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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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SET statement_timeout = 0;
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SET lock_timeout = 0;
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SET client_encoding = 'UTF8';
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SET standard_conforming_strings = on;
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SET check_function_bodies = false;
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SET client_min_messages = warning;
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aaronmk
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--
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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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aaronmk
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--CREATE SCHEMA "TNRS";
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--
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-- Name: SCHEMA "TNRS"; Type: COMMENT; Schema: -; Owner: -
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--
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COMMENT ON SCHEMA "TNRS" IS 'IMPORTANT: when changing this schema, you must also make the same changes on vegbiendev:
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on vegbiendev:
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# back up existing TNRS schema (in case of an accidental incorrect change):
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$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")
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$ svn up
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$ svn di
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# make the changes shown in the diff
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## to change column types:
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SELECT util.set_col_types(''"TNRS".tnrs'', ARRAY[
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(''col'', ''new_type'')
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]::util.col_cast[]); -- runtime: 9 min ("531282 ms")
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$ rm=1 inputs/.TNRS/schema.sql.run
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# repeat until `svn di` shows no diff
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# back up new TNRS schema:
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$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")';
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SET search_path = "TNRS", pg_catalog;
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--
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-- Name: MatchedTaxon_modify(text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION "MatchedTaxon_modify"(view_query text) RETURNS void
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LANGUAGE sql
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AS $_$
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SELECT util.recreate_view('"TNRS"."MatchedTaxon"', $1, $$
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-- **IMPORTANT**: keep these updated as described in the views' comments
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CREATE VIEW "TNRS"."ValidMatchedTaxon" AS
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SELECT *
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FROM "TNRS"."MatchedTaxon"
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WHERE "MatchedTaxon".taxon_scrub__is_valid_match;
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$$||util.mk_set_relation_metadata('"TNRS"."ValidMatchedTaxon"')||$$
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CREATE VIEW "TNRS".taxon_scrub AS
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SELECT *
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FROM "TNRS"."ValidMatchedTaxon"
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LEFT JOIN "TNRS"."taxon_scrub.scrubbed_unique_taxon_name.*" USING (scrubbed_unique_taxon_name);
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$$||util.mk_set_relation_metadata('"TNRS".taxon_scrub')||$$
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$$);
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$_$;
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--
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-- Name: FUNCTION "MatchedTaxon_modify"(view_query text); Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON FUNCTION "MatchedTaxon_modify"(view_query text) IS '
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usage:
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SELECT "TNRS"."MatchedTaxon_modify"($$
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SELECT *, __ AS accepted_morphospecies_binomial
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FROM __
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$$);
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idempotent
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';
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--
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-- Name: batch__fill(); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION batch__fill() RETURNS trigger
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LANGUAGE plpgsql
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AS $$
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BEGIN
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new.id_by_time = new.time_submitted;
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new.id = COALESCE(new.id, new.id_by_time);
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RETURN new;
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END;
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$$;
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--
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-- Name: family_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION family_is_homonym(family text) RETURNS boolean
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LANGUAGE sql STABLE STRICT
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AS $_$
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SELECT EXISTS(SELECT * FROM "IRMNG".family_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
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$_$;
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--
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-- Name: genus_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION genus_is_homonym(genus text) RETURNS boolean
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LANGUAGE sql STABLE STRICT
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AS $_$
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SELECT EXISTS(SELECT * FROM "IRMNG".genus_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
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$_$;
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--
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-- Name: map_taxonomic_status(text, text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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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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SELECT CASE WHEN $2 IS NOT NULL THEN 'accepted' ELSE lower($1) END
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$_$;
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--
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-- Name: taxon_scrub_modify(text); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION taxon_scrub_modify(view_query text) RETURNS void
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LANGUAGE sql
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AS $_$
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SELECT util.recreate_view('"TNRS".taxon_scrub', $1);
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$_$;
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--
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-- Name: FUNCTION taxon_scrub_modify(view_query text); Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON FUNCTION taxon_scrub_modify(view_query text) IS '
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usage:
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SELECT "TNRS".taxon_scrub_modify($$
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SELECT *
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FROM "TNRS"."ValidMatchedTaxon"
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LEFT JOIN "TNRS"."taxon_scrub.scrubbed_unique_taxon_name.*" USING (scrubbed_unique_taxon_name);
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$$);
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idempotent
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';
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--
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-- Name: tnrs_populate_fields(); Type: FUNCTION; Schema: TNRS; Owner: -
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--
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CREATE FUNCTION tnrs_populate_fields() RETURNS trigger
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LANGUAGE plpgsql
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AS $$
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9763
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DECLARE
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"Specific_epithet_is_plant" boolean :=
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(CASE
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WHEN new."Infraspecific_epithet_matched" IS NOT NULL
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OR new."Infraspecific_epithet_2_matched" IS NOT NULL
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OR new."Specific_epithet_score" >= 0.9 -- fuzzy match
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THEN true
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ELSE NULL -- ambiguous
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END);
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never_homonym boolean = COALESCE(new."Author_score" >= 0.6, false);
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-- author disambiguates
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family_is_homonym boolean = NOT never_homonym
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AND "TNRS".family_is_homonym(new."Family_matched");
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genus_is_homonym boolean = NOT never_homonym
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AND "TNRS".genus_is_homonym(new."Genus_matched");
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matched_taxon_name_with_author text = NULLIF(concat_ws(' '
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, NULLIF(NULLIF(new."Name_matched_accepted_family", 'Unknown'),
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new."Name_matched")
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, NULLIF(new."Name_matched", 'No suitable matches found.')
