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Revision 4648

Added by Aaron Marcuse-Kubitza over 12 years ago

filter_out_ci: Filter header instead of passing it through, in order to properly support CSVs without a header, such as the unmapped_terms.csv and new_terms.csv files. For CSVs with a header, the header of the vocabulary should be removed before passing it to filter_out_ci.

View differences:

inputs/CTFS/PlotObservation/unmapped_terms.csv
1 
Description
inputs/FIA/Organism/unmapped_terms.csv
1 
HOM
inputs/VegBank/observation_/unmapped_terms.csv
1 
previousobs_id
2 1 
dateaccuracy
3 2 
covermethod_id
4 3 
coverdispersion
bin/filter_out_ci
1 1 
#!/usr/bin/env python
2 2 
# Finds spreadsheet rows where a column is not in a vocabulary.
3 
# The vocabulary should not have a header. CSVs without a header are supported.
3 4 
# Case- and punctuation-insensitive.
4 5 

  		




  5
  6
  
    
import csv


  		




  ......




  18
  19
  
    
    vocab = set()


  		




  19
  20
  
    
    stream = open(vocab_path, 'rb')


  		




  20
  21
  
    
    reader = csv.reader(stream)


  		




  21
  
  
    
    reader.next() # skip header


  		




  22
  22
  
    
    for row in reader: vocab.add(simplify(row[0]))


  		




  23
  23
  
    
    stream.close()


  		




  24
  24
  
    
    


  		




  25
  25
  
    
    # Filter input


  		




  26
  26
  
    
    reader = csv.reader(sys.stdin)


  		




  27
  27
  
    
    writer = csv.writer(sys.stdout)


  		




  28
  
  
    
    writer.writerow(reader.next()) # pass through header


  		




  29
  28
  
    
    for row in reader:


  		




  30
  29
  
    
        term = simplify(row[col_num])


  		




  31
  30
  
    
        if term not in vocab: writer.writerow(row)


  		












  

    
      inputs/XAL/Specimen/unmapped_terms.csv
    
  





  1
  
  
    
dcterms:modified


  		




  2
  1
  
    
BasisOfRecord


  		




  3
  2
  
    
TypeStatus


  		




  4
  3
  
    
recordNumber/_alt/1


  		












  

    
      inputs/TEAM/VL/unmapped_terms.csv
    
  





  1
  
  
    
max_diam


  		




  2
  1
  
    
max_diam_pom


  		




  3
  2
  
    
ConditionCodes


  		




  4
  3
  
    
LocationCodes


  		












  

    
      inputs/TEAM/VT/unmapped_terms.csv
    
  





  1
  
  
    
dbh_pom


  		




  2
  1
  
    
dbh_new


  		




  3
  2
  
    
dbh_new_pom


  		




  4
  3
  
    
ConditionCodes


  		












  

    
      inputs/NY/Specimen/unmapped_terms.csv
    
  





  1
  
  
    
key


  		




  2
  1
  
    
dcterms:modified


  		




  3
  2
  
    
BasisOfRecord


  		




  4
  3
  
    
TypeStatus


  		












  

    
      inputs/Madidi/Organism/unmapped_terms.csv
    
  





  1
  
  
    
Number of inventory (general)


  		




  2
  1
  
    
Number of inventory (expedition)


  		




  3
  2
  
    
"Type Inventory (C, PP, TP)"


  		




  4
  3
  
    
Similar specimen


  		












  

    
      inputs/Madidi/Plot/unmapped_terms.csv
    
  





  1
  
  
    
Inventory number


  		




  2
  1
  
    
Number of inventory (expedition)


  		




  3
  2
  
    
Installed and evaluated by


  		




  4
  3
  
    
Collaborators


  		












  

    
      inputs/UNCC/Specimen/unmapped_terms.csv
    
  





  1
  
  
    
taxonRank/_alt/1


  		




  2
  1
  
    
taxonRank/_alt/2


  		




  3
  2
  
    
Collector/_merge/1


  		




  4
  3
  
    
Collector/_merge/2


  		












  

    
      inputs/SALVIAS-CSV/Organism/unmapped_terms.csv
    
  





  1
  
  
    
ind_id


  		




  2
  1
  
    
tag/_alt/1


  		




  3
  2
  
    
previousTag/_alt/1


  		




  4
  3
  
    
catalogNumber/_alt/2


  		












  

    
      inputs/SALVIAS-CSV/Plot/unmapped_terms.csv
    
  





  1
  
  
    
"clay/_units:[default=""%"",to=]/value"


  		




  2
  1
  
    
"silt/_units:[default=""%"",to=]/value"


  		




  3
  2
  
    
"sand/_units:[default=""%"",to=]/value"


  		




  4
  3
  
    
"organic/_units:[default=""%"",to=]/value"


  		












