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7844
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aaronmk
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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 VOLATILE
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COST 100;
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| 9 |
9756
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aaronmk
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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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*/
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5183
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aaronmk
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CREATE TABLE tnrs
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5110
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aaronmk
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(
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9513
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aaronmk
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"Time_submitted" timestamp with time zone DEFAULT now(),
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5110
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aaronmk
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"Name_number" text,
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"Name_submitted" text NOT NULL,
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"Overall_score" text,
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"Name_matched" text,
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"Name_matched_rank" text,
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"Name_score" text,
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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" text,
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"Family_matched" text,
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"Family_score" text,
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9529
|
aaronmk
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"Name_matched_accepted_family" text,
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5110
|
aaronmk
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"Genus_matched" text,
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"Genus_score" text,
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"Specific_epithet_matched" text,
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"Specific_epithet_score" text,
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"Infraspecific_rank" text,
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"Infraspecific_epithet_matched" text,
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"Infraspecific_epithet_score" text,
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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" text,
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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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| 44 |
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"Accepted_name_url" text,
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| 45 |
9762
|
aaronmk
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"Accepted_name_species" text,
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"Accepted_name_family" text,
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| 47 |
5110
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aaronmk
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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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7133
|
aaronmk
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"Accepted_scientific_name" text,
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7293
|
aaronmk
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"Max_score" double precision,
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9763
|
aaronmk
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"Is_plant" boolean,
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5110
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aaronmk
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CONSTRAINT tnrs_pkey PRIMARY KEY ("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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| 59 |
7132
|
aaronmk
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| 60 |
7844
|
aaronmk
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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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| 66 |
9765
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aaronmk
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/* IMPORTANT: when changing this function, you must regenerate the derived cols:
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UPDATE tnrs SET "Name_submitted" = "Name_submitted"
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9767
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aaronmk
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runtime: 17 min ("4992166 rows affected, 1019907 ms execution time")
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9765
|
aaronmk
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*/
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9512
|
aaronmk
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CREATE OR REPLACE FUNCTION tnrs_populate_fields()
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| 71 |
7134
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aaronmk
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RETURNS trigger AS
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$BODY$
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| 73 |
9763
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aaronmk
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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"::double precision >= 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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7134
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aaronmk
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BEGIN
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7848
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aaronmk
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new."Accepted_scientific_name" = NULLIF(concat_ws(' '
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| 84 |
9762
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aaronmk
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, NULLIF(NULLIF(new."Accepted_name_family", 'Unknown'), new."Accepted_name")
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7134
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aaronmk
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, new."Accepted_name"
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, new."Accepted_name_author"
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| 87 |
7848
|
aaronmk
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), '');
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| 88 |
7293
|
aaronmk
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new."Max_score" = GREATEST(
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new."Overall_score"::double precision
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, new."Family_score"::double precision
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, new."Genus_score"::double precision
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, new."Specific_epithet_score"::double precision
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);
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9763
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aaronmk
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new."Is_plant" = (CASE
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| 95 |
9764
|
aaronmk
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WHEN new."Family_score"::double precision = 1 THEN true -- exact match
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| 96 |
9763
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aaronmk
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ELSE -- Family_matched IS NULL
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(CASE
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WHEN new."Genus_score"::double precision = 1 -- exact match
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THEN "Specific_epithet_is_plant"
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WHEN new."Genus_score"::double precision >= 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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| 105 |
7134
|
aaronmk
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| 106 |
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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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| 112 |
9512
|
aaronmk
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CREATE TRIGGER tnrs_populate_fields
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| 113 |
7134
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aaronmk
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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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| 116 |
9512
|
aaronmk
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EXECUTE PROCEDURE tnrs_populate_fields();
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| 117 |
7251
|
aaronmk
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| 118 |
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| 119 |
9759
|
aaronmk
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CREATE OR REPLACE VIEW "MatchedTaxon" AS
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| 120 |
7823
|
aaronmk
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SELECT
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"Time_submitted" AS "*Name_matched.Time_submitted"
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| 122 |
7830
|
aaronmk
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, "Name_submitted" AS "concatenatedScientificName"
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| 123 |
7829
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aaronmk
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, "Name_matched" AS "matchedTaxonName"
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| 124 |
7823
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aaronmk
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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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| 130 |
9762
|
aaronmk
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, COALESCE("Name_matched_accepted_family", "Accepted_name_family") AS "matchedFamily"
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| 131 |
7831
|
aaronmk
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, "Genus_matched" AS "matchedGenus"
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| 132 |
7823
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aaronmk
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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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| 139 |
7833
|
aaronmk
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, "Taxonomic_status" AS "taxonomicStatus"
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| 140 |
7823
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aaronmk
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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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| 144 |
9762
|
aaronmk
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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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| 146 |
7823
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aaronmk
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, "Selected" AS "*Name_matched.Selected"
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| 147 |
7828
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aaronmk
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, "Source" AS "*Name_matched.Source"
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| 148 |
7823
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aaronmk
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, "Warnings" AS "*Name_matched.Warnings"
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| 149 |
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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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| 152 |
9616
|
aaronmk
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FROM tnrs
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;
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| 154 |
7823
|
aaronmk
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| 155 |
9759
|
aaronmk
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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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| 161 |
7823
|
aaronmk
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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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| 166 |
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, "Specific_epithet_matched" AS "acceptedSpecificEpithet"
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, "Infraspecific_epithet_matched" AS "acceptedInfraspecificEpithet"
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| 168 |
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, "Annotations" AS "*Accepted_name.Annotations"
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| 169 |
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, "Taxonomic_status" AS "acceptedTaxonomicStatus"
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| 170 |
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, "Selected" AS "*Accepted_name.Selected"
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| 171 |
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, "Source" AS "*Accepted_name.Source"
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| 172 |
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, "Warnings" AS "*Accepted_name.Warnings"
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| 173 |
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, "Accepted_name_lsid" AS "*Accepted_name.Accepted_name_lsid"
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| 174 |
9760
|
aaronmk
|
FROM tnrs
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;
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| 176 |
7823
|
aaronmk
|
|
| 177 |
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CREATE OR REPLACE VIEW "ScrubbedTaxon" AS
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| 178 |
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SELECT *
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| 179 |
9758
|
aaronmk
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FROM "ValidMatchedTaxon"
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| 180 |
7823
|
aaronmk
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NATURAL LEFT JOIN "AcceptedTaxon"
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| 181 |
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;
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