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, new."Name_matched_author"
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), '');
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accepted_taxon_name_with_author text = NULLIF(concat_ws(' '
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11628
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, NULLIF(NULLIF(new."Accepted_name_family", 'Unknown'),
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new."Accepted_name")
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, new."Accepted_name"
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, new."Accepted_name_author"
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), '');
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| 194 |
11643
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aaronmk
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BEGIN
|
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11629
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/* exclude homonyms because these are not valid matches (i.e. TNRS provides
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a name, but the name is not meaningful because it is not unambiguous). */
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11711
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new.is_valid_match = new."Taxonomic_status" != 'Invalid'
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AND COALESCE(CASE
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11628
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WHEN new."Family_score" = 1 AND NOT family_is_homonym -- exact match
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THEN true
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ELSE -- consider genus
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| 202 |
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(CASE
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| 203 |
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WHEN new."Genus_score" = 1 -- exact match
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| 204 |
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THEN
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| 205 |
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(CASE
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| 206 |
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WHEN NOT genus_is_homonym THEN true
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ELSE "Specific_epithet_is_plant"
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| 208 |
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END)
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WHEN new."Genus_score" >= 0.85 -- fuzzy match
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THEN "Specific_epithet_is_plant"
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ELSE NULL -- ambiguous
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| 212 |
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END)
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| 213 |
11629
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aaronmk
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END, false);
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| 214 |
11632
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aaronmk
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new.scrubbed_unique_taxon_name = COALESCE(
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| 215 |
11643
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aaronmk
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accepted_taxon_name_with_author, matched_taxon_name_with_author);
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| 216 |
11628
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aaronmk
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| 217 |
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RETURN new;
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| 218 |
7134
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END;
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| 219 |
10778
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aaronmk
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$$;
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| 220 |
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| 221 |
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--
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| 223 |
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-- Name: FUNCTION tnrs_populate_fields(); Type: COMMENT; Schema: TNRS; Owner: -
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| 224 |
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--
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| 225 |
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| 226 |
10754
