Revision 9529
Added by Aaron Marcuse-Kubitza over 11 years ago
inputs/test_taxonomic_names/_scrub/TNRS.sql | ||
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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_derived_fields(); Type: FUNCTION; Schema: TNRS; Owner: bien
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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_derived_fields() RETURNS trigger
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CREATE FUNCTION tnrs_populate_fields() RETURNS trigger |
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LANGUAGE plpgsql |
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AS $$ |
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BEGIN |
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$$; |
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ALTER FUNCTION "TNRS".tnrs_populate_derived_fields() OWNER TO bien;
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ALTER FUNCTION "TNRS".tnrs_populate_fields() OWNER TO bien; |
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SET default_tablespace = ''; |
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... | ... | |
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-- |
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CREATE TABLE tnrs ( |
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"Time_submitted" timestamp with time zone, |
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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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"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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-- |
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CREATE VIEW "MatchedTaxon" AS |
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SELECT tnrs."Time_submitted" AS "*Name_matched.Time_submitted", 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", 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_species" AS "*Name_matched.Accepted_species", tnrs."Accepted_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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SELECT tnrs."Time_submitted" AS "*Name_matched.Time_submitted", 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", tnrs."Name_matched_accepted_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_species" AS "*Name_matched.Accepted_species", tnrs."Accepted_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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CREATE VIEW "ScrubbedTaxon" AS |
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SELECT "MatchedTaxon"."acceptedScientificName", "MatchedTaxon"."*Name_matched.Time_submitted", "MatchedTaxon"."concatenatedScientificName", "MatchedTaxon"."matchedTaxonName", "MatchedTaxon"."matchedTaxonRank", "MatchedTaxon"."*Name_matched.Name_score", "MatchedTaxon"."matchedScientificNameAuthorship", "MatchedTaxon"."matchedScientificNameID", "MatchedTaxon"."*Name_matched.Author_score", "MatchedTaxon"."matchedFamilyConfidence_fraction", "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_species", "MatchedTaxon"."acceptedFamily", "MatchedTaxon"."*Name_matched.Selected", "MatchedTaxon"."*Name_matched.Source", "MatchedTaxon"."*Name_matched.Warnings", "MatchedTaxon"."*Name_matched.Accepted_name_lsid", "MatchedTaxon"."matchedTaxonConfidence_fraction", "AcceptedTaxon"."*Accepted_name.Time_submitted", "AcceptedTaxon"."acceptedGenus", "AcceptedTaxon"."acceptedSpecificEpithet", "AcceptedTaxon"."acceptedInfraspecificEpithet", "AcceptedTaxon"."*Accepted_name.Annotations", "AcceptedTaxon"."acceptedTaxonomicStatus", "AcceptedTaxon"."*Accepted_name.Selected", "AcceptedTaxon"."*Accepted_name.Source", "AcceptedTaxon"."*Accepted_name.Warnings", "AcceptedTaxon"."*Accepted_name.Accepted_name_lsid" FROM ("MatchedTaxon" NATURAL LEFT JOIN "AcceptedTaxon") WHERE score_ok("MatchedTaxon"."matchedTaxonConfidence_fraction"); |
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SELECT "MatchedTaxon"."acceptedScientificName", "MatchedTaxon"."*Name_matched.Time_submitted", "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_species", "MatchedTaxon"."acceptedFamily", "MatchedTaxon"."*Name_matched.Selected", "MatchedTaxon"."*Name_matched.Source", "MatchedTaxon"."*Name_matched.Warnings", "MatchedTaxon"."*Name_matched.Accepted_name_lsid", "MatchedTaxon"."matchedTaxonConfidence_fraction", "AcceptedTaxon"."*Accepted_name.Time_submitted", "AcceptedTaxon"."acceptedGenus", "AcceptedTaxon"."acceptedSpecificEpithet", "AcceptedTaxon"."acceptedInfraspecificEpithet", "AcceptedTaxon"."*Accepted_name.Annotations", "AcceptedTaxon"."acceptedTaxonomicStatus", "AcceptedTaxon"."*Accepted_name.Selected", "AcceptedTaxon"."*Accepted_name.Source", "AcceptedTaxon"."*Accepted_name.Warnings", "AcceptedTaxon"."*Accepted_name.Accepted_name_lsid" FROM ("MatchedTaxon" NATURAL LEFT JOIN "AcceptedTaxon") WHERE score_ok("MatchedTaxon"."matchedTaxonConfidence_fraction");
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ALTER TABLE "TNRS"."ScrubbedTaxon" OWNER TO bien; |
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-- Data for Name: tnrs; Type: TABLE DATA; Schema: TNRS; Owner: bien |
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-- |
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COPY tnrs ("Time_submitted", "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", "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_species", "Accepted_family", "Selected", "Source", "Warnings", "Accepted_name_lsid", "Accepted_scientific_name", "Max_score") FROM stdin; |
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2013-05-21 19:23:15.278517-07 0 Fam_indet. Boyle#6501 0 No suitable matches found. \N 0 \N \N \N 0 \N 0 \N 0 \N 0 \N \N 0 \N \N 0 \N \N \N \N \N \N \N \N \N true \N \N \N 0
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2013-05-21 19:23:15.278517-07 1 Poa annua var. eriolepis 1 Poa annua var. eriolepis variety 1 E. Desv. http://www.tropicos.org/Name/50119145 \N \N \N \N 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
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2013-05-21 19:23:15.278517-07 2 Poa annua 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 \N \N \N \N 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
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2013-05-21 19:23:15.278517-07 3 Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire 0.77 Silene scouleri subsp. pringlei subspecies 0.77 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N 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
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2013-05-21 19:23:15.278517-07 4 Fabaceae Boyle#6500 0.9 Fabaceae family 1 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \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
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2013-05-21 19:23:15.278517-07 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 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
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2013-05-21 19:23:15.278517-07 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 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
