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--
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-- PostgreSQL database dump
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--
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SET statement_timeout = 0;
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SET client_encoding = 'UTF8';
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SET standard_conforming_strings = on;
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SET check_function_bodies = false;
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SET client_min_messages = warning;
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--
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-- Name: TNRS; Type: SCHEMA; Schema: -; Owner: bien
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--
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CREATE SCHEMA "TNRS";
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ALTER SCHEMA "TNRS" OWNER TO bien;
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SET search_path = "TNRS", pg_catalog;
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--
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-- Name: batch__fill(); Type: FUNCTION; Schema: TNRS; Owner: bien
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--
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CREATE FUNCTION batch__fill() RETURNS trigger
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LANGUAGE plpgsql
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AS $$
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BEGIN
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new.id_by_time = new.time_submitted;
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new.id = COALESCE(new.id, new.id_by_time);
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RETURN new;
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END;
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$$;
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ALTER FUNCTION "TNRS".batch__fill() OWNER TO bien;
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--
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-- Name: family_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: bien
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--
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CREATE FUNCTION family_is_homonym(family text) RETURNS boolean
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LANGUAGE sql STABLE STRICT
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AS $_$
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SELECT EXISTS(SELECT * FROM "IRMNG".family_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
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$_$;
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ALTER FUNCTION "TNRS".family_is_homonym(family text) OWNER TO bien;
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--
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-- Name: genus_is_homonym(text); Type: FUNCTION; Schema: TNRS; Owner: bien
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--
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CREATE FUNCTION genus_is_homonym(genus text) RETURNS boolean
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LANGUAGE sql STABLE STRICT
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AS $_$
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SELECT EXISTS(SELECT * FROM "IRMNG".genus_homonym_epithet WHERE "taxonNameOrEpithet" = $1)
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$_$;
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ALTER FUNCTION "TNRS".genus_is_homonym(genus text) OWNER TO bien;
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--
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-- Name: score_ok(double precision); Type: FUNCTION; Schema: TNRS; Owner: bien
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--
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CREATE FUNCTION score_ok(score double precision) RETURNS boolean
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LANGUAGE sql IMMUTABLE STRICT
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AS $_$
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SELECT $1 >= 0.8
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$_$;
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ALTER FUNCTION "TNRS".score_ok(score double precision) OWNER TO bien;
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--
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-- Name: tnrs_populate_fields(); Type: FUNCTION; Schema: TNRS; Owner: bien
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--
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CREATE FUNCTION tnrs_populate_fields() RETURNS trigger
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LANGUAGE plpgsql
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AS $$
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DECLARE
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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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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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new."Is_plant" = (CASE
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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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END)
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END);
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RETURN new;
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END;
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$$;
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ALTER FUNCTION "TNRS".tnrs_populate_fields() OWNER TO bien;
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--
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-- Name: FUNCTION tnrs_populate_fields(); Type: COMMENT; Schema: TNRS; Owner: bien
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--
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COMMENT ON FUNCTION tnrs_populate_fields() IS '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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SET default_tablespace = '';
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SET default_with_oids = false;
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--
