SELECT *

FROM "nodes.src"

JOIN "names.src" USING (tax_id)

WHERE "name class" = 'scientific name'

;

ALTER TABLE :table ALTER COLUMN tax_id TYPE integer

USING tax_id::integer;

ALTER TABLE :table ALTER COLUMN "parent tax_id" TYPE integer

USING "parent tax_id"::integer;

ALTER TABLE :table ADD PRIMARY KEY (tax_id);

CREATE INDEX ON :table ("parent tax_id");

ALTER TABLE :table ADD FOREIGN KEY ("parent tax_id") REFERENCES :table (tax_id)

    ON UPDATE CASCADE ON DELETE CASCADE;

-- Make name_txt (mostly) globally unique by removing other kingdoms

-- Note that the delete will cascade to descendants

DELETE FROM :table WHERE tax_id IN (

      10239 -- superkingdom Viruses

    , 12884 -- superkingdom Viroids

    , 12908 -- unclassified sequences

    , 28384 -- other sequences

    ,     2 -- superkingdom Bacteria

    ,  2157 -- superkingdom Archaea

    ,  4751 -- kingdom Fungi

    , 33208 -- kingdom Animalia/Metazoa

);

-- Make name_txt completely globally unique by removing duplicates

DELETE FROM :table

WHERE name_txt IN (

    SELECT name_txt

    FROM :table

    GROUP BY name_txt

    HAVING count(*) > 1

)

;