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2013-05-21 19:23:15.278517-07 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 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
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2013-05-21 19:23:15.278517-07 8 Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 \N \N 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
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2013-05-21 19:23:15.278517-07 9 Compositae indet. sp.1 0.9 Compositae family 1 Giseke http://www.tropicos.org/Name/50255940 \N \N Compositae 1 \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
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2013-05-21 19:23:15.278517-07 10 Poa annua fo. lanuginosa 1 Poa annua fo. lanuginosa forma 1 Sennen http://www.tropicos.org/Name/50267771 \N \N \N \N 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
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2013-05-21 19:23:15.278517-07 11 Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire 0.77 Silene scouleri subsp. pringlei subspecies 0.77 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N 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
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2013-05-21 19:23:15.278517-07 12 Fabaceae Inga "fuzzy leaf" 0.9 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 \N \N Fabaceae 1 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
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2013-05-21 19:23:15.278517-07 13 Fabaceae Inga sp.3 0.9 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 \N \N Fabaceae 1 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
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2013-05-21 19:23:15.278517-07 14 Fabaceae unknown #2 0.9 Fabaceae family 1 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \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
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2013-05-21 19:23:19.089938-07 0 Poaceae Poa infirma Kunth 1 Poa infirma species 1 Kunth http://www.tropicos.org/Name/25514158 Kunth 1 Poaceae 1 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
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2013-05-21 19:23:19.089938-07 1 Fabaceae Lindl. 0.5 Fabaceae family 0.5 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \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
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2013-05-21 19:23:19.089938-07 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 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
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2013-05-21 19:23:19.089938-07 3 Fabaceae Inga Mill. 1 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 Mill. 1 Fabaceae 1 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
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2013-05-21 19:23:19.089938-07 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 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
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2013-05-21 19:23:19.089938-07 5 Poaceae Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 Poaceae 1 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
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2013-05-21 19:23:19.089938-07 6 Asteraceae Bercht. & J. Presl 0.4 Asteraceae family 0.5 Bercht. & J. Presl http://www.tropicos.org/Name/50307371 \N \N Asteraceae 1 \N \N \N \N \N \N \N \N \N \N \N Bercht. & J. Presl Accepted Asteraceae Bercht. & J. Presl family http://www.tropicos.org/Name/50307371 \N Asteraceae true tropicos [Partial match] \N Asteraceae Bercht. & J. Presl 1
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2013-05-21 19:23:19.089938-07 7 Poaceae Poa annua var. annua 1 Poa annua var. annua variety 1 \N http://www.tropicos.org/Name/25517736 \N \N Poaceae 1 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
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COPY tnrs ("Time_submitted", "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_species", "Accepted_family", "Selected", "Source", "Warnings", "Accepted_name_lsid", "Accepted_scientific_name", "Max_score") FROM stdin;
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2013-05-23 15:18:27.731914-07 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
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2013-05-23 15:18:27.731914-07 1 Poa annua var. eriolepis 1 Poa annua var. eriolepis variety 1 E. Desv. http://www.tropicos.org/Name/50119145 \N \N \N \N \N 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
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2013-05-23 15:18:27.731914-07 2 Poa annua 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 \N \N \N \N \N 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
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2013-05-23 15:18:27.731914-07 3 Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire 0.77 Silene scouleri subsp. pringlei subspecies 0.77 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N \N 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
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154 |
2013-05-23 15:18:27.731914-07 4 Fabaceae Boyle#6500 0.9 Fabaceae family 1 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \N \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
|
|
155 |
2013-05-23 15:18:27.731914-07 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 \N 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
|
|
156 |
2013-05-23 15:18:27.731914-07 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 \N 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
|
|
157 |
2013-05-23 15:18:27.731914-07 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 \N 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
|
|
158 |
2013-05-23 15:18:27.731914-07 8 Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 \N \N \N 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
|
|
159 |
2013-05-23 15:18:27.731914-07 9 Compositae indet. sp.1 0.9 Compositae family 1 Giseke http://www.tropicos.org/Name/50255940 \N \N Compositae 1 \N \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
|
|
160 |
2013-05-23 15:18:27.731914-07 10 Poa annua fo. lanuginosa 1 Poa annua fo. lanuginosa forma 1 Sennen http://www.tropicos.org/Name/50267771 \N \N \N \N \N 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
|
|
161 |
2013-05-23 15:18:27.731914-07 11 Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire 0.77 Silene scouleri subsp. pringlei subspecies 0.77 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N \N 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
|
|
162 |
2013-05-23 15:18:27.731914-07 12 Fabaceae Inga "fuzzy leaf" 0.9 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 \N \N Fabaceae 1 \N 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
|
|
163 |
2013-05-23 15:18:27.731914-07 13 Fabaceae Inga sp.3 0.9 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 \N \N Fabaceae 1 \N 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
|
|
164 |
2013-05-23 15:18:27.731914-07 14 Fabaceae unknown #2 0.9 Fabaceae family 1 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \N \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
