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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
|
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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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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| 113 |
13868
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aaronmk
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CREATE FUNCTION taxon_match__fill() RETURNS trigger
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| 114 |
13578
|
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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| 135 |
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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| 138 |
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
|
| 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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| 143 |
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(CASE
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| 144 |
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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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| 149 |
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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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| 151 |
13871
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aaronmk
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END, false);
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| 152 |
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END;
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| 153 |
11628
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aaronmk
|
|
| 154 |
13871
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aaronmk
|
DECLARE
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| 155 |
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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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| 157 |
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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
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aaronmk
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), '');
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accepted_taxon_name_with_author text = NULLIF(concat_ws(' '
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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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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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| 172 |
11628
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aaronmk
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RETURN new;
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7134
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aaronmk
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END;
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| 174 |
10778
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aaronmk
|
$$;
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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
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aaronmk
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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"
|
| 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
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aaronmk
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|
| 189 |
7251
|
aaronmk
|
|
| 190 |
13631
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aaronmk
|
--
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| 191 |
14122
|
aaronmk
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-- 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 $$
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| 197 |
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BEGIN
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| 198 |
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new."__accepted_{genus,specific_epithet}" = (SELECT
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| 199 |
14150
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aaronmk
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regexp_split_to_array("*Accepted_name_species", ' '::text)
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| 200 |
14122
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aaronmk
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FROM (SELECT new.*) new);
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| 201 |
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| 202 |
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RETURN new;
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| 203 |
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END;
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| 204 |
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$$;
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| 205 |
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| 206 |
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| 207 |
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--
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| 208 |
13868
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aaronmk
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-- Name: taxon_match__match_num__fill(); Type: FUNCTION; Schema: TNRS; Owner: -
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| 209 |
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--
|
| 210 |
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| 211 |
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CREATE FUNCTION taxon_match__match_num__fill() RETURNS trigger
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| 212 |
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LANGUAGE plpgsql
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| 213 |
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AS $$
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| 214 |
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BEGIN
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| 215 |
|
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IF new.match_num IS NULL THEN
|
| 216 |
13869
|
aaronmk
|
new.match_num = "TNRS".taxon_match__match_num__next();
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| 217 |
13868
|
aaronmk
|
END IF;
|
| 218 |
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RETURN new;
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| 219 |
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END;
|
| 220 |
