Revision 4529
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/VegBank/import_order.txt | ||
|---|---|---|
| 1 | 1 |
plot_ |
| 2 |
observation_ |
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| 2 |
observation_ |
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| 3 |
taxonobservation_ |
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| inputs/VegBank/taxonobservation_/create.sql | ||
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| 1 |
SELECT * |
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| 2 |
FROM taxonobservation |
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LEFT JOIN taxoninterpretation USING (taxonobservation_id) |
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| 4 |
LEFT JOIN plantconcept_ USING (plantconcept_id) |
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; |
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ALTER TABLE :table DROP COLUMN row_num; |
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| inputs/VegBank/taxonobservation_/src.csv | ||
|---|---|---|
| 1 |
VegBank[Veg+],Veg+,Comments |
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| 2 |
plantconcept_id,, |
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| 3 |
taxonobservation_id,, |
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| 4 |
observation_id,, |
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| 5 |
authorplantname,, |
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| 6 |
taxonobservation_reference_id,, |
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| 7 |
taxoninferencearea,, |
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| 8 |
emb_taxonobservation,, |
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| 9 |
int_origplantconcept_id,, |
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| 10 |
int_origplantscifull,, |
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| 11 |
int_origplantscinamenoauth,, |
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| 12 |
int_origplantcommon,, |
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| 13 |
int_origplantcode,, |
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| 14 |
int_currplantconcept_id,, |
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| 15 |
int_currplantscifull,, |
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| 16 |
int_currplantscinamenoauth,, |
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| 17 |
int_currplantcommon,, |
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| 18 |
int_currplantcode,, |
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| 19 |
taxonobservation_accessioncode,, |
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| 20 |
taxoninterpretation_id,, |
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| 21 |
stemlocation_id,, |
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| 22 |
taxoninterpretation_plantname_id,, |
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| 23 |
party_id,, |
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| 24 |
role_id,, |
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| 25 |
interpretationtype,, |
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| 26 |
reference_id,, |
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| 27 |
originalinterpretation,, |
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| 28 |
currentinterpretation,, |
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| 29 |
taxonfit,, |
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| 30 |
taxonconfidence,, |
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| 31 |
collector_id,, |
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collectionnumber,, |
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museum_id,, |
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museumaccessionnumber,, |
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grouptype,, |
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notes,, |
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notespublic,, |
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notesmgt,, |
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| 39 |
revisions,, |
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| 40 |
interpretationdate,, |
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| 41 |
collectiondate,, |
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| 42 |
emb_taxoninterpretation,, |
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taxoninterpretation_accessioncode,, |
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plantname_id,, |
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plantconcept__reference_id,, |
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plantname,, |
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plantcode,, |
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plantdescription,, |
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d_obscount,, |
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d_currentaccepted,, |
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plantconcept__accessioncode,, |
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Kingdom,, |
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Subkingdom,, |
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| 54 |
Superdivision,, |
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Division,, |
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Subdivision,, |
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Class,, |
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| 58 |
Subclass,, |
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| 59 |
Order,, |
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| 60 |
Family,, |
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| 61 |
Genus,, |
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| 62 |
Species,, |
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Subspecies,, |
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| 64 |
Variety,, |
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Forma,, |
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row_num,, |
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| inputs/VegBank/taxonobservation_/header.csv | ||
|---|---|---|
| 1 |
plantconcept_id,taxonobservation_id,observation_id,authorplantname,taxonobservation_reference_id,taxoninferencearea,emb_taxonobservation,int_origplantconcept_id,int_origplantscifull,int_origplantscinamenoauth,int_origplantcommon,int_origplantcode,int_currplantconcept_id,int_currplantscifull,int_currplantscinamenoauth,int_currplantcommon,int_currplantcode,taxonobservation_accessioncode,taxoninterpretation_id,stemlocation_id,taxoninterpretation_plantname_id,party_id,role_id,interpretationtype,reference_id,originalinterpretation,currentinterpretation,taxonfit,taxonconfidence,collector_id,collectionnumber,museum_id,museumaccessionnumber,grouptype,notes,notespublic,notesmgt,revisions,interpretationdate,collectiondate,emb_taxoninterpretation,taxoninterpretation_accessioncode,plantname_id,plantconcept__reference_id,plantname,plantcode,plantdescription,d_obscount,d_currentaccepted,plantconcept__accessioncode,Kingdom,Subkingdom,Superdivision,Division,Subdivision,Class,Subclass,Order,Family,Genus,Species,Subspecies,Variety,Forma,row_num |
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| inputs/VegBank/taxonobservation_/map.csv | ||
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| 1 |
VegBank[Veg+],Veg+,Comments |
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| 2 |
plantconcept_id,, |
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taxonobservation_id,taxonOccurrenceID, |
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| 4 |
observation_id,, |
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authorplantname,verbatimScientificName, |
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taxonobservation_reference_id,, |
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taxoninferencearea,, |
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emb_taxonobservation,, |
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| 9 |
