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Revision 10418

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/CTFS/StemObservation/: translated collisions (missing filters) to postprocessing derived columns, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns

View differences:

inputs/CTFS/StemObservation/postprocess.sql
1 
SELECT util.search_path_append('util');
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  3
  
    
SELECT mk_derived_col((:table_str, 'stemTag'),


  		




  
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$$concat_ws('.', "Tag", "StemTag")$$); -- runtime: 30 s ("Time: 29390.121 ms") @starscream


  		




  
  5
  
    
SELECT mk_derived_col((:table_str, 'tag'), $$"stemTag"$$); -- runtime: 25 s ("Time: 25010.752 ms") @starscream


  		












  

    
      inputs/CTFS/StemObservation/map.csv
    
  





  13
  13
  
    
PrimaryStem,*PrimaryStem,,


  		




  14
  14
  
    
ExactDate,*ExactDate,,


  		




  15
  15
  
    
Stem.src.row_num,*Stem.src.row_num,,


  		




  16
  
  
    
StemTag,tag,,


  		




  
  16
  
    
StemTag,stem_subtag,,


  		




  17
  17
  
    
StemDescription,*StemDescription,,


  		




  18
  18
  
    
Organism.src.row_num,*Organism.src.row_num,,


  		




  19
  19
  
    
QuadratID,subplot,,Not globally unique; unique only within Site


  		




  20
  20
  
    
PlotID,locationID,,


  		




  21
  
  
    
Tag,tag,,


  		




  
  21
  
    
Tag,individual_tag,,


  		




  22
  22
  
    
x,organismX_m,,"Assuming units based on the size of values relative to plot area, which has units of ha. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>."


  		




  23
  23
  
    
y,organismY_m,,"Assuming units based on the size of values relative to plot area, which has units of ha. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>."


  		




  24
  24
  
    
InfraspecificEpithet.src.row_num,*InfraspecificEpithet.src.row_num,,


  		




  ......




  45
  45
  
    
Family.src.row_num,*Family.src.row_num,,


  		




  46
  46
  
    
Family,family,,


  		




  47
  47
  
    
ReferenceID,*ReferenceID,,


  		




  
  48
  
    
stemTag,stemTag,,


  		




  
  49
  
    
tag,tag,,


  		












  

    
      inputs/CTFS/StemObservation/VegBIEN.csv
    
  





  15
  15
  
    
MeasureID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2,


  		




  16
  16
  
    
StemID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode,


  		




  17
  17
  
    
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,Assuming units based on the range and precision of values. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>.


  		




  18
  
  
    
StemTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,


  		




  19
  
  
    
Tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,


  		




  
  18
  
    
tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,


  		




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  19
  
    
x,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,"Assuming units based on the size of values relative to plot area, which has units of ha. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>."


  		




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y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,"Assuming units based on the size of values relative to plot area, which has units of ha. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>."


  		




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CensusID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",


  		




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PlotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",


  		




  24
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MeasureID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists",


  		




  25
  
  
    
StemTag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",


  		




  26
  
  
    
Tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",


  		




  
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tag,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",


  		




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  25
  
    
MeasureID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",


  		




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MeasureID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2",


  		




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SubSpeciesName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet",


  		




  ......




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Stem.src.row_num,,** No join mapping for *Stem.src.row_num ** 


  		




  69
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StemDescription,,** No join mapping for *StemDescription ** 


  		




  70
  68
  
    
StemObservation.src.row_num,,** No join mapping for *StemObservation.src.row_num ** 


  		




  
  69
  
    
StemTag,,** No join mapping for stem_subtag ** 


  		




  71
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SubSpeciesAuthority,,** No join mapping for *SubSpeciesAuthority ** 


  		




  72
  71
  
    
SubSpeciesCurrentTaxonFlag,,** No join mapping for *SubSpeciesCurrentTaxonFlag ** 


  		




  73
  72
  
    
SubSpeciesID,,** No join mapping for *SubSpeciesID ** 


  		




  74
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SubSpeciesMnemonic,,** No join mapping for *SubSpeciesMnemonic ** 


  		




  75
  74
  
    
SubSpeciesObsoleteTaxonFlag,,** No join mapping for *SubSpeciesObsoleteTaxonFlag ** 


  		




  
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Tag,,** No join mapping for individual_tag ** 


  		




  76
  76
  
    
TreeID,,** No join mapping for *TreeID ** 


  		




  
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stemTag,,** No join mapping for stemTag ** 


  		












  

    
      inputs/CTFS/StemObservation/test.xml.ref
    
  





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                                        <stemobservation>


  		




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                                            <authorstemcode>$StemID</authorstemcode>


  		




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                                            <diameterbreastheight_m><_cm_to_m><value>$DBH</value></_cm_to_m></diameterbreastheight_m>


  		




  35
  
  
    
                                            <tag>


  		




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                                                <_alt>


  		




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                                                    <0>$StemTag</0>


  		




  38
  
  
    
                                                    <1>$Tag</1>


  		




  39
  
  
    
                                                </_alt>


  		




  40
  
  
    
                                            </tag>


  		




  
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                                            <tag>$tag</tag>


  		




  41
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                                            <xposition_m>$x</xposition_m>


  		




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                                            <yposition_m>$y</yposition_m>


  		




  43
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                                        </stemobservation>


  		




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                                    </plantobservation>


  		




  45
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                                </aggregateoccurrence>


  		




  46
  
  
    
                                <authortaxoncode>


  		




  47
  
  
    
                                    <_alt>


  		




  48
  
  
    
                                        <0>$StemTag</0>


  		




  49
  
  
    
                                        <1>$Tag</1>


  		




  50
  
  
    
                                    </_alt>


  		




  51
  
  
    
                                </authortaxoncode>


  		




  
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                                <authortaxoncode>$tag</authortaxoncode>


  		




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                                <sourceaccessioncode>$MeasureID</sourceaccessioncode>


  		




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                                <taxondetermination>


  		




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                                    <taxonverbatim_id>


  		












  

    
      inputs/CTFS/StemObservation/unmapped_terms.csv
    
  





  8
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*PrimaryStem


  		




  9
  9
  
    
*ExactDate


  		




  10
  10
  
    
*Stem.src.row_num


  		




  
  11
  
    
stem_subtag


  		




  11
  12
  
    
*StemDescription


  		




  12
  13
  
    
*Organism.src.row_num


  		




  
  14
  
    
individual_tag


  		




  13
  15
  
    
*InfraspecificEpithet.src.row_num


  		




  14
  16
  
    
*SubSpeciesCurrentTaxonFlag


  		




  15
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*SubSpeciesObsoleteTaxonFlag


  		




  ......




  29
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*GenusAuthority


  		




  30
  32
  
    
*Family.src.row_num


  		




  31
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*ReferenceID


  		




  
  34
  
    
stemTag


  		












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