|
|
165 |
2013-05-23 15:18:31.201803-07 0 Poaceae Poa infirma Kunth 1 Poa infirma species 1 Kunth http://www.tropicos.org/Name/25514158 Kunth 1 Poaceae 1 \N 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
|
|
166 |
2013-05-23 15:18:31.201803-07 1 Fabaceae Lindl. 0.5 Fabaceae family 0.5 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \N \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
|
|
167 |
2013-05-23 15:18:31.201803-07 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 \N 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
|
|
168 |
2013-05-23 15:18:31.201803-07 3 Fabaceae Inga Mill. 1 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 Mill. 1 Fabaceae 1 \N 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
|
|
169 |
2013-05-23 15:18:31.201803-07 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 \N 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
|
|
170 |
2013-05-23 15:18:31.201803-07 5 Poaceae Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 Poaceae 1 \N 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
|
|
171 |
2013-05-23 15:18:31.201803-07 6 Asteraceae Bercht. & J. Presl 0.4 Asteraceae family 0.5 Bercht. & J. Presl http://www.tropicos.org/Name/50307371 \N \N Asteraceae 1 \N \N \N \N \N \N \N \N \N \N \N \N Bercht. & J. Presl Accepted Asteraceae Bercht. & J. Presl family http://www.tropicos.org/Name/50307371 \N Asteraceae true tropicos [Partial match] \N Asteraceae Bercht. & J. Presl 1
|
|
172 |
2013-05-23 15:18:31.201803-07 7 Poaceae Poa annua var. annua 1 Poa annua var. annua variety 1 \N http://www.tropicos.org/Name/25517736 \N \N Poaceae 1 \N 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
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|
172 | 173 |
\. |
173 | 174 |
|
174 | 175 |
|
... | ... | |
188 | 189 |
|
189 | 190 |
|
190 | 191 |
-- |
191 |
-- Name: tnrs_populate_derived_fields; Type: TRIGGER; Schema: TNRS; Owner: bien
|
|
192 |
-- Name: tnrs_populate_fields; Type: TRIGGER; Schema: TNRS; Owner: bien |
|
192 | 193 |
-- |
193 | 194 |
|
194 |
CREATE TRIGGER tnrs_populate_derived_fields BEFORE INSERT OR UPDATE ON tnrs FOR EACH ROW EXECUTE PROCEDURE tnrs_populate_derived_fields();
|
|
195 |
CREATE TRIGGER tnrs_populate_fields BEFORE INSERT OR UPDATE ON tnrs FOR EACH ROW EXECUTE PROCEDURE tnrs_populate_fields();
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|
195 | 196 |
|
196 | 197 |
|
197 | 198 |
-- |
inputs/test_taxonomic_names/_scrub/public.test_taxonomic_names.sql | ||
---|---|---|
21 | 21 |
-- Name: SCHEMA "public.test_taxonomic_names"; Type: COMMENT; Schema: -; Owner: bien |
22 | 22 |
-- |
23 | 23 |
|
24 |
COMMENT ON SCHEMA "public.test_taxonomic_names" IS 'Version: public (2013-5-21 19:23:27 PDT)';
|
|
24 |
COMMENT ON SCHEMA "public.test_taxonomic_names" IS 'Version: public (2013-5-23 15:18:39 PDT)';
|
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25 | 25 |
|
26 | 26 |
|
27 | 27 |
SET search_path = "public.test_taxonomic_names", pg_catalog; |
... | ... | |
2681 | 2681 |
-- |
2682 | 2682 |
|
2683 | 2683 |
CREATE VIEW analytical_stem_view AS |
2684 |
SELECT source.shortname AS datasource, sourcelist.name AS "institutionCode", specimenreplicate.collectioncode_dwc AS "collectionCode", specimenreplicate.catalognumber_dwc AS "catalogNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", canon_place.country, canon_place.stateprovince AS "stateProvince", datasource_place.county, location.locationnarrative AS locality, CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.latitude_deg ELSE county_centroids.latitude END AS "decimalLatitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.longitude_deg ELSE county_centroids.longitude END AS "decimalLongitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.coordsaccuracy_m ELSE _km_to_m(county_centroids.error_km) END AS "coordinateUncertaintyInMeters", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN 'source data'::coordinatesource WHEN (county_centroids.row_num IS NOT NULL) THEN 'georeferencing'::coordinatesource ELSE NULL::coordinatesource END AS "coordinateSource_bien", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN NULL::text WHEN (county_centroids.row_num IS NOT NULL) THEN 'county centroid'::text ELSE NULL::text END AS "georeferenceProtocol_bien", (canon_place.geovalid)::integer AS geovalid_bien, ("newWorldCountries"."isNewWorld")::integer AS "isNewWorld_bien", COALESCE(project.sourceaccessioncode, project.projectname) AS "projectID", COALESCE(location.sourceaccessioncode, NULLIF(pg_catalog.concat_ws('; '::text, COALESCE(parent_location.sourceaccessioncode, parent_location.authorlocationcode), location.authorlocationcode), ''::text)) AS "locationID", COALESCE(parent_location.authorlocationcode, location.authorlocationcode) AS "locationName", CASE WHEN (parent_location.location_id IS NOT NULL) THEN location.authorlocationcode ELSE NULL::text END AS subplot, plantobservation.authorplantcode AS "individualCode", COALESCE(location.elevation_m, parent_location.elevation_m) AS "elevationInMeters", _m2_to_ha(COALESCE(location.area_m2, parent_location.area_m2)) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.temperature_c, parent_event.temperature_c) AS "temperature_C", COALESCE(locationevent.precipitation_m, parent_event.precipitation_m) AS precipitation_m, collector.fullname AS "recordedBy", plantobservation.authorplantcode AS "recordNumber", COALESCE(locationevent.obsstartdate, parent_event.obsstartdate, aggregateoccurrence.collectiondate) AS "dateCollected", taxonverbatim.family AS family_verbatim, COALESCE(taxonverbatim.taxonomicname, NULLIF(pg_catalog.concat_ws(' '::text, taxonverbatim.taxonname, taxonverbatim.author), ''::text), taxonlabel.taxonomicname) AS "scientificName_verbatim", identifiedby.fullname AS "identifiedBy", taxondetermination.determinationdate AS "dateIdentified", taxondetermination.notes AS "identificationRemarks", "ScrubbedTaxon"."matchedTaxonName" AS "taxonName_matched", "ScrubbedTaxon"."matchedScientificNameAuthorship" AS "scientificNameAuthorship_matched", family_higher_plant_group.higher_plant_group AS "higherPlantGroup_bien", "ScrubbedTaxon"."acceptedFamily" AS family, "ScrubbedTaxon"."acceptedGenus" AS genus, COALESCE(NULLIF(pg_catalog.concat_ws(' '::text, COALESCE("ScrubbedTaxon"."acceptedGenus", "ScrubbedTaxon"."acceptedFamily"), "ScrubbedTaxon"."acceptedSpecificEpithet", "ScrubbedTaxon"."morphospeciesSuffix"), ''::text), "ScrubbedTaxon"."acceptedTaxonName") AS "speciesBinomialWithMorphospecies", "ScrubbedTaxon"."acceptedTaxonName" AS "taxonName", "ScrubbedTaxon"."acceptedScientificNameAuthorship" AS "scientificNameAuthorship", taxonoccurrence.growthform AS "growthForm", plantobservation.reproductivecondition AS "reproductiveCondition", ((threatened_taxonlabel.taxonlabel_id IS NOT NULL))::integer AS threatened_bien, (((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)))::integer AS cultivated_bien, CASE WHEN (taxonoccurrence.iscultivated IS NOT NULL) THEN taxonoccurrence.cultivatedbasis WHEN (location.iscultivated IS NOT NULL) THEN NULL::text ELSE NULL::text END AS "cultivatedBasis_bien", aggregateoccurrence.notes AS "occurrenceRemarks", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.sourceaccessioncode AS "taxonOccurrenceID", taxonoccurrence.authortaxoncode AS "authorTaxonCode", plantobservation.sourceaccessioncode AS "individualObservationID", stemobservation.authorstemcode AS "authorStemCode" FROM ((((((((((((((((((((((((((((source JOIN location USING (source_id)) LEFT JOIN locationevent USING (location_id)) LEFT JOIN location parent_location ON ((parent_location.location_id = location.parent_id))) LEFT JOIN locationplace ON ((locationplace.location_id = COALESCE(parent_location.location_id, location.location_id)))) LEFT JOIN place datasource_place USING (place_id)) LEFT JOIN place canon_place ON ((canon_place.place_id = datasource_place.canon_place_id))) LEFT JOIN coordinates ON ((coordinates.coordinates_id = canon_place.coordinates_id))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."GADM country" = canon_place.country))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."isoCode" = iso_code_gadm."2-digit iso code"))) LEFT JOIN geoscrub.county_centroids ON ((((canon_place.country = 'United States'::text) AND (county_centroids.state = canon_place.stateprovince)) AND (county_centroids.county = canon_place.county)))) LEFT JOIN taxonoccurrence USING (locationevent_id)) LEFT JOIN locationevent parent_event ON ((parent_event.locationevent_id = locationevent.parent_id))) LEFT JOIN project ON ((project.project_id = COALESCE(locationevent.project_id, parent_event.project_id)))) LEFT JOIN method ON ((method.method_id = COALESCE(locationevent.method_id, parent_event.method_id)))) LEFT JOIN party collector ON ((collector.party_id = taxonoccurrence.collector_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcelist ON ((sourcelist.sourcelist_id = specimenreplicate.institution_id))) LEFT JOIN taxondetermination ON (((taxondetermination.taxonoccurrence_id = taxonoccurrence.taxonoccurrence_id) AND taxondetermination.is_datasource_current))) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel USING (taxonlabel_id)) LEFT JOIN "TNRS"."ScrubbedTaxon" ON (("ScrubbedTaxon"."concatenatedScientificName" = taxonlabel.taxonomicname))) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = "ScrubbedTaxon"."acceptedFamily"))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = "ScrubbedTaxon"."acceptedFamily") AND (cultivated_family_locations.country = canon_place.country)))) LEFT JOIN threatened_taxonlabel USING (taxonlabel_id)) ORDER BY source.shortname; |
|
2684 |
SELECT source.shortname AS datasource, sourcelist.name AS "institutionCode", specimenreplicate.collectioncode_dwc AS "collectionCode", specimenreplicate.catalognumber_dwc AS "catalogNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", canon_place.country, canon_place.stateprovince AS "stateProvince", datasource_place.county, location.locationnarrative AS locality, CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.latitude_deg ELSE county_centroids.latitude END AS "decimalLatitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.longitude_deg ELSE county_centroids.longitude END AS "decimalLongitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.coordsaccuracy_m ELSE _km_to_m(county_centroids.error_km) END AS "coordinateUncertaintyInMeters", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN 'source data'::coordinatesource WHEN (county_centroids.row_num IS NOT NULL) THEN 'georeferencing'::coordinatesource ELSE NULL::coordinatesource END AS "coordinateSource_bien", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN NULL::text WHEN (county_centroids.row_num IS NOT NULL) THEN 'county centroid'::text ELSE NULL::text END AS "georeferenceProtocol_bien", (canon_place.geovalid)::integer AS geovalid_bien, ("newWorldCountries"."isNewWorld")::integer AS "isNewWorld_bien", COALESCE(project.sourceaccessioncode, project.projectname) AS "projectID", COALESCE(location.sourceaccessioncode, NULLIF(pg_catalog.concat_ws('; '::text, COALESCE(parent_location.sourceaccessioncode, parent_location.authorlocationcode), location.authorlocationcode), ''::text)) AS "locationID", COALESCE(parent_location.authorlocationcode, location.authorlocationcode) AS "locationName", CASE WHEN (parent_location.location_id IS NOT NULL) THEN location.authorlocationcode ELSE NULL::text END AS subplot, plantobservation.authorplantcode AS "individualCode", COALESCE(location.elevation_m, parent_location.elevation_m) AS "elevationInMeters", _m2_to_ha(COALESCE(location.area_m2, parent_location.area_m2)) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.temperature_c, parent_event.temperature_c) AS "temperature_C", COALESCE(locationevent.precipitation_m, parent_event.precipitation_m) AS precipitation_m, collector.fullname AS "recordedBy", plantobservation.authorplantcode AS "recordNumber", COALESCE(locationevent.obsstartdate, parent_event.obsstartdate, aggregateoccurrence.collectiondate) AS "dateCollected", taxonverbatim.family AS family_verbatim, COALESCE(taxonverbatim.taxonomicname, NULLIF(pg_catalog.concat_ws(' '::text, taxonverbatim.taxonname, taxonverbatim.author), ''::text), taxonlabel.taxonomicname) AS "scientificName_verbatim", identifiedby.fullname AS "identifiedBy", taxondetermination.determinationdate AS "dateIdentified", taxondetermination.notes AS "identificationRemarks", "ScrubbedTaxon"."matchedFamily" AS family_matched, "ScrubbedTaxon"."matchedTaxonName" AS "taxonName_matched", "ScrubbedTaxon"."matchedScientificNameAuthorship" AS "scientificNameAuthorship_matched", family_higher_plant_group.higher_plant_group AS "higherPlantGroup_bien", "ScrubbedTaxon"."acceptedFamily" AS family, "ScrubbedTaxon"."acceptedGenus" AS genus, COALESCE(NULLIF(pg_catalog.concat_ws(' '::text, COALESCE("ScrubbedTaxon"."acceptedGenus", "ScrubbedTaxon"."acceptedFamily"), "ScrubbedTaxon"."acceptedSpecificEpithet", "ScrubbedTaxon"."morphospeciesSuffix"), ''::text), "ScrubbedTaxon"."acceptedTaxonName") AS "speciesBinomialWithMorphospecies", "ScrubbedTaxon"."acceptedTaxonName" AS "taxonName", "ScrubbedTaxon"."acceptedScientificNameAuthorship" AS "scientificNameAuthorship", taxonoccurrence.growthform AS "growthForm", plantobservation.reproductivecondition AS "reproductiveCondition", ((threatened_taxonlabel.taxonlabel_id IS NOT NULL))::integer AS threatened_bien, (((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)))::integer AS cultivated_bien, CASE WHEN (taxonoccurrence.iscultivated IS NOT NULL) THEN taxonoccurrence.cultivatedbasis WHEN (location.iscultivated IS NOT NULL) THEN NULL::text ELSE NULL::text END AS "cultivatedBasis_bien", aggregateoccurrence.notes AS "occurrenceRemarks", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.sourceaccessioncode AS "taxonOccurrenceID", taxonoccurrence.authortaxoncode AS "authorTaxonCode", plantobservation.sourceaccessioncode AS "individualObservationID", stemobservation.authorstemcode AS "authorStemCode" FROM ((((((((((((((((((((((((((((source JOIN location USING (source_id)) LEFT JOIN locationevent USING (location_id)) LEFT JOIN location parent_location ON ((parent_location.location_id = location.parent_id))) LEFT JOIN locationplace ON ((locationplace.location_id = COALESCE(parent_location.location_id, location.location_id)))) LEFT JOIN place datasource_place