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Revision 10403

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/test_taxonomic_names/_scrub/run: exports/make(): subset the columns to include only the most important to demo how the data is represented

View differences:

inputs/test_taxonomic_names/_scrub/tnrs.csv
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_name_species,Accepted_name_family,Selected,Source,Warnings,Accepted_name_lsid,Accepted_scientific_name,Max_score,Is_homonym,Is_plant
2 
2013-07-24 15:11:44.310741-07,0,Fam_indet. Boyle#6501,0,No suitable matches found.,,0,,,,0,,0,,,0,,0,,,0,,,0,,,,,,,,,,true,, ,,,0,,
3 
2013-07-24 15:11:44.310741-07,1,Poa annua var. eriolepis,1,Poa annua var. eriolepis,variety,1,E. Desv.,http://www.tropicos.org/Name/50119145,,,,,Poaceae,Poa,1,annua,1,var.,eriolepis,1,,,,,,Synonym,Poa annua,L.,species,http://www.tropicos.org/Name/25509881,Poa annua,Poaceae,true,tropicos, ,,Poaceae Poa annua L.,1,f,t
4 
2013-07-24 15:11:44.310741-07,2,Poa annua,1,Poa annua,species,1,L.,http://www.tropicos.org/Name/25509881,,,,,Poaceae,Poa,1,annua,1,,,,,,,,,Accepted,Poa annua,L.,species,http://www.tropicos.org/Name/25509881,Poa annua,Poaceae,true,tropicos, ,,Poaceae Poa annua L.,1,f,t
5 
2013-07-24 15:11:44.310741-07,3,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,,,,,Caryophyllaceae,Silene,1,scouleri,1,subsp.,pringlei,1,,,,,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] ,,Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire,1,t,t
6 
2013-07-24 15:11:44.310741-07,4,Fabaceae Boyle#6500,0.9,Fabaceae,family,1,Lindl.,http://www.tropicos.org/Name/42000184,,,Fabaceae,1,Fabaceae,,,,,,,,,,,,Boyle#6500,Accepted,Fabaceae,Lindl.,family,http://www.tropicos.org/Name/42000184,,Fabaceae,true,tropicos, ,,Fabaceae Lindl.,1,f,t
7 
2013-07-24 15:11:44.310741-07,5,Poa annua subsp. exilis,1,Poa annua subsp. exilis,subspecies,1,(Tomm. ex Freyn) Asch. & Graebn.,http://www.tropicos.org/Name/50063800,,,,,Poaceae,Poa,1,annua,1,subsp.,exilis,1,,,,,,Synonym,Poa infirma,Kunth,species,http://www.tropicos.org/Name/25514158,Poa infirma,Poaceae,true,tropicos, ,,Poaceae Poa infirma Kunth,1,f,t
8 
2013-07-24 15:11:44.310741-07,6,Poa annua ssp. exilis,1,Poa annua subsp. exilis,subspecies,1,(Tomm. ex Freyn) Asch. & Graebn.,http://www.tropicos.org/Name/50063800,,,,,Poaceae,Poa,1,annua,1,subsp.,exilis,1,,,,,,Synonym,Poa infirma,Kunth,species,http://www.tropicos.org/Name/25514158,Poa infirma,Poaceae,true,tropicos, ,,Poaceae Poa infirma Kunth,1,f,t
9 
2013-07-24 15:11:44.310741-07,7,Poa annua subvar. minima,1,Poa annua subvar. minima,subvariety,1,(Schur) Asch. & Graebn.,http://www.tropicos.org/Name/50158097,,,,,Poaceae,Poa,1,annua,1,subvar.,minima,1,,,,,,Accepted,Poa annua subvar. minima,(Schur) Asch. & Graebn.,subvariety,http://www.tropicos.org/Name/50158097,Poa annua,Poaceae,true,tropicos, ,,Poaceae Poa annua subvar. minima (Schur) Asch. & Graebn.,1,f,t
10 
2013-07-24 15:11:44.310741-07,8,Poa annua L.,1,Poa annua,species,1,L.,http://www.tropicos.org/Name/25509881,L.,1,,,Poaceae,Poa,1,annua,1,,,,,,,,,Accepted,Poa annua,L.,species,http://www.tropicos.org/Name/25509881,Poa annua,Poaceae,true,tropicos, ,,Poaceae Poa annua L.,1,f,t
