--

-- PostgreSQL database dump

--

SET statement_timeout = 0;

SET lock_timeout = 0;

SET client_encoding = 'UTF8';

SET standard_conforming_strings = on;

SET check_function_bodies = false;

SET client_min_messages = warning;

--

-- Name: TNRS; Type: SCHEMA; Schema: -; Owner: bien

--

CREATE SCHEMA "TNRS";

ALTER SCHEMA "TNRS" OWNER TO bien;

--

-- Name: SCHEMA "TNRS"; Type: COMMENT; Schema: -; Owner: bien

--

COMMENT ON SCHEMA "TNRS" IS '

IMPORTANT: when changing this schema, you must also make the same changes on vegbiendev:

on vegbiendev:

# back up existing TNRS schema (in case of an accidental incorrect change):

$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")

$ svn up

$ svn di

# make the changes shown in the diff

## to change column types:

SELECT util.set_col_types(''"TNRS".tnrs_match'', ARRAY[

  (''col'', ''new_type'')

]::util.col_cast[]); -- runtime: 9 min ("531282 ms")

$ rm=1 inputs/.TNRS/schema.sql.run

# repeat until `svn di` shows no diff

# back up new TNRS schema:

$ make backups/TNRS.backup-remake # runtime: 3 min ("real 2m44.277s")

';

SET search_path = "TNRS", pg_catalog;

--

-- Name: batch__fill(); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION batch__fill() RETURNS trigger

    LANGUAGE plpgsql

    AS $$

BEGIN

	new.id_by_time = new.time_submitted;

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

	RETURN new;

END;

$$;

ALTER FUNCTION "TNRS".batch__fill() OWNER TO bien;

--

-- Name: family_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION family_is_homonym(family text) RETURNS boolean

    LANGUAGE sql STABLE STRICT

    AS $_$

SELECT EXISTS(SELECT * FROM "IRMNG".family_homonym_epithet WHERE "taxonNameOrEpithet" = $1)

$_$;

ALTER FUNCTION "TNRS".family_is_homonym(family text) OWNER TO bien;

--

-- Name: genus_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION genus_is_homonym(genus text) RETURNS boolean

    LANGUAGE sql STABLE STRICT

    AS $_$

SELECT EXISTS(SELECT * FROM "IRMNG".genus_homonym_epithet WHERE "taxonNameOrEpithet" = $1)

$_$;

ALTER FUNCTION "TNRS".genus_is_homonym(genus text) OWNER TO bien;

--

-- Name: map_taxonomic_status(text, text); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION map_taxonomic_status(taxonomic_status_verbatim text, accepted_taxon_name_no_author text) RETURNS text

    LANGUAGE sql IMMUTABLE

    AS $_$

/* from http://wiki.vegpath.org/2013-11-14_conference_call#taxonomic-fields:

"taxonomic_status should be accepted instead of synonym when an accepted name is

available (this is not always the case when a name is marked as a synonym)" */

SELECT CASE WHEN $2 IS NOT NULL THEN 'accepted' ELSE lower($1) END

$_$;

ALTER FUNCTION "TNRS".map_taxonomic_status(taxonomic_status_verbatim text, accepted_taxon_name_no_author text) OWNER TO bien;

--

-- Name: taxon_name_is_safe(text); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION taxon_name_is_safe(taxon_name text) RETURNS boolean

    LANGUAGE sql IMMUTABLE

    AS $_$

SELECT NOT ($1 = ANY("TNRS".unsafe_taxon_names()))

$_$;

ALTER FUNCTION "TNRS".taxon_name_is_safe(taxon_name text) OWNER TO bien;

--

-- Name: tnrs__batch_begin(); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION tnrs__batch_begin() RETURNS trigger

    LANGUAGE plpgsql

    AS $$

BEGIN

	PERFORM util.seq__reset('pg_temp.tnrs__match_num__seq', 0);

	RETURN NULL;

END;

$$;

ALTER FUNCTION "TNRS".tnrs__batch_begin() OWNER TO bien;

--

-- Name: tnrs__match_num__fill(); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION tnrs__match_num__fill() RETURNS trigger