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$$;
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| 221 |
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| 222 |
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| 223 |
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--
|
| 224 |
13869
|
aaronmk
|
-- Name: taxon_match__match_num__next(); Type: FUNCTION; Schema: TNRS; Owner: -
|
| 225 |
|
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--
|
| 226 |
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| 227 |
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CREATE FUNCTION taxon_match__match_num__next() RETURNS bigint
|
| 228 |
|
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LANGUAGE sql
|
| 229 |
|
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AS $$
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| 230 |
|
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SELECT nextval('pg_temp.taxon_match__match_num__seq');
|
| 231 |
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$$;
|
| 232 |
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|
| 233 |
|
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|
| 234 |
|
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--
|
| 235 |
13868
|
aaronmk
|
-- Name: taxon_match_input__copy_to__insert(); Type: FUNCTION; Schema: TNRS; Owner: -
|
| 236 |
|
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--
|
| 237 |
|
|
|
| 238 |
|
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CREATE FUNCTION taxon_match_input__copy_to__insert() RETURNS trigger
|
| 239 |
|
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LANGUAGE plpgsql
|
| 240 |
|
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AS $$
|
| 241 |
|
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BEGIN
|
| 242 |
|
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INSERT INTO "TNRS".taxon_match_input SELECT new.*;
|
| 243 |
|
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RETURN NULL;
|
| 244 |
|
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END;
|
| 245 |
|
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$$;
|
| 246 |
|
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|
| 247 |
|
|
|
| 248 |
|
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--
|
| 249 |
|
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-- Name: taxon_name_is_safe(text); Type: FUNCTION; Schema: TNRS; Owner: -
|
| 250 |
|
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--
|
| 251 |
|
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|
| 252 |
|
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CREATE FUNCTION taxon_name_is_safe(taxon_name text) RETURNS boolean
|
| 253 |
|
|
LANGUAGE sql IMMUTABLE
|
| 254 |
|
|
AS $_$
|
| 255 |
|
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SELECT NOT ($1 = ANY("TNRS".unsafe_taxon_names()))
|
| 256 |
|
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$_$;
|
| 257 |
|
|
|
| 258 |
|
|
|
| 259 |
|
|
--
|
| 260 |
13631
|
aaronmk
|
-- Name: unsafe_taxon_names(); Type: FUNCTION; Schema: TNRS; Owner: -
|
| 261 |
|
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--
|
| 262 |
|
|
|
| 263 |
|
|
CREATE FUNCTION unsafe_taxon_names() RETURNS text[]
|
| 264 |
|
|
LANGUAGE sql IMMUTABLE
|
| 265 |
|
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AS $$
|
| 266 |
|
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SELECT ARRAY[
|
| 267 |
13686
|
aaronmk
|
]::text[]
|
| 268 |
13631
|
aaronmk
|
$$;
|
| 269 |
|
|
|
| 270 |
|
|
|
| 271 |
10778
|
aaronmk
|
SET default_tablespace = '';
|
| 272 |
|
|
|
| 273 |
|
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SET default_with_oids = false;
|
| 274 |
|
|
|
| 275 |
10728
|
aaronmk
|
--
|
| 276 |
13861
|
aaronmk
|
-- Name: taxon_match; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 277 |
10778
|
aaronmk
|
--
|
| 278 |
7251
|
aaronmk
|
|
| 279 |
13861
|
aaronmk
|
CREATE TABLE taxon_match (
|
| 280 |
10778
|
aaronmk
|
batch text DEFAULT now() NOT NULL,
|
| 281 |
13580
|
aaronmk
|
match_num integer NOT NULL,
|
| 282 |
14111
|
aaronmk
|
"*Name_number" integer NOT NULL,
|
| 283 |
|
|
"*Name_submitted" text NOT NULL,
|
| 284 |
|
|
"*Overall_score" double precision,
|
| 285 |
|
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"*Name_matched" text,
|
| 286 |
|
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"*Name_matched_rank" text,
|
| 287 |
|
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"*Name_score" double precision,
|
| 288 |
|
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"*Name_matched_author" text,
|
| 289 |
|
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"*Name_matched_url" text,
|
| 290 |
|
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"*Author_matched" text,
|
| 291 |
|
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"*Author_score" double precision,
|
| 292 |
|
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"*Family_matched" text,
|
| 293 |
|
|
"*Family_score" double precision,
|
| 294 |
|
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"*Name_matched_accepted_family" text,
|
| 295 |
|
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"*Genus_matched" text,
|
| 296 |
|
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"*Genus_score" double precision,
|
| 297 |
|
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"*Specific_epithet_matched" text,
|
| 298 |
|
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"*Specific_epithet_score" double precision,
|
| 299 |
|
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"*Infraspecific_rank" text,
|
| 300 |
|
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"*Infraspecific_epithet_matched" text,
|
| 301 |
|
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"*Infraspecific_epithet_score" double precision,
|
| 302 |
|
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"*Infraspecific_rank_2" text,
|
| 303 |
|
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"*Infraspecific_epithet_2_matched" text,
|
| 304 |
|
|
"*Infraspecific_epithet_2_score" double precision,
|
| 305 |
|
|
"*Annotations" text,
|
| 306 |
|
|
"*Unmatched_terms" text,
|
| 307 |
|
|
"*Taxonomic_status" text,
|
| 308 |
|
|
"*Accepted_name" text,
|
| 309 |
|
|
"*Accepted_name_author" text,
|
| 310 |
|
|
"*Accepted_name_rank" text,
|
| 311 |
|
|
"*Accepted_name_url" text,
|
| 312 |
|
|
"*Accepted_name_species" text,
|
| 313 |
|
|
"*Accepted_name_family" text,
|
| 314 |
|
|
"*Selected" text,
|
| 315 |
|
|
"*Source" text,
|
| 316 |
|
|
"*Warnings" text,
|
| 317 |
|
|
"*Accepted_name_lsid" text,
|
| 318 |
11628
|
aaronmk
|
is_valid_match boolean NOT NULL,
|
| 319 |
14122
|
aaronmk
|
scrubbed_unique_taxon_name text,
|
| 320 |
|
|
"__accepted_{genus,specific_epithet}" text[],
|
| 321 |
|
|
