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CREATE OR REPLACE FUNCTION score_ok(score double precision)
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RETURNS boolean AS
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3
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$BODY$
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SELECT $1 >= 0.8
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$BODY$
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6
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LANGUAGE sql VOLATILE
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COST 100;
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8
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9
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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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*/
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CREATE TABLE tnrs
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(
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"Time_submitted" timestamp with time zone DEFAULT now(),
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"Name_number" text,
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"Name_submitted" text NOT NULL,
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"Overall_score" text,
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"Name_matched" text,
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"Name_matched_rank" text,
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"Name_score" text,
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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" text,
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"Family_matched" text,
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"Family_score" text,
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"Name_matched_accepted_family" text,
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"Genus_matched" text,
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"Genus_score" text,
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"Specific_epithet_matched" text,
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"Specific_epithet_score" text,
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"Infraspecific_rank" text,
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"Infraspecific_epithet_matched" text,
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"Infraspecific_epithet_score" text,
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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" text,
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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_species" text,
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"Accepted_family" text,
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"Selected" text,
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"Source" text,
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"Warnings" text,
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50
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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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CONSTRAINT tnrs_pkey PRIMARY KEY ("Name_submitted" )
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)
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WITH (
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OIDS=FALSE
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);
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58
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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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64
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65
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CREATE OR REPLACE FUNCTION tnrs_populate_fields()
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RETURNS trigger AS
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67
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$BODY$
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BEGIN
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new."Accepted_scientific_name" = NULLIF(concat_ws(' '
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, NULLIF(NULLIF(new."Accepted_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"::double precision
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, new."Family_score"::double precision
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, new."Genus_score"::double precision
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, new."Specific_epithet_score"::double precision
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);
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80
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RETURN new;
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END;
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83
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$BODY$
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84
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LANGUAGE plpgsql VOLATILE
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85
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COST 100;
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86
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87
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CREATE TRIGGER tnrs_populate_fields
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88
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BEFORE INSERT OR UPDATE
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ON tnrs
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FOR EACH ROW
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EXECUTE PROCEDURE tnrs_populate_fields();
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92
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93
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94
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CREATE OR REPLACE VIEW "ValidMatchedTaxon" AS
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95
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SELECT
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96
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"Time_submitted" AS "*Name_matched.Time_submitted"
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, "Name_submitted" AS "concatenatedScientificName"
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, "Name_matched" AS "matchedTaxonName"
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, "Name_matched_rank" AS "matchedTaxonRank"
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, "Name_score" AS "*Name_matched.Name_score"
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, "Name_matched_author" AS "matchedScientificNameAuthorship"
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, "Name_matched_url" AS "matchedScientificNameID"
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103
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, "Author_score" AS "*Name_matched.Author_score"
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104
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, "Family_score" AS "matchedFamilyConfidence_fraction"
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105
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, COALESCE("Name_matched_accepted_family", "Accepted_family") AS "matchedFamily"
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106
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, "Genus_matched" AS "matchedGenus"
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107
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, "Genus_score" AS "matchedGenusConfidence_fraction"
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108
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, "Specific_epithet_matched" AS "matchedSpecificEpithet"
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109
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, "Specific_epithet_score" AS "matchedSpeciesConfidence_fraction"
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, "Infraspecific_epithet_matched" AS "matchedInfraspecificEpithet"
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111
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, "Infraspecific_epithet_score" AS "*Name_matched.Infraspecific_epithet_score"
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112
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, "Annotations" AS "identificationQualifier"
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113
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, "Unmatched_terms" AS "morphospeciesSuffix"
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114
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, "Taxonomic_status" AS "taxonomicStatus"
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115
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, "Accepted_name" AS "acceptedTaxonName"
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116
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, "Accepted_name_author" AS "acceptedScientificNameAuthorship"
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117
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, "Accepted_name_rank" AS "acceptedTaxonRank"
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118
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, "Accepted_name_url" AS "acceptedScientificNameID"
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119
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, "Accepted_species" AS "*Name_matched.Accepted_species"
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120
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, "Accepted_family" AS "acceptedFamily"
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121
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, "Selected" AS "*Name_matched.Selected"
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122
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, "Source" AS "*Name_matched.Source"
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123
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, "Warnings" AS "*Name_matched.Warnings"
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124
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, "Accepted_name_lsid" AS "*Name_matched.Accepted_name_lsid"
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125
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, "Accepted_scientific_name" AS "acceptedScientificName"
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126
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, "Max_score" AS "matchedTaxonConfidence_fraction"
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127
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FROM tnrs
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128
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WHERE score_ok("Max_score")
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129
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;
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130
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131
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CREATE OR REPLACE VIEW "AcceptedTaxon" AS
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132
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SELECT
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133
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"Time_submitted" AS "*Accepted_name.Time_submitted"
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134
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, "Name_submitted" AS "acceptedScientificName"
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135
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, "Genus_matched" AS "acceptedGenus"
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136
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, "Specific_epithet_matched" AS "acceptedSpecificEpithet"
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137
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, "Infraspecific_epithet_matched" AS "acceptedInfraspecificEpithet"
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138
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, "Annotations" AS "*Accepted_name.Annotations"
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139
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, "Taxonomic_status" AS "acceptedTaxonomicStatus"
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140
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, "Selected" AS "*Accepted_name.Selected"
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141
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, "Source" AS "*Accepted_name.Source"
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142
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, "Warnings" AS "*Accepted_name.Warnings"
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143
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, "Accepted_name_lsid" AS "*Accepted_name.Accepted_name_lsid"
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144
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FROM tnrs;
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145
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146
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CREATE OR REPLACE VIEW "ScrubbedTaxon" AS
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147
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SELECT *
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148
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FROM "ValidMatchedTaxon"
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149
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NATURAL LEFT JOIN "AcceptedTaxon"
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150
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;
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