    LANGUAGE plpgsql

    AS $$

BEGIN

	IF new.match_num IS NULL THEN

		new.match_num = "TNRS".tnrs__match_num__next();

	END IF;

	RETURN new;

END;

$$;

ALTER FUNCTION "TNRS".tnrs__match_num__fill() OWNER TO bien;

--

-- Name: tnrs__match_num__next(); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION tnrs__match_num__next() RETURNS bigint

    LANGUAGE sql

    AS $$

SELECT nextval('pg_temp.tnrs__match_num__seq');

$$;

ALTER FUNCTION "TNRS".tnrs__match_num__next() OWNER TO bien;

--

-- Name: tnrs_populate_fields(); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION tnrs_populate_fields() RETURNS trigger

    LANGUAGE plpgsql

    AS $$

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");

	matched_taxon_name_with_author text = NULLIF(concat_ws(' '

		, NULLIF(NULLIF(new."Name_matched_accepted_family", 'Unknown'),

			new."Name_matched")

		, NULLIF(new."Name_matched", 'No suitable matches found.')

		, new."Name_matched_author"

		), '');

	accepted_taxon_name_with_author text = NULLIF(concat_ws(' '

		, NULLIF(NULLIF(new."Accepted_name_family", 'Unknown'),

			new."Accepted_name")

		, new."Accepted_name"

		, new."Accepted_name_author"

		), '');

BEGIN

	/* exclude homonyms because these are not valid matches (i.e. TNRS provides

	a name, but the name is not meaningful because it is not unambiguous). */

	new.is_valid_match = new."Taxonomic_status" != 'Invalid'

		AND COALESCE(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, false);

	new.scrubbed_unique_taxon_name = COALESCE(

		accepted_taxon_name_with_author, matched_taxon_name_with_author);

	RETURN new;

END;

$$;

ALTER FUNCTION "TNRS".tnrs_populate_fields() OWNER TO bien;

--

-- Name: FUNCTION tnrs_populate_fields(); Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON FUNCTION tnrs_populate_fields() IS '

IMPORTANT: when changing this function, you must regenerate the derived cols:

UPDATE "TNRS".tnrs_match SET "Name_submitted" = "Name_submitted"

runtime: 30 min ("5564082 rows affected, 1918900 ms execution time")

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

runtime: 1.5 min ("92633 ms")

';

--

-- Name: unsafe_taxon_names(); Type: FUNCTION; Schema: TNRS; Owner: bien

--

CREATE FUNCTION unsafe_taxon_names() RETURNS text[]

    LANGUAGE sql IMMUTABLE

    AS $$

SELECT ARRAY[

]::text[]

$$;

ALTER FUNCTION "TNRS".unsafe_taxon_names() OWNER TO bien;

SET default_tablespace = '';

SET default_with_oids = false;

--

-- Name: tnrs_match; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace: 

--

CREATE TABLE tnrs_match (

    batch text DEFAULT now() NOT NULL,

    match_num integer NOT NULL,

    "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,

    is_valid_match boolean NOT NULL,

    scrubbed_unique_taxon_name text

);

ALTER TABLE "TNRS".tnrs_match OWNER TO bien;

--

-- Name: TABLE tnrs_match; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON TABLE tnrs_match IS '

to remove columns or add columns at the end:

$ rm=1 inputs/.TNRS/data.sql.run

$ make schemas/remake

to add columns in the middle:

make the changes in inputs/.TNRS/schema.sql

$ inputs/.TNRS/data.sql.run refresh # re-run TNRS

$ make schemas/remake

to populate a new column:

ALTER TABLE "TNRS".tnrs_match DISABLE TRIGGER tnrs_populate_fields; --speeds up update

UPDATE "TNRS".tnrs_match SET "col" = value;

	-- runtime: 30 min ("5564201 rows affected, 1624829 ms execution time")

ALTER TABLE "TNRS".tnrs_match ENABLE TRIGGER tnrs_populate_fields;

VACUUM ANALYZE "TNRS".tnrs_match --remove previous rows; runtime: 1.5 min ("92633 ms")

to add a constraint: runtime: 3 min ("173620 ms")