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aaronmk
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COMMENT ON FUNCTION tnrs_populate_fields() IS 'IMPORTANT: when changing this function, you must regenerate the derived cols:
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| 227 |
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UPDATE "TNRS".tnrs SET "Name_submitted" = "Name_submitted"
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| 228 |
11715
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aaronmk
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runtime: 30 min ("5564082 rows affected, 1918900 ms execution time")
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| 229 |
10754
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aaronmk
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VACUUM ANALYZE "TNRS".tnrs -- to remove previous rows
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| 230 |
11615
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aaronmk
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runtime: 1.5 min ("92633 ms")';
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| 231 |
7134
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aaronmk
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| 232 |
7251
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aaronmk
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| 233 |
10778
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aaronmk
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SET default_tablespace = '';
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| 234 |
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| 235 |
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SET default_with_oids = false;
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| 236 |
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| 237 |
10728
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aaronmk
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--
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| 238 |
10778
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aaronmk
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-- Name: tnrs; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 239 |
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--
|
| 240 |
7251
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aaronmk
|
|
| 241 |
10778
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aaronmk
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CREATE TABLE tnrs (
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| 242 |
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batch text DEFAULT now() NOT NULL,
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| 243 |
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"Name_number" integer NOT NULL,
|
| 244 |
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"Name_submitted" text NOT NULL,
|
| 245 |
|
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"Overall_score" double precision,
|
| 246 |
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"Name_matched" text,
|
| 247 |
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"Name_matched_rank" text,
|
| 248 |
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"Name_score" double precision,
|
| 249 |
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"Name_matched_author" text,
|
| 250 |
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"Name_matched_url" text,
|
| 251 |
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"Author_matched" text,
|
| 252 |
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"Author_score" double precision,
|
| 253 |
|
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"Family_matched" text,
|
| 254 |
|
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"Family_score" double precision,
|
| 255 |
|
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"Name_matched_accepted_family" text,
|
| 256 |
|
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"Genus_matched" text,
|
| 257 |
|
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"Genus_score" double precision,
|
| 258 |
|
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"Specific_epithet_matched" text,
|
| 259 |
|
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"Specific_epithet_score" double precision,
|
| 260 |
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"Infraspecific_rank" text,
|
| 261 |
|
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"Infraspecific_epithet_matched" text,
|
| 262 |
|
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"Infraspecific_epithet_score" double precision,
|
| 263 |
|
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"Infraspecific_rank_2" text,
|
| 264 |
|
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"Infraspecific_epithet_2_matched" text,
|
| 265 |
|
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"Infraspecific_epithet_2_score" double precision,
