Importar Indivíduos & Vouchers

library(opendatabio)
base_url="https://opendb.inpa.gov.br/api"
token ="GZ1iXcmRvIFQ" #this must be your token not this value
cfg = odb_config(base_url=base_url, token = token)

#the number in the aluminium tag in the forest
to.odb = data.frame(tag='3405.L1', stringsAsFactors=F)

#the collectors (get ids from the server)
(joao = odb_get_persons(params=list(search='joao batista da silva'),odb_cfg=cfg)$id)
(ana = odb_get_persons(params=list(search='ana cristina sega'),odb_cfg=cfg)$id)
#ids concatenated by | pipe
to.odb$collector = paste(joao,ana,sep='|')

#tagged date (lets use an incomplete).
to.odb$date = '2018-07-NA'

#lets place in a Plot location imported with the Location post tutorial
plots = odb_get_locations(params=list(name='A 1ha example plot'),odb_cfg=cfg)
head(plots)
to.odb$location = plots$id


#relative position within parent plot
to.odb$x = 10.4
to.odb$y = 32.5
#or could be
#to.odb$relative_position = paste(x,y,sep=',')

#taxonomic identification
taxon = 'Ocotea guianensis'
#check that exists
(odb_get_taxons(params=list(name='Ocotea guianensis'),odb_cfg=cfg)$id)

#person that identified the individual
to.odb$identifier = odb_get_persons(params=list(search='paulo apostolo'),odb_cfg=cfg)$id
#or you also do to.odb$identifier = "Assunção, P.A.C.L."
#the used form only guarantees the persons is there.

#may add modifers as well [may need to use numeric code instead]
to.odb$modifier = 'cf.'
#or check with  to see you spelling is correct
odb_detModifiers()
#and submit the numeric code instaed
to.odb$modifier = 3

#an incomplete identification date
to.odb$identification_date = list(year=2005)
#or  to.odb$identification_date =  "2005-NA-NA"

odb_import_individuals(to.odb,odb_cfg = cfg)
#lets import this individual
odb_import_individuals(to.odb,odb_cfg = cfg)

#check the job status
odb_get_jobs(params=list(id=130),odb_cfg = cfg)

dataset = odb_get_datasets(params=list(name="Dataset test"),odb_cfg=cfg)
dataset
to.odb$dataset = dataset$id
odb_import_individuals(to.odb,odb_cfg = cfg)

#a fake plant record somewhere in the Amazon
aplant =  data.frame(taxon="Duckeodendron cestroides", date="2021-09-09", latitude=-2.34, longitude=-59.845,angle=NA,distance=NA, collector="Oliveira, A.A. de|João Batista da Silva", tag="3456-A",dataset=1)

#a fake set of vouchers for this individual
herb = data.frame(biocollection=c("INPA","NY","MO"),biocollection_number=c("12345A","574635","ANOTHER FAKE CODE"),biocollection_type=c(2,3,3))

#add this dataframe to the object
aplant$biocollection = NA
aplant$biocollection = list(herb)

#another fake plant
asecondplant =  data.frame(taxon="Ocotea guianensis", date="2021-09-09", latitude=-2.34, longitude=-59.89,angle=240,distance=50, collector="Oliveira, A.A. de|João Batista da Silva", tag="3456",dataset=1)
asecondplant$biocollection = NA

#merge the fake data
to.odb = rbind(aplant,asecondplant)

library(opendatabio)
base_url="https://opendb.inpa.gov.br/api"
token ="GZ1iXcmRvIFQ" #this must be your token not this value
cfg = odb_config(base_url=base_url, token = token)

odb_import_individuals(to.odb, odb_cfg=cfg)

#get the imported individuals using a wildcard
inds = odb_get_individuals(params = list(tag='3456*'),odb_cfg = cfg)
inds[,c("basisOfRecord","scientificName","organismID","decimalLatitude","decimalLongitude","higherGeography") ]

#get the vouchers imported with the first plant data
vouchers = odb_get_vouchers(params = list(individual=inds$id),odb_cfg = cfg)
vouchers[,c("basisOfRecord","scientificName","organismID","collectionCode","catalogNumber") ]

#a holotype voucher with same collector and date as individual
onevoucher = data.frame(individual=1,biocollection="INPA",biocollection_number=1234,biocollection_type=1,dataset=1)
library(opendatabio)
base_url="https://opendb.inpa.gov.br/api"
token ="GZ1iXcmRvIFQ" #this must be your token not this value
cfg = odb_config(base_url=base_url, token = token)

odb_import_vouchers(onevoucher, odb_cfg=cfg)

#get the imported voucher
voucher = odb_get_vouchers(params=list(individual=1),cfg)
vouchers[,c("basisOfRecord","scientificName","occurrenceID","collectionCode","catalogNumber") ]

#one with same date and collector as individual
one = data.frame(individual=2,biocollection="INPA",biocollection_number=1234,dataset=1,collector=NA,number=NA,date=NA)
#this one with different collector and date
two= data.frame(individual=2,biocollection="INPA",biocollection_number=4435,dataset=1,collector="Oliveira, A.A. de|João Batista da Silva",number=3456,date="1991-08-01")


library(opendatabio)
base_url="https://opendb.inpa.gov.br/api"
token ="GZ1iXcmRvIFQ" #this must be your token not this value
cfg = odb_config(base_url=base_url, token = token)


to.odb = rbind(one,two)
odb_import_vouchers(to.odb, odb_cfg=cfg)

#get the imported voucher
voucher = odb_get_vouchers(params=list(individual=2),cfg)
voucher[,c("basisOfRecord","scientificName","occurrenceID","collectionCode","catalogNumber") ]