int_origplantconcept_id,, |
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| 10 |
int_origplantscifull,, |
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| 11 |
int_origplantscinamenoauth,, |
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| 12 |
int_origplantcommon,, |
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int_origplantcode,, |
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| 14 |
int_currplantconcept_id,, |
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| 15 |
int_currplantscifull,, |
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| 16 |
int_currplantscinamenoauth,, |
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| 17 |
int_currplantcommon,, |
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| 18 |
int_currplantcode,, |
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taxonobservation_accessioncode,, |
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| 20 |
taxoninterpretation_id,, |
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stemlocation_id,, |
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taxoninterpretation_plantname_id,, |
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party_id,, |
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role_id,, |
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interpretationtype,, |
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reference_id,, |
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originalinterpretation,, |
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| 28 |
currentinterpretation,, |
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| 29 |
taxonconfidence,, |
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collector_id,, |
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collectionnumber,, |
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| 32 |
museum_id,, |
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| 33 |
museumaccessionnumber,catalogNumber, |
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grouptype,, |
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| 35 |
notespublic,, |
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notesmgt,, |
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| 37 |
revisions,, |
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| 38 |
interpretationdate,identifiedDate, |
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| 39 |
collectiondate,collectedDate, |
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| 40 |
emb_taxoninterpretation,, |
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taxoninterpretation_accessioncode,, |
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plantname_id,, |
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plantconcept__reference_id,, |
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plantname,, |
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| 45 |
plantcode,, |
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| 46 |
plantdescription,, |
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d_obscount,, |
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| 48 |
d_currentaccepted,, |
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| 49 |
plantconcept__accessioncode,, |
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| 50 |
Subkingdom,, |
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| 51 |
Superdivision,, |
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| 52 |
Division,, |
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| 53 |
Subdivision,, |
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| 54 |
Subclass,, |
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Variety,, |
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Forma,, |
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row_num,, |
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| inputs/VegBank/taxonobservation_/map.full.csv | ||
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| 1 |
VegBank[Veg+],Veg+,Comments |
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| 2 |
museumaccessionnumber,catalogNumber, |
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class,class |
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collectiondate,collectedDate, |
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family,family |
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genus,genus |
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interpretationdate,identifiedDate, |
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kingdom,kingdom |
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notes,notes |
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order,order |
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species,species |
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subspecies,subspecies |
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taxonFit,taxonFit |
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taxonobservation_id,taxonOccurrenceID, |
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authorplantname,verbatimScientificName, |
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| inputs/VegBank/taxonobservation_/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank[Veg+],VegBIEN:,Comments |
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museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_join/3/_if[@name=""if indirect voucher""]/else", |
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collectiondate,/location/locationevent/obsenddate/_*/date/_dateRangeEnd/value/_alt/2/_alt/3, |
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collectiondate,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value/_alt/2/_alt/3, |
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collectiondate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_alt/3, |
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notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
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museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
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authorplantname,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_alt/1, |
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taxonobservation_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
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subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/last", |
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species,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname", |
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genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname", |
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family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname", |
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order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=order]/plantname", |
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class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=class]/plantname", |
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kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname", |
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interpretationdate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_*/date/_dateRangeStart/value/_alt/3, |
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taxonFit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
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authorplantname,"/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname", |
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museumaccessionnumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
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| inputs/VegBank/taxonobservation_/test.xml.ref | ||
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| 1 |
Put template: |
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<VegBIEN> |
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<location id="-1"> |
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<authorlocationcode>$museumaccessionnumber</authorlocationcode> |