CONSTRAINT "__accepted_{genus,specific_epithet}" CHECK ((NOT ("__accepted_{genus,specific_epithet}" IS DISTINCT FROM regexp_split_to_array("*Accepted_name_species", ' '::text))))
|
| 322 |
10778
|
aaronmk
|
);
|
| 323 |
7823
|
aaronmk
|
|
| 324 |
9759
|
aaronmk
|
|
| 325 |
10778
|
aaronmk
|
--
|
| 326 |
13861
|
aaronmk
|
-- Name: TABLE taxon_match; Type: COMMENT; Schema: TNRS; Owner: -
|
| 327 |
10778
|
aaronmk
|
--
|
| 328 |
7823
|
aaronmk
|
|
| 329 |
13861
|
aaronmk
|
COMMENT ON TABLE taxon_match IS '
|
| 330 |
14161
|
aaronmk
|
whenever columns are renamed:
|
| 331 |
|
|
SELECT util.derived_cols_sync(''"TNRS".taxon_match'');
|
| 332 |
|
|
|
| 333 |
13577
|
aaronmk
|
to remove columns or add columns at the end:
|
| 334 |
|
|
$ rm=1 inputs/.TNRS/data.sql.run
|
| 335 |
|
|
$ make schemas/remake
|
| 336 |
|
|
|
| 337 |
|
|
to add columns in the middle:
|
| 338 |
|
|
make the changes in inputs/.TNRS/schema.sql
|
| 339 |
|
|
$ inputs/.TNRS/data.sql.run refresh # re-run TNRS
|
| 340 |
|
|
$ make schemas/remake
|
| 341 |
13582
|
aaronmk
|
|
| 342 |
|
|
to populate a new column:
|
| 343 |
13868
|
aaronmk
|
ALTER TABLE "TNRS".taxon_match DISABLE TRIGGER taxon_match__fill; --speeds up update
|
| 344 |
13861
|
aaronmk
|
UPDATE "TNRS".taxon_match SET "col" = value;
|
| 345 |
13582
|
aaronmk
|
-- runtime: 30 min ("5564201 rows affected, 1624829 ms execution time")
|
| 346 |
14132
|
aaronmk
|
CLUSTER "TNRS".taxon_match; -- ensure rows are exported in sorted order
|
| 347 |
13868
|
aaronmk
|
ALTER TABLE "TNRS".taxon_match ENABLE TRIGGER taxon_match__fill;
|
| 348 |
13861
|
aaronmk
|
VACUUM ANALYZE "TNRS".taxon_match --remove previous rows; runtime: 1.5 min ("92633 ms")
|
| 349 |
13584
|
aaronmk
|
|
| 350 |
|
|
to add a constraint: runtime: 3 min ("173620 ms")
|
| 351 |
13575
|
aaronmk
|
';
|
| 352 |
10778
|
aaronmk
|
|
| 353 |
|
|
|
| 354 |
|
|
--
|
| 355 |
13878
|
aaronmk
|
-- Name: taxon_best_match; Type: VIEW; Schema: TNRS; Owner: -
|
| 356 |
|
|
--
|
| 357 |
|
|
|
| 358 |
|
|
CREATE VIEW taxon_best_match AS
|
| 359 |
|
|
SELECT taxon_match.batch,
|
| 360 |
|
|
taxon_match.match_num,
|
| 361 |
14111
|
aaronmk
|
taxon_match."*Name_number",
|
| 362 |
|
|
taxon_match."*Name_submitted",
|
| 363 |
|
|
taxon_match."*Overall_score",
|
| 364 |
|
|
taxon_match."*Name_matched",
|
| 365 |
|
|
taxon_match."*Name_matched_rank",
|
| 366 |
|
|
taxon_match."*Name_score",
|
| 367 |
|
|
taxon_match."*Name_matched_author",
|
| 368 |
|
|
taxon_match."*Name_matched_url",
|
| 369 |
|
|
taxon_match."*Author_matched",
|
| 370 |
|
|
taxon_match."*Author_score",
|
| 371 |
|
|
taxon_match."*Family_matched",
|
| 372 |
|
|
taxon_match."*Family_score",
|
| 373 |
|
|
taxon_match."*Name_matched_accepted_family",
|
| 374 |
|
|
taxon_match."*Genus_matched",
|
| 375 |
|
|
taxon_match."*Genus_score",
|
| 376 |
|
|
taxon_match."*Specific_epithet_matched",
|
| 377 |
|
|
taxon_match."*Specific_epithet_score",
|
| 378 |
|
|
taxon_match."*Infraspecific_rank",
|
| 379 |
|
|
taxon_match."*Infraspecific_epithet_matched",
|
| 380 |
|
|
taxon_match."*Infraspecific_epithet_score",
|
| 381 |
|
|
taxon_match."*Infraspecific_rank_2",
|
| 382 |
|
|
taxon_match."*Infraspecific_epithet_2_matched",
|
| 383 |
|
|
taxon_match."*Infraspecific_epithet_2_score",
|
| 384 |
|
|
taxon_match."*Annotations",
|
| 385 |
|
|
taxon_match."*Unmatched_terms",
|
| 386 |
|
|
taxon_match."*Taxonomic_status",
|
| 387 |
|
|
taxon_match."*Accepted_name",
|
| 388 |
|
|
taxon_match."*Accepted_name_author",
|
| 389 |
|
|
taxon_match."*Accepted_name_rank",
|
| 390 |
|
|
taxon_match."*Accepted_name_url",
|
| 391 |
|
|
taxon_match."*Accepted_name_species",
|
| 392 |
|
|
taxon_match."*Accepted_name_family",
|
| 393 |
|
|
taxon_match."*Selected",
|
| 394 |
|
|
taxon_match."*Source",
|
| 395 |
|
|
taxon_match."*Warnings",
|
| 396 |
|
|
taxon_match."*Accepted_name_lsid",
|
| 397 |
13878
|
aaronmk
|
taxon_match.is_valid_match,
|
| 398 |
|
|
taxon_match.scrubbed_unique_taxon_name
|
| 399 |
|
|
FROM taxon_match
|
| 400 |
14111
|
aaronmk
|
WHERE (taxon_match."*Selected" = 'true'::text);
|
| 401 |
13878
|
aaronmk
|
|
| 402 |
|
|
|
| 403 |
|
|
--
|
| 404 |
|
|
-- Name: VIEW taxon_best_match; Type: COMMENT; Schema: TNRS; Owner: -
|
| 405 |
|
|
--
|
| 406 |
|
|
|
| 407 |
|
|
COMMENT ON VIEW taxon_best_match IS '
|
| 408 |
|
|
to modify:
|
| 409 |
|
|
SELECT util.recreate_view(''"TNRS"."taxon_best_match"'', $$
|
| 410 |
|
|
SELECT __
|
| 411 |
|
|
$$);
|
| 412 |
|
|
';
|
| 413 |
|
|
|
| 414 |
|
|
|
| 415 |
|
|
--
|
| 416 |
10778
|
aaronmk
|
-- Name: MatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
|
| 417 |
|
|
--
|
| 418 |
|
|
|
| 419 |
|
|
CREATE VIEW "MatchedTaxon" AS
|
| 420 |
14110
|
aaronmk
|
SELECT taxon_best_match.batch,
|
| 421 |
|
|
taxon_best_match.match_num,
|
| 422 |
14111
|
aaronmk
|
taxon_best_match."*Name_number",
|
| 423 |
|
|
taxon_best_match."*Name_submitted",
|
| 424 |
|
|
taxon_best_match."*Overall_score",
|
| 425 |
|
|
taxon_best_match."*Name_matched",
|
| 426 |
|
|
taxon_best_match."*Name_matched_rank",
|
| 427 |
|
|
taxon_best_match."*Name_score",
|
| 428 |
|
|
taxon_best_match."*Name_matched_author",
|
| 429 |
|
|
taxon_best_match."*Name_matched_url",
|
| 430 |
|
|
taxon_best_match."*Author_matched",
|
| 431 |
|
|
taxon_best_match."*Author_score",
|
| 432 |
|
|
taxon_best_match."*Family_matched",
|
| 433 |
|
|
taxon_best_match."*Family_score",
|
| 434 |
|
|
taxon_best_match."*Name_matched_accepted_family",
|
| 435 |
|
|
taxon_best_match."*Genus_matched",
|
| 436 |
|
|
taxon_best_match."*Genus_score",
|
| 437 |
|
|
taxon_best_match."*Specific_epithet_matched",
|
| 438 |
|
|
taxon_best_match."*Specific_epithet_score",
|
| 439 |
|
|
taxon_best_match."*Infraspecific_rank",
|
| 440 |
|
|
taxon_best_match."*Infraspecific_epithet_matched",
|
| 441 |
|
|
taxon_best_match."*Infraspecific_epithet_score",
|
| 442 |
|
|
taxon_best_match."*Infraspecific_rank_2",
|
| 443 |
|
|
taxon_best_match."*Infraspecific_epithet_2_matched",
|
| 444 |
|
|
taxon_best_match."*Infraspecific_epithet_2_score",
|
| 445 |
|
|
taxon_best_match."*Annotations",
|
| 446 |
|
|
taxon_best_match."*Unmatched_terms",
|
| 447 |
|
|
taxon_best_match."*Taxonomic_status",
|
| 448 |
|
|
taxon_best_match."*Accepted_name",
|
| 449 |
|
|
taxon_best_match."*Accepted_name_author",
|
| 450 |
|
|
taxon_best_match."*Accepted_name_rank",
|
| 451 |
|
|
taxon_best_match."*Accepted_name_url",
|
| 452 |
|
|
taxon_best_match."*Accepted_name_species",
|
| 453 |
|
|
taxon_best_match."*Accepted_name_family",
|
| 454 |
|
|
taxon_best_match."*Selected",
|
| 455 |
|
|
taxon_best_match."*Source",
|
| 456 |
|
|
taxon_best_match."*Warnings",
|
| 457 |
|
|
taxon_best_match."*Accepted_name_lsid",
|
| 458 |
14110
|
aaronmk
|
taxon_best_match.is_valid_match,
|
| 459 |
|
|
taxon_best_match.scrubbed_unique_taxon_name,
|
| 460 |
14111
|
aaronmk
|
