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Revision 1530

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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