R/meta.R

In dsidavis/RSPARQL: SPARQL client

getClasses =
    # This gets the classes that are defined.
    # not what classes are used, i.e. have instances. That is getTypes
    #XXX add rdfs:subClassOf
function(owl = TRUE, ..., fun = SPARQL, asIs = FALSE)
{

   q = if(!owl) 
       "SELECT DISTINCT * { {  ?s rdfs:class ?class . }
                            UNION {?s owl:class ?class . }
                            UNION { ?s rdfs:subClassOf ?class . }
                            ?class a ?classType
                          }"
       else
           "select distinct ?resource {
                  ?resource rdf:type owl:Class .
                         # FILTER ( NOT isBlank(?resource) )
            }"
    
   ans = fun(q, ns = commonNS, ...)
   if(nrow(ans) > 0) {
      classes = ans[[1]]
      if(asIs)
          classes
      else
          getNamesNS(classes)
   } else
       character()
}

getTypes =
    #  getTypes(fun = qmeamc)    
function(..., fun = SPARQL, asIs = subAbbrevs, subAbbrevs = TRUE)
{
  ans = fun("SELECT DISTINCT ?ty {  ?s rdf:type ?ty . }", ..., subAbbrevs = subAbbrevs)

  ns = commonNS
  if(is.character(subAbbrevs)) {
      ns = subAbbrevs
      subAbbrevs = TRUE
  }
  
  if(subAbbrevs)
     subNSAbbrevs(ans[[1]], ns)
  else if(asIs) {
      ans[[1]]
  } else    
     getNamesNS( ans[[1]])
}

getPredicates =
    # This is used predicates, not defined properties in the RDFS or OWL way.
    # Use a different query for those.
    #
    #  getPredicates(fun = qmeamc)
    #
function(..., fun = SPARQL, asIs = FALSE)
{
  ans = fun("SELECT DISTINCT ?pred {  ?s ?pred ?ty . }", ...)
  if(asIs)
      ans[[1]]
  else
      getNamesNS( ans[[1]])
}


getPredicatesByClass =
function(..., classes = getClasses(..., fun = fun, asIs = TRUE), fun = SPARQL, asIs = FALSE)
{
   queries = sprintf("select ?property {  ?property owl:ObjectProperty %s  . }", classes)

   structure(lapply(queries, function(q) fun(q, ...)) , names = classes)
}



getNamesNS =
    # Take a vector of, e.g.,
    # <http://meamcentral.ucdavis.edu/ontology/mco#personDescription>
    # and return the personDescription values (after the # or at the end of the URL
    # and also use the namespace as the name for that element.
function(values)
{
   tmp = gsub("(^<|>$)", "", values)
   i = grepl("#", tmp)

   ans = character(length(tmp))
   ans[i] = gsub(".*#", "", tmp[i])
   names(ans)[i] = gsub("#.*", "", tmp[i])
   ans[!i] = basename(tmp[!i])
   names(ans)[!i] = dirname(tmp[!i])
   ans
}



getClassPredType = 
function(className, ..., fun = SPARQL, subAbbrevs = TRUE) {
     q = sprintf("SELECT DISTINCT ?pred ?type WHERE {
                                                ?m a %s ;
                                                   ?pred ?obj .
                                                ?obj  a ?type .
                                             }", className)
     ans = fun(q, subAbbrevs = subAbbrevs, ...)
     ans$class = rep(className, nrow(ans))
     ans
}

sparqlMetadata =
function(..., types = getTypes(..., fun = fun, subAbbrevs = subAbbrevs), fun = SPARQL, subAbbrevs = TRUE)
{
  info = lapply(types, getClassPredType, fun = fun, ...)
  info = do.call(rbind, info)
  class(info) = c("SPARQLClassPredType", "SPARQLMetaData", class(info))
  info
}

plot.SPARQLClassPredType =
function(x, ...)
{
   if(!require("igraph"))
       stop("The igraph package is not installed")

   g = graph.edgelist( as.matrix( x[, c("class", "type")] ) )   
   E(g)$label = x$pred
   plot(g, edge.arrow.size = .5, ...)
}