11 
2013-07-24 15:11:44.310741-07,9,Compositae indet. sp.1,0.9,Compositae,family,1,Giseke,http://www.tropicos.org/Name/50255940,,,Compositae,1,Compositae,,,,,,,,,,,,indet. sp.1,Synonym,Asteraceae,Bercht. & J. Presl,family,http://www.tropicos.org/Name/50307371,,Asteraceae,true,tropicos, ,,Asteraceae Bercht. & J. Presl,1,f,t
12 
2013-07-24 15:11:44.310741-07,10,Poa annua fo. lanuginosa,1,Poa annua fo. lanuginosa,forma,1,Sennen,http://www.tropicos.org/Name/50267771,,,,,Poaceae,Poa,1,annua,1,fo.,lanuginosa,1,,,,,,Synonym,Poa annua var. annua,,variety,http://www.tropicos.org/Name/25517736,Poa annua,Poaceae,true,tropicos, ,,Poaceae Poa annua var. annua,1,f,t
13 
2013-07-24 15:11:44.310741-07,11,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,,,,,Caryophyllaceae,Silene,1,scouleri,1,subsp.,pringlei,1,,,,,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] ,,Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire,1,t,t
14 
2013-07-24 15:11:44.310741-07,12,"Fabaceae Inga ""fuzzy leaf""",0.9,Inga,genus,1,Mill.,http://www.tropicos.org/Name/40031040,,,Fabaceae,1,Fabaceae,Inga,1,,,,,,,,,,"""fuzzy leaf""",Accepted,Inga,Mill.,genus,http://www.tropicos.org/Name/40031040,,Fabaceae,true,tropicos, ,,Fabaceae Inga Mill.,1,t,t
15 
2013-07-24 15:11:44.310741-07,13,Fabaceae Inga sp.3,0.9,Inga,genus,1,Mill.,http://www.tropicos.org/Name/40031040,,,Fabaceae,1,Fabaceae,Inga,1,,,,,,,,,,sp.3,Accepted,Inga,Mill.,genus,http://www.tropicos.org/Name/40031040,,Fabaceae,true,tropicos, ,,Fabaceae Inga Mill.,1,t,t
16 
2013-07-24 15:11:44.310741-07,14,Fabaceae unknown #2,0.9,Fabaceae,family,1,Lindl.,http://www.tropicos.org/Name/42000184,,,Fabaceae,1,Fabaceae,,,,,,,,,,,,unknown #2,Accepted,Fabaceae,Lindl.,family,http://www.tropicos.org/Name/42000184,,Fabaceae,true,tropicos, ,,Fabaceae Lindl.,1,f,t
17 
2013-07-24 15:11:47.497803-07,0,Poaceae Poa infirma Kunth,1,Poa infirma,species,1,Kunth,http://www.tropicos.org/Name/25514158,Kunth,1,Poaceae,1,Poaceae,Poa,1,infirma,1,,,,,,,,,Accepted,Poa infirma,Kunth,species,http://www.tropicos.org/Name/25514158,Poa infirma,Poaceae,true,tropicos, ,,Poaceae Poa infirma Kunth,1,f,t
18 
2013-07-24 15:11:47.497803-07,1,Fabaceae Lindl.,0.5,Fabaceae,family,0.5,Lindl.,http://www.tropicos.org/Name/42000184,,,Fabaceae,1,Fabaceae,,,,,,,,,,,,Lindl.,Accepted,Fabaceae,Lindl.,family,http://www.tropicos.org/Name/42000184,,Fabaceae,true,tropicos, [Partial match] ,,Fabaceae Lindl.,1,f,t
19 
2013-07-24 15:11:47.497803-07,2,Poaceae Poa annua subvar. minima (Schur) Asch. & Graebn.,1,Poa annua subvar. minima,subvariety,1,(Schur) Asch. & Graebn.,http://www.tropicos.org/Name/50158097,(Schur) Asch. & Graebn.,1,Poaceae,1,Poaceae,Poa,1,annua,1,subvar.,minima,1,,,,,,Accepted,Poa annua subvar. minima,(Schur) Asch. & Graebn.,subvariety,http://www.tropicos.org/Name/50158097,Poa annua,Poaceae,true,tropicos, ,,Poaceae Poa annua subvar. minima (Schur) Asch. & Graebn.,1,f,t
20 