USING (place_id)) LEFT JOIN place canon_place ON ((canon_place.place_id = datasource_place.canon_place_id))) LEFT JOIN coordinates ON ((coordinates.coordinates_id = canon_place.coordinates_id))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."GADM country" = canon_place.country))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."isoCode" = iso_code_gadm."2-digit iso code"))) LEFT JOIN geoscrub.county_centroids ON ((((canon_place.country = 'United States'::text) AND (county_centroids.state = canon_place.stateprovince)) AND (county_centroids.county = canon_place.county)))) LEFT JOIN taxonoccurrence USING (locationevent_id)) LEFT JOIN locationevent parent_event ON ((parent_event.locationevent_id = locationevent.parent_id))) LEFT JOIN project ON ((project.project_id = COALESCE(locationevent.project_id, parent_event.project_id)))) LEFT JOIN method ON ((method.method_id = COALESCE(locationevent.method_id, parent_event.method_id)))) LEFT JOIN party collector ON ((collector.party_id = taxonoccurrence.collector_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcelist ON ((sourcelist.sourcelist_id = specimenreplicate.institution_id))) LEFT JOIN taxondetermination ON (((taxondetermination.taxonoccurrence_id = taxonoccurrence.taxonoccurrence_id) AND taxondetermination.is_datasource_current))) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel USING (taxonlabel_id)) LEFT JOIN "TNRS"."ScrubbedTaxon" ON (("ScrubbedTaxon"."concatenatedScientificName" = taxonlabel.taxonomicname))) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = "ScrubbedTaxon"."acceptedFamily"))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = "ScrubbedTaxon"."acceptedFamily") AND (cultivated_family_locations.country = canon_place.country)))) LEFT JOIN threatened_taxonlabel USING (taxonlabel_id)) ORDER BY source.shortname;
|
|
2685 | 2685 |
|
2686 | 2686 |
|
2687 | 2687 |
ALTER TABLE "public.test_taxonomic_names".analytical_stem_view OWNER TO bien; |
inputs/.TNRS/tnrs/header.csv | ||
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1 |
Time_submitted,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,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_species,Accepted_family,Selected,Source,Warnings,Accepted_name_lsid,Accepted_scientific_name,Max_score |
|
1 |
Time_submitted,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_species,Accepted_family,Selected,Source,Warnings,Accepted_name_lsid,Accepted_scientific_name,Max_score |
inputs/.TNRS/data.sql | ||
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1 |
COPY tnrs FROM stdin; |
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2 |
2013-05-21 19:23:15.278517-07 0 Fam_indet. Boyle#6501 0 No suitable matches found. \N 0 \N \N \N 0 \N 0 \N 0 \N 0 \N \N 0 \N \N 0 \N \N \N \N \N \N \N \N \N true \N \N \N 0
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3 |
2013-05-21 19:23:15.278517-07 1 Poa annua var. eriolepis 1 Poa annua var. eriolepis variety 1 E. Desv. http://www.tropicos.org/Name/50119145 \N \N \N \N 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
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4 |
2013-05-21 19:23:15.278517-07 2 Poa annua 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 \N \N \N \N 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
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5 |
2013-05-21 19:23:15.278517-07 3 Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire 0.77 Silene scouleri subsp. pringlei subspecies 0.77 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N 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
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6 |
2013-05-21 19:23:15.278517-07 4 Fabaceae Boyle#6500 0.9 Fabaceae family 1 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \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
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7 |
2013-05-21 19:23:15.278517-07 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 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
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8 |
2013-05-21 19:23:15.278517-07 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 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
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9 |
2013-05-21 19:23:15.278517-07 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 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
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10 |
2013-05-21 19:23:15.278517-07 8 Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 \N \N 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
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11 |
2013-05-21 19:23:15.278517-07 9 Compositae indet. sp.1 0.9 Compositae family 1 Giseke http://www.tropicos.org/Name/50255940 \N \N Compositae 1 \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
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12 |
2013-05-21 19:23:15.278517-07 10 Poa annua fo. lanuginosa 1 Poa annua fo. lanuginosa forma 1 Sennen http://www.tropicos.org/Name/50267771 \N \N \N \N 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
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13 |
2013-05-21 19:23:15.278517-07 11 Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire 0.77 Silene scouleri subsp. pringlei subspecies 0.77 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N 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
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14 |
2013-05-21 19:23:15.278517-07 12 Fabaceae Inga "fuzzy leaf" 0.9 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 \N \N Fabaceae 1 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
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15 |
2013-05-21 19:23:15.278517-07 13 Fabaceae Inga sp.3 0.9 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 \N \N Fabaceae 1 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
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16 |
2013-05-21 19:23:15.278517-07 14 Fabaceae unknown #2 0.9 Fabaceae family 1 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \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
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17 |
2013-05-21 19:23:19.089938-07 0 Poaceae Poa infirma Kunth 1 Poa infirma species 1 Kunth http://www.tropicos.org/Name/25514158 Kunth 1 Poaceae 1 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
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18 |
2013-05-21 19:23:19.089938-07 1 Fabaceae Lindl. 0.5 Fabaceae family 0.5 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \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
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19 |
2013-05-21 19:23:19.089938-07 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 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
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20 |
2013-05-21 19:23:19.089938-07 3 Fabaceae Inga Mill. 1 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 Mill. 1 Fabaceae 1 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
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21 |
