Revision 10173
Added by Aaron Marcuse-Kubitza over 11 years ago
| inputs/NCU/Specimen/VegBIEN.csv | ||
|---|---|---|
| 13 | 13 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| 14 | 14 |
SpecimenPK,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 15 | 15 |
firstCollectorRemarks,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Actually the collector's number, not remarks" |
| 16 |
Cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/1/_map:[0=,""-1""=true,*=*]/value","cultivated can only be true or NULL, not false"
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| 16 |
Cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/1/_map:[0=,""-1""=true,*=*]/value","cultivated can only be true or NULL, not false"
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|
| 17 | 17 |
VerbatimLocality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2/_alt/1, |
| 18 | 18 |
CityLocality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2/_alt/2, |
| 19 | 19 |
CollectionDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| ... | ... | |
| 35 | 35 |
firstCollectorName,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 36 | 36 |
SpecimenPK,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 37 | 37 |
firstCollectorRemarks,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Actually the collector's number, not remarks" |
| 38 |
Cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/1/_map:[0=,""-1""=true,*=*]/value","cultivated can only be true or NULL, not false"
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| 38 |
Cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1/_map:[0=,""-1""=true,*=*]/value","cultivated can only be true or NULL, not false"
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| 39 | 39 |
SpecimenPK,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 40 | 40 |
CurrentScientificNameWithAuthor,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
| 41 | 41 |
CurrentScientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
| inputs/bien_web/observation/VegBIEN.csv | ||
|---|---|---|
| 15 | 15 |
elevation_m,/location/elevation_m/_alt/1, |
| 16 | 16 |
collectionNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 17 | 17 |
observationID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 18 |
isCultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/1",
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| 18 |
isCultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/1",
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| 19 | 19 |
plotMethod,/location/locationevent/*_id/method/name, |
| 20 | 20 |
plotCode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
| 21 | 21 |
plotID,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
| ... | ... | |
| 34 | 34 |
collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 35 | 35 |
collectionNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 36 | 36 |
observationID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 37 |
isCultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/1",
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| 37 |
isCultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1",
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| 38 | 38 |
observationID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 39 | 39 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 40 | 40 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 38 | 38 |
HAVING count(*) > 1 |
| 39 | 39 |
-----" |
| 40 | 40 |
collectno,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 41 |
cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/1/_alt/1/_map:[*=true]/value","For our purposes, anything non-NULL should be assumed to be cultivated"
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| 42 |
campus,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/1/_alt/2/_map:[*=true]/value","""this refers to occurrence on the UNCC campus, but I do not know the meaning of the codes. Presumably C = cultivated"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/723/UNCC-validate_rkp_bb_rkp.xlsx#Campus)"
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| 41 |
cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/1/_alt/1/_map:[*=true]/value","For our purposes, anything non-NULL should be assumed to be cultivated"
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| 42 |
campus,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/1/_alt/2/_map:[*=true]/value","""this refers to occurrence on the UNCC campus, but I do not know the meaning of the codes. Presumably C = cultivated"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/723/UNCC-validate_rkp_bb_rkp.xlsx#Campus)"
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| 43 | 43 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
| 44 | 44 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
| 45 | 45 |
collday,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value", |
| ... | ... | |
| 82 | 82 |
collector2,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join/3, |
| 83 | 83 |
collector3,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join/4, |
| 84 | 84 |
collectno,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 85 |
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/1/_alt/1/_map:[*=true]/value","For our purposes, anything non-NULL should be assumed to be cultivated"
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| 86 |
campus,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/1/_alt/2/_map:[*=true]/value","""this refers to occurrence on the UNCC campus, but I do not know the meaning of the codes. Presumably C = cultivated"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/723/UNCC-validate_rkp_bb_rkp.xlsx#Campus)"
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| 85 |
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1/_alt/1/_map:[*=true]/value","For our purposes, anything non-NULL should be assumed to be cultivated"
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| 86 |
campus,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1/_alt/2/_map:[*=true]/value","""this refers to occurrence on the UNCC campus, but I do not know the meaning of the codes. Presumably C = cultivated"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/723/UNCC-validate_rkp_bb_rkp.xlsx#Campus)"
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| 87 | 87 |
usdaRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank/_alt/1", |
| 88 | 88 |
infrarank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank/_alt/2", |
| 89 | 89 |
species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet", |
| inputs/FIA/occurrence_all/VegBIEN.csv | ||
|---|---|---|
| 9 | 9 |
locationID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
| 10 | 10 |
subplot,/location/authorlocationcode, |
| 11 | 11 |
individualObservationID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 12 |
cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/1",
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| 13 |
oldGrowth,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/2/_not/value",
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| 12 |
cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/1",
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| 13 |
oldGrowth,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/2/_not/value",
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| 14 | 14 |
subplot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists", |
| 15 | 15 |
subplotID,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists", |
| 16 | 16 |
authorEventCode,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