map_taxonomic_status(taxon_best_match."*Taxonomic_status", taxon_best_match."*Accepted_name") AS "taxonomicStatus",
|
| 461 |
13498
|
aaronmk
|
CASE
|
| 462 |
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")
|
| 463 |
|
|
WHEN (taxon_best_match."*Accepted_name_rank" = 'genus'::text) THEN concat_ws(' '::text, taxon_best_match."*Accepted_name", taxon_best_match."*Unmatched_terms")
|
| 464 |
|
|
ELSE taxon_best_match."*Accepted_name_species"
|
| 465 |
13498
|
aaronmk
|
END AS accepted_morphospecies_binomial
|
| 466 |
14110
|
aaronmk
|
FROM taxon_best_match;
|
| 467 |
10778
|
aaronmk
|
|
| 468 |
|
|
|
| 469 |
|
|
--
|
| 470 |
13498
|
aaronmk
|
-- Name: VIEW "MatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 471 |
|
|
--
|
| 472 |
|
|
|
| 473 |
|
|
COMMENT ON VIEW "MatchedTaxon" IS '
|
| 474 |
13501
|
aaronmk
|
to modify:
|
| 475 |
13845
|
aaronmk
|
SELECT util.recreate_view(''"TNRS"."MatchedTaxon"'', $$
|
| 476 |
13647
|
aaronmk
|
SELECT __
|
| 477 |
13501
|
aaronmk
|
$$);
|
| 478 |
13498
|
aaronmk
|
';
|
| 479 |
|
|
|
| 480 |
|
|
|
| 481 |
|
|
--
|
| 482 |
10778
|
aaronmk
|
-- Name: ValidMatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
|
| 483 |
|
|
--
|
| 484 |
|
|
|
| 485 |
|
|
CREATE VIEW "ValidMatchedTaxon" AS
|
| 486 |
14108
|
aaronmk
|
SELECT "MatchedTaxon".batch,
|
| 487 |
14105
|
aaronmk
|
"MatchedTaxon".match_num,
|
| 488 |
14111
|
aaronmk
|
"MatchedTaxon"."*Name_number",
|
| 489 |
|
|
"MatchedTaxon"."*Name_submitted",
|
| 490 |
|
|
"MatchedTaxon"."*Overall_score",
|
| 491 |
|
|
"MatchedTaxon"."*Name_matched",
|
| 492 |
|
|
"MatchedTaxon"."*Name_matched_rank",
|
| 493 |
|
|
"MatchedTaxon"."*Name_score",
|
| 494 |
|
|
"MatchedTaxon"."*Name_matched_author",
|
| 495 |
|
|
"MatchedTaxon"."*Name_matched_url",
|
| 496 |
|
|
"MatchedTaxon"."*Author_matched",
|
| 497 |
|
|
"MatchedTaxon"."*Author_score",
|
| 498 |
|
|
"MatchedTaxon"."*Family_matched",
|
| 499 |
|
|
"MatchedTaxon"."*Family_score",
|
| 500 |
|
|
"MatchedTaxon"."*Name_matched_accepted_family",
|
| 501 |
|
|
"MatchedTaxon"."*Genus_matched",
|
| 502 |
|
|
"MatchedTaxon"."*Genus_score",
|
| 503 |
|
|
"MatchedTaxon"."*Specific_epithet_matched",
|
| 504 |
|
|
"MatchedTaxon"."*Specific_epithet_score",
|
| 505 |
|
|
"MatchedTaxon"."*Infraspecific_rank",
|
| 506 |
|
|
"MatchedTaxon"."*Infraspecific_epithet_matched",
|
| 507 |
|
|
"MatchedTaxon"."*Infraspecific_epithet_score",
|
| 508 |
|
|
"MatchedTaxon"."*Infraspecific_rank_2",
|
| 509 |
|
|
"MatchedTaxon"."*Infraspecific_epithet_2_matched",
|
| 510 |
|
|
"MatchedTaxon"."*Infraspecific_epithet_2_score",
|
| 511 |
|
|
"MatchedTaxon"."*Annotations",
|
| 512 |
|
|
"MatchedTaxon"."*Unmatched_terms",
|
| 513 |
|
|
"MatchedTaxon"."*Taxonomic_status",
|
| 514 |
|
|
"MatchedTaxon"."*Accepted_name",
|
| 515 |
|
|
"MatchedTaxon"."*Accepted_name_author",
|
| 516 |
|
|
"MatchedTaxon"."*Accepted_name_rank",
|
| 517 |
|
|
"MatchedTaxon"."*Accepted_name_url",
|
| 518 |
|
|
"MatchedTaxon"."*Accepted_name_species",
|
| 519 |
|
|
"MatchedTaxon"."*Accepted_name_family",
|
| 520 |
|
|
"MatchedTaxon"."*Selected",
|
| 521 |
|
|
"MatchedTaxon"."*Source",
|
| 522 |
|
|
"MatchedTaxon"."*Warnings",
|
| 523 |
|
|
"MatchedTaxon"."*Accepted_name_lsid",
|
| 524 |
14108
|
aaronmk
|
"MatchedTaxon".is_valid_match,
|
| 525 |
13800
|
aaronmk
|
"MatchedTaxon".scrubbed_unique_taxon_name,
|
| 526 |
14103
|
aaronmk
|
"MatchedTaxon"."taxonomicStatus",
|
| 527 |
13498
|
aaronmk
|
"MatchedTaxon".accepted_morphospecies_binomial
|
| 528 |
11708
|
aaronmk
|
FROM "MatchedTaxon"
|
| 529 |
14108
|
aaronmk
|
WHERE "MatchedTaxon".is_valid_match;
|
| 530 |
10778
|
aaronmk
|
|
| 531 |
|
|
|
| 532 |
|
|
--
|
| 533 |
|
|
-- Name: VIEW "ValidMatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 534 |
|
|
--
|
| 535 |
|
|
|
| 536 |
13443
|
aaronmk
|
COMMENT ON VIEW "ValidMatchedTaxon" IS '
|
| 537 |
|
|
to update, use * as the column list
|
| 538 |
|
|
';
|
| 539 |
10778
|
aaronmk
|
|
| 540 |
|
|
|
| 541 |
|
|
--
|
| 542 |
|
|
-- Name: batch; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 543 |
|
|
--
|
| 544 |
|
|
|
| 545 |
|
|
CREATE TABLE batch (
|
| 546 |
|
|
id text NOT NULL,
|
| 547 |
|
|
id_by_time text,
|
| 548 |
|
|
time_submitted timestamp with time zone DEFAULT now(),
|
| 549 |
|
|
client_version text
|
| 550 |
|
|
);
|
| 551 |
|
|
|
| 552 |
|
|
|
| 553 |
|
|
--
|
| 554 |
|
|
-- Name: batch_download_settings; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 555 |
|
|
--
|
| 556 |
|
|
|
| 557 |
|
|
CREATE TABLE batch_download_settings (
|
| 558 |
|
|
id text NOT NULL,
|
| 559 |
|
|
"E-mail" text,
|
| 560 |
|
|
"Id" text,
|
| 561 |
|
|
"Job type" text,
|
| 562 |
|
|
"Contains Id" boolean,
|
| 563 |
|
|
"Start time" text,
|
| 564 |
|
|
"Finish time" text,
|
| 565 |
|
|
"TNRS version" text,
|
| 566 |
|
|
"Sources selected" text,
|
| 567 |
|
|
"Match threshold" double precision,
|
| 568 |
|
|
"Classification" text,
|
| 569 |
|
|
"Allow partial matches?" boolean,
|
| 570 |
|
|
"Sort by source" boolean,
|
| 571 |
|
|
"Constrain by higher taxonomy" boolean
|
| 572 |
|
|
);
|
| 573 |
|
|
|
| 574 |
|
|
|
| 575 |
|
|
--
|
| 576 |
|
|
-- Name: TABLE batch_download_settings; Type: COMMENT; Schema: TNRS; Owner: -
|
| 577 |
|
|
--
|
| 578 |
|
|
|
| 579 |
13575
|
aaronmk
|
COMMENT ON TABLE batch_download_settings IS '
|
| 580 |
|
|
stores data from http://tnrs.iplantcollaborative.org/TNRSapp.html > Submit List > results section > Download settings > settings.txt
|
| 581 |
|
|
';
|
| 582 |
10778
|
aaronmk
|
|
| 583 |
|
|
|
| 584 |
|
|
--
|
| 585 |
|
|
-- Name: client_version; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 586 |
|
|
--
|
| 587 |
|
|
|
| 588 |
|
|
CREATE TABLE client_version (
|
| 589 |
|
|
id text NOT NULL,
|
| 590 |
|
|
global_rev integer NOT NULL,
|
| 591 |
|
|
"/lib/tnrs.py rev" integer,
|
| 592 |
|
|
"/bin/tnrs_db rev" integer
|
| 593 |
|
|
);
|
| 594 |
|
|
|
| 595 |
|
|
|
| 596 |
|
|
--
|
| 597 |
|
|
-- Name: TABLE client_version; Type: COMMENT; Schema: TNRS; Owner: -
|
| 598 |
|
|
--
|
| 599 |
|
|
|
| 600 |
13575
|
aaronmk
|
COMMENT ON TABLE client_version IS '
|
| 601 |
|
|
contains svn revisions
|
| 602 |
|
|
';
|
| 603 |
10778
|
aaronmk
|
|
| 604 |
|
|
|
| 605 |
|
|
--
|
| 606 |
|
|
-- Name: COLUMN client_version.global_rev; Type: COMMENT; Schema: TNRS; Owner: -
|
| 607 |
|
|
--
|
| 608 |
|
|
|
| 609 |
13575
|
aaronmk
|
COMMENT ON COLUMN client_version.global_rev IS '
|
| 610 |
|
|
from `svn info .` > Last Changed Rev
|
| 611 |
|
|
';
|
| 612 |
10778
|
aaronmk
|
|
| 613 |
|
|
|
| 614 |
|
|
--
|
| 615 |
|
|
-- Name: COLUMN client_version."/lib/tnrs.py rev"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 616 |
|
|
--
|
| 617 |
|
|
|
| 618 |
13575
|
aaronmk
|
COMMENT ON COLUMN client_version."/lib/tnrs.py rev" IS '
|
| 619 |
|
|
from `svn info lib/tnrs.py` > Last Changed Rev
|
| 620 |