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-- Name: tnrs; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace:
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--
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CREATE TABLE tnrs (
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batch text DEFAULT now() NOT NULL,
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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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);
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ALTER TABLE "TNRS".tnrs OWNER TO bien;
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--
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-- Name: TABLE tnrs; Type: COMMENT; Schema: TNRS; Owner: bien
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--
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COMMENT ON TABLE tnrs IS '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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-- Name: AcceptedTaxon; Type: VIEW; Schema: TNRS; Owner: bien
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--
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CREATE VIEW "AcceptedTaxon" AS
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SELECT tnrs.batch AS "*Accepted_name.batch", tnrs."Name_submitted" AS "acceptedScientificName", tnrs."Genus_matched" AS "acceptedGenus", tnrs."Specific_epithet_matched" AS "acceptedSpecificEpithet", tnrs."Infraspecific_epithet_matched" AS "acceptedInfraspecificEpithet", tnrs."Taxonomic_status" AS "acceptedTaxonomicStatus", tnrs."Selected" AS "*Accepted_name.Selected", tnrs."Source" AS "*Accepted_name.Source", tnrs."Warnings" AS "*Accepted_name.Warnings", tnrs."Accepted_name_lsid" AS "*Accepted_name.Accepted_name_lsid" FROM tnrs;
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ALTER TABLE "TNRS"."AcceptedTaxon" OWNER TO bien;
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--
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-- Name: MatchedTaxon; Type: VIEW; Schema: TNRS; Owner: bien
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--
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CREATE VIEW "MatchedTaxon" AS
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SELECT tnrs.batch AS "*Name_matched.batch", tnrs."Name_submitted" AS "concatenatedScientificName", tnrs."Name_matched" AS "matchedTaxonName", tnrs."Name_matched_rank" AS "matchedTaxonRank", tnrs."Name_score" AS "*Name_matched.Name_score", tnrs."Name_matched_author" AS "matchedScientificNameAuthorship", tnrs."Name_matched_url" AS "matchedScientificNameID", tnrs."Author_score" AS "*Name_matched.Author_score", tnrs."Family_score" AS "matchedFamilyConfidence_fraction", COALESCE(tnrs."Name_matched_accepted_family", tnrs."Accepted_name_family") AS "matchedFamily", tnrs."Genus_matched" AS "matchedGenus", tnrs."Genus_score" AS "matchedGenusConfidence_fraction", tnrs."Specific_epithet_matched" AS "matchedSpecificEpithet", tnrs."Specific_epithet_score" AS "matchedSpeciesConfidence_fraction", tnrs."Infraspecific_epithet_matched" AS "matchedInfraspecificEpithet", tnrs."Infraspecific_epithet_score" AS "*Name_matched.Infraspecific_epithet_score", tnrs."Annotations" AS "identificationQualifier", tnrs."Unmatched_terms" AS "morphospeciesSuffix", tnrs."Taxonomic_status" AS "taxonomicStatus", tnrs."Accepted_name" AS "acceptedTaxonName", tnrs."Accepted_name_author" AS "acceptedScientificNameAuthorship", tnrs."Accepted_name_rank" AS "acceptedTaxonRank", tnrs."Accepted_name_url" AS "acceptedScientificNameID", tnrs."Accepted_name_species" AS "*Name_matched.Accepted_name_species", tnrs."Accepted_name_family" AS "acceptedFamily", tnrs."Selected" AS "*Name_matched.Selected", tnrs."Source" AS "*Name_matched.Source", tnrs."Warnings" AS "*Name_matched.Warnings", tnrs."Accepted_name_lsid" AS "*Name_matched.Accepted_name_lsid", tnrs."Accepted_scientific_name" AS "acceptedScientificName", tnrs."Max_score" AS "matchedTaxonConfidence_fraction" FROM tnrs;
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ALTER TABLE "TNRS"."MatchedTaxon" OWNER TO bien;
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--
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-- Name: ValidMatchedTaxon; Type: VIEW; Schema: TNRS; Owner: bien
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--
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CREATE VIEW "ValidMatchedTaxon" AS
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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"."acceptedTaxonName", "MatchedTaxon"."acceptedScientificNameAuthorship", "MatchedTaxon"."acceptedTaxonRank", "MatchedTaxon"."acceptedScientificNameID", "MatchedTaxon"."*Name_matched.Accepted_name_species", "MatchedTaxon"."acceptedFamily", "MatchedTaxon"."*Name_matched.Selected", "MatchedTaxon"."*Name_matched.Source", "MatchedTaxon"."*Name_matched.Warnings", "MatchedTaxon"."*Name_matched.Accepted_name_lsid", "MatchedTaxon"."acceptedScientificName", "MatchedTaxon"."matchedTaxonConfidence_fraction" FROM "MatchedTaxon" WHERE score_ok("MatchedTaxon"."matchedTaxonConfidence_fraction");
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ALTER TABLE "TNRS"."ValidMatchedTaxon" OWNER TO bien;
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--
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-- Name: VIEW "ValidMatchedTaxon"; Type: COMMENT; Schema: TNRS; Owner: bien
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--
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COMMENT ON VIEW "ValidMatchedTaxon" IS 'to update, use * as the column list';
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--
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-- Name: ScrubbedTaxon; Type: VIEW; Schema: TNRS; Owner: bien
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| 253 |
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--
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| 254 |
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CREATE VIEW "ScrubbedTaxon" AS
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aaronmk
