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Revision 10313

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/ACAD/: switched to new-style import, using the steps at wiki.vegpath.org/Switching_to_new-style_import#stage-I-source-specific > "run the following for each datasource"

View differences:

inputs/ACAD/Specimen/postprocess.sql
1 1 
SELECT util.search_path_append('util');
2 2 

  		




  3
  3
  
    
SELECT mk_derived_col((:table_str, 'specimenHolderInstitutions'),


  		




  4
  
  
    
$$_map('"Acadia University"=>"ACAD", "*"=>"*"', "institutionCode")$$);


  		




  
  4
  
    
$$_map('"Acadia University"=>"ACAD", "*"=>"*"', "specimenHolderInstitutions_verbatim")$$);


  		












  

    
      inputs/ACAD/Specimen/run
    
  





  
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#!/bin/bash -e


  		




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


  		




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  3
  
    

  		












  

    
      inputs/ACAD/Specimen/test.xml.ref
    
  





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                    <location>


  		




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                        <authorlocationcode>


  		




  11
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                            <_alt>


  		




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                                <1>$id</1>


  		




  
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                                <1>$dataProviderRecordID</1>


  		




  13
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                                <2>


  		




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                                    <_join>


  		




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                                        <1>$specimenHolderInstitutions</1>


  		




  16
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                                        <2>


  		




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                                            <_join>


  		




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                                                <1>$collectionCode</1>


  		




  19
  
  
    
                                                <2>$collectionID</2>


  		




  
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                                                <1>$collection</1>


  		




  
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                                                <2>$collectionURL</2>


  		




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                                            </_join>


  		




  21
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                                        </2>


  		




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                                        <3>$catalogNumber</3>


  		




  
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                                        <3>$accessionNumber</3>


  		




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                                    </_join>


  		




  24
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                                </2>


  		




  25
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                            </_alt>


  		




  ......




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                                <aggregateoccurrence>


  		




  50
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                                    <notes>$occurrenceRemarks</notes>


  		




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                                    <plantobservation>


  		




  52
  
  
    
                                        <authorplantcode>$recordNumber</authorplantcode>


  		




  
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                                        <authorplantcode>$collectorNumber</authorplantcode>


  		




  53
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                                        <reproductivecondition>$reproductiveCondition</reproductivecondition>


  		




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                                        <specimenreplicate>


  		




  55
  
  
    
                                            <catalognumber_dwc>$catalogNumber</catalognumber_dwc>


  		




  
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                                            <catalognumber_dwc>$accessionNumber</catalognumber_dwc>


  		




  56
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                                            <collectioncode_dwc>


  		




  57
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                                                <_alt>


  		




  58
  
  
    
                                                    <1>$collectionCode</1>


  		




  59
  
  
    
                                                    <2>$collectionID</2>


  		




  
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                                                    <1>$collection</1>


  		




  
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                                                    <2>$collectionURL</2>


  		




  60
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                                                </_alt>


  		




  61
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                                            </collectioncode_dwc>


  		




  62
  
  
    
                                            <collectionnumber>$recordNumber</collectionnumber>


  		




  
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                                            <collectionnumber>$collectorNumber</collectionnumber>


  		




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                                            <institution_id>


  		




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                                                <sourcelist>


  		




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                                                    <name>$specimenHolderInstitutions</name>


  		




  ......




  73
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                                                    </sourcename>


  		




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                                                </sourcelist>


  		




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                                            </institution_id>


  		




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                                            <sourceaccessioncode>$id</sourceaccessioncode>


  		




  
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                                            <sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>


  		




  77
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                                        </specimenreplicate>


  		




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                                    </plantobservation>


  		




  79
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                                </aggregateoccurrence>


  		




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                                <collector_id><party><fullname>$recordedBy</fullname></party></collector_id>


  		




  81
  
  
    
                                <sourceaccessioncode>$id</sourceaccessioncode>


  		




  
  81
  
    
                                <sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>


  		




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                                <taxondetermination>


  		




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                                    <party_id><party><fullname>$identifiedBy</fullname></party></party_id>


  		




  84
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                                    <taxonverbatim_id>


  		












  

    
      inputs/ACAD/Specimen/VegBIEN.csv
    
  





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


  		




  2
  
  
    
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists",


  		




  3
  
  
    
id,"/_if[@name=""if specimen""]/cond/_exists",


  		




  4
  
  
    
specimenHolderInstitutions,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",


  		




  5
  
  
    
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1",


  		




  6
  
  
    
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",


  		




  7
  
  
    
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",


  		




  8
  
  
    
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",


  		




  9
  
  
    
specimenHolderInstitutions,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/2",


  		




  10
  
  
    
collectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1",


  		




  11
  
  
    
collectionID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2",


  		




  12
  
  
    
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else",


  		




  13
  
  
    
rights,/location/accessconditions,


  		




  14
  
  
    
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value",


  		




  15
  
  
    
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",


  		




  16
  
  
    
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1,


  		




  17
  
  
    
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3,


  		




  18
  
  
    
