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--
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-- PostgreSQL database dump
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--
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SET statement_timeout = 0;
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SET client_encoding = 'UTF8';
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SET standard_conforming_strings = on;
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SET check_function_bodies = false;
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SET client_min_messages = warning;
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--
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-- Name: TNRS; Type: SCHEMA; Schema: -; Owner: -
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--
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--CREATE SCHEMA "TNRS";
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--
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-- Name: SCHEMA "TNRS"; Type: COMMENT; Schema: -; Owner: -
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--
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COMMENT ON SCHEMA "TNRS" IS '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: 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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55
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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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67 10736 aaronmk
--
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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: 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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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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BEGIN
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	new."Accepted_scientific_name" = NULLIF(concat_ws(' '
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		, NULLIF(NULLIF(new."Accepted_name_family", 'Unknown'),
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			new."Accepted_name")
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		, new."Accepted_name"
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		, new."Accepted_name_author"
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		), '');
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	/* 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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	new.is_valid_match = COALESCE(CASE
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		WHEN new."Family_score" = 1 AND NOT family_is_homonym -- exact match
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			THEN true
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		ELSE -- consider genus
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			(CASE
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			WHEN new."Genus_score" =  1	   -- exact match
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				THEN
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				(CASE
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				WHEN NOT genus_is_homonym THEN true
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				ELSE "Specific_epithet_is_plant"
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				END)
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			WHEN new."Genus_score" >= 0.85 -- fuzzy match
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				THEN "Specific_epithet_is_plant"
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			ELSE NULL -- ambiguous
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			END)
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		END, false);
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	new.scrubbed_unique_taxon_name = COALESCE(
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		new."Accepted_scientific_name", matched_taxon_name_with_author);
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	RETURN new;
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END;
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$$;
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--
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-- Name: FUNCTION tnrs_populate_fields(); Type: COMMENT; Schema: TNRS; Owner: -
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--
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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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UPDATE "TNRS".tnrs SET "Name_submitted" = "Name_submitted"
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runtime: 25 min ("5363526 rows affected, 1351907 ms execution time")
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VACUUM ANALYZE "TNRS".tnrs -- to remove previous rows
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runtime: 1.5 min ("92633 ms")';
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SET default_tablespace = '';
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SET default_with_oids = false;
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--
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-- Name: tnrs; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
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--
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CREATE TABLE tnrs (
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    batch text DEFAULT now() NOT NULL,
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    "Name_number" integer NOT NULL,
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    "Name_submitted" text NOT NULL,
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    "Overall_score" double precision,
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    "Name_matched" text,
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    "Name_matched_rank" text,
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    "Name_score" double precision,
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    "Name_matched_author" text,
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    "Name_matched_url" text,
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    "Author_matched" text,
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    "Author_score" double precision,
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    "Family_matched" text,
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    "Family_score" double precision,
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    "Name_matched_accepted_family" text,
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    "Genus_matched" text,
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    "Genus_score" double precision,
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    "Specific_epithet_matched" text,
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    "Specific_epithet_score" double precision,
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    "Infraspecific_rank" text,
