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CREATE TABLE download_settings
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(
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"Time_submitted" timestamp with time zone 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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CONSTRAINT "Download settings_pkey" PRIMARY KEY ("Time_submitted" )
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)
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WITH (
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OIDS=FALSE
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);
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COMMENT ON TABLE download_settings
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IS 'stores data from http://tnrs.iplantcollaborative.org/TNRSapp.html > Submit List > results section > Download settings > settings.txt';
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CREATE OR REPLACE FUNCTION score_ok(score double precision)
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RETURNS boolean AS
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$BODY$
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SELECT $1 >= 0.8
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$BODY$
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LANGUAGE sql IMMUTABLE STRICT
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COST 100;
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CREATE OR REPLACE FUNCTION family_is_homonym(family text)
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RETURNS boolean AS
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$BODY$
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SELECT EXISTS(SELECT * FROM "IRMNG".family_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
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$BODY$
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LANGUAGE sql STABLE STRICT
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COST 100;
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CREATE OR REPLACE FUNCTION genus_is_homonym(genus text)
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RETURNS boolean AS
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$BODY$
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SELECT EXISTS(SELECT * FROM "IRMNG".genus_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
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$BODY$
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LANGUAGE sql STABLE STRICT
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COST 100;
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/* IMPORTANT: when changing this table's schema, you must regenerate data.sql:
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$ <this_file>/../test_taxonomic_names/test_scrub
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you must also make the same changes on vegbiendev: e.g.
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$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")
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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[]);
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runtime: 4 min ("242100 ms")
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*/
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CREATE TABLE tnrs
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(
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"Time_submitted" timestamp with time zone NOT NULL DEFAULT now(),
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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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"Max_score" double precision,
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"Is_homonym" boolean,
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"Is_plant" boolean,
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CONSTRAINT tnrs_pkey PRIMARY KEY ("Time_submitted" , "Name_number" ),
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CONSTRAINT "tnrs_Name_submitted_key" UNIQUE ("Name_submitted" )
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)
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WITH (
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OIDS=FALSE
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);
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CREATE UNIQUE INDEX tnrs_score_ok
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ON tnrs
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USING btree
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("Name_submitted" )
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WHERE score_ok("Max_score");
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/* 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 ("5221748 rows affected, 1524228 ms execution time")
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VACUUM ANALYZE "TNRS".tnrs -- to remove previous rows
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runtime: 1 min ("62350 ms")
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*/
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CREATE OR REPLACE FUNCTION tnrs_populate_fields()
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RETURNS trigger AS
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$BODY$
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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); -- author disambiguates
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family_is_homonym boolean = NOT never_homonym AND "TNRS".family_is_homonym(new."Family_matched");
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genus_is_homonym boolean = NOT never_homonym AND "TNRS".genus_is_homonym( new."Genus_matched" );
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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'), 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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new."Max_score" = GREATEST(
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new."Overall_score"
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, new."Family_score"
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, new."Genus_score"
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, new."Specific_epithet_score"
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);
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new."Is_homonym" = COALESCE(genus_is_homonym, family_is_homonym);
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new."Is_plant" = (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);
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RETURN new;
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END;
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$BODY$
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LANGUAGE plpgsql VOLATILE
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COST 100;
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CREATE TRIGGER tnrs_populate_fields
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BEFORE INSERT OR UPDATE
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ON tnrs
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FOR EACH ROW
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EXECUTE PROCEDURE tnrs_populate_fields();
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CREATE OR REPLACE VIEW "MatchedTaxon" AS
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SELECT
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"Time_submitted" AS "*Name_matched.Time_submitted"
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, "Name_submitted" AS "concatenatedScientificName"
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, "Name_matched" AS "matchedTaxonName"
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, "Name_matched_rank" AS "matchedTaxonRank"
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, "Name_score" AS "*Name_matched.Name_score"
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, "Name_matched_author" AS "matchedScientificNameAuthorship"
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, "Name_matched_url" AS "matchedScientificNameID"
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, "Author_score" AS "*Name_matched.Author_score"
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, "Family_score" AS "matchedFamilyConfidence_fraction"
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, COALESCE("Name_matched_accepted_family", "Accepted_name_family") AS "matchedFamily"
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, "Genus_matched" AS "matchedGenus"
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, "Genus_score" AS "matchedGenusConfidence_fraction"
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, "Specific_epithet_matched" AS "matchedSpecificEpithet"
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, "Specific_epithet_score" AS "matchedSpeciesConfidence_fraction"
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, "Infraspecific_epithet_matched" AS "matchedInfraspecificEpithet"
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, "Infraspecific_epithet_score" AS "*Name_matched.Infraspecific_epithet_score"
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, "Annotations" AS "identificationQualifier"
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, "Unmatched_terms" AS "morphospeciesSuffix"
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, "Taxonomic_status" AS "taxonomicStatus"
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, "Accepted_name" AS "acceptedTaxonName"
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, "Accepted_name_author" AS "acceptedScientificNameAuthorship"
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, "Accepted_name_rank" AS "acceptedTaxonRank"
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, "Accepted_name_url" AS "acceptedScientificNameID"
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, "Accepted_name_species" AS "*Name_matched.Accepted_name_species"
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, "Accepted_name_family" AS "acceptedFamily"
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, "Selected" AS "*Name_matched.Selected"
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, "Source" AS "*Name_matched.Source"
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, "Warnings" AS "*Name_matched.Warnings"
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, "Accepted_name_lsid" AS "*Name_matched.Accepted_name_lsid"
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, "Accepted_scientific_name" AS "acceptedScientificName"
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, "Max_score" AS "matchedTaxonConfidence_fraction"
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FROM tnrs
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;
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CREATE OR REPLACE VIEW "ValidMatchedTaxon" AS
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SELECT *
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FROM "MatchedTaxon"
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WHERE score_ok("matchedTaxonConfidence_fraction")
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;
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CREATE OR REPLACE VIEW "AcceptedTaxon" AS
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SELECT
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"Time_submitted" AS "*Accepted_name.Time_submitted"
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, "Name_submitted" AS "acceptedScientificName"
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, "Genus_matched" AS "acceptedGenus"
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, "Specific_epithet_matched" AS "acceptedSpecificEpithet"
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, "Infraspecific_epithet_matched" AS "acceptedInfraspecificEpithet"
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, "Taxonomic_status" AS "acceptedTaxonomicStatus"
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, "Selected" AS "*Accepted_name.Selected"
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, "Source" AS "*Accepted_name.Source"
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, "Warnings" AS "*Accepted_name.Warnings"
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, "Accepted_name_lsid" AS "*Accepted_name.Accepted_name_lsid"
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FROM tnrs
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;
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CREATE OR REPLACE VIEW "ScrubbedTaxon" AS
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SELECT *
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FROM "ValidMatchedTaxon"
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NATURAL LEFT JOIN "AcceptedTaxon"
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;
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