Revision 4587
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/SALVIAS/plotObservations/map.csv | ||
|---|---|---|
| 44 | 44 |
common_name,, |
| 45 | 45 |
morphoname,, |
| 46 | 46 |
species_code,, |
| 47 |
Habit,Habit,"Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
|
|
| 47 |
Habit,habit,"Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
|
|
| 48 | 48 |
height_class,, |
| 49 | 49 |
height_m,height, |
| 50 | 50 |
height_m_commercial,, |
| inputs/SALVIAS/plotObservations/map.full.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,Veg+,Comments |
| 2 |
Habit,Habit,"Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
|
| 3 | 2 |
canopy_form,canopyForm, |
| 4 | 3 |
canopy_position,canopyPosition, |
| 5 | 4 |
coll_number,catalogNumber/_alt/1,Brad: Map instead as for voucher_string |
| ... | ... | |
| 18 | 17 |
Family,family, |
| 19 | 18 |
Notes,fieldNotes, |
| 20 | 19 |
Genus,genus, |
| 20 |
Habit,habit,"Brad: This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
|
| 21 | 21 |
height_m,height, |
| 22 | 22 |
ht_first_branch_m,heightFirstBranch, |
| 23 | 23 |
cfaff,identificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank." |
| inputs/U/Specimen/map.csv | ||
|---|---|---|
| 1 | 1 |
U[Veg+],Veg+,Comments |
| 2 |
ID,GlobalUniqueIdentifier,
|
|
| 3 |
Barcode,CatalogNumber,
|
|
| 2 |
ID,globalUniqueIdentifier,
|
|
| 3 |
Barcode,catalogNumber,
|
|
| 4 | 4 |
Collector,Collector/_merge/1, |
| 5 | 5 |
Prefix,,Not used |
| 6 |
Number,RecordNumber,
|
|
| 6 |
Number,recordNumber,
|
|
| 7 | 7 |
Suffix,,Not used |
| 8 | 8 |
Addcoll,Collector/_merge/2, |
| 9 |
Colldd,DayCollected,
|
|
| 10 |
Collmm,MonthCollected,
|
|
| 11 |
Collyy,YearCollected,
|
|
| 9 |
Colldd,dayCollected,
|
|
| 10 |
Collmm,monthCollected,
|
|
| 11 |
Collyy,yearCollected,
|
|
| 12 | 12 |
DateInfo,,Not used |
| 13 |
cf,IdentificationQualifier,
|
|
| 14 |
Detby,IdentifiedBy,
|
|
| 15 |
Detyy,YearIdentified,
|
|
| 13 |
cf,identificationQualifier,
|
|
| 14 |
Detby,identifiedBy,
|
|
| 15 |
Detyy,yearIdentified,
|
|
| 16 | 16 |
Gazetteer,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/1", |
| 17 | 17 |
Newgazett,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row |
| 18 | 18 |
Majorarea,, |
| 19 | 19 |
Locnotes,VerbatimLocality/_merge/2, |
| 20 | 20 |
Coorsyst,, |
| 21 |
Lat,DecimalLatitude,
|
|
| 21 |
Lat,decimalLatitude,
|
|
| 22 | 22 |
NS,, |
| 23 |
Long,DecimalLongitude,
|
|
| 23 |
Long,decimalLongitude,
|
|
| 24 | 24 |
EW,, |
| 25 | 25 |
Alt,,What is this? |
| 26 | 26 |
Alt2,,What is this? |
| 27 |
Ecology,Habitat,
|
|
| 27 |
Ecology,habitat,
|
|
| 28 | 28 |
Phenology,ReproductiveCondition, |
| inputs/U/Specimen/map.full.csv | ||
|---|---|---|
| 1 | 1 |
U[Veg+],Veg+,Comments |
| 2 |
Barcode,CatalogNumber, |
|
| 3 | 2 |
Collector,Collector/_merge/1, |
| 4 | 3 |
Addcoll,Collector/_merge/2, |
| 5 |
Colldd,DayCollected, |
|
| 6 |
Lat,DecimalLatitude, |
|
| 7 |
Long,DecimalLongitude, |
|
| 8 |
ID,GlobalUniqueIdentifier, |
|
| 9 |
Ecology,Habitat, |
|
| 10 |
cf,IdentificationQualifier, |
