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CREATE TABLE client_version
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(
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id text NOT NULL,
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global_rev integer NOT NULL, -- from `svn info .` > Last Changed Rev
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"/lib/tnrs.py rev" integer, -- from `svn info lib/tnrs.py` > Last Changed Rev
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"/bin/tnrs_db rev" integer, -- from `svn info bin/tnrs_db` > Last Changed Rev
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CONSTRAINT client_version_pkey PRIMARY KEY (id )
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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 client_version
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IS 'contains svn revisions';
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COMMENT ON COLUMN client_version.global_rev IS 'from `svn info .` > Last Changed Rev';
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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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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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CREATE TABLE batch
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(
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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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CONSTRAINT batch_pkey PRIMARY KEY (id ),
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CONSTRAINT batch_client_version_fkey FOREIGN KEY (client_version)
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REFERENCES client_version (id) MATCH SIMPLE
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ON UPDATE CASCADE ON DELETE CASCADE,
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CONSTRAINT batch_id_by_time_key UNIQUE (id_by_time )
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)
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WITH (
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OIDS=FALSE
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);
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CREATE OR REPLACE FUNCTION batch__fill()
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RETURNS trigger AS
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$BODY$
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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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$BODY$
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LANGUAGE plpgsql VOLATILE
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COST 100;
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CREATE TRIGGER batch__fill
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BEFORE INSERT OR UPDATE
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ON batch
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FOR EACH ROW
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EXECUTE PROCEDURE batch__fill();
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--
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CREATE TABLE batch_download_settings
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(
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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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CONSTRAINT batch_download_settings_pkey PRIMARY KEY (id ),
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CONSTRAINT batch_download_settings_id_fkey FOREIGN KEY (id)
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REFERENCES "TNRS".batch (id) MATCH SIMPLE
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ON UPDATE CASCADE ON DELETE CASCADE
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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 batch_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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--
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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: 9 min ("531282 ms")
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*/
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CREATE TABLE tnrs
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(
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batch text 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 (batch , "Name_number" ),
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CONSTRAINT tnrs_batch_fkey FOREIGN KEY (batch)
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REFERENCES batch (id) MATCH SIMPLE
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ON UPDATE CASCADE ON DELETE CASCADE,
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CONSTRAINT "tnrs_Name_submitted_key" UNIQUE ("Name_submitted" )
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167
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)
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WITH (
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OIDS=FALSE
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);
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171
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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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184
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CREATE OR REPLACE FUNCTION tnrs_populate_fields()
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185
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RETURNS trigger AS
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186
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$BODY$
|
187
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DECLARE
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188
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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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200
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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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212
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new."Is_plant" = (CASE
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213
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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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226
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END)
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END);
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228
|
|
229
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RETURN new;
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230
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END;
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231
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$BODY$
|
232
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LANGUAGE plpgsql VOLATILE
|
233
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COST 100;
|
234
|
|
235
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CREATE TRIGGER tnrs_populate_fields
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236
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BEFORE INSERT OR UPDATE
|
237
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ON tnrs
|
238
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FOR EACH ROW
|
239
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EXECUTE PROCEDURE tnrs_populate_fields();
|
240
|
|
241
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--
|
242
|
|
243
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CREATE OR REPLACE VIEW "MatchedTaxon" AS
|
244
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SELECT
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245
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"batch" AS "*Name_matched.batch"
|
246
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, "Name_submitted" AS "concatenatedScientificName"
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, "Name_matched" AS "matchedTaxonName"
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248
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, "Name_matched_rank" AS "matchedTaxonRank"
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249
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, "Name_score" AS "*Name_matched.Name_score"
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250
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, "Name_matched_author" AS "matchedScientificNameAuthorship"
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251
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, "Name_matched_url" AS "matchedScientificNameID"
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252
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, "Author_score" AS "*Name_matched.Author_score"
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253
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, "Family_score" AS "matchedFamilyConfidence_fraction"
|
254
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, COALESCE("Name_matched_accepted_family", "Accepted_name_family") AS "matchedFamily"
|
255
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, "Genus_matched" AS "matchedGenus"
|
256
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, "Genus_score" AS "matchedGenusConfidence_fraction"
|
257
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, "Specific_epithet_matched" AS "matchedSpecificEpithet"
|
258
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, "Specific_epithet_score" AS "matchedSpeciesConfidence_fraction"
|
259
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, "Infraspecific_epithet_matched" AS "matchedInfraspecificEpithet"
|
260
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, "Infraspecific_epithet_score" AS "*Name_matched.Infraspecific_epithet_score"
|
261
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, "Annotations" AS "identificationQualifier"
|
262
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, "Unmatched_terms" AS "morphospeciesSuffix"
|
263
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, "Taxonomic_status" AS "taxonomicStatus"
|
264
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, "Accepted_name" AS "acceptedTaxonName"
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265
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, "Accepted_name_author" AS "acceptedScientificNameAuthorship"
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266
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, "Accepted_name_rank" AS "acceptedTaxonRank"
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267
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, "Accepted_name_url" AS "acceptedScientificNameID"
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268
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, "Accepted_name_species" AS "*Name_matched.Accepted_name_species"
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269
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, "Accepted_name_family" AS "acceptedFamily"
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270
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, "Selected" AS "*Name_matched.Selected"
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271
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, "Source" AS "*Name_matched.Source"
|
272
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, "Warnings" AS "*Name_matched.Warnings"
|
273
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, "Accepted_name_lsid" AS "*Name_matched.Accepted_name_lsid"
|
274
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, "Accepted_scientific_name" AS "acceptedScientificName"
|
275
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, "Max_score" AS "matchedTaxonConfidence_fraction"
|
276
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FROM tnrs
|
277
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;
|
278
|
|
279
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CREATE OR REPLACE VIEW "ValidMatchedTaxon" AS
|
280
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SELECT *
|
281
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FROM "MatchedTaxon"
|
282
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WHERE score_ok("matchedTaxonConfidence_fraction")
|
283
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;
|
284
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COMMENT ON VIEW "ValidMatchedTaxon"
|
285
|
IS 'to update, use * as the column list';
|
286
|
|
287
|
CREATE OR REPLACE VIEW "AcceptedTaxon" AS
|
288
|
SELECT
|
289
|
"batch" AS "*Accepted_name.batch"
|
290
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, "Name_submitted" AS "acceptedScientificName"
|
291
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, "Genus_matched" AS "acceptedGenus"
|
292
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, "Specific_epithet_matched" AS "acceptedSpecificEpithet"
|
293
|
, "Infraspecific_epithet_matched" AS "acceptedInfraspecificEpithet"
|
294
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, "Taxonomic_status" AS "acceptedTaxonomicStatus"
|
295
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, "Selected" AS "*Accepted_name.Selected"
|
296
|
, "Source" AS "*Accepted_name.Source"
|
297
|
, "Warnings" AS "*Accepted_name.Warnings"
|
298
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, "Accepted_name_lsid" AS "*Accepted_name.Accepted_name_lsid"
|
299
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FROM tnrs
|
300
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;
|
301
|
|
302
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CREATE OR REPLACE VIEW "ScrubbedTaxon" AS
|
303
|
SELECT *
|
304
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FROM "ValidMatchedTaxon"
|
305
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NATURAL LEFT JOIN "AcceptedTaxon"
|
306
|
;
|
307
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COMMENT ON VIEW "ScrubbedTaxon"
|
308
|
IS 'to update, use * as the column list';
|