';

--

-- Name: MatchedTaxon; Type: VIEW; Schema: TNRS; Owner: bien

--

CREATE VIEW "MatchedTaxon" AS

 SELECT s."*Name_matched.batch",

    s."concatenatedScientificName",

    s."matchedTaxonName",

    s."matchedTaxonRank",

    s."*Name_matched.Name_score",

    s."matchedScientificNameAuthorship",

    s."matchedScientificNameID",

    s."*Name_matched.Author_score",

    s."matchedFamilyConfidence_fraction",

    s."matchedFamily",

    s."matchedGenus",

    s."matchedGenusConfidence_fraction",

    s."matchedSpecificEpithet",

    s."matchedSpeciesConfidence_fraction",

    s."matchedInfraspecificEpithet",

    s."*Name_matched.Infraspecific_epithet_score",

    s."identificationQualifier",

    s."morphospeciesSuffix",

    s."taxonomicStatus",

    s.accepted_taxon_name_no_author,

    s.accepted_author,

    s.accepted_taxon_rank,

    s."acceptedScientificNameID",

    s.accepted_species_binomial,

    s.accepted_family,

    s."*Name_matched.Selected",

    s."*Name_matched.Source",

    s."*Name_matched.Warnings",

    s."*Name_matched.Accepted_name_lsid",

    s.taxon_scrub__is_valid_match,

    s.scrubbed_unique_taxon_name,

        CASE

            WHEN (s.accepted_taxon_rank = 'family'::text) THEN concat_ws(' '::text, s.accepted_family, s."morphospeciesSuffix")

            WHEN (s.accepted_taxon_rank = 'genus'::text) THEN concat_ws(' '::text, s.accepted_taxon_name_no_author, s."morphospeciesSuffix")

            ELSE s.accepted_species_binomial

        END AS accepted_morphospecies_binomial

   FROM ( SELECT tnrs_match.batch AS "*Name_matched.batch",

            tnrs_match."Name_submitted" AS "concatenatedScientificName",

            tnrs_match."Name_matched" AS "matchedTaxonName",

            tnrs_match."Name_matched_rank" AS "matchedTaxonRank",

            tnrs_match."Name_score" AS "*Name_matched.Name_score",

            tnrs_match."Name_matched_author" AS "matchedScientificNameAuthorship",

            tnrs_match."Name_matched_url" AS "matchedScientificNameID",

            tnrs_match."Author_score" AS "*Name_matched.Author_score",

            tnrs_match."Family_score" AS "matchedFamilyConfidence_fraction",

            COALESCE(tnrs_match."Name_matched_accepted_family", tnrs_match."Accepted_name_family") AS "matchedFamily",

            tnrs_match."Genus_matched" AS "matchedGenus",

            tnrs_match."Genus_score" AS "matchedGenusConfidence_fraction",

            tnrs_match."Specific_epithet_matched" AS "matchedSpecificEpithet",

            tnrs_match."Specific_epithet_score" AS "matchedSpeciesConfidence_fraction",

            tnrs_match."Infraspecific_epithet_matched" AS "matchedInfraspecificEpithet",

            tnrs_match."Infraspecific_epithet_score" AS "*Name_matched.Infraspecific_epithet_score",

            tnrs_match."Annotations" AS "identificationQualifier",

            tnrs_match."Unmatched_terms" AS "morphospeciesSuffix",

            map_taxonomic_status(tnrs_match."Taxonomic_status", tnrs_match."Accepted_name") AS "taxonomicStatus",

            tnrs_match."Accepted_name" AS accepted_taxon_name_no_author,

            tnrs_match."Accepted_name_author" AS accepted_author,

            tnrs_match."Accepted_name_rank" AS accepted_taxon_rank,

            tnrs_match."Accepted_name_url" AS "acceptedScientificNameID",

            tnrs_match."Accepted_name_species" AS accepted_species_binomial,

            tnrs_match."Accepted_name_family" AS accepted_family,

            tnrs_match."Selected" AS "*Name_matched.Selected",

            tnrs_match."Source" AS "*Name_matched.Source",

            tnrs_match."Warnings" AS "*Name_matched.Warnings",

            tnrs_match."Accepted_name_lsid" AS "*Name_matched.Accepted_name_lsid",

            tnrs_match.is_valid_match AS taxon_scrub__is_valid_match,

            tnrs_match.scrubbed_unique_taxon_name

           FROM tnrs_match) s;