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SELECT "ValidMatchedTaxon"."acceptedScientificName", "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"."acceptedTaxonName", "ValidMatchedTaxon"."acceptedScientificNameAuthorship", "ValidMatchedTaxon"."acceptedTaxonRank", "ValidMatchedTaxon"."acceptedScientificNameID", "ValidMatchedTaxon"."*Name_matched.Accepted_name_species", "ValidMatchedTaxon"."acceptedFamily", "ValidMatchedTaxon"."*Name_matched.Selected", "ValidMatchedTaxon"."*Name_matched.Source", "ValidMatchedTaxon"."*Name_matched.Warnings", "ValidMatchedTaxon"."*Name_matched.Accepted_name_lsid", "ValidMatchedTaxon"."matchedTaxonConfidence_fraction", "AcceptedTaxon"."*Accepted_name.batch", "AcceptedTaxon"."acceptedGenus", "AcceptedTaxon"."acceptedSpecificEpithet", "AcceptedTaxon"."acceptedInfraspecificEpithet", "AcceptedTaxon"."acceptedTaxonomicStatus", "AcceptedTaxon"."*Accepted_name.Selected", "AcceptedTaxon"."*Accepted_name.Source", "AcceptedTaxon"."*Accepted_name.Warnings", "AcceptedTaxon"."*Accepted_name.Accepted_name_lsid" FROM ("ValidMatchedTaxon" NATURAL LEFT JOIN "AcceptedTaxon");
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ALTER TABLE "TNRS"."ScrubbedTaxon" OWNER TO bien;
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--
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-- Name: VIEW "ScrubbedTaxon"; Type: COMMENT; Schema: TNRS; Owner: bien
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--
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COMMENT ON VIEW "ScrubbedTaxon" IS 'to update, use * as the column list';
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| 268 |
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--
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10395
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-- Name: Source; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace:
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| 270 |
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--
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| 271 |
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| 272 |
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CREATE TABLE "Source" (
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"*row_num" integer NOT NULL,
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"sourceType" text DEFAULT 'aggregator'::text NOT NULL,
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| 275 |
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"datasetURL" text DEFAULT 'http://tnrs.iplantcollaborative.org/TNRSapp.html'::text NOT NULL
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| 276 |
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);
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ALTER TABLE "TNRS"."Source" OWNER TO bien;
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--
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| 282 |
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-- Name: COLUMN "Source"."sourceType"; Type: COMMENT; Schema: TNRS; Owner: bien
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| 283 |
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--
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| 284 |
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COMMENT ON COLUMN "Source"."sourceType" IS 'constant';
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| 287 |
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| 288 |
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--
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-- Name: COLUMN "Source"."datasetURL"; Type: COMMENT; Schema: TNRS; Owner: bien
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| 290 |
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--
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COMMENT ON COLUMN "Source"."datasetURL" IS 'constant';
|
| 293 |
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| 294 |
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| 295 |
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--
|
| 296 |
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-- Name: batch; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace:
|
| 297 |
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--
|
| 298 |
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|
| 299 |
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CREATE TABLE batch (
|
| 300 |
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id text NOT NULL,
|
| 301 |
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id_by_time text,
|
| 302 |
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time_submitted timestamp with time zone DEFAULT now(),
|
| 303 |
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client_version text
|
| 304 |
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);
|
| 305 |
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| 307 |
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ALTER TABLE "TNRS".batch OWNER TO bien;
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--
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-- Name: batch_download_settings; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace:
|
| 311 |
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--
|
| 312 |
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| 313 |
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CREATE TABLE batch_download_settings (
|
| 314 |
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id text NOT NULL,
|
| 315 |
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"E-mail" text,
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| 316 |
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"Id" text,
|
| 317 |
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"Job type" text,
|
| 318 |
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"Contains Id" boolean,
|
| 319 |
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"Start time" text,
|
| 320 |
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"Finish time" text,
|
| 321 |
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"TNRS version" text,
|
| 322 |
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"Sources selected" text,
|
| 323 |
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"Match threshold" double precision,
|
| 324 |
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"Classification" text,
|
| 325 |
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"Allow partial matches?" boolean,
|
| 326 |
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"Sort by source" boolean,
|
| 327 |
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|
"Constrain by higher taxonomy" boolean
|
| 328 |
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|
);
|
| 329 |