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists",


  		




  19
  
  
    
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value",


  		




  20
  
  
    
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value",


  		




  21
  
  
    
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value,


  		




  22
  
  
    
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value,


  		




  23
  
  
    
dateIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value",


  		




  24
  
  
    
occurrenceRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1,


  		




  25
  
  
    
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2,


  		




  26
  
  
    
reproductiveCondition,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/reproductivecondition,


  		




  27
  
  
    
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",


  		




  28
  
  
    
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name


  		




  29
  
  
    
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_alt/2,


  		




  30
  
  
    
recordNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else",


  		




  31
  
  
    
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",


  		




  32
  
  
    
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",


  		




  33
  
  
    
specimenHolderInstitutions,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2",


  		




  34
  
  
    
specimenHolderInstitutions,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value",


  		




  35
  
  
    
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,


  		




  36
  
  
    
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",


  		




  37
  
  
    
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",


  		




  38
  
  
    
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname,


  		




  39
  
  
    
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",


  		




  40
  
  
    
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",


  		




  41
  
  
    
id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,


  		




  42
  
  
    
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,


  		




  43
  
  
    
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",


  		




  44
  
  
    
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",


  		




  45
  
  
    
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",


  		




  46
  
  
    
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",


  		




  47
  
  
    
order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet",


  		




  48
  
  
    
class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet",


  		




  49
  
  
    
phylum,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=phylum]/taxonepithet",


  		




  50
  
  
    
kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet",


  		




  51
  
  
    
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,


  		




  52
  
  
    
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,


  		




  53
  
  
    
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",


  		




  54
  
  
    
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,


  		




  55
  
  
    
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,


  		




  56
  
  
    
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value,


  		




  57
  
  
    
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,


  		




  58
  
  
    
infraspecificEpithet,"/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""]/cond",


  		




  59
  
  
    
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",


  		




  60
  
  
    
infraspecificEpithet,/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/2,


  		




  61
  
  
    
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2,


  		




  62
  
  
    
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,


  		




  63
  
  
    
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,


  		




  64
  
  
    
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,


  		




  65
  
  
    
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,


  		




  66
  
  
    
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,


  		




  67
  
  
    
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,


  		




  68
  
  
    
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,


  		




  69
  
  
    
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",


  		




  70
  
  
    
recordNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then",


  		




  71
  
  
    
locality,/location/locationnarrative/_merge/1,


  		




  72
  
  
    
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"


  		




  73
  
  
    
locationRemarks,/location/locationnarrative/_merge/4,


  		




  74
  
  
    
decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value",


  		




  75
  
  
    
decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value",


  		




  76
  
  
    
continent,/location/locationplace/*_id/place/continent,


  		




  77
  
  
    
country,/location/locationplace/*_id/place/country,


  		




  78
  
  
    
county,/location/locationplace/*_id/place/county,


  		




  79
  
  
    
decimalLatitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"


  		




  80
  
  
    
decimalLongitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"


  		




  81
  
  
    
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2,


  		




  82
  
  
    
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2,


  		




  83
  
  
    
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2,


  		




  84
  
  
    
stateProvince,/location/locationplace/*_id/place/stateprovince,


  		




  85
  
  
    
verbatimElevation,/location/verbatimelevation,


  		




  86
  
  
    
basisOfRecord,,** No join mapping for basisOfRecord ** 


  		




  87
  
  
    
bibliographicCitation,,** No join mapping for bibliographicCitation ** 


  		




  88
  
  
    
dynamicProperties,,** No join mapping for dynamicProperties ** 


  		




  89
  
  
    
geodeticDatum,,** No join mapping for geodeticDatum ** 


  		




  90
  
  
    
georeferenceSources,,** No join mapping for georeferenceSources ** 


  		




  91
  
  
    
georeferenceVerificationStatus,,** No join mapping for georeferenceVerificationStatus ** 


  		




  92
  
  
    
identificationRemarks,,** No join mapping for identificationRemarks ** 


  		




  93
  
  
    
institutionCode,,** No join mapping for specimenHolderInstitutions_verbatim ** 


  		




  94
  
  
    
language,,** No join mapping for language ** 


  		




  95
  
  
    
modified,,** No join mapping for modified ** 


  		




  96
  
  
    
municipality,,** No join mapping for municipality ** 


  		




  97
  
  
    
ownerInstitutionCode,,** No join mapping for specimenOwner ** 


  		




  98
  
  
    
rightsHolder,,** No join mapping for dataOwners ** 


  		




  99
  
  
    
row_num,,** No join mapping for *row_num ** 


  		




  100
  
  
    
type,,** No join mapping for type ** 


  		




  101
  
  
    
verbatimDepth,,** No join mapping for verbatimDepth ** 


  		




  
  1
  
    
link ../../../mappings/VegCore-VegBIEN.csv


  		




  102
  2
  
    

  		












  

    
      inputs/ACAD/run
    
  





  
  1
  
    
#!/bin/bash -e


  		




  
  2
  
    
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run


  		




  0
  3
  
    

  		












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