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    "Infraspecific_epithet_matched" text,
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    "Infraspecific_epithet_score" double precision,
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    "Infraspecific_rank_2" text,
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    "Infraspecific_epithet_2_matched" text,
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    "Infraspecific_epithet_2_score" double precision,
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    "Annotations" text,
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    "Unmatched_terms" text,
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    "Taxonomic_status" text,
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    "Accepted_name" text,
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    "Accepted_name_author" text,
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    "Accepted_name_rank" text,
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    "Accepted_name_url" text,
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    "Accepted_name_species" text,
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    "Accepted_name_family" text,
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    "Selected" text,
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    "Source" text,
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    "Warnings" text,
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    "Accepted_name_lsid" text,
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    "Accepted_scientific_name" text,
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    is_valid_match boolean NOT NULL,
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    scrubbed_unique_taxon_name text
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);
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--
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-- Name: TABLE tnrs; Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON TABLE tnrs IS 'IMPORTANT: when changing this table''s schema, you may need to re-run TNRS:
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$ inputs/.TNRS/data.sql.run refresh';
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--
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-- Name: AcceptedTaxon; Type: VIEW; Schema: TNRS; Owner: -
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--
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CREATE VIEW "AcceptedTaxon" AS
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    SELECT tnrs.batch AS "*Accepted_name.batch", tnrs."Name_submitted" AS "acceptedScientificName", tnrs."Genus_matched" AS "acceptedGenus", tnrs."Specific_epithet_matched" AS "acceptedSpecificEpithet", tnrs."Infraspecific_epithet_matched" AS "acceptedInfraspecificEpithet", tnrs."Taxonomic_status" AS "acceptedTaxonomicStatus", tnrs."Selected" AS "*Accepted_name.Selected", tnrs."Source" AS "*Accepted_name.Source", tnrs."Warnings" AS "*Accepted_name.Warnings", tnrs."Accepted_name_lsid" AS "*Accepted_name.Accepted_name_lsid" FROM tnrs;
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--
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-- Name: MatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
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--
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CREATE VIEW "MatchedTaxon" AS
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    SELECT tnrs.batch AS "*Name_matched.batch", tnrs."Name_submitted" AS "concatenatedScientificName", tnrs."Name_matched" AS "matchedTaxonName", tnrs."Name_matched_rank" AS "matchedTaxonRank", tnrs."Name_score" AS "*Name_matched.Name_score", tnrs."Name_matched_author" AS "matchedScientificNameAuthorship", tnrs."Name_matched_url" AS "matchedScientificNameID", tnrs."Author_score" AS "*Name_matched.Author_score", tnrs."Family_score" AS "matchedFamilyConfidence_fraction", COALESCE(tnrs."Name_matched_accepted_family", tnrs."Accepted_name_family") AS "matchedFamily", tnrs."Genus_matched" AS "matchedGenus", tnrs."Genus_score" AS "matchedGenusConfidence_fraction", tnrs."Specific_epithet_matched" AS "matchedSpecificEpithet", tnrs."Specific_epithet_score" AS "matchedSpeciesConfidence_fraction", tnrs."Infraspecific_epithet_matched" AS "matchedInfraspecificEpithet", tnrs."Infraspecific_epithet_score" AS "*Name_matched.Infraspecific_epithet_score", tnrs."Annotations" AS "identificationQualifier", tnrs."Unmatched_terms" AS "morphospeciesSuffix", tnrs."Taxonomic_status" AS "taxonomicStatus", tnrs."Accepted_name" AS "acceptedTaxonName", tnrs."Accepted_name_author" AS "acceptedScientificNameAuthorship", tnrs."Accepted_name_rank" AS "acceptedTaxonRank", tnrs."Accepted_name_url" AS "acceptedScientificNameID", tnrs."Accepted_name_species" AS "*Name_matched.Accepted_name_species", tnrs."Accepted_name_family" AS "acceptedFamily", tnrs."Selected" AS "*Name_matched.Selected", tnrs."Source" AS "*Name_matched.Source", tnrs."Warnings" AS "*Name_matched.Warnings", tnrs."Accepted_name_lsid" AS "*Name_matched.Accepted_name_lsid", tnrs."Accepted_scientific_name" AS "acceptedScientificName", tnrs.is_valid_match AS taxon_scrub__is_valid_match, tnrs.scrubbed_unique_taxon_name FROM tnrs;
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--
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-- Name: ValidMatchedTaxon; Type: VIEW; Schema: TNRS; Owner: -
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--
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CREATE VIEW "ValidMatchedTaxon" AS
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    SELECT "MatchedTaxon"."*Name_matched.batch", "MatchedTaxon"."concatenatedScientificName", "MatchedTaxon"."matchedTaxonName", "MatchedTaxon"."matchedTaxonRank", "MatchedTaxon"."*Name_matched.Name_score", "MatchedTaxon"."matchedScientificNameAuthorship", "MatchedTaxon"."matchedScientificNameID", "MatchedTaxon"."*Name_matched.Author_score", "MatchedTaxon"."matchedFamilyConfidence_fraction", "MatchedTaxon"."matchedFamily", "MatchedTaxon"."matchedGenus", "MatchedTaxon"."matchedGenusConfidence_fraction", "MatchedTaxon"."matchedSpecificEpithet", "MatchedTaxon"."matchedSpeciesConfidence_fraction", "MatchedTaxon"."matchedInfraspecificEpithet", "MatchedTaxon"."*Name_matched.Infraspecific_epithet_score", "MatchedTaxon"."identificationQualifier", "MatchedTaxon"."morphospeciesSuffix", "MatchedTaxon"."taxonomicStatus", "MatchedTaxon"."acceptedTaxonName", "MatchedTaxon"."acceptedScientificNameAuthorship", "MatchedTaxon"."acceptedTaxonRank", "MatchedTaxon"."acceptedScientificNameID", "MatchedTaxon"."*Name_matched.Accepted_name_species", "MatchedTaxon"."acceptedFamily", "MatchedTaxon"."*Name_matched.Selected", "MatchedTaxon"."*Name_matched.Source", "MatchedTaxon"."*Name_matched.Warnings", "MatchedTaxon"."*Name_matched.Accepted_name_lsid", "MatchedTaxon"."acceptedScientificName", "MatchedTaxon".taxon_scrub__is_valid_match, "MatchedTaxon".scrubbed_unique_taxon_name FROM "MatchedTaxon" WHERE "MatchedTaxon".taxon_scrub__is_valid_match;
