Merge branch 'main' into byebye

DESCRIPTION

@@ -28,7 +28,6 @@ Imports:
     purrr,
     rlang,
     tibble,
-    WikidataQueryServiceR,
     WikidataR,
     xml2,
     xmlparsedata
@@ -37,10 +36,16 @@ Suggests:
     httptest2,
     httpuv,
     knitr,
-    leaflet,
     rmarkdown,
     testthat (>= 3.0.0),
     withr
+Config/Needs/website:
+    DT,
+    ggplot2,
+    leaflet,
+    lvaudor/sequins,
+    sf,
+    tidyr
 VignetteBuilder: 
     knitr,
     rmarkdown
@@ -49,3 +54,4 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
+

R/send_sparql.R

@@ -96,15 +96,23 @@ send_sparql = function(query_string,
     request_type = request_control[["request_type"]]
   }
 
-  # if endpoint wikidata, use WikidataQueryServiceR::query_wikidata()
-  if (endpoint == "https://query.wikidata.org/") {
-    return(purrr::quietly(WikidataQueryServiceR::query_wikidata)(query_string)$result)
+  initial_request = httr2::request(endpoint) %>%
+    httr2::req_method("POST")
+
+  if (request_type == "url") {
+    initial_request = initial_request %>%
+    httr2::req_headers(
+      Accept = "application/sparql-results+json",
+      `Content-length` = 0
+    )
+  } else {
+    initial_request = initial_request %>%
+      httr2::req_headers(
+        Accept = "application/sparql-results+json"
+      )
   }
-  # else, use httr2
 
-  initial_request = httr2::request(endpoint) %>%
-    httr2::req_method("POST") %>%
-    httr2::req_headers(Accept = "application/sparql-results+json") %>%
+  initial_request = initial_request %>%
     httr2::req_user_agent(user_agent) %>%
     httr2::req_retry(max_tries = max_tries, max_seconds = max_seconds) %>%
     httr2::req_timeout(timeout)
@@ -141,34 +149,30 @@ send_sparql = function(query_string,
 
     # Adapted from https://github.com/wikimedia/WikidataQueryServiceR/blob/accff89a06ad4ac4af1bef369f589175c92837b6/R/query.R#L56
     if (length(content$results$bindings) > 0) {
-      parse_binding = function(binding, name) {
-        type <- sub(
-          "http://www.w3.org/2001/XMLSchema#", "",
-          binding[["datatype"]] %||% "http://www.w3.org/2001/XMLSchema#character"
-        )
 
-        parse = function(x, type) {
-          switch(
-          type,
-          character = x,
-            # easier for now as dbpedia can return different things with the same name
-          integer = ifelse(endpoint == "https://dbpedia.org/sparql", x, as.integer(x)),
-          datetime = anytime::anytime(x),
-            x
+      parsed_results = purrr::map(
+        content[["results"]][["bindings"]],
+        parse_result,
+        endpoint = endpoint
+      )
+      data_frame = try(
+        dplyr::bind_rows(parsed_results),
+        silent = TRUE
+      )
+
+      # for instance this can happen with HAL
+      binding_failed <- inherits(data_frame, "try-error")
+
+      if (binding_failed) {
+        parsed_results <- purrr::map(
+          content$results$bindings,
+          parse_result,
+          simple = TRUE,
+          endpoint = endpoint
         )
-        }
-        value = parse(binding[["value"]], type)
-        tibble::tibble(.rows = 1) %>%
-          dplyr::mutate({{name}} := value)
-      }
-
-      parse_result = function(result) {
-        purrr::map2(result, names(result), parse_binding) %>%
-        dplyr::bind_cols()
+        data_frame <- dplyr::bind_rows(parsed_results)
       }
 
-      data_frame <- purrr::map_df(content$results$bindings, parse_result)
-
       } else {
         data_frame <- dplyr::as_tibble(
           matrix(
@@ -183,3 +187,42 @@ send_sparql = function(query_string,
 }
 
 utils::globalVariables("usual_endpoints")
+
+parse_result = function(result, simple = FALSE, endpoint) {
+
+  purrr::map2(
+    result,
+    names(result),
+    parse_binding,
+    simple = simple,
+    endpoint = endpoint
+  ) %>%
+  dplyr::bind_cols()
+}
+
+parse_binding = function(binding, name, simple, endpoint) {
+  type <- tolower(sub(
+    "http://www.w3.org/2001/XMLSchema#", "",
+    binding[["datatype"]] %||% "http://www.w3.org/2001/XMLSchema#character"
+  ))
+
+  parse = if (!simple) {
+    function(x, type, endpoint) {
+    switch(
+      type,
+      character = x,
+      # easier for now as dbpedia can return different things with the same name
+      integer = ifelse(endpoint == "https://dbpedia.org/sparql", x, as.integer(x)),
+      datetime = anytime::anytime(x),
+      x
+    )
+    }
+  } else {
+    function(x, type, endpoint) {
+      as.character(x)
+    }
+  }
+  value = parse(binding[["value"]], type, endpoint = endpoint)
+  tibble::tibble(.rows = 1) %>%
+    dplyr::mutate({{name}} := value)
+}

_pkgdown.yml

@@ -55,7 +55,7 @@ navbar:
       href: articles/explore.html
     - text: glitter for dataBNF
       href: articles/glitter_for_dataBNF.html
-    - text: Bibliometry with HAL
-      href: articles/glitter_for_hal.html
+    - text: Bibliometry with HAL (French)
+      href: articles/glitter_bibliometry.html
     - text: Learn more about how glitter works
       href: articles/internals.html

data-raw/usual_endpoints.csv

@@ -1,5 +1,5 @@
 name,url
-wikidata,https://query.wikidata.org/
+wikidata,https://query.wikidata.org/sparql
 dbpedia,https://dbpedia.org/sparql
 databnf,https://data.bnf.fr/sparql
 isidore,https://isidore.science/sparql