CREATE TABLE batch

(

  id text NOT NULL,

  id_by_time text,

  time_submitted timestamp with time zone DEFAULT now(),

  CONSTRAINT batch_pkey PRIMARY KEY (id ),

  CONSTRAINT download_settings_id_by_time_key UNIQUE (id_by_time )

)

WITH (

  OIDS=FALSE

);

CREATE OR REPLACE FUNCTION batch__fill()

  RETURNS trigger AS

$BODY$

BEGIN

	new.id_by_time = new.time_submitted;

	new.id = COALESCE(new.id, new.id_by_time);

	RETURN new;

END;

$BODY$

  LANGUAGE plpgsql VOLATILE

  COST 100;

CREATE TRIGGER batch__fill

  BEFORE INSERT OR UPDATE

  ON batch

  FOR EACH ROW

  EXECUTE PROCEDURE batch__fill();

--

CREATE TABLE download_settings

(

  id text NOT NULL,

  "E-mail" text,

  "Id" text,

  "Job type" text,

  "Contains Id" boolean,

  "Start time" text,

  "Finish time" text,

  "TNRS version" text,

  "Sources selected" text,

  "Match threshold" double precision,

  "Classification" text,

  "Allow partial matches?" boolean,

  "Sort by source" boolean,

  "Constrain by higher taxonomy" boolean,

  CONSTRAINT download_settings_pkey PRIMARY KEY (id )

)

WITH (

  OIDS=FALSE

);

COMMENT ON TABLE download_settings

  IS 'stores data from http://tnrs.iplantcollaborative.org/TNRSapp.html > Submit List > results section > Download settings > settings.txt';

--

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: 25 min ("5221748 rows affected, 1524228 ms execution time")

VACUUM ANALYZE "TNRS".tnrs -- to remove previous rows

runtime: 1 min ("62350 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"

, "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"

;