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--
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-- Name: VIEW "ValidMatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON VIEW "ValidMatchedTaxon" IS 'to update, use * as the column list';
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--
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-- Name: ScrubbedTaxon; Type: VIEW; Schema: TNRS; Owner: -
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--
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CREATE VIEW "ScrubbedTaxon" AS
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    SELECT "ValidMatchedTaxon"."acceptedScientificName", "ValidMatchedTaxon"."*Name_matched.batch", "ValidMatchedTaxon"."concatenatedScientificName", "ValidMatchedTaxon"."matchedTaxonName", "ValidMatchedTaxon"."matchedTaxonRank", "ValidMatchedTaxon"."*Name_matched.Name_score", "ValidMatchedTaxon"."matchedScientificNameAuthorship", "ValidMatchedTaxon"."matchedScientificNameID", "ValidMatchedTaxon"."*Name_matched.Author_score", "ValidMatchedTaxon"."matchedFamilyConfidence_fraction", "ValidMatchedTaxon"."matchedFamily", "ValidMatchedTaxon"."matchedGenus", "ValidMatchedTaxon"."matchedGenusConfidence_fraction", "ValidMatchedTaxon"."matchedSpecificEpithet", "ValidMatchedTaxon"."matchedSpeciesConfidence_fraction", "ValidMatchedTaxon"."matchedInfraspecificEpithet", "ValidMatchedTaxon"."*Name_matched.Infraspecific_epithet_score", "ValidMatchedTaxon"."identificationQualifier", "ValidMatchedTaxon"."morphospeciesSuffix", "ValidMatchedTaxon"."taxonomicStatus", "ValidMatchedTaxon"."acceptedTaxonName", "ValidMatchedTaxon"."acceptedScientificNameAuthorship", "ValidMatchedTaxon"."acceptedTaxonRank", "ValidMatchedTaxon"."acceptedScientificNameID", "ValidMatchedTaxon"."*Name_matched.Accepted_name_species", "ValidMatchedTaxon"."acceptedFamily", "ValidMatchedTaxon"."*Name_matched.Selected", "ValidMatchedTaxon"."*Name_matched.Source", "ValidMatchedTaxon"."*Name_matched.Warnings", "ValidMatchedTaxon"."*Name_matched.Accepted_name_lsid", "ValidMatchedTaxon".taxon_scrub__is_valid_match, "ValidMatchedTaxon".scrubbed_unique_taxon_name, "AcceptedTaxon"."*Accepted_name.batch", "AcceptedTaxon"."acceptedGenus", "AcceptedTaxon"."acceptedSpecificEpithet", "AcceptedTaxon"."acceptedInfraspecificEpithet", "AcceptedTaxon"."acceptedTaxonomicStatus", "AcceptedTaxon"."*Accepted_name.Selected", "AcceptedTaxon"."*Accepted_name.Source", "AcceptedTaxon"."*Accepted_name.Warnings", "AcceptedTaxon"."*Accepted_name.Accepted_name_lsid" FROM ("ValidMatchedTaxon" NATURAL LEFT JOIN "AcceptedTaxon");
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--
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-- Name: batch; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
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--
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CREATE TABLE batch (
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    id text NOT NULL,
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    id_by_time text,
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    time_submitted timestamp with time zone DEFAULT now(),
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    client_version text
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);
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--
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-- Name: batch_download_settings; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
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--
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CREATE TABLE batch_download_settings (
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    id text NOT NULL,
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    "E-mail" text,
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    "Id" text,
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    "Job type" text,
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    "Contains Id" boolean,
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    "Start time" text,
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    "Finish time" text,
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    "TNRS version" text,
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    "Sources selected" text,
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    "Match threshold" double precision,
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    "Classification" text,
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    "Allow partial matches?" boolean,
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    "Sort by source" boolean,
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    "Constrain by higher taxonomy" boolean
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);
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--
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-- Name: TABLE batch_download_settings; Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON TABLE batch_download_settings IS 'stores data from http://tnrs.iplantcollaborative.org/TNRSapp.html > Submit List > results section > Download settings > settings.txt';
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--
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-- Name: client_version; Type: TABLE; Schema: TNRS; Owner: -; Tablespace:
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--
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CREATE TABLE client_version (
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    id text NOT NULL,
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    global_rev integer NOT NULL,
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    "/lib/tnrs.py rev" integer,
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    "/bin/tnrs_db rev" integer
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);
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--
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-- Name: TABLE client_version; Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON TABLE client_version IS 'contains svn revisions';
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--
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-- Name: COLUMN client_version.global_rev; Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON COLUMN client_version.global_rev IS 'from `svn info .` > Last Changed Rev';
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--
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-- Name: COLUMN client_version."/lib/tnrs.py rev"; Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON COLUMN client_version."/lib/tnrs.py rev" IS 'from `svn info lib/tnrs.py` > Last Changed Rev';
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--
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-- Name: COLUMN client_version."/bin/tnrs_db rev"; Type: COMMENT; Schema: TNRS; Owner: -
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--
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COMMENT ON COLUMN client_version."/bin/tnrs_db rev" IS 'from `svn info bin/tnrs_db` > Last Changed Rev';