2013-05-21 19:23:19.089938-07 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 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
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22 |
2013-05-21 19:23:19.089938-07 5 Poaceae Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 Poaceae 1 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
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23 |
2013-05-21 19:23:19.089938-07 6 Asteraceae Bercht. & J. Presl 0.4 Asteraceae family 0.5 Bercht. & J. Presl http://www.tropicos.org/Name/50307371 \N \N Asteraceae 1 \N \N \N \N \N \N \N \N \N \N \N Bercht. & J. Presl Accepted Asteraceae Bercht. & J. Presl family http://www.tropicos.org/Name/50307371 \N Asteraceae true tropicos [Partial match] \N Asteraceae Bercht. & J. Presl 1
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24 |
2013-05-21 19:23:19.089938-07 7 Poaceae Poa annua var. annua 1 Poa annua var. annua variety 1 \N http://www.tropicos.org/Name/25517736 \N \N Poaceae 1 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
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1 |
COPY tnrs ("Time_submitted", "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_species", "Accepted_family", "Selected", "Source", "Warnings", "Accepted_name_lsid", "Accepted_scientific_name", "Max_score") FROM stdin;
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2 |
2013-05-23 15:18:27.731914-07 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
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3 |
2013-05-23 15:18:27.731914-07 1 Poa annua var. eriolepis 1 Poa annua var. eriolepis variety 1 E. Desv. http://www.tropicos.org/Name/50119145 \N \N \N \N \N 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
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4 |
2013-05-23 15:18:27.731914-07 2 Poa annua 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 \N \N \N \N \N 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
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5 |
2013-05-23 15:18:27.731914-07 3 Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire 0.77 Silene scouleri subsp. pringlei subspecies 0.77 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N \N 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
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6 |
2013-05-23 15:18:27.731914-07 4 Fabaceae Boyle#6500 0.9 Fabaceae family 1 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \N \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
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7 |
2013-05-23 15:18:27.731914-07 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 \N 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
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8 |
2013-05-23 15:18:27.731914-07 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 \N 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
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9 |
2013-05-23 15:18:27.731914-07 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 \N 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
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10 |
2013-05-23 15:18:27.731914-07 8 Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 \N \N \N 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
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11 |
2013-05-23 15:18:27.731914-07 9 Compositae indet. sp.1 0.9 Compositae family 1 Giseke http://www.tropicos.org/Name/50255940 \N \N Compositae 1 \N \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
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12 |
2013-05-23 15:18:27.731914-07 10 Poa annua fo. lanuginosa 1 Poa annua fo. lanuginosa forma 1 Sennen http://www.tropicos.org/Name/50267771 \N \N \N \N \N 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
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13 |
2013-05-23 15:18:27.731914-07 11 Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire 0.77 Silene scouleri subsp. pringlei subspecies 0.77 (S. Watson) C.L. Hitchc. & Maguire http://www.tropicos.org/Name/6303627 \N \N \N \N \N 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
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14 |
2013-05-23 15:18:27.731914-07 12 Fabaceae Inga "fuzzy leaf" 0.9 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 \N \N Fabaceae 1 \N 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
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15 |
2013-05-23 15:18:27.731914-07 13 Fabaceae Inga sp.3 0.9 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 \N \N Fabaceae 1 \N 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
|
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16 |
2013-05-23 15:18:27.731914-07 14 Fabaceae unknown #2 0.9 Fabaceae family 1 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \N \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
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17 |
2013-05-23 15:18:31.201803-07 0 Poaceae Poa infirma Kunth 1 Poa infirma species 1 Kunth http://www.tropicos.org/Name/25514158 Kunth 1 Poaceae 1 \N 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
|
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18 |
2013-05-23 15:18:31.201803-07 1 Fabaceae Lindl. 0.5 Fabaceae family 0.5 Lindl. http://www.tropicos.org/Name/42000184 \N \N Fabaceae 1 \N \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
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19 |
2013-05-23 15:18:31.201803-07 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 \N 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
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20 |
2013-05-23 15:18:31.201803-07 3 Fabaceae Inga Mill. 1 Inga genus 1 Mill. http://www.tropicos.org/Name/40031040 Mill. 1 Fabaceae 1 \N 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
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21 |
2013-05-23 15:18:31.201803-07 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 \N 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
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22 |
2013-05-23 15:18:31.201803-07 5 Poaceae Poa annua L. 1 Poa annua species 1 L. http://www.tropicos.org/Name/25509881 L. 1 Poaceae 1 \N 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
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23 |
2013-05-23 15:18:31.201803-07 6 Asteraceae Bercht. & J. Presl 0.4 Asteraceae family 0.5 Bercht. & J. Presl http://www.tropicos.org/Name/50307371 \N \N Asteraceae 1 \N \N \N \N \N \N \N \N \N \N \N \N Bercht. & J. Presl Accepted Asteraceae Bercht. & J. Presl family http://www.tropicos.org/Name/50307371 \N Asteraceae true tropicos [Partial match] \N Asteraceae Bercht. & J. Presl 1
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24 |
2013-05-23 15:18:31.201803-07 7 Poaceae Poa annua var. annua 1 Poa annua var. annua variety 1 \N http://www.tropicos.org/Name/25517736 \N \N Poaceae 1 \N 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
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25 | 25 |
\. |
inputs/.TNRS/schema.sql | ||
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22 | 22 |
"Author_score" text, |
23 | 23 |
"Family_matched" text, |
24 | 24 |