ALTER TABLE "TNRS"."MatchedTaxon" OWNER TO bien;

--

-- Name: VIEW "MatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON VIEW "MatchedTaxon" IS '

to modify:

SELECT util.recreate_view(''"TNRS"."MatchedTaxon"'', $$

SELECT __

$$);

';

--

-- Name: Source; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace: 

--

CREATE TABLE "Source" (

    "*row_num" integer NOT NULL,

    "sourceType" text DEFAULT 'aggregator'::text NOT NULL,

    "datasetURL" text DEFAULT 'http://tnrs.iplantcollaborative.org/TNRSapp.html'::text NOT NULL,

    CONSTRAINT nulls_mapped CHECK (true)

);

ALTER TABLE "TNRS"."Source" OWNER TO bien;

--

-- Name: COLUMN "Source"."sourceType"; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON COLUMN "Source"."sourceType" IS '

constant

';

--

-- Name: COLUMN "Source"."datasetURL"; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON COLUMN "Source"."datasetURL" IS '

constant

';

--

-- Name: ValidMatchedTaxon; Type: VIEW; Schema: TNRS; Owner: bien

--

CREATE VIEW "ValidMatchedTaxon" AS

 SELECT "MatchedTaxon"."*Name_matched.batch",

    "MatchedTaxon"."concatenatedScientificName",

    "MatchedTaxon"."matchedTaxonName",

    "MatchedTaxon"."matchedTaxonRank",

    "MatchedTaxon"."*Name_matched.Name_score",

    "MatchedTaxon"."matchedScientificNameAuthorship",

    "MatchedTaxon"."matchedScientificNameID",

    "MatchedTaxon"."*Name_matched.Author_score",

    "MatchedTaxon"."matchedFamilyConfidence_fraction",

    "MatchedTaxon"."matchedFamily",

    "MatchedTaxon"."matchedGenus",

    "MatchedTaxon"."matchedGenusConfidence_fraction",

    "MatchedTaxon"."matchedSpecificEpithet",

    "MatchedTaxon"."matchedSpeciesConfidence_fraction",

    "MatchedTaxon"."matchedInfraspecificEpithet",

    "MatchedTaxon"."*Name_matched.Infraspecific_epithet_score",

    "MatchedTaxon"."identificationQualifier",

    "MatchedTaxon"."morphospeciesSuffix",

    "MatchedTaxon"."taxonomicStatus",

    "MatchedTaxon".accepted_taxon_name_no_author,

    "MatchedTaxon".accepted_author,

    "MatchedTaxon".accepted_taxon_rank,

    "MatchedTaxon"."acceptedScientificNameID",

    "MatchedTaxon".accepted_species_binomial,

    "MatchedTaxon".accepted_family,

    "MatchedTaxon"."*Name_matched.Selected",

    "MatchedTaxon"."*Name_matched.Source",

    "MatchedTaxon"."*Name_matched.Warnings",

    "MatchedTaxon"."*Name_matched.Accepted_name_lsid",

    "MatchedTaxon".taxon_scrub__is_valid_match,

    "MatchedTaxon".scrubbed_unique_taxon_name,

    "MatchedTaxon".accepted_morphospecies_binomial

   FROM "MatchedTaxon"

  WHERE "MatchedTaxon".taxon_scrub__is_valid_match;

ALTER TABLE "TNRS"."ValidMatchedTaxon" OWNER TO bien;

--

-- Name: VIEW "ValidMatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON VIEW "ValidMatchedTaxon" IS '

to update, use * as the column list

';

--

-- Name: batch; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace: 

--

CREATE TABLE batch (

    id text NOT NULL,

    id_by_time text,

    time_submitted timestamp with time zone DEFAULT now(),

    client_version text

);

ALTER TABLE "TNRS".batch OWNER TO bien;