|
| 266 |
|
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"Annotations" text,
|
| 267 |
|
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"Unmatched_terms" text,
|
| 268 |
|
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"Taxonomic_status" text,
|
| 269 |
|
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"Accepted_name" text,
|
| 270 |
|
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"Accepted_name_author" text,
|
| 271 |
|
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"Accepted_name_rank" text,
|
| 272 |
|
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"Accepted_name_url" text,
|
| 273 |
|
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"Accepted_name_species" text,
|
| 274 |
|
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"Accepted_name_family" text,
|
| 275 |
|
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"Selected" text,
|
| 276 |
|
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"Source" text,
|
| 277 |
|
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"Warnings" text,
|
| 278 |
|
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"Accepted_name_lsid" text,
|
| 279 |
11628
|
aaronmk
|
is_valid_match boolean NOT NULL,
|
| 280 |
11632
|
aaronmk
|
scrubbed_unique_taxon_name text
|
| 281 |
10778
|
aaronmk
|
);
|
| 282 |
7823
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aaronmk
|
|
| 283 |
9759
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aaronmk
|
|
| 284 |
10778
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aaronmk
|
--
|
| 285 |
|
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-- Name: TABLE tnrs; Type: COMMENT; Schema: TNRS; Owner: -
|
| 286 |
|
|
--
|
| 287 |
7823
|
aaronmk
|
|
| 288 |
10787
|
aaronmk
|
COMMENT ON TABLE tnrs IS 'IMPORTANT: when changing this table''s schema, you may need to re-run TNRS:
|
| 289 |
11614
|
aaronmk
|
$ inputs/.TNRS/data.sql.run refresh';
|
| 290 |
10778
|
aaronmk
|
|
| 291 |
|
|
|
| 292 |
|
|
--
|
| 293 |
|
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-- Name: MatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
|
| 294 |
|
|
--
|
| 295 |
|
|
|
| 296 |
|
|
CREATE VIEW "MatchedTaxon" AS
|
| 297 |
13498
|
aaronmk
|
SELECT s."*Name_matched.batch",
|
| 298 |
|
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s."concatenatedScientificName",
|
| 299 |
|
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s."matchedTaxonName",
|
| 300 |
|
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s."matchedTaxonRank",
|
| 301 |
|
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s."*Name_matched.Name_score",
|
| 302 |
|
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s."matchedScientificNameAuthorship",
|
| 303 |
|
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s."matchedScientificNameID",
|
| 304 |
|
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s."*Name_matched.Author_score",
|
| 305 |
|
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s."matchedFamilyConfidence_fraction",
|
| 306 |
|
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s."matchedFamily",
|
| 307 |
|
|
s."matchedGenus",
|
| 308 |
|
|
s."matchedGenusConfidence_fraction",
|
| 309 |
|
|
s."matchedSpecificEpithet",
|
| 310 |
|
|
s."matchedSpeciesConfidence_fraction",
|
| 311 |
|
|
s."matchedInfraspecificEpithet",
|
| 312 |
|
|
s."*Name_matched.Infraspecific_epithet_score",
|
| 313 |
|
|
s."identificationQualifier",
|
| 314 |
|
|
s."morphospeciesSuffix",
|
| 315 |
|
|
s."taxonomicStatus",
|
| 316 |
|
|
s.accepted_taxon_name_no_author,
|
| 317 |
|
|
s.accepted_author,
|
| 318 |
|
|
s.accepted_taxon_rank,
|
| 319 |
|
|
s."acceptedScientificNameID",
|
| 320 |
|
|
s.accepted_species_binomial,
|
| 321 |
|
|
s.accepted_family,
|
| 322 |
|
|
s."*Name_matched.Selected",
|
| 323 |
|
|
s."*Name_matched.Source",
|
| 324 |
|
|
s."*Name_matched.Warnings",
|
| 325 |
|
|
s."*Name_matched.Accepted_name_lsid",
|
| 326 |
|
|
s.taxon_scrub__is_valid_match,
|
| 327 |
|
|
s.scrubbed_unique_taxon_name,
|
| 328 |
|
|
CASE
|
| 329 |
|
|
WHEN (s.accepted_taxon_rank = 'family'::text) THEN concat_ws(' '::text, s.accepted_family, s."morphospeciesSuffix")
|
| 330 |
|
|
WHEN (s.accepted_taxon_rank = 'genus'::text) THEN concat_ws(' '::text, s.accepted_taxon_name_no_author, s."morphospeciesSuffix")
|
| 331 |
|
|
ELSE s.accepted_species_binomial
|
| 332 |
|
|
END AS accepted_morphospecies_binomial
|
| 333 |
|
|
FROM ( SELECT tnrs.batch AS "*Name_matched.batch",
|
| 334 |
|
|
tnrs."Name_submitted" AS "concatenatedScientificName",
|
| 335 |
|
|
tnrs."Name_matched" AS "matchedTaxonName",
|
| 336 |
|
|
tnrs."Name_matched_rank" AS "matchedTaxonRank",
|
| 337 |
|
|
tnrs."Name_score" AS "*Name_matched.Name_score",
|
| 338 |
|
|
tnrs."Name_matched_author" AS "matchedScientificNameAuthorship",
|
| 339 |
|
|
tnrs."Name_matched_url" AS "matchedScientificNameID",
|
| 340 |
|
|