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--
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-- Name: batch_download_settings_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
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--
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ALTER TABLE ONLY batch_download_settings
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    ADD CONSTRAINT batch_download_settings_pkey PRIMARY KEY (id);
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--
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-- Name: batch_id_by_time_key; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
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--
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ALTER TABLE ONLY batch
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    ADD CONSTRAINT batch_id_by_time_key UNIQUE (id_by_time);
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--
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-- Name: batch_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
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--
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ALTER TABLE ONLY batch
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    ADD CONSTRAINT batch_pkey PRIMARY KEY (id);
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--
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-- Name: client_version_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
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--
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ALTER TABLE ONLY client_version
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    ADD CONSTRAINT client_version_pkey PRIMARY KEY (id);
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--
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-- Name: tnrs_Name_submitted_key; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
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--
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ALTER TABLE ONLY tnrs
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    ADD CONSTRAINT "tnrs_Name_submitted_key" UNIQUE ("Name_submitted");
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--
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-- Name: tnrs_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: -; Tablespace:
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--
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ALTER TABLE ONLY tnrs
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    ADD CONSTRAINT tnrs_pkey PRIMARY KEY (batch, "Name_number");
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--
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-- Name: batch_client_version_idx; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
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--
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CREATE INDEX batch_client_version_idx ON batch USING btree (client_version);
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--
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-- Name: tnrs__valid_match; Type: INDEX; Schema: TNRS; Owner: -; Tablespace:
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--
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CREATE UNIQUE INDEX tnrs__valid_match ON tnrs USING btree ("Name_submitted") WHERE is_valid_match;
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--
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-- Name: batch__fill; Type: TRIGGER; Schema: TNRS; Owner: -
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--
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CREATE TRIGGER batch__fill BEFORE INSERT OR UPDATE ON batch FOR EACH ROW EXECUTE PROCEDURE batch__fill();
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--
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-- Name: tnrs_populate_fields; Type: TRIGGER; Schema: TNRS; Owner: -
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--
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CREATE TRIGGER tnrs_populate_fields BEFORE INSERT OR UPDATE ON tnrs FOR EACH ROW EXECUTE PROCEDURE tnrs_populate_fields();
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--
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-- Name: batch_client_version_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
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--
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ALTER TABLE ONLY batch
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    ADD CONSTRAINT batch_client_version_fkey FOREIGN KEY (client_version) REFERENCES client_version(id) ON UPDATE CASCADE ON DELETE CASCADE;
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--
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-- Name: batch_download_settings_id_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
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--
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ALTER TABLE ONLY batch_download_settings
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    ADD CONSTRAINT batch_download_settings_id_fkey FOREIGN KEY (id) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
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--
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-- Name: tnrs_batch_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: -
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--
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ALTER TABLE ONLY tnrs
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    ADD CONSTRAINT tnrs_batch_fkey FOREIGN KEY (batch) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
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--
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-- Name: TNRS; Type: ACL; Schema: -; Owner: -
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--
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REVOKE ALL ON SCHEMA "TNRS" FROM PUBLIC;
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REVOKE ALL ON SCHEMA "TNRS" FROM bien;
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GRANT ALL ON SCHEMA "TNRS" TO bien;
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GRANT USAGE ON SCHEMA "TNRS" TO bien_read;
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--
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-- Name: tnrs; Type: ACL; Schema: TNRS; Owner: -
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--
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REVOKE ALL ON TABLE tnrs FROM PUBLIC;
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REVOKE ALL ON TABLE tnrs FROM bien;
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GRANT ALL ON TABLE tnrs TO bien;
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GRANT SELECT ON TABLE tnrs TO bien_read;
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--
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-- PostgreSQL database dump complete
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--