--

-- Name: batch_download_settings; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace: 

--

CREATE TABLE batch_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

);

ALTER TABLE "TNRS".batch_download_settings OWNER TO bien;

--

-- Name: TABLE batch_download_settings; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON TABLE batch_download_settings IS '

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

';

--

-- Name: client_version; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace: 

--

CREATE TABLE client_version (

    id text NOT NULL,

    global_rev integer NOT NULL,

    "/lib/tnrs.py rev" integer,

    "/bin/tnrs_db rev" integer

);

ALTER TABLE "TNRS".client_version OWNER TO bien;

--

-- Name: TABLE client_version; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON TABLE client_version IS '

contains svn revisions

';

--

-- Name: COLUMN client_version.global_rev; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON COLUMN client_version.global_rev IS '

from `svn info .` > Last Changed Rev

';

--

-- Name: COLUMN client_version."/lib/tnrs.py rev"; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON COLUMN client_version."/lib/tnrs.py rev" IS '

from `svn info lib/tnrs.py` > Last Changed Rev

';

--

-- Name: COLUMN client_version."/bin/tnrs_db rev"; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON COLUMN client_version."/bin/tnrs_db rev" IS '

from `svn info bin/tnrs_db` > Last Changed Rev

';

--

-- Name: taxon_scrub.scrubbed_unique_taxon_name.*; Type: VIEW; Schema: TNRS; Owner: bien

--

CREATE VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" AS

 SELECT tnrs_match."Name_submitted" AS scrubbed_unique_taxon_name,

    tnrs_match."Name_matched_rank" AS scrubbed_taxon_rank,

    COALESCE(tnrs_match."Name_matched_accepted_family", tnrs_match."Family_matched") AS scrubbed_family,

    tnrs_match."Genus_matched" AS scrubbed_genus,

    tnrs_match."Specific_epithet_matched" AS scrubbed_specific_epithet,

    tnrs_match."Infraspecific_rank" AS scrubbed_infraspecific_rank,

    tnrs_match."Infraspecific_epithet_matched" AS scrubbed_infraspecific_epithet,

    tnrs_match."Name_matched_author" AS scrubbed_author,

    tnrs_match."Name_matched" AS scrubbed_taxon_name_no_author,

    (tnrs_match."Name_matched" || COALESCE((' '::text || tnrs_match."Name_matched_author"), ''::text)) AS scrubbed_taxon_name_with_author

   FROM tnrs_match;

ALTER TABLE "TNRS"."taxon_scrub.scrubbed_unique_taxon_name.*" OWNER TO bien;

--

-- Name: VIEW "taxon_scrub.scrubbed_unique_taxon_name.*"; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON VIEW "taxon_scrub.scrubbed_unique_taxon_name.*" IS '

to modify:

SELECT util.recreate_view(''"TNRS"."taxon_scrub.scrubbed_unique_taxon_name.*"'', $$

SELECT __

$$);

scrubbed_family: Name_matched_accepted_family was missing from the TNRS results at one point, so Family_matched is used as a workaround to populate this. the workaround is for *accepted names only*, as no opinion names do not have an Accepted_name_family to prepend to the scrubbed name to parse.

';