tnrs."Author_score" AS "*Name_matched.Author_score",
|
| 341 |
|
|
tnrs."Family_score" AS "matchedFamilyConfidence_fraction",
|
| 342 |
|
|
COALESCE(tnrs."Name_matched_accepted_family", tnrs."Accepted_name_family") AS "matchedFamily",
|
| 343 |
|
|
tnrs."Genus_matched" AS "matchedGenus",
|
| 344 |
|
|
tnrs."Genus_score" AS "matchedGenusConfidence_fraction",
|
| 345 |
|
|
tnrs."Specific_epithet_matched" AS "matchedSpecificEpithet",
|
| 346 |
|
|
tnrs."Specific_epithet_score" AS "matchedSpeciesConfidence_fraction",
|
| 347 |
|
|
tnrs."Infraspecific_epithet_matched" AS "matchedInfraspecificEpithet",
|
| 348 |
|
|
tnrs."Infraspecific_epithet_score" AS "*Name_matched.Infraspecific_epithet_score",
|
| 349 |
|
|
tnrs."Annotations" AS "identificationQualifier",
|
| 350 |
|
|
tnrs."Unmatched_terms" AS "morphospeciesSuffix",
|
| 351 |
13508
|
aaronmk
|
map_taxonomic_status(tnrs."Taxonomic_status", tnrs."Accepted_name") AS "taxonomicStatus",
|
| 352 |
13498
|
aaronmk
|
tnrs."Accepted_name" AS accepted_taxon_name_no_author,
|
| 353 |
|
|
tnrs."Accepted_name_author" AS accepted_author,
|
| 354 |
|
|
tnrs."Accepted_name_rank" AS accepted_taxon_rank,
|
| 355 |
|
|
tnrs."Accepted_name_url" AS "acceptedScientificNameID",
|
| 356 |
|
|
tnrs."Accepted_name_species" AS accepted_species_binomial,
|
| 357 |
|
|
tnrs."Accepted_name_family" AS accepted_family,
|
| 358 |
|
|
tnrs."Selected" AS "*Name_matched.Selected",
|
| 359 |
|
|
tnrs."Source" AS "*Name_matched.Source",
|
| 360 |
|
|
tnrs."Warnings" AS "*Name_matched.Warnings",
|
| 361 |
|
|
tnrs."Accepted_name_lsid" AS "*Name_matched.Accepted_name_lsid",
|
| 362 |
|
|
tnrs.is_valid_match AS taxon_scrub__is_valid_match,
|
| 363 |
|
|
tnrs.scrubbed_unique_taxon_name
|
| 364 |
|
|
FROM tnrs) s;
|
| 365 |
10778
|
aaronmk
|
|
| 366 |
|
|
|
| 367 |
|
|
--
|
| 368 |
13498
|
aaronmk
|
-- Name: VIEW "MatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 369 |
|
|
--
|
| 370 |
|
|
|
| 371 |
|
|
COMMENT ON VIEW "MatchedTaxon" IS '
|
| 372 |
13501
|
aaronmk
|
to modify:
|
| 373 |
13507
|
aaronmk
|
SELECT "TNRS"."MatchedTaxon_modify"($$
|
| 374 |
|
|
SELECT *, __ AS accepted_morphospecies_binomial
|
| 375 |
|
|
FROM __
|
| 376 |
13501
|
aaronmk
|
$$);
|
| 377 |
13498
|
aaronmk
|
';
|
| 378 |
|
|
|
| 379 |
|
|
|
| 380 |
|
|
--
|
| 381 |
10778
|
aaronmk
|
-- Name: ValidMatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
|
| 382 |
|
|
--
|
| 383 |
|
|
|
| 384 |
|
|
CREATE VIEW "ValidMatchedTaxon" AS
|
| 385 |
11708
|
aaronmk
|
SELECT "MatchedTaxon"."*Name_matched.batch",
|
| 386 |
|
|
"MatchedTaxon"."concatenatedScientificName",
|
| 387 |
|
|
"MatchedTaxon"."matchedTaxonName",
|
| 388 |
|
|
"MatchedTaxon"."matchedTaxonRank",
|
| 389 |
|
|
"MatchedTaxon"."*Name_matched.Name_score",
|
| 390 |
|
|
"MatchedTaxon"."matchedScientificNameAuthorship",
|
| 391 |
|
|
"MatchedTaxon"."matchedScientificNameID",
|
| 392 |
|
|
"MatchedTaxon"."*Name_matched.Author_score",
|
| 393 |
|
|
"MatchedTaxon"."matchedFamilyConfidence_fraction",
|
| 394 |
|
|
"MatchedTaxon"."matchedFamily",
|
| 395 |
|
|
"MatchedTaxon"."matchedGenus",
|
| 396 |
|
|
"MatchedTaxon"."matchedGenusConfidence_fraction",
|
| 397 |
|
|
"MatchedTaxon"."matchedSpecificEpithet",
|
| 398 |
|
|
"MatchedTaxon"."matchedSpeciesConfidence_fraction",
|
| 399 |
|
|
"MatchedTaxon"."matchedInfraspecificEpithet",
|
| 400 |
|
|
"MatchedTaxon"."*Name_matched.Infraspecific_epithet_score",
|
| 401 |
|
|
"MatchedTaxon"."identificationQualifier",
|
| 402 |
|
|
"MatchedTaxon"."morphospeciesSuffix",
|
| 403 |
|
|
"MatchedTaxon"."taxonomicStatus",
|
| 404 |
13441
|
aaronmk
|
"MatchedTaxon".accepted_taxon_name_no_author,
|
| 405 |
|
|
"MatchedTaxon".accepted_author,
|
| 406 |
|
|
"MatchedTaxon".accepted_taxon_rank,
|
| 407 |
11708
|
aaronmk
|
"MatchedTaxon"."acceptedScientificNameID",
|
| 408 |
13444
|
aaronmk
|
"MatchedTaxon".accepted_species_binomial,
|
| 409 |
13441
|
aaronmk
|
"MatchedTaxon".accepted_family,
|
| 410 |
11708
|
aaronmk
|
"MatchedTaxon"."*Name_matched.Selected",
|
| 411 |
|
|
"MatchedTaxon"."*Name_matched.Source",
|
| 412 |
|
|
"MatchedTaxon"."*Name_matched.Warnings",
|
| 413 |
|
|
"MatchedTaxon"."*Name_matched.Accepted_name_lsid",
|
| 414 |
|
|
"MatchedTaxon".taxon_scrub__is_valid_match,
|
| 415 |
13498
|
aaronmk
|
"MatchedTaxon".scrubbed_unique_taxon_name,
|
| 416 |
|
|
"MatchedTaxon".accepted_morphospecies_binomial
|
| 417 |
11708
|
aaronmk
|
FROM "MatchedTaxon"
|
| 418 |
|
|
WHERE "MatchedTaxon".taxon_scrub__is_valid_match;
|
| 419 |
10778
|
aaronmk
|
|
| 420 |
|
|
|
| 421 |
|
|
--
|
| 422 |
|
|
-- Name: VIEW "ValidMatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 423 |
|
|
--
|
| 424 |
|
|
|
| 425 |
13443
|
aaronmk
|
COMMENT ON VIEW "ValidMatchedTaxon" IS '
|
| 426 |
|
|
to update, use * as the column list
|
| 427 |
|
|
';
|
| 428 |
10778
|
aaronmk
|
|
| 429 |
|
|
|
| 430 |
|
|
--
|
| 431 |
|
|
-- Name: batch; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 432 |
