R/client.R

In ropenscilabs/sparqldsl: SPARQL DSL Client

#' Sparql Connection Client
#' 
#' Low level Sparql connection client with query methods
#'
#' @export
#' @keywords internal
#' @details
#' \strong{Methods}
#'   \describe{
#'    \item{\code{make_url(x)}}{
#'      construct the complete url
#'    }
#'    \item{\code{query(query, format = "json", ...)}}{
#'      query the endpoint
#'    }
#'  }
#' @format NULL
#' @usage NULL
#' @examples \dontrun{
#' # dbpedia
#' (x <- SparqlClient$new(url = "dbpedia.org", path = "sparql"))
#' x$query("SELECT * WHERE { ?s ?p ?o } OFFSET 100 LIMIT 10")
#' 
#' # open citations
#' (x <- SparqlClient$new(url = "opencitations.net", path = "sparql"))
#' x$url
#' x$path
#' x$scheme
#' x$make_base()
#' x$make_url()
#' 
#' query <- I("PREFIX+cito%3A+<http%3A%2F%2Fpurl.org%2Fspar%2Fcito%2F>%0APREFIX+dcterms%3A+<http%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F>%0APREFIX+datacite%3A+<http%3A%2F%2Fpurl.org%2Fspar%2Fdatacite%2F>%0APREFIX+literal%3A+<http%3A%2F%2Fwww.essepuntato.it%2F2010%2F06%2Fliteralreification%2F>%0APREFIX+biro%3A+<http%3A%2F%2Fpurl.org%2Fspar%2Fbiro%2F>%0APREFIX+frbr%3A+<http%3A%2F%2Fpurl.org%2Fvocab%2Ffrbr%2Fcore%23>%0APREFIX+c4o%3A+<http%3A%2F%2Fpurl.org%2Fspar%2Fc4o%2F>%0ASELECT+%3Fcited+%3Fcited_ref+%3Ftitle+%3Furl+WHERE+%7B%0A%09<https%3A%2F%2Fw3id.org%2Foc%2Fcorpus%2Fbr%2F1>+cito%3Acites+%3Fcited+.%0A%09OPTIONAL+%7B+%0A%09%09<https%3A%2F%2Fw3id.org%2Foc%2Fcorpus%2Fbr%2F1>+frbr%3Apart+%3Fref+.%0A%09%09%3Fref+biro%3Areferences+%3Fcited+%3B%0A%09%09%09c4o%3AhasContent+%3Fcited_ref+%0A%09%7D%0A%09OPTIONAL+%7B+%3Fcited+dcterms%3Atitle+%3Ftitle+%7D%0A%09OPTIONAL+%7B%0A%09%09%3Fcited+datacite%3AhasIdentifier+%5B%0A%09%09%09datacite%3AusesIdentifierScheme+datacite%3Aurl+%3B%0A%09%09%09literal%3AhasLiteralValue+%3Furl%0A%09%09%5D%0A%09%7D%0A%7D")
#' x$query(query, verbose = TRUE)
#' 
#' # get PMID and PMCID identifiers from DOI
#' qry <- 'PREFIX datacite: <http://purl.org/spar/datacite/>
#' PREFIX literal: <http://www.essepuntato.it/2010/06/literalreification/>
#' SELECT ?paper ?pmid ?pmcid WHERE {
#'   ?paper datacite:hasIdentifier [ 
#'       datacite:usesIdentifierScheme datacite:doi ;
#'       literal:hasLiteralValue "10.1097/igc.0000000000000609"
#'   ] .
#'   
#'   OPTIONAL {
#'     ?paper datacite:hasIdentifier [ 
#'       datacite:usesIdentifierScheme datacite:pmid ;
#'       literal:hasLiteralValue ?pmid
#'     ] .
#'   }
#'   
#'   OPTIONAL {
#'     ?paper datacite:hasIdentifier [ 
#'       datacite:usesIdentifierScheme datacite:pmcid ;
#'       literal:hasLiteralValue ?pmcid
#'     ] .
#'   }
#' }'
#' x$query(qry, verbose = TRUE)
#' 
#' # with DSL
#' sparql_dsl("http://opencitations.net/sparql") %>%
#'  prefix(datacite = "http://purl.org/spar/datacite/", 
#'         literal = "http://www.essepuntato.it/2010/06/literalreification/") %>% 
#'  select(paper, pmid, pmcid) %>% 
#'  where(
#'   list(paper, datacite:usesIdentifierScheme datacite:doi, literal:hasLiteralValue "10.1097/igc.0000000000000609"),
#'   optional(
#'     paper, datacite:usesIdentifierScheme datacite:pmid, literal:hasLiteralValue pmid
#'   ),
#'   optional(
#'     paper, datacite:usesIdentifierScheme datacite:pmcid, literal:hasLiteralValue pmcid
#'   )
#'  )
#' }
SparqlClient <- R6::R6Class(
  'SparqlClient',
  public = list(
    url = NULL,
    path = NULL,
    scheme = NULL,

    print = function(x, ...) {
      cat("<sparql client> ", sep = "\n")
      cat(paste0("  url: ", self$url), sep = "\n")
      cat(paste0("  path: ", self$path), sep = "\n")
      cat(paste0("  scheme: ", self$scheme), sep = "\n")
      invisible(self)
    },

    initialize = function(url, path = "", scheme = "http") {
      self$url <- url
      self$path <- path
      self$scheme <- scheme
    },

    make_base = function() {
      file.path(paste0(self$scheme, ":/"), self$url)
    },
  
    make_url = function() {
      file.path(paste0(self$scheme, ":/"), self$url, self$path)
    },

    query = function(query, format = "json", flatten = TRUE, ...) {
      sparql_GET(self$make_base(), self$path, query, format, 
        flatten = flatten, ...)
    }
  )
)