"Family_score" text, |
25 |
"Name_matched_accepted_family" text, |
|
25 | 26 |
"Genus_matched" text, |
26 | 27 |
"Genus_score" text, |
27 | 28 |
"Specific_epithet_matched" text, |
... | ... | |
99 | 100 |
, "Name_matched_url" AS "matchedScientificNameID" |
100 | 101 |
, "Author_score" AS "*Name_matched.Author_score" |
101 | 102 |
, "Family_score" AS "matchedFamilyConfidence_fraction" |
103 |
, "Name_matched_accepted_family" AS "matchedFamily" |
|
102 | 104 |
, "Genus_matched" AS "matchedGenus" |
103 | 105 |
, "Genus_score" AS "matchedGenusConfidence_fraction" |
104 | 106 |
, "Specific_epithet_matched" AS "matchedSpecificEpithet" |
schemas/vegbien.sql | ||
---|---|---|
2487 | 2487 |
-- |
2488 | 2488 |
|
2489 | 2489 |
CREATE VIEW analytical_stem_view AS |
2490 |
SELECT source.shortname AS datasource, sourcelist.name AS "institutionCode", specimenreplicate.collectioncode_dwc AS "collectionCode", specimenreplicate.catalognumber_dwc AS "catalogNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", canon_place.country, canon_place.stateprovince AS "stateProvince", datasource_place.county, location.locationnarrative AS locality, CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.latitude_deg ELSE county_centroids.latitude END AS "decimalLatitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.longitude_deg ELSE county_centroids.longitude END AS "decimalLongitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.coordsaccuracy_m ELSE _km_to_m(county_centroids.error_km) END AS "coordinateUncertaintyInMeters", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN 'source data'::coordinatesource WHEN (county_centroids.row_num IS NOT NULL) THEN 'georeferencing'::coordinatesource ELSE NULL::coordinatesource END AS "coordinateSource_bien", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN NULL::text WHEN (county_centroids.row_num IS NOT NULL) THEN 'county centroid'::text ELSE NULL::text END AS "georeferenceProtocol_bien", (canon_place.geovalid)::integer AS geovalid_bien, ("newWorldCountries"."isNewWorld")::integer AS "isNewWorld_bien", COALESCE(project.sourceaccessioncode, project.projectname) AS "projectID", COALESCE(location.sourceaccessioncode, NULLIF(pg_catalog.concat_ws('; '::text, COALESCE(parent_location.sourceaccessioncode, parent_location.authorlocationcode), location.authorlocationcode), ''::text)) AS "locationID", COALESCE(parent_location.authorlocationcode, location.authorlocationcode) AS "locationName", CASE WHEN (parent_location.location_id IS NOT NULL) THEN location.authorlocationcode ELSE NULL::text END AS subplot, plantobservation.authorplantcode AS "individualCode", COALESCE(location.elevation_m, parent_location.elevation_m) AS "elevationInMeters", _m2_to_ha(COALESCE(location.area_m2, parent_location.area_m2)) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.temperature_c, parent_event.temperature_c) AS "temperature_C", COALESCE(locationevent.precipitation_m, parent_event.precipitation_m) AS precipitation_m, collector.fullname AS "recordedBy", plantobservation.authorplantcode AS "recordNumber", COALESCE(locationevent.obsstartdate, parent_event.obsstartdate, aggregateoccurrence.collectiondate) AS "dateCollected", taxonverbatim.family AS family_verbatim, COALESCE(taxonverbatim.taxonomicname, NULLIF(pg_catalog.concat_ws(' '::text, taxonverbatim.taxonname, taxonverbatim.author), ''::text), taxonlabel.taxonomicname) AS "scientificName_verbatim", identifiedby.fullname AS "identifiedBy", taxondetermination.determinationdate AS "dateIdentified", taxondetermination.notes AS "identificationRemarks", "ScrubbedTaxon"."matchedTaxonName" AS "taxonName_matched", "ScrubbedTaxon"."matchedScientificNameAuthorship" AS "scientificNameAuthorship_matched", family_higher_plant_group.higher_plant_group AS "higherPlantGroup_bien", "ScrubbedTaxon"."acceptedFamily" AS family, "ScrubbedTaxon"."acceptedGenus" AS genus, COALESCE(NULLIF(pg_catalog.concat_ws(' '::text, COALESCE("ScrubbedTaxon"."acceptedGenus", "ScrubbedTaxon"."acceptedFamily"), "ScrubbedTaxon"."acceptedSpecificEpithet", "ScrubbedTaxon"."morphospeciesSuffix"), ''::text), "ScrubbedTaxon"."acceptedTaxonName") AS "speciesBinomialWithMorphospecies", "ScrubbedTaxon"."acceptedTaxonName" AS "taxonName", "ScrubbedTaxon"."acceptedScientificNameAuthorship" AS "scientificNameAuthorship", taxonoccurrence.growthform AS "growthForm", plantobservation.reproductivecondition AS "reproductiveCondition", ((threatened_taxonlabel.taxonlabel_id IS NOT NULL))::integer AS threatened_bien, (((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)))::integer AS cultivated_bien, CASE WHEN (taxonoccurrence.iscultivated IS NOT NULL) THEN taxonoccurrence.cultivatedbasis WHEN (location.iscultivated IS NOT NULL) THEN NULL::text ELSE NULL::text END AS "cultivatedBasis_bien", aggregateoccurrence.notes AS "occurrenceRemarks", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.sourceaccessioncode AS "taxonOccurrenceID", taxonoccurrence.authortaxoncode AS "authorTaxonCode", plantobservation.sourceaccessioncode AS "individualObservationID", stemobservation.authorstemcode AS "authorStemCode" FROM ((((((((((((((((((((((((((((source JOIN location USING (source_id)) LEFT JOIN locationevent USING (location_id)) LEFT JOIN location parent_location ON ((parent_location.location_id = location.parent_id))) LEFT JOIN locationplace ON ((locationplace.location_id = COALESCE(parent_location.location_id, location.location_id)))) LEFT JOIN place datasource_place USING (place_id)) LEFT JOIN place canon_place ON ((canon_place.place_id = datasource_place.canon_place_id))) LEFT JOIN coordinates ON ((coordinates.coordinates_id = canon_place.coordinates_id))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."GADM country" = canon_place.country))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."isoCode" = iso_code_gadm."2-digit iso code"))) LEFT JOIN geoscrub.county_centroids ON ((((canon_place.country = 'United States'::text) AND (county_centroids.state = canon_place.stateprovince)) AND (county_centroids.county = canon_place.county)))) LEFT JOIN taxonoccurrence USING (locationevent_id)) LEFT JOIN locationevent parent_event ON ((parent_event.locationevent_id = locationevent.parent_id))) LEFT JOIN project ON ((project.project_id = COALESCE(locationevent.project_id, parent_event.project_id)))) LEFT JOIN method ON ((method.method_id = COALESCE(locationevent.method_id, parent_event.method_id)))) LEFT JOIN party collector ON ((collector.party_id = taxonoccurrence.collector_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcelist ON ((sourcelist.sourcelist_id = specimenreplicate.institution_id))) LEFT JOIN taxondetermination ON (((taxondetermination.taxonoccurrence_id = taxonoccurrence.taxonoccurrence_id) AND taxondetermination.is_datasource_current))) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel USING (taxonlabel_id)) LEFT JOIN "TNRS"."ScrubbedTaxon" ON (("ScrubbedTaxon"."concatenatedScientificName" = taxonlabel.taxonomicname))) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = "ScrubbedTaxon"."acceptedFamily"))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = "ScrubbedTaxon"."acceptedFamily") AND (cultivated_family_locations.country = canon_place.country)))) LEFT JOIN threatened_taxonlabel USING (taxonlabel_id)) ORDER BY source.shortname; |
