CREATE OR REPLACE FUNCTION score_ok(score double precision)
  RETURNS boolean AS
$BODY$
SELECT $1 >= 0.8
$BODY$
  LANGUAGE sql IMMUTABLE STRICT
  COST 100;

CREATE OR REPLACE FUNCTION family_is_homonym(family text)
  RETURNS boolean AS
$BODY$
SELECT EXISTS(SELECT * FROM "IRMNG".family_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
$BODY$
  LANGUAGE sql STABLE STRICT
  COST 100;

CREATE OR REPLACE FUNCTION genus_is_homonym(genus text)
  RETURNS boolean AS
$BODY$
SELECT EXISTS(SELECT * FROM "IRMNG".genus_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
$BODY$
  LANGUAGE sql STABLE STRICT
  COST 100;

/* IMPORTANT: when changing this table's schema, you must regenerate data.sql:
$ <this_file>/../test_taxonomic_names/test_scrub
you must also make the same changes on vegbiendev: e.g.
$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")
SELECT util.set_col_types('"TNRS".tnrs', ARRAY[
  ('col', 'new_type')
]::util.col_cast[]);
runtime: 4 min ("242100 ms")
*/
CREATE TABLE tnrs
(
  "Time_submitted" timestamp with time zone NOT NULL DEFAULT now(),
  "Name_number" integer NOT NULL,
  "Name_submitted" text NOT NULL,
  "Overall_score" double precision,
  "Name_matched" text,
  "Name_matched_rank" text,
  "Name_score" double precision,
  "Name_matched_author" text,
  "Name_matched_url" text,
  "Author_matched" text,
  "Author_score" double precision,
  "Family_matched" text,
  "Family_score" double precision,
  "Name_matched_accepted_family" text,
  "Genus_matched" text,
  "Genus_score" double precision,
  "Specific_epithet_matched" text,
  "Specific_epithet_score" double precision,
  "Infraspecific_rank" text,
  "Infraspecific_epithet_matched" text,
  "Infraspecific_epithet_score" double precision,
  "Infraspecific_rank_2" text,
  "Infraspecific_epithet_2_matched" text,
  "Infraspecific_epithet_2_score" double precision,
  "Annotations" text,
  "Unmatched_terms" text,
  "Taxonomic_status" text,
  "Accepted_name" text,
  "Accepted_name_author" text,
  "Accepted_name_rank" text,
  "Accepted_name_url" text,
  "Accepted_name_species" text,
  "Accepted_name_family" text,
  "Selected" text,
  "Source" text,
  "Warnings" text,
  "Accepted_name_lsid" text,
  "Accepted_scientific_name" text,
  "Max_score" double precision,
  "Is_homonym" boolean,
  "Is_plant" boolean,
  CONSTRAINT tnrs_pkey PRIMARY KEY ("Time_submitted" , "Name_number" ),
  CONSTRAINT "tnrs_Name_submitted_key" UNIQUE ("Name_submitted" )
)
WITH (
  OIDS=FALSE
);

CREATE UNIQUE INDEX tnrs_score_ok
  ON tnrs
  USING btree
  ("Name_submitted" )
  WHERE score_ok("Max_score");

/* IMPORTANT: when changing this function, you must regenerate the derived cols:
UPDATE "TNRS".tnrs SET "Name_submitted" = "Name_submitted"
runtime: 16 min ("5052509 rows affected, 980692 ms execution time")
VACUUM ANALYZE "TNRS".tnrs -- to remove previous rows
runtime: 50 s ("48264 ms")
*/
CREATE OR REPLACE FUNCTION tnrs_populate_fields()
  RETURNS trigger AS
$BODY$
DECLARE
    "Specific_epithet_is_plant" boolean :=
        (CASE
        WHEN   new."Infraspecific_epithet_matched"   IS NOT NULL
            OR new."Infraspecific_epithet_2_matched" IS NOT NULL
            OR new."Specific_epithet_score" >= 0.9 -- fuzzy match
            THEN true
        ELSE NULL -- ambiguous
        END);
    never_homonym boolean = COALESCE(new."Author_score" >= 0.6, false); -- author disambiguates
    family_is_homonym boolean = NOT never_homonym AND "TNRS".family_is_homonym(new."Family_matched");
    genus_is_homonym  boolean = NOT never_homonym AND "TNRS".genus_is_homonym( new."Genus_matched" );
BEGIN
    new."Accepted_scientific_name" = NULLIF(concat_ws(' '
        , NULLIF(NULLIF(new."Accepted_name_family", 'Unknown'), new."Accepted_name")
        , new."Accepted_name"
        , new."Accepted_name_author"
    ), '');
    new."Max_score" = GREATEST(
          new."Overall_score"
        , new."Family_score"
        , new."Genus_score"
        , new."Specific_epithet_score"
    );
    new."Is_homonym" = COALESCE(genus_is_homonym, family_is_homonym);
    new."Is_plant" = (CASE
        WHEN new."Family_score" = 1 AND NOT family_is_homonym -- exact match
            THEN true
        ELSE -- consider genus
            (CASE
            WHEN new."Genus_score" =  1    -- exact match
                THEN
                (CASE
                WHEN NOT genus_is_homonym THEN true
                ELSE "Specific_epithet_is_plant"
                END)
            WHEN new."Genus_score" >= 0.85 -- fuzzy match
                THEN "Specific_epithet_is_plant"
            ELSE NULL -- ambiguous
            END)
        END);
    
