fix setting of a base uri in jsonld

uses localhost:// as base uri for now, configurable as option "rdflib_base_uri", though not documented. (since really users wanting a particular base_uri should probably be declaring their own base explicitly in the json-ld rather than setting it here).  closes #5

NAMESPACE

@@ -15,6 +15,8 @@ importClassesFrom(redland,Serializer)
 importClassesFrom(redland,Statement)
 importClassesFrom(redland,Storage)
 importClassesFrom(redland,World)
+importFrom(jsonld,jsonld_compact)
+importFrom(jsonld,jsonld_expand)
 importFrom(jsonld,jsonld_to_rdf)
 importFrom(utils,download.file)
 importMethodsFrom(redland,addStatement)

R/rdf.R

@@ -68,11 +68,15 @@ rdf_parse <- function(doc,
   doc <- text_or_url_to_doc(doc)
 
   ## redlands doesn't support jsonld. So rewrite as nquads using jsonld package
+  ## We use tmp to avoid altering input doc, since parsing a local file should
+  ## be a read-only task!
   if(format == "jsonld"){
     tmp <- tempfile()
-    writeLines(jsonld::jsonld_to_rdf(doc), tmp)
-    doc <- tmp
+    tmp <- add_base_uri(doc, tmp)
+    rdf <- jsonld::jsonld_to_rdf(tmp)
+    writeLines(rdf, tmp)
     format <- "nquads"
+    doc <- tmp
   }
 
   x <- rdf()
@@ -83,6 +87,22 @@ rdf_parse <- function(doc,
   x
 }
 
+# Whenever we convert JSON-LD to RDF we should set a @base if not set.
+# https://json-ld.org/playground does this (with it's own url) but jsonld R package does not.
+# For details, see https://github.com/cboettig/rdflib/issues/5
+#
+#' @importFrom jsonld jsonld_expand jsonld_compact
+add_base_uri <- function(doc, tmp = tempfile()){
+
+  ## Cannot assume it has context, may already be expanded (e.g. from rdf_serialize)
+  ## Expanding will also make any preset @base context take precedence 
+  expanded <- jsonld::jsonld_expand(doc)
+  base <- getOption("rdflib_base_uri", "localhost://")
+  context <- paste0('{"@base": "', base, '"}')
+  compact <- jsonld::jsonld_compact(expanded, context)
+  writeLines(compact, tmp)
+  tmp
+}
 
 
 #' Serialize RDF docs
@@ -127,7 +147,7 @@ rdf_serialize <- function(x,
   format <- match.arg(format)
 
 
-  ## redlands doesn't support jsonld. So write as nquads and then trnasform
+  ## redlands doesn't support jsonld. So write as nquads and then transform
   jsonld_output <- format == "jsonld"
   if(jsonld_output){
     format <- "nquads"
@@ -201,7 +221,7 @@ rdf_query <- function(x, query, ...){
   rectangularize_query_results(out)
 }
 
-## FIXME: cast data type based on Type-string?
+## FIXME: coerce data type based on Type-string?
 rectangularize_query_results <- function(out){
   vars <- unique(names(out))
   X <- lapply(vars, function(v) 

tests/testthat/test-rdf.R

@@ -1,7 +1,7 @@
 testthat::context("test-rdf.R")
 
 doc <- system.file("extdata/example.rdf", package="redland")
-out <- tempfile()
+out <- "testing.rdf"
 
 testthat::test_that("we can parse (in rdfxml)
                     and serialize (in nquads) a simple rdf graph", {
@@ -19,7 +19,7 @@ testthat::test_that("we can make sparql queries", {
 
   rdf <- rdf_parse(doc)
   match <- rdf_query(rdf, sparql)
-  expect_length(match, 2)
+  testthat::expect_length(match, 2)
 })
 
 testthat::test_that("we can initialize add triples to rdf graph", {