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|
| 330 |
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|
| 331 |
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ALTER TABLE "TNRS".batch_download_settings OWNER TO bien;
|
| 332 |
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|
| 333 |
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--
|
| 334 |
|
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-- Name: TABLE batch_download_settings; Type: COMMENT; Schema: TNRS; Owner: bien
|
| 335 |
|
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--
|
| 336 |
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|
| 337 |
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COMMENT ON TABLE batch_download_settings IS 'stores data from http://tnrs.iplantcollaborative.org/TNRSapp.html > Submit List > results section > Download settings > settings.txt';
|
| 338 |
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|
| 339 |
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|
| 340 |
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--
|
| 341 |
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-- Name: client_version; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace:
|
| 342 |
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--
|
| 343 |
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|
| 344 |
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CREATE TABLE client_version (
|
| 345 |
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id text NOT NULL,
|
| 346 |
|
|
global_rev integer NOT NULL,
|
| 347 |
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"/lib/tnrs.py rev" integer,
|
| 348 |
|
|
"/bin/tnrs_db rev" integer
|
| 349 |
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);
|
| 350 |
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|
| 351 |
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| 352 |
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ALTER TABLE "TNRS".client_version OWNER TO bien;
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| 353 |
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|
| 354 |
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--
|
| 355 |
|
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-- Name: TABLE client_version; Type: COMMENT; Schema: TNRS; Owner: bien
|
| 356 |
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--
|
| 357 |
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|
| 358 |
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COMMENT ON TABLE client_version IS 'contains svn revisions';
|
| 359 |
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|
| 360 |
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|
| 361 |
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--
|
| 362 |
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-- Name: COLUMN client_version.global_rev; Type: COMMENT; Schema: TNRS; Owner: bien
|
| 363 |
|
|
--
|
| 364 |
|
|
|
| 365 |
|
|
COMMENT ON COLUMN client_version.global_rev IS 'from `svn info .` > Last Changed Rev';
|
| 366 |
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|
|
| 367 |
|
|
|
| 368 |
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--
|
| 369 |
|
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-- Name: COLUMN client_version."/lib/tnrs.py rev"; Type: COMMENT; Schema: TNRS; Owner: bien
|
| 370 |
|
|
--
|
| 371 |
|
|
|
| 372 |
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COMMENT ON COLUMN client_version."/lib/tnrs.py rev" IS 'from `svn info lib/tnrs.py` > Last Changed Rev';
|
| 373 |
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|
| 374 |
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|
| 375 |
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--
|
| 376 |
|
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-- Name: COLUMN client_version."/bin/tnrs_db rev"; Type: COMMENT; Schema: TNRS; Owner: bien
|
| 377 |
|
|
--
|
| 378 |
|
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|
| 379 |
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COMMENT ON COLUMN client_version."/bin/tnrs_db rev" IS 'from `svn info bin/tnrs_db` > Last Changed Rev';
|
| 380 |
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|
| 381 |
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|
|
| 382 |
|
|
--
|
| 383 |
10395
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|
-- Name: ~Source.map; Type: TABLE; Schema: TNRS; Owner: bien; Tablespace:
|
| 384 |
|
|
--
|
| 385 |
|
|
|
| 386 |
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CREATE TABLE "~Source.map" (
|
| 387 |
|
|
"from" text NOT NULL,
|
| 388 |
|
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"to" text,
|
| 389 |
|
|
filter text,
|
| 390 |
|
|
notes text
|
| 391 |
|
|
);
|
| 392 |
|
|
|
| 393 |
|
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|
| 394 |
|
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ALTER TABLE "TNRS"."~Source.map" OWNER TO bien;
|
| 395 |
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|
|
| 396 |
|
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--
|
| 397 |
|
|
-- Data for Name: Source; Type: TABLE DATA; Schema: TNRS; Owner: bien
|
| 398 |
|
|
--
|
| 399 |
|
|
|
| 400 |
10786
|
aaronmk
|
COPY "Source" ("*row_num", "sourceType", "datasetURL") FROM stdin;
|
| 401 |
10395
|
aaronmk
|
\.
|
| 402 |
|
|
|
| 403 |
|
|
|
| 404 |
|
|
--
|
| 405 |
10786
|
aaronmk
|
-- Data for Name: batch; Type: TABLE DATA; Schema: TNRS; Owner: bien
|
| 406 |
|
|
--
|
| 407 |
|
|
|
| 408 |
|
|
COPY batch (id, id_by_time, time_submitted, client_version) FROM stdin;
|
| 409 |
|
|
2013-08-27 22:02:36.042579-07 2013-08-27 22:02:36.042579-07 2013-08-27 22:02:36.042579-07 \N
|
| 410 |
|
|
2013-08-27 22:02:41.03229-07 2013-08-27 22:02:41.03229-07 2013-08-27 22:02:41.03229-07 \N
|
| 411 |
|
|
2013-08-27 22:02:43.024394-07 2013-08-27 22:02:43.024394-07 2013-08-27 22:02:43.024394-07 \N
|
| 412 |
|
|
\.
|
| 413 |
|
|
|
| 414 |
|
|
|
| 415 |
|
|
--
|
| 416 |
|
|
-- Data for Name: batch_download_settings; Type: TABLE DATA; Schema: TNRS; Owner: bien
|
| 417 |
|
|
--
|
| 418 |
|
|
|
| 419 |
|
|
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;
|
| 420 |
|
|
\.
|
| 421 |
|
|
|
| 422 |
|
|
|
| 423 |
|
|
--
|
| 424 |
|
|
-- Data for Name: client_version; Type: TABLE DATA; Schema: TNRS; Owner: bien
|
| 425 |
|
|
--
|
| 426 |
|
|
|
| 427 |
|
|
COPY client_version (id, global_rev, "/lib/tnrs.py rev", "/bin/tnrs_db rev") FROM stdin;
|
| 428 |
|
|
\.
