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Revision 1530

Added by Aaron Marcuse-Kubitza almost 13 years ago

input.Makefile: Generate VegBIEN maps from full via maps in order to include all input columns if a src map was provided. This causes the VegBIEN join process to produce all the "No join mapping" errors for that datasource, not just those for fields in the (non-full) via map. maps/src.join.*.csv should no longer be needed for producing "No join mapping" errors.

View differences:

inputs/ARIZ/maps/VegBIEN.specimens.csv
42 42 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
43 43 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
44 44 
AgeClass,,** No join mapping for lifeStage **
45 
BasisOfRecord,,** No join mapping for BasisOfRecord **
45 46 
CatalogNumber,,Map to nothing so it doesn't overwrite CatalogNumberNumeric
47 
DateLastModified,,** No join mapping for DateLastModified **
46 48 
GenBankNum,,"** No join mapping for associatedSequences/_label[label=""GenBank""]/value ** "
47 49 
GeorefMethod,,** No join mapping for georeferenceProtocol **
50 
HigherGeography,,** No join mapping for HigherGeography **
48 51 
HorizontalDatum,,Not used
49 52 
IdentificationModifier,,** No join mapping for identificationQualifier **
53 
IndividualCount,,** No join mapping for IndividualCount **
54 
InstitutionCode,,** No join mapping for InstitutionCode **
55 
Island,,** No join mapping for Island **
56 
IslandGroup,,** No join mapping for IslandGroup **
57 
JulianDay,,** No join mapping for JulianDay **
50 58 
LatLongComments,,** No join mapping for georeferenceRemarks **
51 59 
OriginalCoordinateSystem,,** No join mapping for verbatimSRS **
52 60 
OtherCatalogNumbers,,** No join mapping for RelatedCatalogItem **
61 
Preparations,,** No join mapping for Preparations **
53 62 
RelatedCatalogedItems,,"** No join mapping for RelatedCatalogItem ** Used only when OtherCatalogNumbers is NULL, so _alt not needed"
54 63 
TimeCollected,,** No join mapping for TimeOfDay **
55 64 
Tissues,,Not used
65 
TypeStatus,,** No join mapping for TypeStatus **
66 
VerbatimDepth,,** No join mapping for VerbatimDepth **
67 
VerbatimElevation,,** No join mapping for VerbatimElevation **
inputs/NY/maps/VegBIEN.specimens.csv
41 41 
UniqueNYInternalRecordNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/sourceaccessioncode","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
42 42 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
43 43 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
44 
BasisOfRecord,,** No join mapping for BasisOfRecord **
45 
DateLastModified,,** No join mapping for DateLastModified **
46 
IndividualCount,,** No join mapping for IndividualCount **
47 
InstitutionCode,,** No join mapping for InstitutionCode **
48 
JulianDay,,** No join mapping for JulianDay **
49 
PreparationType,,** No join mapping for PreparationType **
50 
PreviousCatalogNumber,,** No join mapping for PreviousCatalogNumber **
51 
RelatedCatalogItem,,** No join mapping for RelatedCatalogItem **
52 
RelationshipType,,** No join mapping for RelationshipType **
53 
TimeOfDay,,** No join mapping for TimeOfDay **
54 
TypeStatus,,** No join mapping for TypeStatus **
44 55 
key,,
inputs/SpeciesLink/maps/VegBIEN.specimens.csv
48 48 
GlobalUniqueIdentifier,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/sourceaccessioncode","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
49 49 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
50 50 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
51 
BasisOfRecord,,** No join mapping for BasisOfRecord **
52 
DateLastModified,,** No join mapping for DateLastModified **
51 53 
DayOfYear,,** No join mapping for JulianDay **
54 
GeodeticDatum,,** No join mapping for GeodeticDatum **
55 
IndividualCount,,** No join mapping for IndividualCount **
56 
InstitutionCode,,** No join mapping for InstitutionCode **
57 
JulianDay,,** No join mapping for JulianDay **
58 
PreparationType,,** No join mapping for PreparationType **
59 
PreviousCatalogNumber,,** No join mapping for PreviousCatalogNumber **
60 
RelatedCatalogItem,,** No join mapping for RelatedCatalogItem **
61 
RelationshipType,,** No join mapping for RelationshipType **
62 
TimeOfDay,,** No join mapping for TimeOfDay **
63 
TypeStatus,,** No join mapping for TypeStatus **
inputs/MO/maps/VegBIEN.specimens.csv
24 24 
notes,/description/_merge/1,,
25 25 
CatalogNumber,":[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel,*_id/taxonoccurrence]/catalognumber_dwc","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
26 26 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22
27 
BasisOfRecord,,** No join mapping for BasisOfRecord **
28 
DateLastModified,,** No join mapping for DateLastModified **
29 
IndividualCount,,** No join mapping for IndividualCount **
30 
InstitutionCode,,** No join mapping for InstitutionCode **
31 
TypeStatus,,** No join mapping for TypeStatus **
27 32 
convertednotes,,
inputs/input.Makefile
123 123 
joinSrcMap = $(if $(wildcard maps/src.$*.csv),$(bin)/in_place $@\
124 124 
$(bin)/intersect maps/src.$*.csv 0)
125 125 

  		




  126
  
  
    
maps/VegBIEN.%.csv: maps/$(via).%.csv $(coreMap)


  		




  127
  
  
    
	$(join) <$+ >$@


  		




  128
  
  
    
	$(joinSrcMap)


  		




  129
  
  
    
maps += $(autogenMaps)


  		




  130
  
  
    

  		




  131
  126
  
    
makeFullCsv = $(if $(shell test -e $(word 2,$+) && echo t),\


  		




  132
  127
  
    
env ignore=1 $(bin)/union <$+|$(bin)/sort_map >$@,$(CP) $< $@)


  		




  133
  128
  
    
# can't use $(wildcard) because it won't recheck file after $(coreSelfMap) runs


  		




  ......




  137
  132
  
    
	$(joinSrcMap)


  		




  138
  133
  
    
maps += $(patsubst maps/%.csv,maps/%.full.csv,$(viaMaps))


  		




  139
  134
  
    

  		




  
  135
  
    
maps/VegBIEN.%.csv: maps/$(via).%.full.csv $(coreMap)


  		




  
  136
  
    
	$(bin)/join <$+|$(bin)/sort_map >$@


  		




  
  137
  
    
maps += $(autogenMaps)


  		




  
  138
  
    

  		




  140
  139
  
    
maps/src.join.%.csv: maps/src.%.csv maps/$(via).%.full.csv $(noEmptyMap)


  		




  141
  140
  
    
	$(selfMap) <$<|$(bin)/join $(word 2,$+)|$(join) $(word 3,$+) >$@


  		




  142
  141
  
    
maps += $(srcJoinMaps)


  		












  

    
      inputs/REMIB/maps/VegBIEN.specimens.csv
    
  





  19
  19
  
    
lat_sec,,


  		




  20
  20
  
    
long_min,,


  		




  21
  21
  
    
long_sec,,


  		




  
  22
  
    
preparation,,** No join mapping for preparation ** 


  		












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