|
|
--
|
| 433 |
|
|
|
| 434 |
|
|
CREATE TABLE batch (
|
| 435 |
|
|
id text NOT NULL,
|
| 436 |
|
|
id_by_time text,
|
| 437 |
|
|
time_submitted timestamp with time zone DEFAULT now(),
|
| 438 |
|
|
client_version text
|
| 439 |
|
|
);
|
| 440 |
|
|
|
| 441 |
|
|
|
| 442 |
|
|
--
|
| 443 |
|
|
-- Name: batch_download_settings; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 444 |
|
|
--
|
| 445 |
|
|
|
| 446 |
|
|
CREATE TABLE batch_download_settings (
|
| 447 |
|
|
id text NOT NULL,
|
| 448 |
|
|
"E-mail" text,
|
| 449 |
|
|
"Id" text,
|
| 450 |
|
|
"Job type" text,
|
| 451 |
|
|
"Contains Id" boolean,
|
| 452 |
|
|
"Start time" text,
|
| 453 |
|
|
"Finish time" text,
|
| 454 |
|
|
"TNRS version" text,
|
| 455 |
|
|
"Sources selected" text,
|
| 456 |
|
|
"Match threshold" double precision,
|
| 457 |
|
|
"Classification" text,
|
| 458 |
|
|
"Allow partial matches?" boolean,
|
| 459 |
|
|
"Sort by source" boolean,
|
| 460 |
|
|
"Constrain by higher taxonomy" boolean
|
| 461 |
|
|
);
|
| 462 |
|
|
|
| 463 |
|
|
|
| 464 |
|
|
--
|
| 465 |
|
|
-- Name: TABLE batch_download_settings; Type: COMMENT; Schema: TNRS; Owner: -
|
| 466 |
|
|
--
|
| 467 |
|
|
|
| 468 |
|
|
COMMENT ON TABLE batch_download_settings IS 'stores data from http://tnrs.iplantcollaborative.org/TNRSapp.html > Submit List > results section > Download settings > settings.txt';
|
| 469 |
|
|
|
| 470 |
|
|
|
| 471 |
|
|
--
|
| 472 |
|
|
-- Name: client_version; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
|
| 473 |
|
|
--
|
| 474 |
|
|
|
| 475 |
|
|
CREATE TABLE client_version (
|
| 476 |
|
|
id text NOT NULL,
|
| 477 |
|
|
global_rev integer NOT NULL,
|
| 478 |
|
|
"/lib/tnrs.py rev" integer,
|
| 479 |
|
|
"/bin/tnrs_db rev" integer
|
| 480 |
|
|
);
|
| 481 |
|
|
|
| 482 |
|
|
|
| 483 |
|
|
--
|
| 484 |
|
|
-- Name: TABLE client_version; Type: COMMENT; Schema: TNRS; Owner: -
|
| 485 |
|
|
--
|
| 486 |
|
|
|
| 487 |
|
|
COMMENT ON TABLE client_version IS 'contains svn revisions';
|
| 488 |
|
|
|
| 489 |
|
|
|
| 490 |
|
|
--
|
| 491 |
|
|
-- Name: COLUMN client_version.global_rev; Type: COMMENT; Schema: TNRS; Owner: -
|
| 492 |
|
|
--
|
| 493 |
|
|
|
| 494 |
|
|
COMMENT ON COLUMN client_version.global_rev IS 'from `svn info .` > Last Changed Rev';
|
| 495 |
|
|
|
| 496 |
|
|
|
| 497 |
|
|
--
|
| 498 |
|
|
-- Name: COLUMN client_version."/lib/tnrs.py rev"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 499 |
|
|
--
|
| 500 |
|
|
|
| 501 |
|
|
COMMENT ON COLUMN client_version."/lib/tnrs.py rev" IS 'from `svn info lib/tnrs.py` > Last Changed Rev';
|
| 502 |
|
|
|
| 503 |
|
|
|
| 504 |
|
|
--
|
| 505 |
|
|
-- Name: COLUMN client_version."/bin/tnrs_db rev"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 506 |
|
|
--
|
| 507 |
|
|
|
| 508 |
|
|
COMMENT ON COLUMN client_version."/bin/tnrs_db rev" IS 'from `svn info bin/tnrs_db` > Last Changed Rev';
|
| 509 |
|
|
|
| 510 |
|
|
|
| 511 |
|
|
--
|
| 512 |
11964
|
aaronmk
|
-- Name: taxon_scrub.scrubbed_unique_taxon_name.*; Type: VIEW; Schema: TNRS; Owner: -
|
| 513 |
|
|
--
|
| 514 |
|
|
|
| 515 |
|
|
CREATE VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" AS
|
| 516 |
|
|
SELECT tnrs."Name_submitted" AS scrubbed_unique_taxon_name,
|
| 517 |
13441
|
aaronmk
|
tnrs."Name_matched_rank" AS scrubbed_taxon_rank,
|
| 518 |
|
|
COALESCE(tnrs."Name_matched_accepted_family", tnrs."Family_matched") AS scrubbed_family,
|
| 519 |
11964
|
aaronmk
|
tnrs."Genus_matched" AS scrubbed_genus,
|
| 520 |
|
|
tnrs."Specific_epithet_matched" AS scrubbed_specific_epithet,
|
| 521 |
|
|
tnrs."Infraspecific_rank" AS scrubbed_infraspecific_rank,
|
| 522 |
|
|
tnrs."Infraspecific_epithet_matched" AS scrubbed_infraspecific_epithet,
|
| 523 |
13441
|
aaronmk
|
tnrs."Name_matched_author" AS scrubbed_author,
|
| 524 |
|
|
tnrs."Name_matched" AS scrubbed_taxon_name_no_author
|
| 525 |
11964
|
aaronmk
|
FROM tnrs;
|
| 526 |
|
|
|
| 527 |
|
|
|
| 528 |
|
|
--
|
| 529 |
11965
|
aaronmk
|
-- Name: VIEW "taxon_scrub.scrubbed_unique_taxon_name.*"; Type: COMMENT; Schema: TNRS; Owner: -
|
| 530 |
|
|
--
|
| 531 |
|
|
|
| 532 |
|
|
COMMENT ON VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" IS '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.';
|
| 533 |
|
|
|
| 534 |
|
|
|
| 535 |
|
|
--
|
| 536 |
11964
|
aaronmk
|
-- Name: taxon_scrub; Type: VIEW; Schema: TNRS; Owner: -
|
| 537 |
|
|
--
|
| 538 |
|
|
|
| 539 |
|
|
CREATE VIEW taxon_scrub AS
|
| 540 |
|
|
SELECT "ValidMatchedTaxon".scrubbed_unique_taxon_name,
|
| 541 |
|
|
"ValidMatchedTaxon"."*Name_matched.batch",
|
| 542 |
|
|
"ValidMatchedTaxon"."concatenatedScientificName",
|
| 543 |
|
|
"ValidMatchedTaxon"."matchedTaxonName",
|
| 544 |
|
|
"ValidMatchedTaxon"."matchedTaxonRank",
|
| 545 |
|
|
"ValidMatchedTaxon"."*Name_matched.Name_score",
|
| 546 |
|
|
"ValidMatchedTaxon"."matchedScientificNameAuthorship",
|
| 547 |
