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https://github.com/inbo/etnservice

R package to serve data from the European Tracking Network over a restful api
https://github.com/inbo/etnservice

animal-movement animal-tracking api biologging data-access fish lifewatch opencpu oscibio r r-package rstats

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R package to serve data from the European Tracking Network over a restful api

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README 

        
---

output: github_document

---



```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```



# etnservice



[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)

[![R-CMD-check](https://github.com/inbo/etnservice/actions/workflows/R-CMD-check-lite.yaml/badge.svg)](https://github.com/inbo/etnservice/actions/workflows/R-CMD-check-lite.yaml)



The goal of etnservice is to to serve data from the European Tracking Network as a restful API.



## About/Data Policy



Etn provides functionality to access data from the [European Tracking

Network (ETN)](http://www.lifewatch.be/etn/) database hosted by the

Flanders Marine Institute (VLIZ) as part of the Flemish contribution to

LifeWatch. ETN data is subject to the [ETN data

policy](http://www.lifewatch.be/etn/assets/docs/ETN-DataPolicy.pdf) and

can be:



  - restricted: under moratorium and only accessible to logged-in data

    owners/collaborators

  - unrestricted: publicly accessible without login and routinely

    published to international biodiversity facilities



The ETN infrastructure currently requires the package to be run within

the [LifeWatch.be RStudio server](http://rstudio.lifewatch.be/), which

is password protected. A login can be requested at

.



## Installation



etnservice needs direct access to the [ETN](https://lifewatch.be/etn/) database, thus a local install will not function without a copy of this database.



You can install the development version of etnservice from [GitHub](https://github.com/) with:



``` r

# install.packages("devtools")

devtools::install_github("inbo/etnservice")

```



## How to use the API



This is a basic example which shows you how adress the API directly:



```{r example, eval = FALSE}

library(httr) # to talk to the internet

library(magrittr) # to use pipes

library(jsonlite) # to work with JSON files

library(askpass) # to safly enter a password in R



# To access the ETN database, we need a login (username + password). We'll ask

# for the password dynamically because that's safer than storing it as an object

username <- ""

# All functions can be adressed directly in the URL

endpoint <- "https://opencpu.lifewatch.be/library/etn/R/list_animal_ids"

# Request the result of the function to be a json, and put in a request

response <-

    httr::POST(paste(endpoint, "json", sep = "/"),

      body = list(

        credentials = glue::glue('list(username = "{username}", password = "{askpass::askpass()}")')

      )

    )

# Take the response of the server, and convert it into an R object we can use

response %>%

    httr::content(as = "text", encoding = "UTF-8") %>%

    jsonlite::fromJSON(simplifyVector = TRUE)



```



However, a fork of the [etn package](https://github.com/inbo/etn) is currently in development that will allow you to do this using built in functions. 



Another example of the same request as above, but now using [curl](https://curl.se/):

```{bash,eval = FALSE}

#! /bin/bash

curl --location --request POST 'https://opencpu.lifewatch.be/library/etnservice/R/list_animal_ids/json' \

--header 'Content-Type: application/json' \

--header 'Cookie: vliz_webc=vliz_webc2' \

--data-raw '{

    "credentials": {

        "username": "",

        "password": ""

    }

}'

```