$(root)/bin/join_union_sort <$+ >$@

#!/bin/sh

# Inner-joins two map spreadsheets and sorts the output on the output column

selfDir="$(dirname -- "$0")"

"$selfDir/join" "$@"|env ignore=1 "$selfDir/union" "$@"|"$selfDir/sort" 1 0

country,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""area|country|territory""])/placename",Brad: Required; reject record if this field NULL,63

stateProvince,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=""region|state|province""])/placename",,65

county,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination(/*_id/namedplace[placesystem=county])/placename,,66

coordinatePrecision,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy,,89

coordinatePrecision/_noCV/value,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/coordsaccuracy/_noCV/value,,89

footprintWKT,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationdetermination[!namedplace_id]/footprintgeometry_dwc,,91

locality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/1,,68

verbatimLocality,/*_id/taxonoccurrence/*_id/locationevent/*_id/location/locationnarrative/_alt/2,"Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69

maximumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/max,elevationrange/_range/to}",,72

minimumElevationInMeters,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{elevation/_alt/2/_avg/min,elevationrange/_range/from}",,71

decimalLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/latitude,centerlatitude}/_alt/1/_nullIf:[null=0,type=float]/value",,85

verbatimLatitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/latitude,centerlatitude}/_alt/2/_nullIf:[null=0,type=float]/value",,81

decimalLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/longitude,centerlongitude}/_alt/1/_nullIf:[null=0,type=float]/value",,86

verbatimLongitude,"/*_id/taxonoccurrence/*_id/locationevent/*_id/location/{locationdetermination[!namedplace_id]/longitude,centerlongitude}/_alt/2/_nullIf:[null=0,type=float]/value",,82

habitat,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52

habitat/_merge/1,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/1,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52

habitat/_merge/2,/*_id/taxonoccurrence/*_id/locationevent/commclass/commdetermination/*_id/commconcept/*_id/*/commname/_merge/2,"Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?",52

bien.substrate,/*_id/taxonoccurrence/*_id/locationevent/landscapenarrative,,

eventDate,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate,,44

eventDate/_alt/2/_date/day,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_alt/2/_date/day,,44

eventDate/_alt/2/_date/month,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_alt/2/_date/month,,44

eventDate/_alt/2/_date/year,/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_alt/2/_date/year,,44

maximumDepthInMeters,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/max,,75

minimumDepthInMeters,/*_id/taxonoccurrence/*_id/locationevent/waterdepth/min,,74

scientificNameAuthorship,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Authority]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname","Brad: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author",153

sex,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/definedvalue[*_id/userdefined[tablename=taxondetermination,userdefinedname=sex]]:[@fkey=tableRecord_ID]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26

dateIdentified,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate",,120

dateIdentified/_alt/2/_date/day,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate/_alt/2/_date/day",,120

dateIdentified/_alt/2/_date/month,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate/_alt/2/_date/month",,120

dateIdentified/_alt/2/_date/year,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]/determinationdate/_alt/2/_date/year",,120

identifiedBy,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]:[determinationtype=Author,iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119

scientificName,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Binomial]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname","Brad: Bob, Nick, please is this mapping OK?",134

class,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Class]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,144

family,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Family]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,146

genus,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Genus]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,147

kingdom,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Kingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,142

order,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Order]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,145

specificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Species]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,149

phylum,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Subkingdom]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,143

infraspecificEpithet,"/*_id/taxonoccurrence/taxondetermination[*_id/role/rolecode=identifier,*_id/plantconcept/*_id/plantname/rank=Subspecies]:[determinationtype=Author,isoriginal=true,iscurrent=true]/*_id/plantconcept/*_id/*/plantname",,150

recordedBy,/*_id/taxonoccurrence/verbatimcollectorname,,23

collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12

fieldNotes,/description,,

fieldNotes/_merge/1,/description/_merge/1,,

"fieldNotes/_merge/2/_label[label=""plant fungus""]/value","/description/_merge/2/_label[label=""plant fungus""]/value",,

catalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/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

recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1,,22

collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9

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

institutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,,

occurrenceID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/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

acceptedNameUsage,,,135

acceptedNameUsageID,,,128

associatedMedia,,,36

associatedOccurrences,,,38

associatedReferences,,,37

associatedSequences,,,39

associatedTaxa,,,40

basisOfRecord,,Brad: OMIT? See http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord for definition of this term.,15