|
|
"ValidMatchedTaxon"."matchedScientificNameID",
|
| 548 |
|
|
"ValidMatchedTaxon"."*Name_matched.Author_score",
|
| 549 |
|
|
"ValidMatchedTaxon"."matchedFamilyConfidence_fraction",
|
| 550 |
|
|
"ValidMatchedTaxon"."matchedFamily",
|
| 551 |
|
|
"ValidMatchedTaxon"."matchedGenus",
|
| 552 |
|
|
"ValidMatchedTaxon"."matchedGenusConfidence_fraction",
|
| 553 |
|
|
"ValidMatchedTaxon"."matchedSpecificEpithet",
|
| 554 |
|
|
"ValidMatchedTaxon"."matchedSpeciesConfidence_fraction",
|
| 555 |
|
|
"ValidMatchedTaxon"."matchedInfraspecificEpithet",
|
| 556 |
|
|
"ValidMatchedTaxon"."*Name_matched.Infraspecific_epithet_score",
|
| 557 |
|
|
"ValidMatchedTaxon"."identificationQualifier",
|
| 558 |
|
|
"ValidMatchedTaxon"."morphospeciesSuffix",
|
| 559 |
|
|
"ValidMatchedTaxon"."taxonomicStatus",
|
| 560 |
13441
|
aaronmk
|
"ValidMatchedTaxon".accepted_taxon_name_no_author,
|
| 561 |
|
|
"ValidMatchedTaxon".accepted_author,
|
| 562 |
|
|
"ValidMatchedTaxon".accepted_taxon_rank,
|
| 563 |
11964
|
aaronmk
|
"ValidMatchedTaxon"."acceptedScientificNameID",
|
| 564 |
13444
|
aaronmk
|
"ValidMatchedTaxon".accepted_species_binomial,
|
| 565 |
13441
|
aaronmk
|
"ValidMatchedTaxon".accepted_family,
|
| 566 |
11964
|
aaronmk
|
"ValidMatchedTaxon"."*Name_matched.Selected",
|
| 567 |
|
|
"ValidMatchedTaxon"."*Name_matched.Source",
|
| 568 |
|
|
"ValidMatchedTaxon"."*Name_matched.Warnings",
|
| 569 |
|
|
"ValidMatchedTaxon"."*Name_matched.Accepted_name_lsid",
|
| 570 |
|
|
"ValidMatchedTaxon".taxon_scrub__is_valid_match,
|
| 571 |
13498
|
aaronmk
|
"ValidMatchedTaxon".accepted_morphospecies_binomial,
|
| 572 |
13441
|
aaronmk
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_rank,
|
| 573 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_family,
|
| 574 |
11964
|
aaronmk
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus,
|
| 575 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet,
|
| 576 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_rank,
|
| 577 |
|
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_epithet,
|
| 578 |
13441
|
aaronmk
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_author,
|
| 579 |
13532
|
aaronmk
|
"taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_no_author,
|
| 580 |
|
|
CASE
|
| 581 |
|
|
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"."morphospeciesSuffix")
|
| 582 |
|
|
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"."morphospeciesSuffix")
|
| 583 |
|
|
ELSE (("taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus || ' '::text) || "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet)
|
| 584 |
|
|
END AS scrubbed_morphospecies_binomial
|
| 585 |
11964
|
aaronmk
|
FROM ("ValidMatchedTaxon"
|
| 586 |
|
|
LEFT JOIN "taxon_scrub.scrubbed_unique_taxon_name.*" USING (scrubbed_unique_taxon_name));
|
| 587 |
|
|
|
| 588 |
|
|
|
| 589 |
|
|
--
|
| 590 |
|
|
-- Name: VIEW taxon_scrub; Type: COMMENT; Schema: TNRS; Owner: -
|
| 591 |
|
|
--
|
| 592 |
|
|
|
| 593 |
13443
|
aaronmk
|
COMMENT ON VIEW taxon_scrub IS '
|
| 594 |
13531
|
aaronmk
|
to modify:
|
| 595 |
|
|
SELECT "TNRS".taxon_scrub_modify($$
|
| 596 |
|
|
SELECT *
|
| 597 |
|
|
FROM "TNRS"."ValidMatchedTaxon"
|
| 598 |
|
|
LEFT JOIN "TNRS"."taxon_scrub.scrubbed_unique_taxon_name.*" USING (scrubbed_unique_taxon_name);
|
| 599 |
|
|
$$);
|
| 600 |
13443
|
aaronmk
|
';
|
| 601 |
11964
|
aaronmk
|
|
| 602 |
|
|
|
| 603 |
|
|
--
|
| 604 |
10778
|
aaronmk
|
-- Name: batch_download_settings_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 605 |
|
|
--
|
| 606 |
|
|
|
| 607 |
|
|
ALTER TABLE ONLY batch_download_settings
|
| 608 |
|
|
ADD CONSTRAINT batch_download_settings_pkey PRIMARY KEY (id);
|
| 609 |
|
|
|
| 610 |
|
|
|
| 611 |
|
|
--
|
| 612 |
|
|
-- Name: batch_id_by_time_key; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 613 |
|
|
--
|
| 614 |
|
|
|
| 615 |
|
|
ALTER TABLE ONLY batch
|
| 616 |
|
|
ADD CONSTRAINT batch_id_by_time_key UNIQUE (id_by_time);
|
| 617 |
|
|
|
| 618 |
|
|
|
| 619 |
|
|
--
|
| 620 |
|
|
-- Name: batch_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 621 |
|
|
--
|
| 622 |
|
|
|
| 623 |
|
|
ALTER TABLE ONLY batch
|
| 624 |
|
|
ADD CONSTRAINT batch_pkey PRIMARY KEY (id);
|
| 625 |
|
|
|
| 626 |
|
|
|
| 627 |
|
|
--
|
| 628 |
|
|
-- Name: client_version_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 629 |
|
|
--
|
| 630 |
|
|
|
| 631 |
|
|
ALTER TABLE ONLY client_version
|
| 632 |
|
|
ADD CONSTRAINT client_version_pkey PRIMARY KEY (id);
|
| 633 |
|
|
|
| 634 |
|
|
|
| 635 |
|
|
--
|
| 636 |
|
|
-- Name: tnrs_Name_submitted_key; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 637 |
|
|
--
|
| 638 |
|
|
|
| 639 |
|
|
ALTER TABLE ONLY tnrs
|
| 640 |
|
|
ADD CONSTRAINT "tnrs_Name_submitted_key" UNIQUE ("Name_submitted");
|
| 641 |
|
|
|
| 642 |
|
|
|
| 643 |
|
|
--
|
| 644 |
|
|
-- Name: tnrs_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
|