|
2490 |
SELECT source.shortname AS datasource, sourcelist.name AS "institutionCode", specimenreplicate.collectioncode_dwc AS "collectionCode", specimenreplicate.catalognumber_dwc AS "catalogNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", canon_place.country, canon_place.stateprovince AS "stateProvince", datasource_place.county, location.locationnarrative AS locality, CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.latitude_deg ELSE county_centroids.latitude END AS "decimalLatitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.longitude_deg ELSE county_centroids.longitude END AS "decimalLongitude", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN coordinates.coordsaccuracy_m ELSE _km_to_m(county_centroids.error_km) END AS "coordinateUncertaintyInMeters", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN 'source data'::coordinatesource WHEN (county_centroids.row_num IS NOT NULL) THEN 'georeferencing'::coordinatesource ELSE NULL::coordinatesource END AS "coordinateSource_bien", CASE WHEN (coordinates.latitude_deg IS NOT NULL) THEN NULL::text WHEN (county_centroids.row_num IS NOT NULL) THEN 'county centroid'::text ELSE NULL::text END AS "georeferenceProtocol_bien", (canon_place.geovalid)::integer AS geovalid_bien, ("newWorldCountries"."isNewWorld")::integer AS "isNewWorld_bien", COALESCE(project.sourceaccessioncode, project.projectname) AS "projectID", COALESCE(location.sourceaccessioncode, NULLIF(pg_catalog.concat_ws('; '::text, COALESCE(parent_location.sourceaccessioncode, parent_location.authorlocationcode), location.authorlocationcode), ''::text)) AS "locationID", COALESCE(parent_location.authorlocationcode, location.authorlocationcode) AS "locationName", CASE WHEN (parent_location.location_id IS NOT NULL) THEN location.authorlocationcode ELSE NULL::text END AS subplot, plantobservation.authorplantcode AS "individualCode", COALESCE(location.elevation_m, parent_location.elevation_m) AS "elevationInMeters", _m2_to_ha(COALESCE(location.area_m2, parent_location.area_m2)) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.temperature_c, parent_event.temperature_c) AS "temperature_C", COALESCE(locationevent.precipitation_m, parent_event.precipitation_m) AS precipitation_m, collector.fullname AS "recordedBy", plantobservation.authorplantcode AS "recordNumber", COALESCE(locationevent.obsstartdate, parent_event.obsstartdate, aggregateoccurrence.collectiondate) AS "dateCollected", taxonverbatim.family AS family_verbatim, COALESCE(taxonverbatim.taxonomicname, NULLIF(pg_catalog.concat_ws(' '::text, taxonverbatim.taxonname, taxonverbatim.author), ''::text), taxonlabel.taxonomicname) AS "scientificName_verbatim", identifiedby.fullname AS "identifiedBy", taxondetermination.determinationdate AS "dateIdentified", taxondetermination.notes AS "identificationRemarks", "ScrubbedTaxon"."matchedFamily" AS family_matched, "ScrubbedTaxon"."matchedTaxonName" AS "taxonName_matched", "ScrubbedTaxon"."matchedScientificNameAuthorship" AS "scientificNameAuthorship_matched", family_higher_plant_group.higher_plant_group AS "higherPlantGroup_bien", "ScrubbedTaxon"."acceptedFamily" AS family, "ScrubbedTaxon"."acceptedGenus" AS genus, COALESCE(NULLIF(pg_catalog.concat_ws(' '::text, COALESCE("ScrubbedTaxon"."acceptedGenus", "ScrubbedTaxon"."acceptedFamily"), "ScrubbedTaxon"."acceptedSpecificEpithet", "ScrubbedTaxon"."morphospeciesSuffix"), ''::text), "ScrubbedTaxon"."acceptedTaxonName") AS "speciesBinomialWithMorphospecies", "ScrubbedTaxon"."acceptedTaxonName" AS "taxonName", "ScrubbedTaxon"."acceptedScientificNameAuthorship" AS "scientificNameAuthorship", taxonoccurrence.growthform AS "growthForm", plantobservation.reproductivecondition AS "reproductiveCondition", ((threatened_taxonlabel.taxonlabel_id IS NOT NULL))::integer AS threatened_bien, (((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)))::integer AS cultivated_bien, CASE WHEN (taxonoccurrence.iscultivated IS NOT NULL) THEN taxonoccurrence.cultivatedbasis WHEN (location.iscultivated IS NOT NULL) THEN NULL::text ELSE NULL::text END AS "cultivatedBasis_bien", aggregateoccurrence.notes AS "occurrenceRemarks", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.sourceaccessioncode AS "taxonOccurrenceID", taxonoccurrence.authortaxoncode AS "authorTaxonCode", plantobservation.sourceaccessioncode AS "individualObservationID", stemobservation.authorstemcode AS "authorStemCode" FROM ((((((((((((((((((((((((((((source JOIN location USING (source_id)) LEFT JOIN locationevent USING (location_id)) LEFT JOIN location parent_location ON ((parent_location.location_id = location.parent_id))) LEFT JOIN locationplace ON ((locationplace.location_id = COALESCE(parent_location.location_id, location.location_id)))) LEFT JOIN place datasource_place USING (place_id)) LEFT JOIN place canon_place ON ((canon_place.place_id = datasource_place.canon_place_id))) LEFT JOIN coordinates ON ((coordinates.coordinates_id = canon_place.coordinates_id))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."GADM country" = canon_place.country))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."isoCode" = iso_code_gadm."2-digit iso code"))) LEFT JOIN geoscrub.county_centroids ON ((((canon_place.country = 'United States'::text) AND (county_centroids.state = canon_place.stateprovince)) AND (county_centroids.county = canon_place.county)))) LEFT JOIN taxonoccurrence USING (locationevent_id)) LEFT JOIN locationevent parent_event ON ((parent_event.locationevent_id = locationevent.parent_id))) LEFT JOIN project ON ((project.project_id = COALESCE(locationevent.project_id, parent_event.project_id)))) LEFT JOIN method ON ((method.method_id = COALESCE(locationevent.method_id, parent_event.method_id)))) LEFT JOIN party collector ON ((collector.party_id = taxonoccurrence.collector_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcelist ON ((sourcelist.sourcelist_id = specimenreplicate.institution_id))) LEFT JOIN taxondetermination ON (((taxondetermination.taxonoccurrence_id = taxonoccurrence.taxonoccurrence_id) AND taxondetermination.is_datasource_current))) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel USING (taxonlabel_id)) LEFT JOIN "TNRS"."ScrubbedTaxon" ON (("ScrubbedTaxon"."concatenatedScientificName" = taxonlabel.taxonomicname))) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = "ScrubbedTaxon"."acceptedFamily"))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = "ScrubbedTaxon"."acceptedFamily") AND (cultivated_family_locations.country = canon_place.country)))) LEFT JOIN threatened_taxonlabel USING (taxonlabel_id)) ORDER BY source.shortname;
|
|
2491 | 2491 |
|
2492 | 2492 |
|
2493 | 2493 |
-- |
Also available in: Unified diff
inputs/.TNRS/schema.sql, data.sql: updated TNRS CSV columns to preserve Name_matched_accepted_family even though it isn't present in the current TNRS CSVs. this way, Name_matched_accepted_family can still be used for previously-scrubbed names, and family_matched can be added back to analytical_stem_view. (now that bin/tnrs_db uses an explicit columns list in COPY TO, the absence of a column in the CSV is no longer a problem.)