bed,,,117

behavior,,,29

continent,,Brad: OMIT,59

coordinateUncertaintyInMeters,,,88

countryCode,,,64

dataGeneralizations,,,17

datasetID,,,10

datasetName,,,13

day,,Brad: OMIT,50

dcterms:accessRights,,,5

dcterms:bibliographicCitation,,,6

dcterms:language,,,2

dcterms:modified,,"Brad: Mapping to VegX is incorrect. I think is this merely an internal timestamp indicated when record last modified, not necessarily when determination (taxon name) last modified. Probably we should omit this field, although might be useful for updating changed records from this source.",1

dcterms:references,,,7

dcterms:rights,,,3

dcterms:rightsHolder,,,4

dcterms:type,,,0

disposition,,,33

dynamicProperties,,,18

earliestAgeOrLowestStage,,,109

earliestEonOrLowestEonothem,,,101

earliestEpochOrLowestSeries,,,107

earliestEraOrLowestErathem,,,103

earliestPeriodOrLowestSystem,,,105

endDayOfYear,,,47

establishmentMeans,,,30

eventID,,,41

eventRemarks,,,55

eventTime,,Brad: OMIT,45

footprintSRS,,,92

footprintSpatialFit,,,93

formation,,,115

geodeticDatum,,,87

geologicalContextID,,,100

georeferenceProtocol,,,96

georeferenceRemarks,,,99

georeferenceSources,,,97

georeferenceVerificationStatus,,,98

georeferencedBy,,Brad: Correct for VB. Nick: is there a way to specifically identify this party as collector of a specimen?,94

georeferencedDate,,,95

group,,,114

higherClassification,,,141

higherGeography,,,58

higherGeographyID,,,57

highestBiostratigraphicZone,,,112

identificationID,,,118

identificationQualifier,,,124

identificationReferences,,,121

identificationRemarks,,,123

identificationVerificationStatus,,,122

individualCount,,Brad: OMIT; not relevant for DwC plant specimen data.,25

individualID,,"Brad: OMIT; db-specific element, not relevant to VB/VX",24

informationWithheld,,,16

institutionID,,,8

island,,,62

islandGroup,,,61

latestAgeOrHighestStage,,,110

latestEonOrHighestEonothem,,,102

latestEpochOrHighestSeries,,,108

latestEraOrHighestErathem,,,104

latestPeriodOrHighestSystem,,,106

lifeStage,,,27

lithostratigraphicTerms,,,113

locationAccordingTo,,,78

locationID,,,56

locationRemarks,,,79

lowestBiostratigraphicZone,,,111

maximumDistanceAboveSurfaceInMeters,,,77

measurementAccuracy,,,169

measurementDeterminedBy,,,172

measurementDeterminedDate,,,171

measurementID,,,166

measurementMethod,,,173

measurementRemarks,,,174

measurementType,,,167

measurementUnit,,,170

measurementValue,,,168

member,,,116

minimumDistanceAboveSurfaceInMeters,,,76

month,,,49

municipality,,,67

nameAccordingTo,,,138

nameAccordingToID,,,131

namePublishedIn,,,139

namePublishedInID,,,132

namePublishedInYear,,,140

nomenclaturalCode,,,155

nomenclaturalStatus,,,157

occurrenceRemarks,,,21

occurrenceStatus,,,31

originalNameUsage,,,137

originalNameUsageID,,,130

otherCatalogNumbers,,,34

ownerInstitutionCode,,,14

parentNameUsage,,,136

parentNameUsageID,,,129

pointRadiusSpatialFit,,,90

preparations,,Brad: OMIT,32

previousIdentifications,,Brad: OMIT,35

relatedResourceID,,Brad: OMIT,161

relationshipAccordingTo,,,163

relationshipEstablishedDate,,,164

relationshipOfResource,,Brad: OMIT,162

relationshipRemarks,,,165

reproductiveCondition,,,28

resourceID,,,160

resourceRelationshipID,,,159

samplingEffort,,,43

samplingProtocol,,,42

scientificNameID,,,127

startDayOfYear,,,46

subgenus,,,148

taxonConceptID,,,133

taxonID,,,126

taxonRank,,,151

taxonRemarks,,,158

taxonomicStatus,,,156

typeStatus,,Brad: OMIT (?). Indicates whether this specimen served as type for taxon name. Probably not relevant for BIEN,125

verbatimCoordinateSystem,,,83

verbatimCoordinates,,,80

verbatimDepth,,,73

verbatimElevation,,,70

verbatimEventDate,,,51

verbatimSRS,,,84

verbatimTaxonRank,,,152

vernacularName,,,154

waterBody,,,60

year,,,48

	$(bin)/join_union_sort <$+ >$@

DwC-VegBIEN.specimens.csv: DwC2-VegBIEN.specimens.csv DwC1-VegBIEN.specimens.csv