| 645 |
|
|
--
|
| 646 |
|
|
|
| 647 |
|
|
ALTER TABLE ONLY tnrs
|
| 648 |
|
|
ADD CONSTRAINT tnrs_pkey PRIMARY KEY (batch, "Name_number");
|
| 649 |
|
|
|
| 650 |
|
|
|
| 651 |
|
|
--
|
| 652 |
10793
|
aaronmk
|
-- Name: batch_client_version_idx; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 653 |
|
|
--
|
| 654 |
|
|
|
| 655 |
|
|
CREATE INDEX batch_client_version_idx ON batch USING btree (client_version);
|
| 656 |
|
|
|
| 657 |
|
|
|
| 658 |
|
|
--
|
| 659 |
11607
|
aaronmk
|
-- Name: tnrs__valid_match; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
|
| 660 |
|
|
--
|
| 661 |
|
|
|
| 662 |
|
|
CREATE UNIQUE INDEX tnrs__valid_match ON tnrs USING btree ("Name_submitted") WHERE is_valid_match;
|
| 663 |
|
|
|
| 664 |
|
|
|
| 665 |
|
|
--
|
| 666 |
10778
|
aaronmk
|
-- Name: batch__fill; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 667 |
|
|
--
|
| 668 |
|
|
|
| 669 |
|
|
CREATE TRIGGER batch__fill BEFORE INSERT OR UPDATE ON batch FOR EACH ROW EXECUTE PROCEDURE batch__fill();
|
| 670 |
|
|
|
| 671 |
|
|
|
| 672 |
|
|
--
|
| 673 |
|
|
-- Name: tnrs_populate_fields; Type: TRIGGER; Schema: TNRS; Owner: -
|
| 674 |
|
|
--
|
| 675 |
|
|
|
| 676 |
|
|
CREATE TRIGGER tnrs_populate_fields BEFORE INSERT OR UPDATE ON tnrs FOR EACH ROW EXECUTE PROCEDURE tnrs_populate_fields();
|
| 677 |
|
|
|
| 678 |
|
|
|
| 679 |
|
|
--
|
| 680 |
|
|
-- Name: batch_client_version_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
| 681 |
|
|
--
|
| 682 |
|
|
|
| 683 |
|
|
ALTER TABLE ONLY batch
|
| 684 |
|
|
ADD CONSTRAINT batch_client_version_fkey FOREIGN KEY (client_version) REFERENCES client_version(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 685 |
|
|
|
| 686 |
|
|
|
| 687 |
|
|
--
|
| 688 |
|
|
-- Name: batch_download_settings_id_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
| 689 |
|
|
--
|
| 690 |
|
|
|
| 691 |
|
|
ALTER TABLE ONLY batch_download_settings
|
| 692 |
|
|
ADD CONSTRAINT batch_download_settings_id_fkey FOREIGN KEY (id) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 693 |
|
|
|
| 694 |
|
|
|
| 695 |
|
|
--
|
| 696 |
|
|
-- Name: tnrs_batch_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
|
| 697 |
|
|
--
|
| 698 |
|
|
|
| 699 |
|
|
ALTER TABLE ONLY tnrs
|
| 700 |
|
|
ADD CONSTRAINT tnrs_batch_fkey FOREIGN KEY (batch) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 701 |
|
|
|
| 702 |
|
|
|
| 703 |
|
|
--
|
| 704 |
|
|
-- Name: TNRS; Type: ACL; Schema: -; Owner: -
|
| 705 |
|
|
--
|
| 706 |
|
|
|
| 707 |
|
|
REVOKE ALL ON SCHEMA "TNRS" FROM PUBLIC;
|
| 708 |
|
|
REVOKE ALL ON SCHEMA "TNRS" FROM bien;
|
| 709 |
|
|
GRANT ALL ON SCHEMA "TNRS" TO bien;
|
| 710 |
|
|
GRANT USAGE ON SCHEMA "TNRS" TO bien_read;
|
| 711 |
|
|
|
| 712 |
|
|
|
| 713 |
|
|
--
|
| 714 |
|
|
-- Name: tnrs; Type: ACL; Schema: TNRS; Owner: -
|
| 715 |
|
|
--
|
| 716 |
|
|
|
| 717 |
|
|
REVOKE ALL ON TABLE tnrs FROM PUBLIC;
|
| 718 |
|
|
REVOKE ALL ON TABLE tnrs FROM bien;
|
| 719 |
|
|
GRANT ALL ON TABLE tnrs TO bien;
|
| 720 |
|
|
GRANT SELECT ON TABLE tnrs TO bien_read;
|
| 721 |
|
|
|
| 722 |
|
|
|
| 723 |
|
|
--
|
| 724 |
11912
|
aaronmk
|
-- Name: MatchedTaxon; Type: ACL; Schema: TNRS; Owner: -
|
| 725 |
|
|
--
|
| 726 |
|
|
|
| 727 |
|
|
REVOKE ALL ON TABLE "MatchedTaxon" FROM PUBLIC;
|
| 728 |
|
|
REVOKE ALL ON TABLE "MatchedTaxon" FROM bien;
|
| 729 |
|
|
GRANT ALL ON TABLE "MatchedTaxon" TO bien;
|
| 730 |
|
|
GRANT SELECT ON TABLE "MatchedTaxon" TO bien_read;
|
| 731 |
|
|
|
| 732 |
|
|
|
| 733 |
|
|
--
|
| 734 |
|
|
-- Name: ValidMatchedTaxon; Type: ACL; Schema: TNRS; Owner: -
|
| 735 |
|
|
--
|
| 736 |
|
|
|
| 737 |
|
|
REVOKE ALL ON TABLE "ValidMatchedTaxon" FROM PUBLIC;
|
| 738 |
|
|
REVOKE ALL ON TABLE "ValidMatchedTaxon" FROM bien;
|
| 739 |
|
|
GRANT ALL ON TABLE "ValidMatchedTaxon" TO bien;
|
| 740 |
|
|
GRANT SELECT ON TABLE "ValidMatchedTaxon" TO bien_read;
|
| 741 |
|
|
|
| 742 |
|
|
|
| 743 |
|
|
--
|
| 744 |
|
|
-- Name: taxon_scrub.scrubbed_unique_taxon_name.*; Type: ACL; Schema: TNRS; Owner: -
|
| 745 |
|
|
--
|
| 746 |
|
|
|
| 747 |
|
|
REVOKE ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" FROM PUBLIC;
|
| 748 |
|
|
REVOKE ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" FROM bien;
|
| 749 |
|
|
GRANT ALL ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" TO bien;
|
| 750 |
|
|
GRANT SELECT ON TABLE "taxon_scrub.scrubbed_unique_taxon_name.*" TO bien_read;
|
| 751 |
|
|
|
| 752 |
|
|
|
| 753 |
|
|
--
|
| 754 |
|
|
-- Name: taxon_scrub; Type: ACL; Schema: TNRS; Owner: -
|
| 755 |
|
|
--
|
| 756 |
|
|
|
| 757 |
|
|
REVOKE ALL ON TABLE taxon_scrub FROM PUBLIC;
|
| 758 |
|
|
REVOKE ALL ON TABLE taxon_scrub FROM bien;
|
| 759 |
|
|
GRANT ALL ON TABLE taxon_scrub TO bien;
|
| 760 |
|
|
GRANT SELECT ON TABLE taxon_scrub TO bien_read;
|
| 761 |
|
|
|
| 762 |
|
|
|
| 763 |
|
|
--
|
| 764 |
10778
|
aaronmk
|
-- PostgreSQL database dump complete
|
| 765 |
|
|
--
|
