#401 gemet vocab implementation

Author: eblondel

DESCRIPTION

@@ -45,7 +45,6 @@ Imports:
   mime,
   digest,
   dplyr,
-  plyr,
   readr,
   arrow,
   zip,

NAMESPACE

@@ -118,7 +118,6 @@ import(jsonlite)
 import(methods)
 import(mime)
 import(ows4R)
-import(plyr)
 import(readr)
 import(sf)
 import(sfarrow)

R/geoflow.R

@@ -24,12 +24,11 @@
 #' @import httr
 #' @import mime
 #' @import jsonlite
-#' @import dplyr
 #' @import yaml
 #' @import XML
 #' @import xml2
 #' @import mime
-#' @import plyr
+#' @import dplyr
 #' @import readr
 #' @import arrow
 #' @import sf

R/geoflow_entity.R

@@ -2059,7 +2059,7 @@ geoflow_entity <- R6Class("geoflow_entity",
     #'@return a list of \code{geoflow_contact} or a \code{data.frame}
     getContacts = function(pretty = FALSE){
       if(pretty){
-        out <- do.call("rbind.fill", lapply(self$contacts, function(contact){
+        out <- do.call(dplyr::bind_rows, lapply(self$contacts, function(contact){
           contact.df <- data.frame(
             id = contact$id,
             stringsAsFactors = FALSE
@@ -2095,7 +2095,7 @@ geoflow_entity <- R6Class("geoflow_entity",
     #'@return a list of \code{geoflow_subject} or a \code{data.frame}
     getSubjects = function(pretty = FALSE, keywords = FALSE){
       if(pretty){
-        out <- do.call("rbind.fill", lapply(self$subjects, function(subject){
+        out <- do.call(dplyr::bind_rows, lapply(self$subjects, function(subject){
           subject.df <- data.frame(
             subject_name = subject$name,
             subject_uri = ifelse(is.null(subject$uri),NA,subject$uri),
@@ -2124,7 +2124,7 @@ geoflow_entity <- R6Class("geoflow_entity",
     #'@return a list of \code{geoflow_relation} or a \code{data.frame}
     getRelations = function(pretty = FALSE){
       if(pretty){
-        out <- do.call("rbind.fill", lapply(self$relations, function(relation){
+        out <- do.call(dplyr::bind_rows, lapply(self$relations, function(relation){
           relation.df <- data.frame(
             key = relation$key,
             stringsAsFactors = FALSE

R/geoflow_vocabulary.R

@@ -201,7 +201,7 @@ geoflow_skos_vocabulary <- R6Class("geoflow_skos_vocabulary",
             }
             ORDER BY ?concept
           ")
-          self$query(str = str, mimetype = mimetype)
+          self$query(str = str, mimetype = "text/csv")
         },
         "R" = {
           filter_by_language <- function(df, language) {
@@ -219,7 +219,7 @@ geoflow_skos_vocabulary <- R6Class("geoflow_skos_vocabulary",
             mimetype = "text/csv"
           )
           # Create a hierarchy data.frame
-          sparql_result %>%
+          out1 = sparql_result %>%
             dplyr::filter(p == "http://www.w3.org/2004/02/skos/core#broader") %>%
             dplyr::rename(concept = s, broaderConcept = o) %>%
             dplyr::select(concept, broaderConcept) %>%
@@ -232,6 +232,19 @@ geoflow_skos_vocabulary <- R6Class("geoflow_skos_vocabulary",
               by = "broaderConcept"
             ) %>%
             dplyr::select(broaderConcept, broaderPrefLabel, concept, prefLabel)
+          #add broader concepts as concepts for root
+          out2 = do.call("rbind", lapply(unique(out1$broaderConcept), function(broaderConcept){
+            res = NULL
+            if(nrow(out1[out1$concept == broaderConcept,])==0){
+              res = out1[out1$broaderConcept == broaderConcept,][1,]
+              res$concept = res$broaderConcept
+              res$prefLabel = res$broaderPrefLabel
+              res$broaderConcept = NA
+              res$broaderPrefLabel = NA
+            }
+            res
+          }))
+          rbind(out1,out2)
         }
       )