Revision 1530
Added by Aaron Marcuse-Kubitza almost 13 years ago
inputs/ARIZ/maps/VegBIEN.specimens.csv | ||
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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 ** |
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48 | 51 |
HorizontalDatum,,Not used |
49 | 52 |
IdentificationModifier,,** No join mapping for identificationQualifier ** |
53 |
IndividualCount,,** No join mapping for IndividualCount ** |
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54 |
InstitutionCode,,** No join mapping for InstitutionCode ** |
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55 |
Island,,** No join mapping for Island ** |
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56 |
IslandGroup,,** No join mapping for IslandGroup ** |
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57 |
JulianDay,,** No join mapping for JulianDay ** |
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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 ** |
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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 ** |
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66 |
VerbatimDepth,,** No join mapping for VerbatimDepth ** |
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67 |
VerbatimElevation,,** No join mapping for VerbatimElevation ** |
inputs/NY/maps/VegBIEN.specimens.csv | ||
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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=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53 |
44 |
BasisOfRecord,,** No join mapping for BasisOfRecord ** |
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45 |
DateLastModified,,** No join mapping for DateLastModified ** |
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46 |
IndividualCount,,** No join mapping for IndividualCount ** |
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47 |
InstitutionCode,,** No join mapping for InstitutionCode ** |
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48 |
JulianDay,,** No join mapping for JulianDay ** |
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49 |
PreparationType,,** No join mapping for PreparationType ** |
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50 |
PreviousCatalogNumber,,** No join mapping for PreviousCatalogNumber ** |
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51 |
RelatedCatalogItem,,** No join mapping for RelatedCatalogItem ** |
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52 |
RelationshipType,,** No join mapping for RelationshipType ** |
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53 |
TimeOfDay,,** No join mapping for TimeOfDay ** |
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54 |
TypeStatus,,** No join mapping for TypeStatus ** |
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44 | 55 |
key,, |
inputs/SpeciesLink/maps/VegBIEN.specimens.csv | ||
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48 | 48 |
GlobalUniqueIdentifier,":[datasource_id/party/organizationname/_alt/2=$/_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 ** |
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52 |
DateLastModified,,** No join mapping for DateLastModified ** |
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51 | 53 |
DayOfYear,,** No join mapping for JulianDay ** |
54 |
GeodeticDatum,,** No join mapping for GeodeticDatum ** |
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55 |
IndividualCount,,** No join mapping for IndividualCount ** |
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56 |
InstitutionCode,,** No join mapping for InstitutionCode ** |
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57 |
JulianDay,,** No join mapping for JulianDay ** |
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58 |
PreparationType,,** No join mapping for PreparationType ** |
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59 |
PreviousCatalogNumber,,** No join mapping for PreviousCatalogNumber ** |
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60 |
RelatedCatalogItem,,** No join mapping for RelatedCatalogItem ** |
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61 |
RelationshipType,,** No join mapping for RelationshipType ** |
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62 |
TimeOfDay,,** No join mapping for TimeOfDay ** |
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63 |
TypeStatus,,** No join mapping for TypeStatus ** |
inputs/MO/maps/VegBIEN.specimens.csv | ||
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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 ** |
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28 |
DateLastModified,,** No join mapping for DateLastModified ** |
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29 |
IndividualCount,,** No join mapping for IndividualCount ** |
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30 |
InstitutionCode,,** No join mapping for InstitutionCode ** |
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31 |
TypeStatus,,** No join mapping for TypeStatus ** |
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27 | 32 |
convertednotes,, |
inputs/input.Makefile | ||
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123 | 123 |
joinSrcMap = $(if $(wildcard maps/src.$*.csv),$(bin)/in_place $@\ |
124 | 124 |
$(bin)/intersect maps/src.$*.csv 0) |
125 | 125 |
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maps/VegBIEN.%.csv: maps/$(via).%.csv $(coreMap) |
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$(join) <$+ >$@ |
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$(joinSrcMap) |
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maps += $(autogenMaps) |
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130 |
|
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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 |
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maps/VegBIEN.%.csv: maps/$(via).%.full.csv $(coreMap) |
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$(bin)/join <$+|$(bin)/sort_map >$@ |
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maps += $(autogenMaps) |
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|
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140 | 139 |
maps/src.join.%.csv: maps/src.%.csv maps/$(via).%.full.csv $(noEmptyMap) |
141 | 140 |
$(selfMap) <$<|$(bin)/join $(word 2,$+)|$(join) $(word 3,$+) >$@ |
142 | 141 |
maps += $(srcJoinMaps) |
inputs/REMIB/maps/VegBIEN.specimens.csv | ||
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19 | 19 |
lat_sec,, |
20 | 20 |
long_min,, |
21 | 21 |
long_sec,, |
22 |
preparation,,** No join mapping for preparation ** |
Also available in: Unified diff
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.