|
|
';
|
| 621 |
10778
|
aaronmk
|
|
| 622 |
|
|
|
| 623 |
|
|
--
|
| 624 |
|
|
-- Name: COLUMN client_version."/bin/tnrs_db rev"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 625 |
|
|
--
|
| 626 |
|
|
|
| 627 |
13575
|
aaronmk
|
COMMENT ON COLUMN client_version."/bin/tnrs_db rev" IS '
|
| 628 |
|
|
from `svn info bin/tnrs_db` > Last Changed Rev
|
| 629 |
|
|
';
|
| 630 |
10778
|
aaronmk
|
|
| 631 |
|
|
|
| 632 |
|
|
--
|
| 633 |
13866
|
aaronmk
|
-- Name: taxon_match_input; Type: VIEW; Schema: TNRS; Owner: -
|
| 634 |
|
|
--
|
| 635 |
|
|
|
| 636 |
|
|
CREATE VIEW taxon_match_input AS
|
| 637 |
14111
|
aaronmk
|
SELECT taxon_match."*Name_number" AS "Name_number",
|
| 638 |
|
|
taxon_match."*Name_submitted" AS "Name_submitted",
|
| 639 |
|
|
taxon_match."*Overall_score" AS "Overall_score",
|
| 640 |
|
|
taxon_match."*Name_matched" AS "Name_matched",
|
| 641 |
|
|
taxon_match."*Name_matched_rank" AS "Name_matched_rank",
|
| 642 |
|
|
taxon_match."*Name_score" AS "Name_score",
|
| 643 |
|
|
taxon_match."*Name_matched_author" AS "Name_matched_author",
|
| 644 |
|
|
taxon_match."*Name_matched_url" AS "Name_matched_url",
|
| 645 |
|
|
taxon_match."*Author_matched" AS "Author_matched",
|
| 646 |
|
|
taxon_match."*Author_score" AS "Author_score",
|
| 647 |
|
|
taxon_match."*Family_matched" AS "Family_matched",
|
| 648 |
|
|
taxon_match."*Family_score" AS "Family_score",
|
| 649 |
|
|
taxon_match."*Name_matched_accepted_family" AS "Name_matched_accepted_family",
|
| 650 |
|
|
taxon_match."*Genus_matched" AS "Genus_matched",
|
| 651 |
|
|
taxon_match."*Genus_score" AS "Genus_score",
|
| 652 |
|
|
taxon_match."*Specific_epithet_matched" AS "Specific_epithet_matched",
|
| 653 |
|
|
taxon_match."*Specific_epithet_score" AS "Specific_epithet_score",
|
| 654 |
|
|
taxon_match."*Infraspecific_rank" AS "Infraspecific_rank",
|
| 655 |
|
|
taxon_match."*Infraspecific_epithet_matched" AS "Infraspecific_epithet_matched",
|
| 656 |
|
|
taxon_match."*Infraspecific_epithet_score" AS "Infraspecific_epithet_score",
|
| 657 |
|
|
taxon_match."*Infraspecific_rank_2" AS "Infraspecific_rank_2",
|
| 658 |
|
|
taxon_match."*Infraspecific_epithet_2_matched" AS "Infraspecific_epithet_2_matched",
|
| 659 |
|
|
taxon_match."*Infraspecific_epithet_2_score" AS "Infraspecific_epithet_2_score",
|
| 660 |
|
|
taxon_match."*Annotations" AS "Annotations",
|
| 661 |
|
|
taxon_match."*Unmatched_terms" AS "Unmatched_terms",
|
| 662 |
|
|
taxon_match."*Taxonomic_status" AS "Taxonomic_status",
|
| 663 |
|
|
taxon_match."*Accepted_name" AS "Accepted_name",
|
| 664 |
|
|
taxon_match."*Accepted_name_author" AS "Accepted_name_author",
|
| 665 |
|
|
taxon_match."*Accepted_name_rank" AS "Accepted_name_rank",
|
| 666 |
|
|
taxon_match."*Accepted_name_url" AS "Accepted_name_url",
|
| 667 |
|
|
taxon_match."*Accepted_name_species" AS "Accepted_name_species",
|
| 668 |
|
|
taxon_match."*Accepted_name_family" AS "Accepted_name_family",
|
| 669 |
|
|
taxon_match."*Selected" AS "Selected",
|
| 670 |
|
|
taxon_match."*Source" AS "Source",
|
| 671 |
|
|
taxon_match."*Warnings" AS "Warnings",
|
| 672 |
|
|
taxon_match."*Accepted_name_lsid" AS "Accepted_name_lsid"
|
| 673 |
13866
|
aaronmk
|
FROM taxon_match;
|
| 674 |
|
|
|
| 675 |
|
|
|
| 676 |
|
|
--
|
| 677 |
|
|
-- Name: taxon_match_input__copy_to; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 678 |
|
|
--
|
| 679 |
|
|
|
| 680 |
|
|
CREATE TABLE taxon_match_input__copy_to (
|
| 681 |
|
|
"Name_number" integer,
|
| 682 |
|
|
"Name_submitted" text,
|
| 683 |
|
|
"Overall_score" double precision,
|
| 684 |
|
|
"Name_matched" text,
|
| 685 |
|
|
"Name_matched_rank" text,
|
| 686 |
|
|
"Name_score" double precision,
|
| 687 |
|
|
"Name_matched_author" text,
|
| 688 |
|
|
"Name_matched_url" text,
|
| 689 |
|
|
"Author_matched" text,
|
| 690 |
|
|
"Author_score" double precision,
|
| 691 |
|
|
"Family_matched" text,
|
| 692 |
|
|
"Family_score" double precision,
|
| 693 |
|
|
"Name_matched_accepted_family" text,
|
| 694 |
|
|
"Genus_matched" text,
|
| 695 |
|
|
"Genus_score" double precision,
|
| 696 |
|
|
"Specific_epithet_matched" text,
|
| 697 |
|
|
"Specific_epithet_score" double precision,
|
| 698 |
|
|
"Infraspecific_rank" text,
|
| 699 |
|
|
"Infraspecific_epithet_matched" text,
|
| 700 |
|
|
"Infraspecific_epithet_score" double precision,
|
| 701 |
|
|
"Infraspecific_rank_2" text,
|
| 702 |
|
|
"Infraspecific_epithet_2_matched" text,
|
| 703 |
|
|
"Infraspecific_epithet_2_score" double precision,
|
| 704 |
|
|
"Annotations" text,
|
| 705 |
|
|
"Unmatched_terms" text,
|
| 706 |
|
|
"Taxonomic_status" text,
|
| 707 |
|
|
"Accepted_name" text,
|
| 708 |
|
|
"Accepted_name_author" text,
|
| 709 |
|
|
"Accepted_name_rank" text,
|
| 710 |
|
|
"Accepted_name_url" text,
|
| 711 |
|
|
"Accepted_name_species" text,
|
| 712 |
|
|
"Accepted_name_family" text,
|
| 713 |
|
|
"Selected" text,
|
| 714 |
|
|
"Source" text,
|
| 715 |
|
|
"Warnings" text,
|
| 716 |
|
|
"Accepted_name_lsid" text
|
| 717 |
|
|
);
|
| 718 |
|
|
|
| 719 |
|
|
|
| 720 |
|
|
--
|
| 721 |
11964
|
aaronmk
|
-- Name: taxon_scrub.scrubbed_unique_taxon_name.*; Type: VIEW; Schema: TNRS; Owner: -
|
| 722 |
|
|
--
|
| 723 |
|
|
|
| 724 |
|
|
CREATE VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" AS
|
| 725 |
14111
|
aaronmk
|
SELECT taxon_match."*Name_submitted" AS scrubbed_unique_taxon_name,
|
| 726 |
|
|
taxon_match."*Name_matched_rank" AS scrubbed_taxon_rank,
|
| 727 |
|
|
COALESCE(taxon_match."*Name_matched_accepted_family", taxon_match."*Family_matched") AS scrubbed_family,
|
| 728 |
|
|
taxon_match."*Genus_matched" AS scrubbed_genus,
|
| 729 |
|
|
taxon_match."*Specific_epithet_matched" AS scrubbed_specific_epithet,
|
| 730 |
|
|
taxon_match."*Infraspecific_rank" AS scrubbed_infraspecific_rank,
|
| 731 |
|
|
taxon_match."*Infraspecific_epithet_matched" AS scrubbed_infraspecific_epithet,
|
| 732 |
|
|
taxon_match."*Name_matched_author" AS scrubbed_author,
|
| 733 |
|
|
taxon_match."*Name_matched" AS scrubbed_taxon_name_no_author,
|
| 734 |
|
|
(taxon_match."*Name_matched" || COALESCE((' '::text || taxon_match."*Name_matched_author"), ''::text)) AS scrubbed_taxon_name_with_author
|
| 735 |
13861
|
aaronmk
|
FROM taxon_match;
|
| 736 |
11964
|
aaronmk
|
|
| 737 |
|
|
|
| 738 |
|
|
--
|
| 739 |
11965
|
aaronmk
|
-- Name: VIEW "taxon_scrub.scrubbed_unique_taxon_name.*"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 740 |
|
|
--
|
| 741 |
|
|
|
| 742 |
13575
|
aaronmk
|
COMMENT ON VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" IS '
|
| 743 |
13846
|
aaronmk
|
to modify:
|
| 744 |
|
|
SELECT util.recreate_view(''"TNRS"."taxon_scrub.scrubbed_unique_taxon_name.*"'', $$
|
| 745 |
|
|
SELECT __
|
| 746 |
|
|
$$);
|
| 747 |
|
|
|
| 748 |
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.
