SPARQL function for R

SPARQL.r

# Script to query the triple store
library(stringr)
library(httr)
library(jsonlite)

# SPARQL endpoint where the triple store endpoint is located
endpoint = "http://localhost:7200/repositories/wur_unlock_hivghana_drp0070"

# create a named character vector of URLs and prefixes
url_dict <- c("http://example.com/" = "ex:",
              "http://gbol.life/0.1/" = "gbol:",
              "http://www.w3.org/1999/02/22-rdf-syntax-ns#" = "rdf:",
              "http://www.w3.org/2000/01/rdf-schema#" = "rdfs:",
              "http://www.w3.org/2002/07/owl#" = "owl:",
              "http://www.w3.org/2001/XMLSchema#" = "xsd:",
              "http://purl.org/dc/terms/" = "dcterms:",
              "http://purl.org/dc/elements/1.1/" = "dc:",
              "http://purl.org/dc/dcmitype/" = "dcmitype:",
              "http://purl.org/dc/dcam/" = "dcam:",
              "http://purl.org/dc/qualifiers/1.0/" = "dcq:"
              )

prefix_cleaner <- function(x, prefixes = url_dict) {
  x <- as.character(x)
  for (u in names(url_dict)) {
    x <- str_replace(x, u, url_dict[u])
  }
  return(x)
}

# SPARQL function to query the triple store
sparql <- function(query, endpoint, prefixes = NULL) {
  res <- httr::GET(endpoint, query = list(query = query, format = "json"))
  if (res$status_code != 200) {
    stop("Error: ", res$status_code, " ", res$reason)
  }
  # return(content(res, "text", encoding = "UTF-8"))
  dfGraph = jsonlite::fromJSON(content(res, "text", encoding = "UTF-8"))
  dfGraph <- as.data.table(dfGraph$results$bindings)
  # Keep only the columns that contain the value
  table = dfGraph[,grep(".value", names(dfGraph), value=TRUE), with=FALSE]
  # Clean the table
  table <- mapply(prefix_cleaner, table, prefixes)
  # table$library.value <- prefix(table$library.value)
  return(as.data.frame(table))
}