SELECT util.search_path_append('util');

SELECT create_if_not_exists($$CREATE INDEX "Specimen.specimen_duplicate_institutions" ON $$||:table_str||$$ ("specimen_duplicate_institutions")$$);

-- remove frameshifted rows

DELETE FROM :table WHERE "specimen_duplicate_institutions" IS NULL;

DELETE FROM :table WHERE "yearCollected" !~ '^(?:1[7-9]|20)\d{2}$';

DELETE FROM :table WHERE country_verbatim ~ '\d';

DELETE FROM :table WHERE longitude_deg_verbatim ~ '[[:alpha:]]' AND longitude_deg_verbatim NOT IN ('RESTRINGIDO');

DELETE FROM :table WHERE longitude_min_verbatim !~ '^\d*$';

DELETE FROM :table WHERE longitude_sec_verbatim !~ '^\d*$';

DELETE FROM :table WHERE latitude_min_verbatim  !~ '^\d*$';

DELETE FROM :table WHERE latitude_sec_verbatim  !~ '^\d*$';

-- Remove institutions that we have direct data for

DELETE FROM :table

WHERE "specimen_duplicate_institutions" IN (

    -- Comments are from e-mail from Brad Boyle on 2013-1-16

    'MO' -- "all MO records in REMIB are also available from MO's own website"

    --, 'ARIZ' -- Some REMIB ARIZ specimens not yet in ARIZ itself

    --, 'NY' -- Some REMIB NY specimens not yet in NY itself

    , 'TEX'

)

/* list obtained using the following on r9459:

SELECT DISTINCT dataprovider

FROM sourcelist

JOIN provider_count ON provider_count.dataprovider = sourcelist.name

WHERE source_id = (SELECT source_by_shortname('REMIB'))

ORDER BY dataprovider

*/

;

-- map_nulls() derived cols

-- runtime: 7.5 min ("real 7m27.083s") @vegbiendev

CREATE OR REPLACE FUNCTION map_nulls__text(value text)

  RETURNS text AS

$BODY$

-- "ND = no disponible = not available" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)

SELECT util.map_nulls('{ND,NA}', $1)

$BODY$

  LANGUAGE sql IMMUTABLE

  COST 100;

SELECT mk_derived_col((:table_str, 'country'      ), $$map_nulls__text("country_verbatim"      )$$); -- runtime: 35 s ("Time: 35690.797 ms") @vegbiendev

SELECT mk_derived_col((:table_str, 'stateProvince'), $$map_nulls__text("stateProvince_verbatim")$$); -- runtime: 35 s ("Time: 36074.430 ms") @vegbiendev

SELECT mk_derived_col((:table_str, 'county'       ), $$map_nulls__text("county_verbatim"       )$$); -- runtime: 35 s ("Time: 36096.911 ms") @vegbiendev

SELECT mk_derived_col((:table_str, 'locality'     ), $$map_nulls__text("locality_verbatim"     )$$); -- runtime: 35 s ("Time: 36076.364 ms") @vegbiendev

SELECT mk_derived_col((:table_str, 'habitat'      ), $$map_nulls__text("habitat_verbatim"      )$$); -- runtime: 35 s ("Time: 35481.828 ms") @vegbiendev

CREATE OR REPLACE FUNCTION map_nulls__coord__longitude(value text)

  RETURNS double precision AS

$BODY$

-- TODO: sometimes also +-99, but not when min/sec are valid

SELECT util.map_nulls('{-999,999,1000}',

       util.map_nulls('{RESTRINGIDO}', $1)::double precision)

$BODY$

  LANGUAGE sql IMMUTABLE

  COST 100;

CREATE OR REPLACE FUNCTION map_nulls__coord__other(value text)

  RETURNS double precision AS

$BODY$

-- also map nulls that are valid longitudes

SELECT util.map_nulls('{-99,99}', map_nulls__coord__longitude($1))

$BODY$

  LANGUAGE sql IMMUTABLE

  COST 100;

SELECT mk_derived_col((:table_str, 'longitude_deg'), $$map_nulls__coord__longitude("longitude_deg_verbatim")$$); -- runtime: 40 s ("Time: 39417.099 ms") @vegbiendev

SELECT mk_derived_col((:table_str, 'longitude_min'), $$map_nulls__coord__other    ("longitude_min_verbatim")$$); -- runtime: 40 s ("Time: 41929.772 ms") @vegbiendev

SELECT mk_derived_col((:table_str, 'longitude_sec'), $$map_nulls__coord__other    ("longitude_sec_verbatim")$$); -- runtime: 40 s ("Time: 42106.205 ms") @vegbiendev

SELECT mk_derived_col((:table_str, 'latitude_deg' ), $$map_nulls__coord__other    ("latitude_deg_verbatim" )$$); -- runtime: 40 s ("Time: 42187.294 ms") @vegbiendev

SELECT mk_derived_col((:table_str, 'latitude_min' ), $$map_nulls__coord__other    ("latitude_min_verbatim" )$$); -- runtime: 40 s ("Time: 43220.851 ms") @vegbiendev

SELECT mk_derived_col((:table_str, 'latitude_sec' ), $$map_nulls__coord__other    ("latitude_sec_verbatim" )$$); -- runtime: 40 s ("Time: 42267.566 ms") @vegbiendev