|
| 11 |
Detby,IdentifiedBy, |
|
| 12 |
Collmm,MonthCollected, |
|
| 13 |
Number,RecordNumber, |
|
| 14 | 4 |
Phenology,ReproductiveCondition, |
| 15 | 5 |
Gazetteer,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/1", |
| 16 | 6 |
Newgazett,"VerbatimLocality/_merge/1/_label[label=""gazetteer""]/value/_merge/2",Only used in 1 row |
| 17 | 7 |
Locnotes,VerbatimLocality/_merge/2, |
| 18 |
Collyy,YearCollected, |
|
| 19 |
Detyy,YearIdentified, |
|
| 8 |
Barcode,catalogNumber, |
|
| 20 | 9 |
country,country |
| 10 |
Colldd,dayCollected, |
|
| 11 |
Lat,decimalLatitude, |
|
| 12 |
Long,decimalLongitude, |
|
| 21 | 13 |
family,family |
| 22 | 14 |
genus,genus |
| 15 |
ID,globalUniqueIdentifier, |
|
| 16 |
Ecology,habitat, |
|
| 17 |
cf,identificationQualifier, |
|
| 18 |
Detby,identifiedBy, |
|
| 19 |
Collmm,monthCollected, |
|
| 23 | 20 |
notes,notes |
| 21 |
Number,recordNumber, |
|
| 22 |
Collyy,yearCollected, |
|
| 23 |
Detyy,yearIdentified, |
|
| inputs/ARIZ/Specimen/map.csv | ||
|---|---|---|
| 4 | 4 |
FieldNumber,OMIT,"Usage inconsistent with DwC definition: meaning is recordNumber. Identical to CollectorNumber [1], so does not need to be mapped. |
| 5 | 5 |
|
| 6 | 6 |
[1] The following query returns no rows: SELECT * FROM ""ARIZ"".""Specimen"" WHERE ""CollectorNumber"" IS DISTINCT FROM ""FieldNumber""" |
| 7 |
TimeCollected,TimeOfDay,
|
|
| 7 |
TimeCollected,timeOfDay,
|
|
| 8 | 8 |
VerbatimCollectingDate,dateCollected/_alt/0, |
| 9 | 9 |
HorizontalDatum,,Not used |
| 10 | 10 |
OriginalCoordinateSystem,verbatimSRS, |
| inputs/ARIZ/Specimen/map.full.csv | ||
|---|---|---|
| 8 | 8 |
RelatedCatalogedItems,RelatedCatalogItem/_alt/2,Used only when OtherCatalogNumbers is NULL |
| 9 | 9 |
ScientificNameAuthor,ScientificName/_alt/1,Contains the binomial in addition to the authority |
| 10 | 10 |
ScientificName,ScientificName/_alt/2, |
| 11 |
TimeCollected,TimeOfDay, |
|
| 12 | 11 |
GenBankNum,"associatedSequences/_label[label=""GenBank""]/value", |
| 13 | 12 |
boundingBox,boundingBox |
| 14 | 13 |
class,class |
| ... | ... | |
| 50 | 49 |
species,species |
| 51 | 50 |
stateProvince,stateProvince |
| 52 | 51 |
subspecies,subspecies |
| 52 |
TimeCollected,timeOfDay, |
|
| 53 | 53 |
verbatimElevation,verbatimElevation |
| 54 | 54 |
verbatimLatitude,verbatimLatitude |
| 55 | 55 |
verbatimLongitude,verbatimLongitude |
| inputs/ARIZ/Specimen/VegBIEN.csv | ||
|---|---|---|
| 70 | 70 |
OriginalCoordinateSystem,,** No join mapping for verbatimSRS ** |
| 71 | 71 |
OtherCatalogNumbers,,** No join mapping for RelatedCatalogItem/_alt/1 ** |
| 72 | 72 |
RelatedCatalogedItems,,** No join mapping for RelatedCatalogItem/_alt/2 ** Used only when OtherCatalogNumbers is NULL |
| 73 |
TimeCollected,,** No join mapping for TimeOfDay ** |
|
| 73 |
TimeCollected,,** No join mapping for timeOfDay ** |
|
| inputs/GBIF/Specimen/map.csv | ||
|---|---|---|
| 1 | 1 |
GBIF[Veg+],Veg+,Comments |
| 2 | 2 |
LatestDateCollected,dateCollected, |
| 3 |
InstitutionCD,InstitutionCode,
|
|