2013-07-24 15:11:47.497803-07,3,Fabaceae Inga Mill.,1,Inga,genus,1,Mill.,http://www.tropicos.org/Name/40031040,Mill.,1,Fabaceae,1,Fabaceae,Inga,1,,,,,,,,,,,Accepted,Inga,Mill.,genus,http://www.tropicos.org/Name/40031040,,Fabaceae,true,tropicos, ,,Fabaceae Inga Mill.,1,f,t
21 
2013-07-24 15:11:47.497803-07,4,Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire,1,Silene scouleri subsp. pringlei,subspecies,1,(S. Watson) C.L. Hitchc. & Maguire,http://www.tropicos.org/Name/6303627,(S. Watson) C.L. Hitchc. & Maguire,1,Caryophyllaceae,1,Caryophyllaceae,Silene,1,scouleri,1,subsp.,pringlei,1,,,,,,Accepted,Silene scouleri subsp. pringlei,(S. Watson) C.L. Hitchc. & Maguire,subspecies,http://www.tropicos.org/Name/6303627,Silene scouleri,Caryophyllaceae,true,tropicos, ,,Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire,1,f,t
22 
2013-07-24 15:11:47.497803-07,5,Poaceae Poa annua L.,1,Poa annua,species,1,L.,http://www.tropicos.org/Name/25509881,L.,1,Poaceae,1,Poaceae,Poa,1,annua,1,,,,,,,,,Accepted,Poa annua,L.,species,http://www.tropicos.org/Name/25509881,Poa annua,Poaceae,true,tropicos, ,,Poaceae Poa annua L.,1,f,t
23 
2013-07-24 15:11:47.497803-07,6,Asteraceae Bercht. & J. Presl,0.4,Asteraceae,family,0.5,,http://compositae.landcareresearch.co.nz/default.aspx,,,Asteraceae,1,,,,,,,,,,,,,Bercht. & J. Presl,Accepted,Asteraceae,,family,http://compositae.landcareresearch.co.nz/default.aspx,,,true,gcc, [Partial match] ,,Asteraceae,1,f,t
24 
2013-07-24 15:11:47.497803-07,7,Poaceae Poa annua var. annua,1,Poa annua var. annua,variety,1,,http://www.tropicos.org/Name/25517736,,,Poaceae,1,Poaceae,Poa,1,annua,1,var.,annua,1,,,,,,Accepted,Poa annua var. annua,,variety,http://www.tropicos.org/Name/25517736,Poa annua,Poaceae,true,tropicos, ,,Poaceae Poa annua var. annua,1,f,t
25 
2013-07-24 15:11:49.527902-07,0,Asteraceae,1,Asteraceae,family,1,,http://compositae.landcareresearch.co.nz/default.aspx,,,Asteraceae,1,,,,,,,,,,,,,,Accepted,Asteraceae,,family,http://compositae.landcareresearch.co.nz/default.aspx,,,true,gcc, ,,Asteraceae,1,f,t
1 
Name_number,Name_submitted,Family_matched,Genus_matched,Specific_epithet_matched,Taxonomic_status,Accepted_scientific_name
2 
0,Fam_indet. Boyle#6501,,,,,
3 
1,Poa annua var. eriolepis,,Poa,annua,Synonym,Poaceae Poa annua L.
4 
2,Poa annua,,Poa,annua,Accepted,Poaceae Poa annua L.
5 
3,Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire,,Silene,scouleri,Accepted,Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire
6 
4,Fabaceae Boyle#6500,Fabaceae,,,Accepted,Fabaceae Lindl.
7 
5,Poa annua subsp. exilis,,Poa,annua,Synonym,Poaceae Poa infirma Kunth
8 
6,Poa annua ssp. exilis,,Poa,annua,Synonym,Poaceae Poa infirma Kunth
9 
7,Poa annua subvar. minima,,Poa,annua,Accepted,Poaceae Poa annua subvar. minima (Schur) Asch. & Graebn.
10 
8,Poa annua L.,,Poa,annua,Accepted,Poaceae Poa annua L.
11 
9,Compositae indet. sp.1,Compositae,,,Synonym,Asteraceae Bercht. & J. Presl
12 
10,Poa annua fo. lanuginosa,,Poa,annua,Synonym,Poaceae Poa annua var. annua
13 
11,Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire,,Silene,scouleri,Accepted,Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire
14 
