Getting data with OpenDataBio-R

Getting data using the OpenDataBio R client

The Opendatabio-R package was created to allow users to interact with an OpenDataBio server, to both obtain (GET) data or to import (POST) data into the database. This tutorial is a basic example of how to get data.

Set up the connection

  1. Set up the connection to the OpenDataBio server using the odb_config() function. The most important parameters for this function are base_url, which should point to the API url for your OpenDataBio server, and token, which is the access token used to authenticate your user.
  2. The token is only need to get data from datasets that have one of the restricted access policies. Data from datasets of public access can be extracted without the token specification.
  3. Your token is avaliable in your profile in the web interface
library(opendatabio)
base_url="http://localhost:8080/api"
token ="GZ1iXcmRvIFQ"
cfg = odb_config(base_url=base_url, token = token)

More advanced configuration involves setting a specific API version, a custom User Agent, or other HTTP headers, but this is not covered here.

Test your connection

The function odb_test() may be used to check if the connection was successful, and whether your user was correctly identified:

odb_test(cfg)
#will output
Host: http://localhost:8080/api/v0
Versions: server 0.9.1-alpha1 api v0
$message
[1] "Success!"

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

As an alternative, you can specify these parameters as systems variables. Before starting R, set this up on your shell (or add this to the end of your .bashrc file):

export ODB_TOKEN="YourToken"
export ODB_BASE_URL="http://localhost:8080/api"
export ODB_API_VERSION="v0"

GET Data

Check the GET API Quick-Reference for a full list of endpoints and request parameters.

For data of public access the token is optional. Below two examples for the Locations and Taxons endpoints. Follow a similar reasoning for using the remaining endpoints. See the package help in R for all available odb_get_{endpoint} functions.

Getting Taxon names

See GET API Taxon Endpoint request parameters and a list of response fields.

base_url="http://localhost:8080/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)

If the server used the seed data provided and the default language is portuguese, the result will be:

  id scientificName taxonRank parent_id  parentName
1 25    Magnoliidae     Clado        20 Angiosperms
2 43     Canellales     Ordem        25 Magnoliidae
3 62       Laurales     Ordem        25 Magnoliidae
4 65    Magnoliales     Ordem        25 Magnoliidae
5 74      Piperales     Ordem        25 Magnoliidae
6 93  Chloranthales     Ordem        25 Magnoliidae

Getting Locations

See GET API Location Endpoint request parameters and a list of response fields.

Get some fields listing all Conservation Units (adm_level==99) registered in the server:

base_url="http://localhost:8080/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)

If the server used the seed data provided and the default language is portuguese, the result will be:

id                                                           name
1 5628                              Estação Ecológica Mico-Leão-Preto
2 5698          Área de Relevante Interesse Ecológico Ilha do Ameixal
3 5700 Área de Relevante Interesse Ecológico da Mata de Santa Genebra
4 5703     Área de Relevante Interesse Ecológico Buriti de Vassununga
5 5707                                Reserva Extrativista do Mandira
6 5728                                   Floresta Nacional de Ipanema
parent_id parentName
1         6  São Paulo
2         6  São Paulo
3         6  São Paulo
4         6  São Paulo
5         6  São Paulo
6         6  São Paulo

Get the plots imported in the import locations tutorial. To obtain a spatial object in R, use the readWKT function of the rgeos package.

library(rgeos)
library(opendatabio)
base_url="http://localhost:8080/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')
  }
}

Figure generated:

Last modified September 23, 2021 : Updated to GitLab (36f655e)