| 4 |
CollectionCD,CollectionCode,
|
|
| 5 |
CatalogNO,CatalogNumber,
|
|
| 6 |
LastDateModified,DateLastModified,
|
|
| 3 |
InstitutionCD,institutionCode,
|
|
| 4 |
CollectionCD,collectionCode,
|
|
| 5 |
CatalogNO,catalogNumber,
|
|
| 6 |
LastDateModified,dateLastModified,
|
|
| 7 | 7 |
ScientificNameOriginal,verbatimScientificName, |
| 8 |
AuthorOfScientificName,ScientificNameAuthor,
|
|
| 8 |
AuthorOfScientificName,scientificNameAuthor,
|
|
| 9 | 9 |
GBIFFamilyOriginal,verbatimFamily, |
| 10 | 10 |
GBIFGenusOriginal,verbatimGenus, |
| 11 |
MinimumElevationInMeter,MinimumElevationInMeters, |
|
| 12 |
MaximumElevationInMeter,MaximumElevationInMeters, |
|
| 11 |
MinimumElevationInMeter,minimumElevationInMeters, |
|
| 12 |
MaximumElevationInMeter,maximumElevationInMeters, |
|
| inputs/GBIF/Specimen/map.full.csv | ||
|---|---|---|
| 1 | 1 |
GBIF[Veg+],Veg+,Comments |
| 2 |
CatalogNO,CatalogNumber, |
|
| 3 |
CollectionCD,CollectionCode, |
|
| 4 |
LastDateModified,DateLastModified, |
|
| 5 |
InstitutionCD,InstitutionCode, |
|
| 6 |
MaximumElevationInMeter,MaximumElevationInMeters, |
|
| 7 |
MinimumElevationInMeter,MinimumElevationInMeters, |
|
| 8 |
AuthorOfScientificName,ScientificNameAuthor, |
|
| 2 |
CatalogNO,catalogNumber, |
|
| 3 |
CollectionCD,collectionCode, |
|
| 9 | 4 |
collector,collector |
| 10 | 5 |
country,country |
| 11 | 6 |
county,county |
| 12 | 7 |
LatestDateCollected,dateCollected, |
| 8 |
LastDateModified,dateLastModified, |
|
| 13 | 9 |
decimalLatitude,decimalLatitude |
| 14 | 10 |
decimalLongitude,decimalLongitude |
| 15 | 11 |
family,family |
| 16 | 12 |
genus,genus |
| 17 | 13 |
identifiedBy,identifiedBy |
| 18 | 14 |
infraspecificEpithet,infraspecificEpithet |
| 15 |
InstitutionCD,institutionCode, |
|
| 19 | 16 |
locality,locality |
| 17 |
MaximumElevationInMeter,maximumElevationInMeters, |
|
| 18 |
MinimumElevationInMeter,minimumElevationInMeters, |
|
| 20 | 19 |
scientificName,scientificName |
| 20 |
AuthorOfScientificName,scientificNameAuthor, |
|
| 21 | 21 |
specificEpithet,specificEpithet |
| 22 | 22 |
stateProvince,stateProvince |
| 23 | 23 |
GBIFFamilyOriginal,verbatimFamily, |
| inputs/GBIF/Specimen/VegBIEN.csv | ||
|---|---|---|
| 35 | 35 |
collector,/location/locationevent/taxonoccurrence/verbatimcollectorname, |
| 36 | 36 |
CatalogNO,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 37 | 37 |
locality,/location/locationnarrative/_merge/1, |
| 38 |
LastDateModified,,** No join mapping for DateLastModified ** |
|
| 38 |
LastDateModified,,** No join mapping for dateLastModified ** |
|
| inputs/NCU-NCSC/Specimen/map.csv | ||
|---|---|---|
| 1 | 1 |
NCU-NCSC[Veg+],Veg+,Comments |
| 2 | 2 |
Accession Number,occurrenceID, |
| 3 |
SeriesName,CollectionCode,
|
|
| 4 |
Barcode,CatalogNumber,
|
|
| 5 |
Full Taxon Name,ScientificName,
|
|
| 6 |
Collect Date,CollectedDate,
|
|
| 3 |
SeriesName,collectionCode,
|
|
| 4 |
Barcode,catalogNumber,
|
|
| 5 |
Full Taxon Name,scientificName,
|
|
| 6 |
Collect Date,collectedDate,
|
|
| 7 | 7 |