12,"Fabaceae Inga ""fuzzy leaf""",Fabaceae,Inga,,Accepted,Fabaceae Inga Mill.
15 
13,Fabaceae Inga sp.3,Fabaceae,Inga,,Accepted,Fabaceae Inga Mill.
16 
14,Fabaceae unknown #2,Fabaceae,,,Accepted,Fabaceae Lindl.
17 
0,Poaceae Poa infirma Kunth,Poaceae,Poa,infirma,Accepted,Poaceae Poa infirma Kunth
18 
1,Fabaceae Lindl.,Fabaceae,,,Accepted,Fabaceae Lindl.
19 
2,Poaceae Poa annua subvar. minima (Schur) Asch. & Graebn.,Poaceae,Poa,annua,Accepted,Poaceae Poa annua subvar. minima (Schur) Asch. & Graebn.
20 
3,Fabaceae Inga Mill.,Fabaceae,Inga,,Accepted,Fabaceae Inga Mill.
21 
4,Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire,Caryophyllaceae,Silene,scouleri,Accepted,Caryophyllaceae Silene scouleri subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire
22 
5,Poaceae Poa annua L.,Poaceae,Poa,annua,Accepted,Poaceae Poa annua L.
23 
6,Asteraceae Bercht. & J. Presl,Asteraceae,,,Accepted,Asteraceae
24 
7,Poaceae Poa annua var. annua,Poaceae,Poa,annua,Accepted,Poaceae Poa annua var. annua
25 
0,Asteraceae,Asteraceae,,,Accepted,Asteraceae
inputs/test_taxonomic_names/_scrub/taxonlabel.csv
1 
taxonlabel_id,source_id,sourceaccessioncode,taxonstatus,canon_label_id,matched_label_id,parent_id,taxonepithet,rank,taxonomicname
2 
2,2,1,,2,,,,,Poa annua
3 
4,2,2,,4,,,,,Poa annua L.
4 
6,2,3,,6,,,,,Poa annua var. eriolepis
5 
8,2,4,,8,,,,,Poa annua subsp. exilis
6 
10,2,5,,10,,,,,Poa annua ssp. exilis
7 
12,2,6,,12,,,,,Poa annua subvar. minima
8 
14,2,7,,14,,,,,Poa annua fo. lanuginosa
9 
16,2,8,,16,,,,,Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire
10 
18,2,9,,18,,,,,Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire
11 
20,2,10,,20,,,,,Fabaceae Inga sp.3
12 
22,2,11,,22,,,,,"Fabaceae Inga ""fuzzy leaf"""
13 
24,2,12,,24,,,,,Fabaceae unknown #2
14 
26,2,13,,26,,,,,Fabaceae Boyle#6500
15 
28,2,14,,28,,,,,Fam_indet. Boyle#6501
16 
30,2,15,,30,,,,,Compositae indet. sp.1
1 
taxonlabel_id,taxonomicname
2 
2,Poa annua
3 
4,Poa annua L.
4 
6,Poa annua var. eriolepis
5 
8,Poa annua subsp. exilis
6 
10,Poa annua ssp. exilis
7 
12,Poa annua subvar. minima
8 
14,Poa annua fo. lanuginosa
9 
16,Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire
10 
18,Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire
11 
20,Fabaceae Inga sp.3
12 
22,"Fabaceae Inga ""fuzzy leaf"""
13 
24,Fabaceae unknown #2
14 
26,Fabaceae Boyle#6500
15 
28,Fam_indet. Boyle#6501
16 
30,Compositae indet. sp.1
inputs/test_taxonomic_names/_scrub/run
10 10 
exports/make()
11 11 
{
12 12 
	echo_func
13 
	(schema=public."$schema"
14 
		cols=* pg_export_tables_to_dir taxonverbatim
15 
		cols=* pg_export_tables_to_dir taxonlabel
13 
	(schema=public.$schema
14 
		cols=(taxonverbatim_id taxonlabel_id taxonname); \
15 
pg_export_tables_to_dir taxonverbatim
16 
		cols=(taxonlabel_id taxonomicname); pg_export_tables_to_dir taxonlabel
16 17 
	)
17 18 
	(schema=TNRS
18 
		cols=* pg_export_tables_to_dir tnrs
19 
		cols=(Name_number Name_submitted Family_matched Genus_matched
20 
Specific_epithet_matched Taxonomic_status Accepted_scientific_name); \
21 
pg_export_tables_to_dir tnrs
19 22 
	)
20 23 
}
21 24 