  

    
      inputs/CVS/Organism/unmapped_terms.csv
    
  





  1
  1
  
    
OMIT


  		




  2
  
  
    
OMIT


  		




  3
  2
  
    
confidentialityStatus


  		












  

    
      inputs/REMIB/Specimen/unmapped_terms.csv
    
  





  1
  
  
    
long_min


  		




  2
  1
  
    
long_sec


  		




  3
  2
  
    
lat_min


  		




  4
  3
  
    
lat_sec


  		












  

    
      inputs/CTFS/StemObservation/unmapped_terms.csv
    
  





  1
  
  
    
FamilyID


  		




  2
  1
  
    
GenusID


  		




  3
  2
  
    
SpeciesID


  		




  4
  3
  
    
SubSpeciesID


  		












  

    
      inputs/CTFS/Subplot/unmapped_terms.csv
    
  





  1
  
  
    
OMIT


  		




  2
  1
  
    
DimX


  		




  3
  2
  
    
DimY


  		












  

    
      inputs/CTFS/TaxonOccurrence/unmapped_terms.csv
    
  





  1
  
  
    
FamilyID


  		




  2
  1
  
    
GenusID


  		




  3
  2
  
    
SpeciesID


  		




  4
  3
  
    
SubSpeciesID


  		












  

    
      inputs/CTFS/Plot/unmapped_terms.csv
    
  





  1
  
  
    
CountryID


  		




  2
  1
  
    
ReferenceX


  		




  3
  2
  
    
ReferenceY


  		




  4
  3
  
    
row_num


  		












  

    
      inputs/SALVIAS/plotMetadata/unmapped_terms.csv
    
  





  1
  
  
    
orig_filename


  		




  2
  1
  
    
AccessCode


  		




  3
  2
  
    
PrimOwnerID


  		




  4
  3
  
    
SiteName


  		












  

    
      inputs/SALVIAS/projects/unmapped_terms.csv
    
  





  1
  
  
    
project_pi


  		




  2
  1
  
    
allow_download_all


  		




  3
  2
  
    
ipr_specific


  		




  4
  3
  
    
ipr_specific_updated


  		












  

    
      inputs/SALVIAS/stems/unmapped_terms.csv
    
  





  1
  
  
    
origrecord_id_stems


  		




  2
  1
  
    
tmp_del


  		




  3
  2
  
    
plotobs_id_index


  		












  

    
      inputs/SALVIAS/plotObservations/unmapped_terms.csv
    
  





  1
  
  
    
OrigRecordID


  		




  2
  1
  
    
ind_id


  		




  3
  2
  
    
dist


  		




  4
  3
  
    
perp_dist


  		












  

    
      inputs/U/Specimen/unmapped_terms.csv
    
  





  1
  
  
    
Collector/_merge/1


  		




  2
  1
  
    
Prefix


  		




  3
  2
  
    
Suffix


  		




  4
  3
  
    
Collector/_merge/2


  		












  

    
      inputs/ARIZ/Specimen/unmapped_terms.csv
    
  





  1
  
  
    
dcterms:modified


  		




  2
  1
  
    
BasisOfRecord


  		




  3
  2
  
    
CatalogNumber/_alt/2


  		




  4
  3
  
    
CatalogNumber/_alt/1


  		












  

    
      inputs/GBIF/Specimen/unmapped_terms.csv
    
  





  1
  
  
    
0


  		




  2
  1
  
    
1


  		




  3
  2
  
    
3


  		




  4
  3
  
    
dcterms:modified


  		












  

    
      inputs/NCU-NCSC/Specimen/unmapped_terms.csv
    
  





  1
  
  
    
"Latitude/_replace:[""\?$""=]/value"


  		




  2
  1
  
    
"Longitude/_replace:[""\?$""=]/value"


  		




  3
  2
  
    
FIPS


  		




  4
  3
  
    
Alt N/S


  		












  

    
      inputs/SpeciesLink/Specimen/unmapped_terms.csv
    
  





  1
  
  
    
dcterms:modified


  		




  2
  1
  
    
BasisOfRecord


  		




  3
  2
  
    
ScientificNameAuthor/_alt/3


  		




  4
  3
  
    
JulianDay/_alt/2


  		












  

    
      inputs/VegBank/taxonobservation_/unmapped_terms.csv
    
  





  1
  
  
    
plantconcept_id


  		




  2
  1
  
    
taxonobservation_reference_id


  		




  3
  2
  
    
taxoninferencearea


  		




  4
  3
  
    
emb_taxonobservation


  		












  

    
      inputs/VegBank/plot_/unmapped_terms.csv
    
  





  1
  
  
    
reference_id


  		




  2
  1
  
    
parentPlotID


  		




  3
  2
  
    
OMIT


  		




  4
  3
  
    
OMIT


  		












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