|
| 749 |
|
|
';
|
| 750 |
11965
|
aaronmk
|
|
| 751 |
|
|
|
| 752 |
|
|
--
|
| 753 |
11964
|
aaronmk
|
-- Name: taxon_scrub; Type: VIEW; Schema: TNRS; Owner: -
|
| 754 |
|
|
--
|
| 755 |
|
|
|
| 756 |
|
|
CREATE VIEW taxon_scrub AS
|
| 757 |
13800
|
aaronmk
|
SELECT "ValidMatchedTaxon".scrubbed_unique_taxon_name,
|
| 758 |
14108
|
aaronmk
|
"ValidMatchedTaxon".batch,
|
| 759 |
14105
|
aaronmk
|
"ValidMatchedTaxon".match_num,
|
| 760 |
14111
|
aaronmk
|
"ValidMatchedTaxon"."*Name_number",
|
| 761 |
|
|
"ValidMatchedTaxon"."*Name_submitted",
|
| 762 |
|
|
"ValidMatchedTaxon"."*Overall_score",
|
| 763 |
|
|
"ValidMatchedTaxon"."*Name_matched",
|
| 764 |
|
|
"ValidMatchedTaxon"."*Name_matched_rank",
|
| 765 |
|
|
"ValidMatchedTaxon"."*Name_score",
|
| 766 |
|
|
"ValidMatchedTaxon"."*Name_matched_author",
|
| 767 |
|
|
"ValidMatchedTaxon"."*Name_matched_url",
|
| 768 |
|
|
"ValidMatchedTaxon"."*Author_matched",
|
| 769 |
|
|
"ValidMatchedTaxon"."*Author_score",
|
| 770 |
|
|
"ValidMatchedTaxon"."*Family_matched",
|
| 771 |
|
|
"ValidMatchedTaxon"."*Family_score",
|
| 772 |
|
|
"ValidMatchedTaxon"."*Name_matched_accepted_family",
|
| 773 |
|
|
"ValidMatchedTaxon"."*Genus_matched",
|
| 774 |
|
|
"ValidMatchedTaxon"."*Genus_score",
|
| 775 |
|
|
"ValidMatchedTaxon"."*Specific_epithet_matched",
|
| 776 |
|
|
"ValidMatchedTaxon"."*Specific_epithet_score",
|
| 777 |
|
|
"ValidMatchedTaxon"."*Infraspecific_rank",
|
| 778 |
|
|
"ValidMatchedTaxon"."*Infraspecific_epithet_matched",
|
| 779 |
|
|
"ValidMatchedTaxon"."*Infraspecific_epithet_score",
|
| 780 |
|
|
"ValidMatchedTaxon"."*Infraspecific_rank_2",
|
| 781 |
|
|
"ValidMatchedTaxon"."*Infraspecific_epithet_2_matched",
|
| 782 |
|
|
"ValidMatchedTaxon"."*Infraspecific_epithet_2_score",
|
| 783 |
|
|
"ValidMatchedTaxon"."*Annotations",
|
| 784 |
|
|
"ValidMatchedTaxon"."*Unmatched_terms",
|
| 785 |
|
|
"ValidMatchedTaxon"."*Taxonomic_status",
|
| 786 |
|
|
"ValidMatchedTaxon"."*Accepted_name",
|
| 787 |
|
|
"ValidMatchedTaxon"."*Accepted_name_author",
|
| 788 |
|
|
"ValidMatchedTaxon"."*Accepted_name_rank",
|
| 789 |
|
|
"ValidMatchedTaxon"."*Accepted_name_url",
|
| 790 |
|
|
"ValidMatchedTaxon"."*Accepted_name_species",
|
| 791 |
|
|
"ValidMatchedTaxon"."*Accepted_name_family",
|
| 792 |
|
|
"ValidMatchedTaxon"."*Selected",
|
| 793 |
|
|
"ValidMatchedTaxon"."*Source",
|
| 794 |
|
|
"ValidMatchedTaxon"."*Warnings",
|
| 795 |
|
|
"ValidMatchedTaxon"."*Accepted_name_lsid",
|
| 796 |
14108
|
aaronmk
|
"ValidMatchedTaxon".is_valid_match,
|
| 797 |
14103
|
aaronmk
|
"ValidMatchedTaxon"."taxonomicStatus",
|
| 798 |
13800
|
aaronmk
|
"ValidMatchedTaxon".accepted_morphospecies_binomial,
|
| 799 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_rank,
|
| 800 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_family,
|
| 801 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus,
|
| 802 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet,
|
| 803 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_rank,
|
| 804 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_epithet,
|
| 805 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_author,
|
| 806 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_no_author,
|
| 807 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_with_author,
|
| 808 |
13532
|
aaronmk
|
CASE
|
| 809 |
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")
|
| 810 |
|
|
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")
|
| 811 |
13532
|
aaronmk
|
ELSE (("taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus || ' '::text) || "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet)
|
| 812 |
|
|
END AS scrubbed_morphospecies_binomial
|
| 813 |
11964
|
aaronmk
|
FROM ("ValidMatchedTaxon"
|
| 814 |
|
|
LEFT JOIN "taxon_scrub.scrubbed_unique_taxon_name.*" USING (scrubbed_unique_taxon_name));
|
| 815 |
|
|
|
| 816 |
|
|
|
| 817 |
|
|
--
|
| 818 |
|
|
-- Name: VIEW taxon_scrub; Type: COMMENT; Schema: TNRS; Owner: -
|
| 819 |
|
|
--
|
| 820 |
|
|
|
| 821 |
13443
|
aaronmk
|
COMMENT ON VIEW taxon_scrub IS '
|
| 822 |
13531
|
aaronmk
|
to modify:
|
| 823 |
13845
|
aaronmk
|
SELECT util.recreate_view(''"TNRS".taxon_scrub'', $$
|
| 824 |
13647
|
aaronmk
|
SELECT __
|
| 825 |
13531
|
aaronmk
|
$$);
|
| 826 |
13443
|
aaronmk
|
';
|
| 827 |
11964
|
aaronmk
|
|
| 828 |
|
|
|
| 829 |
|
|
--
|
| 830 |
10778
|
aaronmk
|
-- Name: batch_download_settings_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 831 |
|
|
--
|
| 832 |
|
|
|
| 833 |
|
|
ALTER TABLE ONLY batch_download_settings
|
| 834 |
|
|
ADD CONSTRAINT batch_download_settings_pkey PRIMARY KEY (id);
|
| 835 |
|
|
|
| 836 |
|
|
|