  		












  

    
      inputs/test_taxonomic_names/_scrub/taxonverbatim.csv
    
  





  1
  
  
    
taxonverbatim_id,source_id,taxonlabel_id,verbatimrank,taxonomicname,taxonname,author,family,genus,specific_epithet,morphospecies,morphoname,growthform,description


  		




  2
  
  
    
2,2,2,,,Poa annua,,,,,,,,


  		




  3
  
  
    
4,2,4,,,Poa annua L.,,,,,,,,


  		




  4
  
  
    
6,2,6,,,Poa annua var. eriolepis,,,,,,,,


  		




  5
  
  
    
8,2,8,,,Poa annua subsp. exilis,,,,,,,,


  		




  6
  
  
    
10,2,10,,,Poa annua ssp. exilis,,,,,,,,


  		




  7
  
  
    
12,2,12,,,Poa annua subvar. minima,,,,,,,,


  		




  8
  
  
    
14,2,14,,,Poa annua fo. lanuginosa,,,,,,,,


  		




  9
  
  
    
16,2,16,,,Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire,,,,,,,,


  		




  10
  
  
    
18,2,18,,,Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire,,,,,,,,


  		




  11
  
  
    
20,2,20,,,Fabaceae Inga sp.3,,,,,,,,


  		




  12
  
  
    
22,2,22,,,"Fabaceae Inga ""fuzzy leaf""",,,,,,,,


  		




  13
  
  
    
24,2,24,,,Fabaceae unknown #2,,,,,,,,


  		




  14
  
  
    
26,2,26,,,Fabaceae Boyle#6500,,,,,,,,


  		




  15
  
  
    
28,2,28,,,Fam_indet. Boyle#6501,,,,,,,,


  		




  16
  
  
    
30,2,30,,,Compositae indet. sp.1,,,,,,,,


  		




  
  1
  
    
taxonverbatim_id,taxonlabel_id,taxonname


  		




  
  2
  
    
2,2,Poa annua


  		




  
  3
  
    
4,4,Poa annua L.


  		




  
  4
  
    
6,6,Poa annua var. eriolepis


  		




  
  5
  
    
8,8,Poa annua subsp. exilis


  		




  
  6
  
    
10,10,Poa annua ssp. exilis


  		




  
  7
  
    
12,12,Poa annua subvar. minima


  		




  
  8
  
    
14,14,Poa annua fo. lanuginosa


  		




  
  9
  
    
16,16,Silene scouleri subsp. pringlei var. grisea C.L. Hitchc. & Maguire


  		




  
  10
  
    
18,18,Silene scouleri Hook. subsp. pringlei (S. Watson) C.L. Hitchc. & Maguire var. grisea C.L. Hitchc. & Maguire


  		




  
  11
  
    
20,20,Fabaceae Inga sp.3


  		




  
  12
  
    
22,22,"Fabaceae Inga ""fuzzy leaf"""


  		




  
  13
  
    
24,24,Fabaceae unknown #2


  		




  
  14
  
    
26,26,Fabaceae Boyle#6500


  		




  
  15
  
    
28,28,Fam_indet. Boyle#6501


  		




  
  16
  
    
30,30,Compositae indet. sp.1


  		












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