|
| 429 |
|
|
|
| 430 |
|
|
|
| 431 |
|
|
--
|
| 432 |
9493
|
aaronmk
|
-- Data for Name: tnrs; Type: TABLE DATA; Schema: TNRS; Owner: bien
|
| 433 |
5423
|
aaronmk
|
--
|
| 434 |
|
|
|
| 435 |
10786
|
aaronmk
|
COPY tnrs (batch, "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", "Accepted_scientific_name", "Max_score", "Is_homonym", "Is_plant") FROM stdin;
|
| 436 |
|
|
2013-08-27 22:02:36.042579-07 0 Fam_indet. Boyle#6501 0 No suitable matches found. \N 0 \N \N \N 0 \N 0 \N \N 0 \N 0 \N \N 0 \N \N 0 \N \N \N \N \N \N \N \N \N true \N \N \N 0 \N \N
|
| 437 |
|
|
2013-08-27 22:02:36.042579-07 1 Poa annua var. eriolepis 1 Poa annua var. eriolepis variety 1 E. Desv. http://www.tropicos.org/Name/50119145 \N \N \N \N Poaceae Poa 1 annua 1 var. eriolepis 1 \N \N \N \N \N Synonym Poa annua L. species http://www.tropicos.org/Name/25509881 Poa annua Poaceae true tropicos \N Poaceae Poa annua L. 1 f t
|
| 438 |
|
|
2013-08-27 22:02:36.042579-07 2 Poa annua 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 \N \N \N \N Poaceae Poa 1 annua 1 \N \N \N \N \N \N \N \N Accepted Poa annua L. species http://www.tropicos.org/Name/25509881 Poa annua Poaceae true tropicos \N Poaceae Poa annua L. 1 f t
|
| 439 |
|
|
2013-08-27 22:02:36.042579-07 3 Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire 0.770000000000000018 Silene scouleri subsp. pringlei subspecies 0.770000000000000018 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N Caryophyllaceae Silene 1 scouleri 1 subsp. pringlei 1 \N \N \N \N var. grisea Accepted Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire subspecies http://www.tropicos.org/Name/6303627 Silene scouleri Caryophyllaceae true tropicos [Partial match] \N Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire 1 t t
|
| 440 |
|
|
2013-08-27 22:02:36.042579-07 4 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 Fabaceae Lindl. 1 f t
|
| 441 |
|
|
2013-08-27 22:02:36.042579-07 5 Poa annua subsp. exilis 1 Poa annua subsp. exilis subspecies 1 (Tomm. ex Freyn) Asch. & Graebn. http://www.tropicos.org/Name/50063800 \N \N \N \N Poaceae Poa 1 annua 1 subsp. exilis 1 \N \N \N \N \N Synonym Poa infirma Kunth species http://www.tropicos.org/Name/25514158 Poa infirma Poaceae true tropicos \N Poaceae Poa infirma Kunth 1 f t
|
| 442 |
|
|
2013-08-27 22:02:36.042579-07 6 Poa annua ssp. exilis 1 Poa annua subsp. exilis subspecies 1 (Tomm. ex Freyn) Asch. & Graebn. http://www.tropicos.org/Name/50063800 \N \N \N \N Poaceae Poa 1 annua 1 subsp. exilis 1 \N \N \N \N \N Synonym Poa infirma Kunth species http://www.tropicos.org/Name/25514158 Poa infirma Poaceae true tropicos \N Poaceae Poa infirma Kunth 1 f t
|
| 443 |
|
|
2013-08-27 22:02:36.042579-07 7 Poa annua subvar. minima 1 Poa annua subvar. minima subvariety 1 (Schur) Asch. & Graebn. http://www.tropicos.org/Name/50158097 \N \N \N \N Poaceae Poa 1 annua 1 subvar. minima 1 \N \N \N \N \N Accepted Poa annua subvar. minima (Schur) Asch. & Graebn. subvariety http://www.tropicos.org/Name/50158097 Poa annua Poaceae true tropicos \N Poaceae Poa annua subvar. minima (Schur) Asch. & Graebn. 1 f t
|
| 444 |
|
|
2013-08-27 22:02:36.042579-07 8 Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 \N \N Poaceae Poa 1 annua 1 \N \N \N \N \N \N \N \N Accepted Poa annua L. species http://www.tropicos.org/Name/25509881 Poa annua Poaceae true tropicos \N Poaceae Poa annua L. 1 f t
|
| 445 |
|
|
2013-08-27 22:02:36.042579-07 9 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 true tropicos \N Asteraceae Bercht. & J. Presl 1 f t
|
| 446 |
|
|
2013-08-27 22:02:36.042579-07 10 Poa annua fo. lanuginosa 1 Poa annua fo. lanuginosa forma 1 Sennen http://www.tropicos.org/Name/50267771 \N \N \N \N Poaceae Poa 1 annua 1 fo. lanuginosa 1 \N \N \N \N \N Synonym Poa annua var. annua \N variety http://www.tropicos.org/Name/25517736 Poa annua Poaceae true tropicos \N Poaceae Poa annua var. annua 1 f t
|
| 447 |
|
|
2013-08-27 22:02:36.042579-07 11 Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire 0.770000000000000018 Silene scouleri subsp. pringlei subspecies 0.770000000000000018 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N Caryophyllaceae Silene 1 scouleri 1 subsp. pringlei 1 \N \N \N \N var. grisea Accepted Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire subspecies http://www.tropicos.org/Name/6303627 Silene scouleri Caryophyllaceae true tropicos [Partial match] \N Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire 1 t t
|
| 448 |
|
|
2013-08-27 22:02:36.042579-07 12 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 true tropicos \N Fabaceae Inga Mill. 1 t t
|
| 449 |
|
|
2013-08-27 22:02:36.042579-07 13 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 true tropicos \N Fabaceae Inga Mill. 1 t t
|
| 450 |
|
|