| 837 |
|
|
--
|
| 838 |
|
|
-- Name: batch_id_by_time_key; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 839 |
|
|
--
|
| 840 |
|
|
|
| 841 |
|
|
ALTER TABLE ONLY batch
|
| 842 |
|
|
ADD CONSTRAINT batch_id_by_time_key UNIQUE (id_by_time);
|
| 843 |
|
|
|
| 844 |
|
|
|
| 845 |
|
|
--
|
| 846 |
|
|
-- Name: batch_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 847 |
|
|
--
|
| 848 |
|
|
|
| 849 |
|
|
ALTER TABLE ONLY batch
|
| 850 |
|
|
ADD CONSTRAINT batch_pkey PRIMARY KEY (id);
|
| 851 |
|
|
|
| 852 |
|
|
|
| 853 |
|
|
--
|
| 854 |
|
|
-- Name: client_version_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 855 |
|
|
--
|
| 856 |
|
|
|
| 857 |
|
|
ALTER TABLE ONLY client_version
|
| 858 |
|
|
ADD CONSTRAINT client_version_pkey PRIMARY KEY (id);
|
| 859 |
|
|
|
| 860 |
|
|
|
| 861 |
|
|
--
|
| 862 |
13868
|
aaronmk
|
-- Name: taxon_match_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 863 |
10778
|
aaronmk
|
--
|
| 864 |
|
|
|
| 865 |
13861
|
aaronmk
|
ALTER TABLE ONLY taxon_match
|
| 866 |
13868
|
aaronmk
|
ADD CONSTRAINT taxon_match_pkey PRIMARY KEY (batch, match_num);
|
| 867 |
10778
|
aaronmk
|
|
| 868 |
14125
|
aaronmk
|
ALTER TABLE taxon_match CLUSTER ON taxon_match_pkey;
|
| 869 |
10778
|
aaronmk
|
|
| 870 |
14125
|
aaronmk
|
|
| 871 |
10778
|
aaronmk
|
--
|
| 872 |
10793
|
aaronmk
|
-- Name: batch_client_version_idx; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 873 |
|
|
--
|
| 874 |
|
|
|
| 875 |
|
|
CREATE INDEX batch_client_version_idx ON batch USING btree (client_version);
|
| 876 |
|
|
|
| 877 |
|
|
|
| 878 |
|
|
--
|
| 879 |
13879
|
aaronmk
|
-- Name: taxon_best_match__valid_match; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 880 |
13589
|
aaronmk
|
--
|
| 881 |
|
|
|
| 882 |
14111
|
aaronmk
|
CREATE INDEX taxon_best_match__valid_match ON taxon_match USING btree ("*Name_submitted") WHERE (("*Selected" = 'true'::text) AND is_valid_match);
|
| 883 |
13589
|
aaronmk
|
|
| 884 |
|
|
|
| 885 |
|
|
--
|
| 886 |
13879
|
aaronmk
|
-- Name: taxon_match_Name_submitted_idx; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 887 |
13874
|
aaronmk
|
--
|
| 888 |
|
|
|
| 889 |
14111
|
aaronmk
|
CREATE INDEX "taxon_match_Name_submitted_idx" ON taxon_match USING btree ("*Name_submitted");
|
| 890 |
13874
|
aaronmk
|
|
| 891 |
|
|
|
| 892 |
|
|
--
|
| 893 |
13879
|
aaronmk
|
-- Name: taxon_match__one_selected_match; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 894 |
11607
|
aaronmk
|
--
|
| 895 |
|
|
|
| 896 |
14111
|
aaronmk
|
CREATE UNIQUE INDEX taxon_match__one_selected_match ON taxon_match USING btree (batch, "*Name_number") WHERE ("*Selected" = 'true'::text);
|
| 897 |
11607
|
aaronmk
|
|
| 898 |
|
|
|
| 899 |
|
|
--
|
| 900 |
10778
|
aaronmk
|
-- Name: batch__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 901 |
|
|
--
|
| 902 |
|
|
|
| 903 |
|
|
CREATE TRIGGER batch__fill BEFORE INSERT OR UPDATE ON batch FOR EACH ROW EXECUTE PROCEDURE batch__fill();
|
| 904 |
|
|
|
| 905 |
|
|
|
| 906 |
|
|
--
|
| 907 |
13868
|
aaronmk
|
-- Name: taxon_match__batch_begin; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 908 |
13866
|
aaronmk
|
--
|
| 909 |
|
|
|
| 910 |
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();
|
| 911 |
13866
|
aaronmk
|
|
| 912 |
|
|
|
| 913 |
|
|
--
|
| 914 |
13868
|
aaronmk
|
-- Name: taxon_match__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 915 |
13567
|
aaronmk
|
--
|
| 916 |
|
|
|
| 917 |
13868
|
aaronmk
|
CREATE TRIGGER taxon_match__fill BEFORE INSERT OR UPDATE ON taxon_match FOR EACH ROW EXECUTE PROCEDURE taxon_match__fill();
|
| 918 |
13567
|
aaronmk
|
|
| 919 |
|
|
|
| 920 |
|
|
--
|
| 921 |
14122
|
aaronmk
|
-- Name: taxon_match__fill_derived; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 922 |
|
|
--
|
| 923 |
|
|
|
| 924 |
|
|
CREATE TRIGGER taxon_match__fill_derived BEFORE INSERT OR UPDATE ON taxon_match FOR EACH ROW EXECUTE PROCEDURE taxon_match__fill_derived();
|
| 925 |
|
|
|
| 926 |
|
|
|
| 927 |
|
|
--
|
| 928 |
13868
|
aaronmk
|
-- Name: taxon_match__match_num__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 929 |
13578
|
aaronmk
|
--
|
| 930 |
|
|
|
| 931 |
13868
|
aaronmk
|
CREATE TRIGGER taxon_match__match_num__fill BEFORE INSERT ON taxon_match FOR EACH ROW EXECUTE PROCEDURE taxon_match__match_num__fill();
|
| 932 |
13578
|
aaronmk
|
|
| 933 |
|
|
|
| 934 |
|
|
--
|
| 935 |
13868
|
aaronmk
|
-- Name: taxon_match_input__copy_to__insert; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 936 |
10778
|
aaronmk
|
--
|
| 937 |
|
|
|
| 938 |
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();
|
| 939 |
10778
|
aaronmk
|
|
| 940 |
|
|
|
