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Revision 10098

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/.NCBI/: added new-style import runscripts, which renamed the staging table columns to VegCore

View differences:

inputs/.NCBI/Source/run
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#!/bin/bash -e
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      inputs/.NCBI/run
    
  





  
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#!/bin/bash -e


  		




  
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run


  		




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      inputs/.NCBI/nodes/run
    
  





  
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#!/bin/bash -e


  		




  
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run


  		




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      inputs/.NCBI/nodes/VegBIEN.csv
    
  





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NCBI,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments


  		




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parent tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode,


  		




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parent tax_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/cond/_exists",


  		




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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",


  		




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rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,


  		




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tax_id,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,


  		




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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",


  		




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name_txt,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then",


  		




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rank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",


  		




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name_txt,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3,


  		




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rank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,


  		




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4,,** No join mapping for *4 ** 


  		




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5,,** No join mapping for *5 ** 


  		




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6,,** No join mapping for *6 ** 


  		




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7,,** No join mapping for *7 ** 


  		




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8,,** No join mapping for *8 ** 


  		




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9,,** No join mapping for *9 ** 


  		




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embl code,,** No join mapping for *embl code ** 


  		




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name class,,** No join mapping for *name class ** 


  		




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


  		




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


  		




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unique name,,** No join mapping for *unique name ** 


  		




  
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NCBI,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Filter; Comments,Comments


  		




  
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parentTaxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_taxonlabel_set_parent_id/parent_id/taxonlabel/sourceaccessioncode,


  		




  
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parentTaxonID,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/cond/_exists",


  		




  
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taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",


  		




  
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taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,


  		




  
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taxonID,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/sourceaccessioncode,


  		




  
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taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",


  		




  
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taxonNameOrEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/then",


  		




  
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taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",


  		




  
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taxonNameOrEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/3,


  		




  
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taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,


  		




  
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*4,,** No join mapping for *4 ** 


  		




  
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*5,,** No join mapping for *5 ** 


  		




  
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*6,,** No join mapping for *6 ** 


  		




  
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*7,,** No join mapping for *7 ** 


  		




  
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*8,,** No join mapping for *8 ** 


  		




  
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*9,,** No join mapping for *9 ** 


  		




  
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*embl code,,** No join mapping for *embl code ** 


  		




  
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*name class,,** No join mapping for *name class ** 


  		




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


  		




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


  		




  
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*unique name,,** No join mapping for *unique name ** 


  		












  

    
      inputs/.NCBI/nodes/test.xml.ref
    
  





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                                        <taxonverbatim>


  		




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                                            <taxonlabel_id>


  		




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                                                <taxonlabel>


  		




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                                                    <_taxonlabel_set_parent_id><parent_id><taxonlabel><sourceaccessioncode>$parent tax_id</sourceaccessioncode></taxonlabel></parent_id></_taxonlabel_set_parent_id>


  		




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                                                    <rank>$rank</rank>


  		




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                                                    <sourceaccessioncode>$tax_id</sourceaccessioncode>


  		




  
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                                                    <_taxonlabel_set_parent_id><parent_id><taxonlabel><sourceaccessioncode>$parentTaxonID</sourceaccessioncode></taxonlabel></parent_id></_taxonlabel_set_parent_id>


  		




  
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                                                    <rank>$taxonRank</rank>


  		




  
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                                                    <sourceaccessioncode>$taxonID</sourceaccessioncode>


  		




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                                                    <taxonepithet>


  		




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                                                        <_if name="if taxonomic name is epithet">


  		




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                                                            <cond>


  		




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                                                                <_alt>


  		




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                                                                    <2>true</2>


  		




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                                                                    <1><_taxonomic_name_is_epithet><rank>$rank</rank></_taxonomic_name_is_epithet></1>


  		




  
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                                                                    <1><_taxonomic_name_is_epithet><rank>$taxonRank</rank></_taxonomic_name_is_epithet></1>


  		




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                                                                </_alt>


  		




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                                                            </cond>


  		




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                                                            <then>$name_txt</then>


  		




  
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                                                            <then>$taxonNameOrEpithet</then>


  		




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                                                        </_if>


  		




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                                                    </taxonepithet>


  		




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                                                    <taxonomicname>$name_txt</taxonomicname>


  		




  
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                                                    <taxonomicname>$taxonNameOrEpithet</taxonomicname>


  		




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                                                </taxonlabel>


  		




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                                            </taxonlabel_id>


  		




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                                            <verbatimrank>$rank</verbatimrank>


  		




  
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                                            <verbatimrank>$taxonRank</verbatimrank>


  		




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                                        </taxonverbatim>


  		




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                                    </taxonverbatim_id>


  		




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                                </taxondetermination>


  		












  

    
      inputs/.NCBI/table.run
    
  





  
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#!/bin/bash -e


  		




  
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/table.run


  		




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      inputs/.NCBI/Makefile
    
  





  
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include ../input.Makefile


  		












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