--

-- Name: taxon_scrub; Type: VIEW; Schema: TNRS; Owner: bien

--

CREATE VIEW taxon_scrub AS

 SELECT "ValidMatchedTaxon".scrubbed_unique_taxon_name,

    "ValidMatchedTaxon"."*Name_matched.batch",

    "ValidMatchedTaxon"."concatenatedScientificName",

    "ValidMatchedTaxon"."matchedTaxonName",

    "ValidMatchedTaxon"."matchedTaxonRank",

    "ValidMatchedTaxon"."*Name_matched.Name_score",

    "ValidMatchedTaxon"."matchedScientificNameAuthorship",

    "ValidMatchedTaxon"."matchedScientificNameID",

    "ValidMatchedTaxon"."*Name_matched.Author_score",

    "ValidMatchedTaxon"."matchedFamilyConfidence_fraction",

    "ValidMatchedTaxon"."matchedFamily",

    "ValidMatchedTaxon"."matchedGenus",

    "ValidMatchedTaxon"."matchedGenusConfidence_fraction",

    "ValidMatchedTaxon"."matchedSpecificEpithet",

    "ValidMatchedTaxon"."matchedSpeciesConfidence_fraction",

    "ValidMatchedTaxon"."matchedInfraspecificEpithet",

    "ValidMatchedTaxon"."*Name_matched.Infraspecific_epithet_score",

    "ValidMatchedTaxon"."identificationQualifier",

    "ValidMatchedTaxon"."morphospeciesSuffix",

    "ValidMatchedTaxon"."taxonomicStatus",

    "ValidMatchedTaxon".accepted_taxon_name_no_author,

    "ValidMatchedTaxon".accepted_author,

    "ValidMatchedTaxon".accepted_taxon_rank,

    "ValidMatchedTaxon"."acceptedScientificNameID",

    "ValidMatchedTaxon".accepted_species_binomial,

    "ValidMatchedTaxon".accepted_family,

    "ValidMatchedTaxon"."*Name_matched.Selected",

    "ValidMatchedTaxon"."*Name_matched.Source",

    "ValidMatchedTaxon"."*Name_matched.Warnings",

    "ValidMatchedTaxon"."*Name_matched.Accepted_name_lsid",

    "ValidMatchedTaxon".taxon_scrub__is_valid_match,

    "ValidMatchedTaxon".accepted_morphospecies_binomial,

    "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_rank,

    "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_family,

    "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus,

    "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet,

    "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_rank,

    "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_infraspecific_epithet,

    "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_author,

    "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_no_author,

    "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_with_author,

        CASE

            WHEN ("taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_rank = 'family'::text) THEN concat_ws(' '::text, "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_family, "ValidMatchedTaxon"."morphospeciesSuffix")

            WHEN ("taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_rank = 'genus'::text) THEN concat_ws(' '::text, "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_taxon_name_no_author, "ValidMatchedTaxon"."morphospeciesSuffix")

            ELSE (("taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_genus || ' '::text) || "taxon_scrub.scrubbed_unique_taxon_name.*".scrubbed_specific_epithet)

        END AS scrubbed_morphospecies_binomial

   FROM ("ValidMatchedTaxon"

   LEFT JOIN "taxon_scrub.scrubbed_unique_taxon_name.*" USING (scrubbed_unique_taxon_name));

ALTER TABLE "TNRS".taxon_scrub OWNER TO bien;

--

-- Name: VIEW taxon_scrub; Type: COMMENT; Schema: TNRS; Owner: bien

--

COMMENT ON VIEW taxon_scrub IS '

to modify:

SELECT util.recreate_view(''"TNRS".taxon_scrub'', $$

SELECT __

$$);

';

--

-- Name: ~Source.map; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace: 

--

CREATE TABLE "~Source.map" (

    "from" text NOT NULL,

    "to" text,

    filter text,

    notes text

);

ALTER TABLE "TNRS"."~Source.map" OWNER TO bien;

--

-- Data for Name: Source; Type: TABLE DATA; Schema: TNRS; Owner: bien

--

COPY "Source" ("*row_num", "sourceType", "datasetURL") FROM stdin;

1	aggregator	http://tnrs.iplantcollaborative.org/TNRSapp.html

\.

--

-- Data for Name: batch; Type: TABLE DATA; Schema: TNRS; Owner: bien

--

COPY batch (id, id_by_time, time_submitted, client_version) FROM stdin;

2014-06-25 16:26:37.716529-07	2014-06-25 16:26:37.716529-07	2014-06-25 16:26:37.716529-07	\N

\.

--

-- Data for Name: batch_download_settings; Type: TABLE DATA; Schema: TNRS; Owner: bien

--

COPY batch_download_settings (id, "E-mail", "Id", "Job type", "Contains Id", "Start time", "Finish time", "TNRS version", "Sources selected", "Match threshold", "Classification", "Allow partial matches?", "Sort by source", "Constrain by higher taxonomy") FROM stdin;

\.