| ... | ... | |
| 36 | 36 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
| 37 | 37 |
taxonName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
| 38 | 38 |
individualObservationID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 39 |
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/1",
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| 40 |
oldGrowth,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/2/_not/value",
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| 39 |
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1",
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| 40 |
oldGrowth,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/2/_not/value",
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| 41 | 41 |
individualObservationID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/1", |
| 42 | 42 |
forma,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=forma]/taxonepithet", |
| 43 | 43 |
variety,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=variety]/taxonepithet", |
| inputs/FIA/occurrence_all/test.xml.ref | ||
|---|---|---|
| 58 | 58 |
</plantobservation> |
| 59 | 59 |
</aggregateoccurrence> |
| 60 | 60 |
<authortaxoncode>$individualCode</authortaxoncode> |
| 61 |
<iscultivated> |
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| 62 |
<_alt> |
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| 63 |
<1>$cultivated</1> |
|
| 64 |
<2><_not><value>$oldGrowth</value></_not></2> |
|
| 65 |
</_alt> |
|
| 66 |
</iscultivated> |
|
| 61 |
<iscultivated>$cultivated</iscultivated> |
|
| 67 | 62 |
<sourceaccessioncode>$individualObservationID</sourceaccessioncode> |
| 68 | 63 |
<taxondetermination> |
| 69 | 64 |
<taxonverbatim_id> |
| inputs/ARIZ/omoccurrences/VegBIEN.csv | ||
|---|---|---|
| 15 | 15 |
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 16 | 16 |
occid,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_first/1", |
| 17 | 17 |
occurrenceID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_first/2",Not populated for all rows |
| 18 |
cultivationStatus,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/1/_map:[0=,*=*]/value","cultivated can only be true or NULL, not false "
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| 18 |
cultivationStatus,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/1/_map:[0=,*=*]/value","cultivated can only be true or NULL, not false "
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| 19 | 19 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
| 20 | 20 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
| 21 | 21 |
samplingProtocol,/location/locationevent/*_id/method/name, |
| ... | ... | |
| 45 | 45 |
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 46 | 46 |
occid,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_first/1", |
| 47 | 47 |
occurrenceID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_first/2",Not populated for all rows |
| 48 |
cultivationStatus,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/1/_map:[0=,*=*]/value","cultivated can only be true or NULL, not false "
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| 48 |
cultivationStatus,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1/_map:[0=,*=*]/value","cultivated can only be true or NULL, not false "
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| 49 | 49 |
occid,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3/_first/1, |
| 50 | 50 |
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3/_first/2,Not populated for all rows |
| 51 | 51 |
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| inputs/MO/Specimen/VegBIEN.csv | ||
|---|---|---|
| 7 | 7 |
minimumelevation,/location/elevation_m/_alt/2/_avg/1,Setting units to m for now because only 4% of rows have valid elevationunits other than Meters (these rows all have units of Feet) |
| 8 | 8 |
maximumelevation,/location/elevation_m/_alt/2/_avg/2,Setting units to m for now because only 4% of rows have valid elevationunits other than Meters (these rows all have units of Feet) |
| 9 | 9 |
collectionnumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 10 |
iscultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/1",
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| 10 |
iscultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/1",
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| 11 | 11 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
| 12 | 12 |
determinationyear,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value", |
| 13 | 13 |
qualifier,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit", |
| ... | ... | |
| 24 | 24 |
collectorstring,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 25 | 25 |
collectionnumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 26 | 26 |
specimenid,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 27 |
iscultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/1",
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| 27 |
iscultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1",
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| 28 | 28 |
specimenid,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
| 29 | 29 |
determinedby,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname, |
| 30 | 30 |
rankabbreviation,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank", |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 43 | 43 |
individualObservationID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 44 | 44 |
occurrenceID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 45 | 45 |
taxonOccurrenceID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 46 |
cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/1",
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| 47 |
oldGrowth,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/2/_not/value",
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| 46 |
cultivated,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/1",
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| 47 |
oldGrowth,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_first/2/_not/value",
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| 48 | 48 |
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
| 49 | 49 |
verbatimLocality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/2, |
| 50 | 50 |
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3, |
| ... | ... | |
| 229 | 229 |
individualObservationID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 230 | 230 |
occurrenceID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 231 | 231 |
taxonOccurrenceID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 232 |
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/1",
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| 233 |
oldGrowth,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/2/_not/value",
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| 232 |
cultivated,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/1",
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| 233 |
oldGrowth,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_first/2/_not/value",
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| 234 | 234 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
| 235 | 235 |
establishmentMeans,"/location/locationevent/taxonoccurrence/isnative/_map:[native=t,exotic=f,*=]/value", |
| 236 | 236 |
taxonOccurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: cultivated, oldGrowth: use just cultivated if it's provided, rather than /_alt-ing it back with oldGrowth (which it was generated from)