| 941 |
|
|
--
|
| 942 |
|
|
-- Name: batch_client_version_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
| 943 |
|
|
--
|
| 944 |
|
|
|
| 945 |
|
|
ALTER TABLE ONLY batch
|
| 946 |
|
|
ADD CONSTRAINT batch_client_version_fkey FOREIGN KEY (client_version) REFERENCES client_version(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 947 |
|
|
|
| 948 |
|
|
|
| 949 |
|
|
--
|
| 950 |
|
|
-- Name: batch_download_settings_id_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
| 951 |
|
|
--
|
| 952 |
|
|
|
| 953 |
|
|
ALTER TABLE ONLY batch_download_settings
|
| 954 |
|
|
ADD CONSTRAINT batch_download_settings_id_fkey FOREIGN KEY (id) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 955 |
|
|
|
| 956 |
|
|
|
| 957 |
|
|
--
|
| 958 |
13868
|
aaronmk
|
-- Name: taxon_match_batch_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
| 959 |
10778
|
aaronmk
|
--
|
| 960 |
|
|
|
| 961 |
13861
|
aaronmk
|
ALTER TABLE ONLY taxon_match
|
| 962 |
13868
|
aaronmk
|
ADD CONSTRAINT taxon_match_batch_fkey FOREIGN KEY (batch) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 963 |
10778
|
aaronmk
|
|
| 964 |
|
|
|
| 965 |
|
|
--
|
| 966 |
|
|
-- Name: TNRS; Type: ACL; Schema: -; Owner: -
|
| 967 |
|
|
--
|
| 968 |
|
|
|
| 969 |
|
|
REVOKE ALL ON SCHEMA "TNRS" FROM PUBLIC;
|
| 970 |
|
|
REVOKE ALL ON SCHEMA "TNRS" FROM bien;
|
| 971 |
|
|
GRANT ALL ON SCHEMA "TNRS" TO bien;
|
| 972 |
|
|
GRANT USAGE ON SCHEMA "TNRS" TO bien_read;
|
| 973 |
|
|
|
| 974 |
|
|
|
| 975 |
|
|
--
|
| 976 |
13861
|
aaronmk
|
-- Name: taxon_match; Type: ACL; Schema: TNRS; Owner: -
|
| 977 |
10778
|
aaronmk
|
--
|
| 978 |
|
|
|
| 979 |
13861
|
aaronmk
|
REVOKE ALL ON TABLE taxon_match FROM PUBLIC;
|
| 980 |
|
|
REVOKE ALL ON TABLE taxon_match FROM bien;
|
| 981 |
|
|
GRANT ALL ON TABLE taxon_match TO bien;
|
| 982 |
|
|
GRANT SELECT ON TABLE taxon_match TO bien_read;
|
| 983 |
10778
|
aaronmk
|
|
| 984 |
|
|
|
| 985 |
|
|
--
|
| 986 |
13878
|
aaronmk
|
-- Name: taxon_best_match; Type: ACL; Schema: TNRS; Owner: -
|
| 987 |
|
|
--
|
| 988 |
|
|
|
| 989 |
|
|
REVOKE ALL ON TABLE taxon_best_match FROM PUBLIC;
|
| 990 |
|
|
REVOKE ALL ON TABLE taxon_best_match FROM bien;
|
| 991 |
|
|
GRANT ALL ON TABLE taxon_best_match TO bien;
|
| 992 |
|
|
GRANT SELECT ON TABLE taxon_best_match TO bien_read;
|
| 993 |
|
|
|
| 994 |
|
|
|
| 995 |
|
|
--
|
| 996 |
11912
|
aaronmk
|
-- Name: MatchedTaxon; Type: ACL; Schema: TNRS; Owner: -
|
| 997 |
|
|
--
|
| 998 |
|
|
|
| 999 |
|
|
REVOKE ALL ON TABLE "MatchedTaxon" FROM PUBLIC;
|
| 1000 |
|
|
REVOKE ALL ON TABLE "MatchedTaxon" FROM bien;
|
| 1001 |
|
|
GRANT ALL ON TABLE "MatchedTaxon" TO bien;
|
| 1002 |
|
|
GRANT SELECT ON TABLE "MatchedTaxon" TO bien_read;
|
| 1003 |
|
|
|
| 1004 |
|
|
|
| 1005 |
|
|
--
|
| 1006 |
|
|
-- Name: ValidMatchedTaxon; Type: ACL; Schema: TNRS; Owner: -
|
| 1007 |
|
|
--
|
| 1008 |
|
|
|
| 1009 |
|
|
REVOKE ALL ON TABLE "ValidMatchedTaxon" FROM PUBLIC;
|
| 1010 |
|
|
REVOKE ALL ON TABLE "ValidMatchedTaxon" FROM bien;
|
| 1011 |
|
|
GRANT ALL ON TABLE "ValidMatchedTaxon" TO bien;
|
| 1012 |
|
|
GRANT SELECT ON TABLE "ValidMatchedTaxon" TO bien_read;
|
| 1013 |
|
|
|
| 1014 |
|
|
|
| 1015 |
|
|
--
|
| 1016 |
13866
|
aaronmk
|
-- Name: taxon_match_input; Type: ACL; Schema: TNRS; Owner: -
|
| 1017 |
|
|
--
|
| 1018 |
|
|
|
| 1019 |
|
|
REVOKE ALL ON TABLE taxon_match_input FROM PUBLIC;
|
| 1020 |
|
|
REVOKE ALL ON TABLE taxon_match_input FROM bien;
|
| 1021 |
|
|
GRANT ALL ON TABLE taxon_match_input TO bien;
|
| 1022 |
|
|
GRANT SELECT ON TABLE taxon_match_input TO bien_read;
|
| 1023 |
|
|
|
| 1024 |
|
|
|
| 1025 |
|
|
--
|
| 1026 |
11912
|
aaronmk
|
-- Name: taxon_scrub.scrubbed_unique_taxon_name.*; Type: ACL; Schema: TNRS; Owner: -
|
| 1027 |
|
|
--
|
| 1028 |
|
|
|
| 1029 |
|
|
REVOKE ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" FROM PUBLIC;
|
| 1030 |
|
|
REVOKE ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" FROM bien;
|
| 1031 |
|
|
GRANT ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" TO bien;
|
| 1032 |
|
|
GRANT SELECT ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" TO bien_read;
|
| 1033 |
|
|
|
| 1034 |
|
|
|
| 1035 |
|
|
--
|
| 1036 |
|
|
-- Name: taxon_scrub; Type: ACL; Schema: TNRS; Owner: -
|
| 1037 |
|
|
--
|
| 1038 |
|
|
|
| 1039 |
|
|
REVOKE ALL ON TABLE taxon_scrub FROM PUBLIC;
|
| 1040 |
|
|
REVOKE ALL ON TABLE taxon_scrub FROM bien;
|
| 1041 |
|
|
GRANT ALL ON TABLE taxon_scrub TO bien;
|
| 1042 |
|
|
GRANT SELECT ON TABLE taxon_scrub TO bien_read;
|
| 1043 |
|
|
|
| 1044 |
|
|
|
| 1045 |
|
|
--
|
| 1046 |
10778
|
aaronmk
|
-- PostgreSQL database dump complete
|
| 1047 |
|
|
--
|
