schema: TNRS; Owner: -
|
| 1921 |
10778
|
aaronmk
|
--
|
| 1922 |
|
|
|
| 1923 |
13861
|
aaronmk
|
REVOKE ALL ON TABLE taxon_match FROM PUBLIC;
|
| 1924 |
|
|
REVOKE ALL ON TABLE taxon_match FROM bien;
|
| 1925 |
|
|
GRANT ALL ON TABLE taxon_match TO bien;
|
| 1926 |
|
|
GRANT SELECT ON TABLE taxon_match TO bien_read;
|
| 1927 |
10778
|
aaronmk
|
|
| 1928 |
|
|
|
| 1929 |
|
|
--
|
| 1930 |
13878
|
aaronmk
|
-- Name: taxon_best_match; Type: ACL; Schema: TNRS; Owner: -
|
| 1931 |
|
|
--
|
| 1932 |
|
|
|
| 1933 |
|
|
REVOKE ALL ON TABLE taxon_best_match FROM PUBLIC;
|
| 1934 |
|
|
REVOKE ALL ON TABLE taxon_best_match FROM bien;
|
| 1935 |
|
|
GRANT ALL ON TABLE taxon_best_match TO bien;
|
| 1936 |
|
|
GRANT SELECT ON TABLE taxon_best_match TO bien_read;
|
| 1937 |
|
|
|
| 1938 |
|
|
|
| 1939 |
|
|
--
|
| 1940 |
11912
|
aaronmk
|
-- Name: MatchedTaxon; Type: ACL; Schema: TNRS; Owner: -
|
| 1941 |
|
|
--
|
| 1942 |
|
|
|
| 1943 |
|
|
REVOKE ALL ON TABLE "MatchedTaxon" FROM PUBLIC;
|
| 1944 |
|
|
REVOKE ALL ON TABLE "MatchedTaxon" FROM bien;
|
| 1945 |
|
|
GRANT ALL ON TABLE "MatchedTaxon" TO bien;
|
| 1946 |
|
|
GRANT SELECT ON TABLE "MatchedTaxon" TO bien_read;
|
| 1947 |
|
|
|
| 1948 |
|
|
|
| 1949 |
|
|
--
|
| 1950 |
|
|
-- Name: ValidMatchedTaxon; Type: ACL; Schema: TNRS; Owner: -
|
| 1951 |
|
|
--
|
| 1952 |
|
|
|
| 1953 |
|
|
REVOKE ALL ON TABLE "ValidMatchedTaxon" FROM PUBLIC;
|
| 1954 |
|
|
REVOKE ALL ON TABLE "ValidMatchedTaxon" FROM bien;
|
| 1955 |
|
|
GRANT ALL ON TABLE "ValidMatchedTaxon" TO bien;
|
| 1956 |
|
|
GRANT SELECT ON TABLE "ValidMatchedTaxon" TO bien_read;
|
| 1957 |
|
|
|
| 1958 |
|
|
|
| 1959 |
|
|
--
|
| 1960 |
13866
|
aaronmk
|
-- Name: taxon_match_input; Type: ACL; Schema: TNRS; Owner: -
|
| 1961 |
|
|
--
|
| 1962 |
|
|
|
| 1963 |
|
|
REVOKE ALL ON TABLE taxon_match_input FROM PUBLIC;
|
| 1964 |
|
|
REVOKE ALL ON TABLE taxon_match_input FROM bien;
|
| 1965 |
|
|
GRANT ALL ON TABLE taxon_match_input TO bien;
|
| 1966 |
|
|
GRANT SELECT ON TABLE taxon_match_input TO bien_read;
|
| 1967 |
|
|
|
| 1968 |
|
|
|
| 1969 |
|
|
--
|
| 1970 |
11912
|
aaronmk
|
-- Name: taxon_scrub.scrubbed_unique_taxon_name.*; Type: ACL; Schema: TNRS; Owner: -
|
| 1971 |
|
|
--
|
| 1972 |
|
|
|
| 1973 |
|
|
REVOKE ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" FROM PUBLIC;
|
| 1974 |
|
|
REVOKE ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" FROM bien;
|
| 1975 |
|
|
GRANT ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" TO bien;
|
| 1976 |
|
|
GRANT SELECT ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" TO bien_read;
|
| 1977 |
|
|
|
| 1978 |
|
|
|
| 1979 |
|
|
--
|
| 1980 |
|
|
-- Name: taxon_scrub; Type: ACL; Schema: TNRS; Owner: -
|
| 1981 |
|
|
--
|
| 1982 |
|
|
|
| 1983 |
|
|
REVOKE ALL ON TABLE taxon_scrub FROM PUBLIC;
|
| 1984 |
|
|
REVOKE ALL ON TABLE taxon_scrub FROM bien;
|
| 1985 |
|
|
GRANT ALL ON TABLE taxon_scrub TO bien;
|
| 1986 |
|
|
GRANT SELECT ON TABLE taxon_scrub TO bien_read;
|
| 1987 |
|
|
|
| 1988 |
|
|
|
| 1989 |
|
|
--
|
| 1990 |
10778
|
aaronmk
|
-- PostgreSQL database dump complete
|
| 1991 |
|
|
--
|