Cultivated?,cultivated, |
| 8 |
Elevation,VerbatimElevation,
|
|
| 8 |
Elevation,verbatimElevation,
|
|
| 9 | 9 |
Lat (-=S),"Latitude/_replace:[""\?$""=]/value", |
| 10 | 10 |
Long (-=W),"Longitude/_replace:[""\?$""=]/value", |
| 11 |
Accuracy,CoordinateUncertaintyInMeters,
|
|
| 11 |
Accuracy,coordinateUncertaintyInMeters,
|
|
| 12 | 12 |
FIPS,,FIPS county code |
| 13 | 13 |
Alt N/S,, |
| 14 | 14 |
Alt E/W,, |
| 15 |
Format,PreparationType,
|
|
| 15 |
Format,preparationType,
|
|
| 16 | 16 |
Typology,typeStatus, |
| inputs/NCU-NCSC/Specimen/map.full.csv | ||
|---|---|---|
| 1 | 1 |
NCU-NCSC[Veg+],Veg+,Comments |
| 2 |
Barcode,CatalogNumber, |
|
| 3 |
Collect Date,CollectedDate, |
|
| 4 |
SeriesName,CollectionCode, |
|
| 5 |
Accuracy,CoordinateUncertaintyInMeters, |
|
| 6 | 2 |
Lat (-=S),"Latitude/_replace:[""\?$""=]/value", |
| 7 | 3 |
Long (-=W),"Longitude/_replace:[""\?$""=]/value", |
| 8 |
Format,PreparationType, |
|
| 9 |
Full Taxon Name,ScientificName, |
|
| 10 |
Elevation,VerbatimElevation, |
|
| 4 |
Barcode,catalogNumber, |
|
| 5 |
Collect Date,collectedDate, |
|
| 6 |
SeriesName,collectionCode, |
|
| 7 |
Accuracy,coordinateUncertaintyInMeters, |
|
| 11 | 8 |
country,country |
| 12 | 9 |
county,county |
| 13 | 10 |
Cultivated?,cultivated, |
| 14 | 11 |
Accession Number,occurrenceID, |
| 12 |
Format,preparationType, |
|
| 13 |
Full Taxon Name,scientificName, |
|
| 15 | 14 |
state,state |
| 16 | 15 |
Typology,typeStatus, |
| 16 |
Elevation,verbatimElevation, |
|
| inputs/NCU-NCSC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
Cultivated?,/location/locationevent/taxonoccurrence/iscultivated/_alt/1, |
| 18 | 18 |
Full Taxon Name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname", |
| 19 | 19 |
Barcode,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 20 |
Format,,** No join mapping for PreparationType **
|
|
| 20 |
Format,,** No join mapping for preparationType **
|
|
| 21 | 21 |
Typology,,** No join mapping for typeStatus ** |
| inputs/input.Makefile | ||
|---|---|---|
| 144 | 144 |
|
| 145 | 145 |
coreMap := $(mappings)/$(via)-VegBIEN.csv |
| 146 | 146 |
coreSelfMap := $(mappings)/$(via).self.csv |
| 147 |
vocab := $(mappings)/$(via).vocab.csv |
|
| 147 | 148 |
|
| 148 | 149 |
viaMaps := $(wildcard $(tables:%=%/map.csv)) |
| 149 | 150 |
viaMaps += $(filter-out $(viaMaps),$(srcMaps:%/src.csv=%/map.csv)) |
| ... | ... | |
| 280 | 281 |
|
| 281 | 282 |
# Via maps cleanup |
| 282 | 283 |
ifneq ($(filter %/.map.csv.last_cleanup,$(MAKECMDGOALS)),) |
| 283 |
%/.map.csv.last_cleanup: %/map.csv $(coreMap) |
|
| 284 |
%/.map.csv.last_cleanup: %/map.csv $(coreMap) $(vocab) |
|
| 285 |
$(bin)/in_place $< $(bin)/canon 1 $(word 3,$+) |
|
| 284 | 286 |
$(bin)/in_place $< env ignore=1 $(bin)/subtract $(word 2,$+) 0 1 2 |
| 285 | 287 |
touch $@ |
| 286 | 288 |
# Include comment column so commented mappings are never removed |
Also available in: Unified diff
input.Makefile: Maps building: %/.map.csv.last_cleanup: Canonicalize map.csv using $(mappings)/$(via).vocab.csv