--

-- Data for Name: client_version; Type: TABLE DATA; Schema: TNRS; Owner: bien

--

COPY client_version (id, global_rev, "/lib/tnrs.py rev", "/bin/tnrs_db rev") FROM stdin;

\.

--

-- Data for Name: tnrs_match; Type: TABLE DATA; Schema: TNRS; Owner: bien

--

COPY tnrs_match (batch, match_num, "Name_number", "Name_submitted", "Overall_score", "Name_matched", "Name_matched_rank", "Name_score", "Name_matched_author", "Name_matched_url", "Author_matched", "Author_score", "Family_matched", "Family_score", "Name_matched_accepted_family", "Genus_matched", "Genus_score", "Specific_epithet_matched", "Specific_epithet_score", "Infraspecific_rank", "Infraspecific_epithet_matched", "Infraspecific_epithet_score", "Infraspecific_rank_2", "Infraspecific_epithet_2_matched", "Infraspecific_epithet_2_score", "Annotations", "Unmatched_terms", "Taxonomic_status", "Accepted_name", "Accepted_name_author", "Accepted_name_rank", "Accepted_name_url", "Accepted_name_species", "Accepted_name_family", "Selected", "Source", "Warnings", "Accepted_name_lsid", is_valid_match, scrubbed_unique_taxon_name) FROM stdin;

2014-06-25 16:26:37.716529-07	0	0	Compositae indet. sp.1	0.900000000000000022	Compositae	family	1	\N	http://www.theplantlist.org/1.1/browse/A/Compositae/	\N	\N	Compositae	1	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	indet. sp.1	Accepted	Compositae	\N	family	http://www.theplantlist.org/1.1/browse/A/Compositae/	\N	\N	true	tpl	 [Ambiguous match] 	\N	t	Compositae

2014-06-25 16:26:37.716529-07	1	0	Compositae indet. sp.1	0.900000000000000022	Compositae	family	1	\N	\N	\N	\N	Compositae	1	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	indet. sp.1	Accepted	Compositae	\N	family	\N	\N	\N	false	tpl	 [Ambiguous match] 	\N	t	Compositae

2014-06-25 16:26:37.716529-07	2	0	Compositae indet. sp.1	0.900000000000000022	Compositae	family	1	Giseke	http://www.tropicos.org/Name/50255940	\N	\N	Compositae	1	Compositae	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	indet. sp.1	Synonym	Asteraceae	Bercht. & J. Presl	family	http://www.tropicos.org/Name/50307371	\N	Asteraceae	false	tropicos	 	\N	t	Asteraceae Bercht. & J. Presl

2014-06-25 16:26:37.716529-07	3	1	Fabaceae Boyle#6500	0.839999999999999969	Fagaceae	family	0.939999999999999947	\N	;http://plants.usda.gov/java/nameSearch	\N	\N	Fagaceae	0.880000000000000004	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	Boyle#6500	Accepted	Fagaceae	\N	family	;http://plants.usda.gov/java/nameSearch	\N	\N	true	tpl;usda	 	\N	f	Fagaceae

2014-06-25 16:26:37.716529-07	4	1	Fabaceae Boyle#6500	0.900000000000000022	Fabaceae	family	1	Lindl.	http://www.tropicos.org/Name/42000184	\N	\N	Fabaceae	1	Fabaceae	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	Boyle#6500	Accepted	Fabaceae	Lindl.	family	http://www.tropicos.org/Name/42000184	\N	Fabaceae	true	tropicos	 	\N	t	Fabaceae Lindl.

2014-06-25 16:26:37.716529-07	5	1	Fabaceae Boyle#6500	0.839999999999999969	Fagaceae	family	0.939999999999999947	Dumort.	http://www.tropicos.org/Name/42000062	\N	\N	Fagaceae	0.880000000000000004	Fagaceae	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	Boyle#6500	Accepted	Fagaceae	Dumort.	family	http://www.tropicos.org/Name/42000062	\N	Fagaceae	false	tropicos	 	\N	f	Fagaceae Dumort.