2013-08-27 22:02:36.042579-07 14 Fabaceae unknown #2 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 unknown #2 Accepted Fabaceae Lindl. family http://www.tropicos.org/Name/42000184 \N Fabaceae true tropicos \N Fabaceae Lindl. 1 f t
|
| 451 |
|
|
2013-08-27 22:02:41.03229-07 0 Poaceae Poa infirma Kunth 1 Poa infirma species 1 Kunth http://www.tropicos.org/Name/25514158 Kunth 1 Poaceae 1 Poaceae Poa 1 infirma 1 \N \N \N \N \N \N \N \N Accepted Poa infirma Kunth species http://www.tropicos.org/Name/25514158 Poa infirma Poaceae true tropicos \N Poaceae Poa infirma Kunth 1 f t
|
| 452 |
|
|
2013-08-27 22:02:41.03229-07 1 Fabaceae Lindl. 0.5 Fabaceae family 0.5 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 Fabaceae \N \N \N \N \N \N \N \N \N \N \N Lindl. Accepted Fabaceae Lindl. family http://www.tropicos.org/Name/42000184 \N Fabaceae true tropicos [Partial match] \N Fabaceae Lindl. 1 f t
|
| 453 |
|
|
2013-08-27 22:02:41.03229-07 2 Poaceae Poa annua subvar. minima (Schur) Asch. & Graebn. 1 Poa annua subvar. minima subvariety 1 (Schur) Asch. & Graebn. http://www.tropicos.org/Name/50158097 (Schur) Asch. & Graebn. 1 Poaceae 1 Poaceae Poa 1 annua 1 subvar. minima 1 \N \N \N \N \N Accepted Poa annua subvar. minima (Schur) Asch. & Graebn. subvariety http://www.tropicos.org/Name/50158097 Poa annua Poaceae true tropicos \N Poaceae Poa annua subvar. minima (Schur) Asch. & Graebn. 1 f t
|
| 454 |
|
|
2013-08-27 22:02:41.03229-07 3 Fabaceae Inga Mill. 1 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 Mill. 1 Fabaceae 1 Fabaceae Inga 1 \N \N \N \N \N \N \N \N \N \N Accepted Inga Mill. genus http://www.tropicos.org/Name/40031040 \N Fabaceae true tropicos \N Fabaceae Inga Mill. 1 f t
|
| 455 |
|
|
2013-08-27 22:02:41.03229-07 4 Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire 1 Silene scouleri subsp. pringlei subspecies 1 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 (S. Watson) C.L. Hitchc. & Maguire 1 Caryophyllaceae 1 Caryophyllaceae Silene 1 scouleri 1 subsp. pringlei 1 \N \N \N \N \N Accepted Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire subspecies http://www.tropicos.org/Name/6303627 Silene scouleri Caryophyllaceae true tropicos \N Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire 1 f t
|
| 456 |
|
|
2013-08-27 22:02:41.03229-07 5 Poaceae Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 Poaceae 1 Poaceae Poa 1 annua 1 \N \N \N \N \N \N \N \N Accepted Poa annua L. species http://www.tropicos.org/Name/25509881 Poa annua Poaceae true tropicos \N Poaceae Poa annua L. 1 f t
|
| 457 |
|
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2013-08-27 22:02:41.03229-07 6 Asteraceae Bercht. & J. Presl 0.400000000000000022 Asteraceae family 0.5 \N http://compositae.landcareresearch.co.nz/default.aspx \N \N Asteraceae 1 \N \N \N \N \N \N \N \N \N \N \N \N Bercht. & J. Presl Accepted Asteraceae \N family http://compositae.landcareresearch.co.nz/default.aspx \N \N true gcc [Partial match] \N Asteraceae 1 f t
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| 458 |
|
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2013-08-27 22:02:41.03229-07 7 Poaceae Poa annua var. annua 1 Poa annua var. annua variety 1 \N http://www.tropicos.org/Name/25517736 \N \N Poaceae 1 Poaceae Poa 1 annua 1 var. annua 1 \N \N \N \N \N Accepted Poa annua var. annua \N variety http://www.tropicos.org/Name/25517736 Poa annua Poaceae true tropicos \N Poaceae Poa annua var. annua 1 f t
|
| 459 |
|
|
2013-08-27 22:02:43.024394-07 0 Asteraceae 1 Asteraceae family 1 \N http://compositae.landcareresearch.co.nz/default.aspx \N \N Asteraceae 1 \N \N \N \N \N \N \N \N \N \N \N \N \N Accepted Asteraceae \N family http://compositae.landcareresearch.co.nz/default.aspx \N \N true gcc \N Asteraceae 1 f t
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| 460 |
5917
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aaronmk
|
\.
|
| 461 |
5423
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aaronmk
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|
| 462 |
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|
| 463 |
5917
|
aaronmk
|
--
|
| 464 |
10395
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aaronmk
|
-- Data for Name: ~Source.map; Type: TABLE DATA; Schema: TNRS; Owner: bien
|
| 465 |
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--
|
| 466 |
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|
| 467 |
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COPY "~Source.map" ("from", "to", filter, notes) FROM stdin;
|
| 468 |
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row_num *row_num \N \N
|
| 469 |
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:aggregator sourceType \N \N
|
| 470 |
10786
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aaronmk
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:http://tnrs.iplantcollaborative.org/TNRSapp.html datasetURL \N \N
|
| 471 |
10395
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aaronmk
|
\.