    RETURN new;
END;
$BODY$
  LANGUAGE plpgsql VOLATILE
  COST 100;

CREATE TRIGGER tnrs_populate_fields
  BEFORE INSERT OR UPDATE
  ON tnrs
  FOR EACH ROW
  EXECUTE PROCEDURE tnrs_populate_fields();


CREATE OR REPLACE VIEW "MatchedTaxon" AS
SELECT
  "Time_submitted" AS "*Name_matched.Time_submitted"
, "Name_submitted" AS "concatenatedScientificName"
, "Name_matched" AS "matchedTaxonName"
, "Name_matched_rank" AS "matchedTaxonRank"
, "Name_score" AS "*Name_matched.Name_score"
, "Name_matched_author" AS "matchedScientificNameAuthorship"
, "Name_matched_url" AS "matchedScientificNameID"
, "Author_score" AS "*Name_matched.Author_score"
, "Family_score" AS "matchedFamilyConfidence_fraction"
, COALESCE("Name_matched_accepted_family", "Accepted_name_family") AS "matchedFamily"
, "Genus_matched" AS "matchedGenus"
, "Genus_score" AS "matchedGenusConfidence_fraction"
, "Specific_epithet_matched" AS "matchedSpecificEpithet"
, "Specific_epithet_score" AS "matchedSpeciesConfidence_fraction"
, "Infraspecific_epithet_matched" AS "matchedInfraspecificEpithet"
, "Infraspecific_epithet_score" AS "*Name_matched.Infraspecific_epithet_score"
, "Annotations" AS "identificationQualifier"
, "Unmatched_terms" AS "morphospeciesSuffix"
, "Taxonomic_status" AS "taxonomicStatus"
, "Accepted_name" AS "acceptedTaxonName"
, "Accepted_name_author" AS "acceptedScientificNameAuthorship"
, "Accepted_name_rank" AS "acceptedTaxonRank"
, "Accepted_name_url" AS "acceptedScientificNameID"
, "Accepted_name_species" AS "*Name_matched.Accepted_name_species"
, "Accepted_name_family" AS "acceptedFamily"
, "Selected" AS "*Name_matched.Selected"
, "Source" AS "*Name_matched.Source"
, "Warnings" AS "*Name_matched.Warnings"
, "Accepted_name_lsid" AS "*Name_matched.Accepted_name_lsid"
, "Accepted_scientific_name" AS "acceptedScientificName"
, "Max_score" AS "matchedTaxonConfidence_fraction"
FROM tnrs
;

CREATE OR REPLACE VIEW "ValidMatchedTaxon" AS
SELECT *
FROM "MatchedTaxon"
WHERE score_ok("matchedTaxonConfidence_fraction")
;

CREATE OR REPLACE VIEW "AcceptedTaxon" AS
SELECT
  "Time_submitted" AS "*Accepted_name.Time_submitted"
, "Name_submitted" AS "acceptedScientificName"
, "Genus_matched" AS "acceptedGenus"
, "Specific_epithet_matched" AS "acceptedSpecificEpithet"
, "Infraspecific_epithet_matched" AS "acceptedInfraspecificEpithet"
, "Annotations" AS "*Accepted_name.Annotations"
, "Taxonomic_status" AS "acceptedTaxonomicStatus"
, "Selected" AS "*Accepted_name.Selected"
, "Source" AS "*Accepted_name.Source"
, "Warnings" AS "*Accepted_name.Warnings"
, "Accepted_name_lsid" AS "*Accepted_name.Accepted_name_lsid"
FROM tnrs
;

CREATE OR REPLACE VIEW "ScrubbedTaxon" AS
SELECT *
FROM "ValidMatchedTaxon"
NATURAL LEFT JOIN "AcceptedTaxon"
;