2014-06-25 16:26:37.716529-07	6	1	Fabaceae Boyle#6500	0.67000000000000004	Ficaceae	family	0.770000000000000018	Bercht. & J. Presl	http://www.tropicos.org/Name/100353631	\N	\N	Ficaceae	0.75	Ficaceae	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	Boyle#6500	No opinion	\N	\N	\N	\N	\N	\N	false	tropicos	 	\N	f	Ficaceae Bercht. & J. Presl

2014-06-25 16:26:37.716529-07	7	1	Fabaceae Boyle#6500	0.67000000000000004	Fucaceae	family	0.770000000000000018	\N	http://www.tropicos.org/Name/100371040	\N	\N	Fucaceae	0.75	Fucaceae	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	Boyle#6500	No opinion	\N	\N	\N	\N	\N	\N	false	tropicos	 	\N	f	Fucaceae

2014-06-25 16:26:37.716529-07	8	1	Fabaceae Boyle#6500	0.900000000000000022	Fabaceae	family	1	\N	http://plants.usda.gov/java/nameSearch	\N	\N	Fabaceae	1	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	\N	Boyle#6500	Accepted	Fabaceae	\N	family	http://plants.usda.gov/java/nameSearch	\N	\N	false	usda	 	\N	t	Fabaceae

2014-06-25 16:26:37.716529-07	9	2	Fabaceae Inga "fuzzy leaf"	0.900000000000000022	Inga	genus	1	\N	http://www.theplantlist.org/1.1/browse/A/Leguminosae/Inga/;http://plants.usda.gov/java/profile?symbol=INGA	\N	\N	Fabaceae	1	Fabaceae	Inga	1	\N	\N	\N	\N	\N	\N	\N	\N	\N	"fuzzy leaf"	Accepted	Inga	\N	genus	http://www.theplantlist.org/1.1/browse/A/Leguminosae/Inga/;http://plants.usda.gov/java/profile?symbol=INGA	\N	Fabaceae	true	tpl;usda	 	\N	t	Fabaceae Inga

2014-06-25 16:26:37.716529-07	10	2	Fabaceae Inga "fuzzy leaf"	0.900000000000000022	Inga	genus	1	Mill.	http://www.tropicos.org/Name/40031040	\N	\N	Fabaceae	1	Fabaceae	Inga	1	\N	\N	\N	\N	\N	\N	\N	\N	\N	"fuzzy leaf"	Accepted	Inga	Mill.	genus	http://www.tropicos.org/Name/40031040	\N	Fabaceae	false	tropicos	 	\N	t	Fabaceae Inga Mill.

2014-06-25 16:26:37.716529-07	11	2	Fabaceae Inga "fuzzy leaf"	0.900000000000000022	Inga	genus	1	Scop.	http://www.tropicos.org/Name/50215121	\N	\N	Fabaceae	1	Fabaceae	Inga	1	\N	\N	\N	\N	\N	\N	\N	\N	\N	"fuzzy leaf"	Illegitimate	\N	\N	\N	\N	\N	\N	false	tropicos	 	\N	t	Fabaceae Inga Scop.

2014-06-25 16:26:37.716529-07	12	3	Fabaceae Inga sp.3	0.900000000000000022	Inga	genus	1	\N	http://www.theplantlist.org/1.1/browse/A/Leguminosae/Inga/;http://plants.usda.gov/java/profile?symbol=INGA	\N	\N	Fabaceae	1	Fabaceae	Inga	1	\N	\N	\N	\N	\N	\N	\N	\N	\N	sp.3	Accepted	Inga	\N	genus	http://www.theplantlist.org/1.1/browse/A/Leguminosae/Inga/;http://plants.usda.gov/java/profile?symbol=INGA	\N	Fabaceae	true	tpl;usda	 	\N	t	Fabaceae Inga

2014-06-25 16:26:37.716529-07	13	3	Fabaceae Inga sp.3	0.900000000000000022	Inga	genus	1	Mill.	http://www.tropicos.org/Name/40031040	\N	\N	Fabaceae	1	Fabaceae	Inga	1	\N	\N	\N	\N	\N	\N	\N	\N	\N	sp.3	Accepted	Inga	Mill.	genus	http://www.tropicos.org/Name/40031040	\N	Fabaceae	false	tropicos	 	\N	t	Fabaceae Inga Mill.