|
| 472 |
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|
| 473 |
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|
| 474 |
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--
|
| 475 |
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-- Name: Source_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: bien; Tablespace:
|
| 476 |
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--
|
| 477 |
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|
|
| 478 |
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ALTER TABLE ONLY "Source"
|
| 479 |
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ADD CONSTRAINT "Source_pkey" PRIMARY KEY ("*row_num");
|
| 480 |
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|
| 481 |
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|
| 482 |
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--
|
| 483 |
10786
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aaronmk
|
-- Name: batch_download_settings_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: bien; Tablespace:
|
| 484 |
|
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--
|
| 485 |
|
|
|
| 486 |
|
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ALTER TABLE ONLY batch_download_settings
|
| 487 |
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ADD CONSTRAINT batch_download_settings_pkey PRIMARY KEY (id);
|
| 488 |
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|
|
| 489 |
|
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|
| 490 |
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--
|
| 491 |
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-- Name: batch_id_by_time_key; Type: CONSTRAINT; Schema: TNRS; Owner: bien; Tablespace:
|
| 492 |
|
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--
|
| 493 |
|
|
|
| 494 |
|
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ALTER TABLE ONLY batch
|
| 495 |
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ADD CONSTRAINT batch_id_by_time_key UNIQUE (id_by_time);
|
| 496 |
|
|
|
| 497 |
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|
| 498 |
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--
|
| 499 |
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-- Name: batch_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: bien; Tablespace:
|
| 500 |
|
|
--
|
| 501 |
|
|
|
| 502 |
|
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ALTER TABLE ONLY batch
|
| 503 |
|
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ADD CONSTRAINT batch_pkey PRIMARY KEY (id);
|
| 504 |
|
|
|
| 505 |
|
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|
| 506 |
|
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--
|
| 507 |
|
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-- Name: client_version_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: bien; Tablespace:
|
| 508 |
|
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--
|
| 509 |
|
|
|
| 510 |
|
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ALTER TABLE ONLY client_version
|
| 511 |
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ADD CONSTRAINT client_version_pkey PRIMARY KEY (id);
|
| 512 |
|
|
|
| 513 |
|
|
|
| 514 |
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--
|
| 515 |
9972
|
aaronmk
|
-- Name: tnrs_Name_submitted_key; Type: CONSTRAINT; Schema: TNRS; Owner: bien; Tablespace:
|
| 516 |
|
|
--
|
| 517 |
|
|
|
| 518 |
|
|
ALTER TABLE ONLY tnrs
|
| 519 |
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|
ADD CONSTRAINT "tnrs_Name_submitted_key" UNIQUE ("Name_submitted");
|
| 520 |
|
|
|
| 521 |
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|
| 522 |
|
|
--
|
| 523 |
9493
|
aaronmk
|
-- Name: tnrs_pkey; Type: CONSTRAINT; Schema: TNRS; Owner: bien; Tablespace:
|
| 524 |
5917
|
aaronmk
|
--
|
| 525 |
5423
|
aaronmk
|
|
| 526 |
9493
|
aaronmk
|
ALTER TABLE ONLY tnrs
|
| 527 |
10786
|
aaronmk
|
ADD CONSTRAINT tnrs_pkey PRIMARY KEY (batch, "Name_number");
|
| 528 |