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<locationevent> |
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<obsenddate><_date><date><_dateRangeEnd><value>$collectiondate</value></_dateRangeEnd></date></_date></obsenddate> |
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<obsstartdate><_date><date><_dateRangeStart><value>$collectiondate</value></_dateRangeStart></date></_date></obsstartdate> |
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<taxonoccurrence> |
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<aggregateoccurrence> |
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<collectiondate><_date><date>$collectiondate</date></_date></collectiondate> |
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<notes>$notes</notes> |
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<plantobservation><specimenreplicate><catalognumber_dwc>$museumaccessionnumber</catalognumber_dwc></specimenreplicate></plantobservation> |
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</aggregateoccurrence> |
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<authortaxoncode>$authorplantname</authortaxoncode> |
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<sourceaccessioncode>$taxonobservation_id</sourceaccessioncode> |
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<taxondetermination> |
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<plantconcept_id> |
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<plantconcept> |
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<plantname_id> |
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<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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<plantname> |
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<rank>binomial</rank> |
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<parent_id> |
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<plantname> |
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<rank>authority</rank> |
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<parent_id> |
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<plantname> |
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<rank>subspecies</rank> |
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<plantname>$Subspecies</plantname> |
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<parent_id> |
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<plantname> |
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<rank>species</rank> |
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<plantname>$Species</plantname> |
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<parent_id> |
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<plantname> |
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<rank>genus</rank> |
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<plantname>$Genus</plantname> |
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<parent_id> |
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| 41 |
<plantname> |
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<rank>family</rank> |
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<plantname>$Family</plantname> |
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<parent_id> |
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| 45 |
<plantname> |
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<rank>order</rank> |
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<plantname>$Order</plantname> |
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| 48 |
<parent_id> |
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<plantname> |
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<rank>class</rank> |
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<plantname>$Class</plantname> |
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<parent_id> |
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<plantname> |
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<rank>subkingdom</rank> |
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<parent_id> |
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<plantname> |
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<rank>kingdom</rank> |
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<plantname>$Kingdom</plantname> |
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</plantname> |
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</parent_id> |
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</plantname> |
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</parent_id> |
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</plantname> |
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</parent_id> |
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</plantname> |
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</parent_id> |
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</plantname> |
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</parent_id> |
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</plantname> |
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</parent_id> |
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</plantname> |
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</parent_id> |
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</plantname> |
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</parent_id> |
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</plantname> |
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</parent_id> |
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</plantname> |
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</path> |
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</_simplifyPath> |
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</plantname_id> |
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</plantconcept> |
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</plantconcept_id> |
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<determinationdate><_date><date><_dateRangeStart><value>$interpretationdate</value></_dateRangeStart></date></_date></determinationdate> |
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<taxonfit>$taxonfit</taxonfit> |
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</taxondetermination> |
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<taxondetermination> |
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<isoriginal>true</isoriginal> |
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| 88 |
<plantconcept_id> |
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| 89 |
<plantconcept> |
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| 90 |
<plantname_id> |
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| 91 |
<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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<plantname> |
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<rank>binomial</rank> |
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<plantname>$authorplantname</plantname> |
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</plantname> |
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</path> |
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</_simplifyPath> |
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</plantname_id> |
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</plantconcept> |
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</plantconcept_id> |
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| 103 |
</taxondetermination> |
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</taxonoccurrence> |
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</locationevent> |
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</location> |
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</VegBIEN> |
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Inserted 18 new rows into database |
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Also available in: Unified diff
inputs/VegBank/: Added taxonobservation_/