Getting data with OpenDataBio-R

library(opendatabio)
base_url="https://opendb.inpa.gov.br/api"
token ="GZ1iXcmRvIFQ"
cfg = odb_config(base_url=base_url, token = token)

odb_test(cfg)
#will output
Host: https://opendb.inpa.gov.br/api/v0
Versions: server 0.9.1-alpha1 api v0
$message
[1] "Success!"

$user
[1] "admin@example.org"

export ODB_TOKEN="YourToken"
export ODB_BASE_URL="https://opendb.inpa.gov.br/api"
export ODB_API_VERSION="v0"

base_url="https://opendb.inpa.gov.br/api"
cfg = odb_config(base_url=base_url)
#get id for a taxon
mag.id = odb_get_taxons(params=list(name='Magnoliidae',fields='id,name'),odb_cfg = cfg)
#use this id to get all descendants of this taxon
odb_taxons = odb_get_taxons(params=list(root=mag.id$id,fields='id,scientificName,taxonRank,parent_id,parentName'),odb_cfg = cfg)
head(odb_taxons)

base_url="https://opendb.inpa.gov.br/api"
cfg = odb_config(base_url=base_url)
odblocais = odb_get_locations(params = list(fields='id,name,parent_id,parentName',adm_level=99),odb_cfg = cfg)
head(odblocais)

library(rgeos)
library(opendatabio)
base_url="https://opendb.inpa.gov.br/api"
cfg = odb_config(base_url=base_url)

locais = odb_get_locations(params=list(adm_level=100),odb_cfg = cfg)
locais[,c('id','locationName','parentName')]
colnames(locais)
for(i in 1:nrow(locais)) {
  geom = readWKT(locais$footprintWKT[i])
  if (i==1) {
    plot(geom,main=locais$locationName[i],cex.main=0.8)
    axis(side=1,cex.axis=0.5)
    axis(side=2,cex.axis=0.5,las=2)
  } else {
    plot(geom,main=locais$locationName[i],add=T,col='red')
  }
}

#conect to database
library(opendatabio)
base_url="http://localhost/opendatabio/api"
token ="your token is mandatory in this case"
cfg = odb_config(base_url=base_url, token = token)
odb_test(cfg)

#fake data
dados = data.frame(
  latitude = sample(seq(-2,2,by=0.00001),10),
  longitude = sample(seq(-60,-59,by=0.00001),10)
)

#submit job for validation
jb = odb_validate_locations(dados,odb_cfg = cfg)

#monitor job execution
odb_get_jobs(params=list(id=jb$id),odb_cfg = cfg)

#get results
dadosValidados = odb_get_jobs(params=list(id=jb$id,get_file=T),odb_cfg = cfg)

library(opendatabio)
base_url = "https://opendb.inpa.gov.br/api"
token = "YOUR TOKEN HERE"

# Set the connection configuration
cfg = odb_config(base_url = base_url, token = token)

# DIRECT DOWNLOAD – if you want to download a small amount of data
inds = odb_get_individuals(params = list(limit = 100), odb_cfg = cfg)

# PREPARE FILE ON SERVER – if your query will return a large number of records
# Download all records you have access to or public ones
# Save the process, since the result is likely to be large
jobid = odb_get_individuals(params = list(save_job = TRUE), odb_cfg = cfg)
# Check the status of the job
odb_get_jobs(params = list(id = jobid$job_id), odb_cfg = cfg)
# When it finishes, get the data here (or download the file via the web interface)
all_inds = odb_get_jobs(params = list(id = jobid$job_id), odb_cfg = cfg)

# FETCHING SPECIFIC DATA

# All individuals identified as taxon X
params = list(taxon = "Licaria cannela tenuicarpa")
licarias = odb_get_individuals(params = params, odb_cfg = cfg)

# All individuals identified as taxon X or its descendants
params = list(taxon_root = "Licaria")
licarias = odb_get_individuals(params = params, odb_cfg = cfg)

# All individuals from dataset X
params = list(dataset = "MyDataset name or id")
inds = odb_get_individuals(params = params, odb_cfg = cfg)
# Or use save_job above if the dataset is large

# You can view the list of available datasets
datasets = odb_get_datasets(odb_cfg = cfg)

library(opendatabio)
base_url="https://opendb.inpa.gov.br/api"
token="YOUR TOKEN HERE"

#establishes the connection configuration
cfg = odb_config(base_url=base_url, token = token)

#100 first measurements of the dataset X with id=10
measurements = odb_get_measurements(params=list(dataset=10,limit=100),odb_cfg=cfg)

#100 first measurements of the dataset X with id=10 for the variable whose export_name is treeDbh
measurements = odb_get_measurements(params=list(trait="treeDbh",dataset=10,limit=100),odb_cfg=cfg)

#Measurements of the dataset X with id=10 for the variable whose export_name is treeDbh
#only for Lauraceae
measurements = odb_get_measurements(params=list(trait="treeDbh",dataset=10,taxon_root="Lauraceae"),odb_cfg=cfg)

#linking data of individuals measurements
laurels = odb_get_individuals(params=list(dataset=10,taxon_root="Lauraceae"),odb_cfg=cfg)
filter = grep("Individu",measurements$measured_type) #optional, depends on what is in measurements
g = match(measurements$measured_id[filter],laurels$id)
measurements$location = NA
measurements$location[filter] = laurels$locationName[g]

library(opendatabio)
base_url="https://opendb.inpa.gov.br/api"
token="YOUR TOKEN HERE"

#set the connection configuration
cfg = odb_config(base_url=base_url, token = token)

#the first 50 media files of a dataset that has images
imgs = odb_get_media(params=list(dataset=97,limit=50),odb_cfg=cfg)

#see this metadata
head(imgs)

#from this metadata, download the media files
#create a function for this:
getImagesByURL <- function(url,downloadFolder='img') {
dir.create(downloadFolder,showWarnings = F)
fn = strsplit(url,"\\/")[[1]]
fn = fn[length(fn)]
nname = paste(downloadFolder,fn,sep="/")
img = httr::GET(url=url) 
writeBin(httr::content(img, "raw"), nname)
}
#use the function to download images to a folder
sapply(imgs$file_url,getImagesByURL,downloadFolder='testeImgsFromOdb') 

library(opendatabio)
base_url="https://opendb.inpa.gov.br/api"
token="YOUR TOKEN HERE"

#establishes the connection configuration
cfg = odb_config(base_url=base_url, token = token)

#first 100 vouchers registered in a biocollection
vouchers = odb_get_vouchers(params=list(biocollection="INPA",limit=100),odb_cfg=cfg)

#vouchers in location x (id, or name, as registered in the database)
vouchers = odb_get_vouchers(params=list(location="Reserva Florestal Adolpho Ducke, Parcela PDBFF-100ha",limit=100),odb_cfg=cfg)