5917
|
aaronmk
|
|
| 529 |
|
|
|
| 530 |
5423
|
aaronmk
|
--
|
| 531 |
10395
|
aaronmk
|
-- Name: ~Source.map_from_key; Type: CONSTRAINT; Schema: TNRS; Owner: bien; Tablespace:
|
| 532 |
|
|
--
|
| 533 |
|
|
|
| 534 |
|
|
ALTER TABLE ONLY "~Source.map"
|
| 535 |
|
|
ADD CONSTRAINT "~Source.map_from_key" UNIQUE ("from");
|
| 536 |
|
|
|
| 537 |
|
|
|
| 538 |
|
|
--
|
| 539 |
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-- Name: ~Source.map_to_key; Type: CONSTRAINT; Schema: TNRS; Owner: bien; Tablespace:
|
| 540 |
|
|
--
|
| 541 |
|
|
|
| 542 |
|
|
ALTER TABLE ONLY "~Source.map"
|
| 543 |
|
|
ADD CONSTRAINT "~Source.map_to_key" UNIQUE ("to");
|
| 544 |
|
|
|
| 545 |
|
|
|
| 546 |
|
|
--
|
| 547 |
9493
|
aaronmk
|
-- Name: tnrs_score_ok; Type: INDEX; Schema: TNRS; Owner: bien; Tablespace:
|
| 548 |
5917
|
aaronmk
|
--
|
| 549 |
|
|
|
| 550 |
9493
|
aaronmk
|
CREATE UNIQUE INDEX tnrs_score_ok ON tnrs USING btree ("Name_submitted") WHERE score_ok("Max_score");
|
| 551 |
5917
|
aaronmk
|
|
| 552 |
|
|
|
| 553 |
|
|
--
|
| 554 |
10786
|
aaronmk
|
-- Name: batch__fill; Type: TRIGGER; Schema: TNRS; Owner: bien
|
| 555 |
|
|
--
|
| 556 |
|
|
|
| 557 |
|
|
CREATE TRIGGER batch__fill BEFORE INSERT OR UPDATE ON batch FOR EACH ROW EXECUTE PROCEDURE batch__fill();
|
| 558 |
|
|
|
| 559 |
|
|
|
| 560 |
|
|
--
|
| 561 |
10395
|
aaronmk
|
-- Name: map_filter_insert; Type: TRIGGER; Schema: TNRS; Owner: bien
|
| 562 |
|
|
--
|
| 563 |
|
|
|
| 564 |
|
|
CREATE TRIGGER map_filter_insert BEFORE INSERT ON "~Source.map" FOR EACH ROW EXECUTE PROCEDURE util.map_filter_insert();
|
| 565 |
|
|
|
| 566 |
|
|
ALTER TABLE "~Source.map" DISABLE TRIGGER map_filter_insert;
|
| 567 |
|
|
|
| 568 |
|
|
|
| 569 |
|
|
--
|
| 570 |
9529
|
aaronmk
|
-- Name: tnrs_populate_fields; Type: TRIGGER; Schema: TNRS; Owner: bien
|
| 571 |
5917
|
aaronmk
|
--
|
| 572 |
|
|
|
| 573 |
9529
|
aaronmk
|
CREATE TRIGGER tnrs_populate_fields BEFORE INSERT OR UPDATE ON tnrs FOR EACH ROW EXECUTE PROCEDURE tnrs_populate_fields();
|
| 574 |
5917
|
aaronmk
|
|
| 575 |
|
|
|
| 576 |
|
|
--
|
| 577 |
10786
|
aaronmk
|
-- Name: batch_client_version_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: bien
|
| 578 |
|
|
--
|
| 579 |
|
|
|
| 580 |
|
|
ALTER TABLE ONLY batch
|
| 581 |
|
|
ADD CONSTRAINT batch_client_version_fkey FOREIGN KEY (client_version) REFERENCES client_version(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 582 |
|
|
|
| 583 |
|
|
|
| 584 |
|
|
--
|
| 585 |
|
|
-- Name: batch_download_settings_id_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: bien
|
| 586 |
|
|
--
|
| 587 |
|
|
|
| 588 |
|
|
ALTER TABLE ONLY batch_download_settings
|
| 589 |
|
|
ADD CONSTRAINT batch_download_settings_id_fkey FOREIGN KEY (id) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 590 |
|
|
|
| 591 |
|
|
|
| 592 |
|
|
--
|
| 593 |
|
|
-- Name: tnrs_batch_fkey; Type: FK CONSTRAINT; Schema: TNRS; Owner: bien
|
| 594 |
|
|
--
|
| 595 |
|
|
|
| 596 |
|
|
ALTER TABLE ONLY tnrs
|
| 597 |
|
|
ADD CONSTRAINT tnrs_batch_fkey FOREIGN KEY (batch) REFERENCES batch(id) ON UPDATE CASCADE ON DELETE CASCADE;
|
| 598 |
|
|
|
| 599 |
|
|
|
| 600 |
|
|
--
|
| 601 |
10395
|
aaronmk
|
-- Name: TNRS; Type: ACL; Schema: -; Owner: bien
|
| 602 |
|
|
--
|
| 603 |
|
|
|
| 604 |
|
|
REVOKE ALL ON SCHEMA "TNRS" FROM PUBLIC;
|
| 605 |
|
|
REVOKE ALL ON SCHEMA "TNRS" FROM bien;
|
| 606 |
|
|
GRANT ALL ON SCHEMA "TNRS" TO bien;
|
| 607 |
|
|
GRANT USAGE ON SCHEMA "TNRS" TO bien_read;
|
| 608 |
|
|
|
| 609 |
|
|
|
| 610 |
|
|
--
|
| 611 |
|
|
-- Name: tnrs; Type: ACL; Schema: TNRS; Owner: bien
|
| 612 |
|
|
--
|
| 613 |
|
|
|
| 614 |
|
|
REVOKE ALL ON TABLE tnrs FROM PUBLIC;
|
| 615 |
|
|
REVOKE ALL ON TABLE tnrs FROM bien;
|
| 616 |
|
|
GRANT ALL ON TABLE tnrs TO bien;
|
| 617 |
|
|
GRANT SELECT ON TABLE tnrs TO bien_read;
|
| 618 |
|
|
|
| 619 |
|
|
|
| 620 |
|
|
--
|
| 621 |
5423
|
aaronmk
|
-- PostgreSQL database dump complete
|
| 622 |
|
|
--
|
