feat: new function get_coverage_tax #2

R/get_attributes.R

@@ -162,22 +162,9 @@ parse_attribute <- function(x) {
   att <- att[!grepl("methods", names(att))]
 
   ## Alter names to be consistent with other tools
-  names(att) <- gsub("missingValueCode.code",
-                      "missingValueCode",
-                      names(att),
-                      fixed = TRUE)
   names(att) <- gsub("standardUnit|customUnit",
                       "unit",
                       names(att))
-  ## Alter names of annotation label fields for accessibility
-  names(att) <- gsub("annotation.valueURI.label",
-                      "valueLabel",
-                      names(att),
-                      fixed = TRUE)
-  names(att) <- gsub("annotation.propertyURI.label",
-                      "propertyLabel",
-                      names(att),
-                      fixed = TRUE)
   names(att) <- gsub(".+\\.+",
                       "",
                       names(att))

R/get_coverage_tax.R

@@ -0,0 +1,72 @@
+#' Title
+#'
+#' @param corpus
+#'
+#' @return
+#' @export
+#'
+#' @examples
+get_coverage_tax <- function(corpus) {
+  get_multilevel_element(
+    corpus = corpus,
+    element_names = c("coverage", "taxonomicCoverage"),
+    parse_function = parse_taxcov
+  )
+}
+
+#' Title
+#'
+#' @param x
+#'
+#' @return
+#'
+#' @examples
+parse_taxcov <- function(x) {
+  a <- handle_one(x$taxonomicClassification)
+  return(data.table::rbindlist(
+    lapply(seq_along(a), function(x)
+      parse_taxonomic_classification(a[[x]], i = x)),
+    fill = TRUE
+  ))
+}
+
+#' Title
+#'
+#' @param x
+#' @param i
+#' @param j
+#'
+#' @return
+#'
+#' @examples
+parse_taxonomic_classification <- function(x, i, j) {
+  t <- list()
+  j <- i
+  if ("taxonomicClassification" %in% names(x)) {
+    i <- i + 1
+    t[[j]] <-
+      data.frame(
+        taxonrecordid = i,
+        parenttaxonid = j,
+        taxonrankname = null2na(x$taxonRankName),
+        taxonrankvalue = null2na(x$taxonRankValue),
+        commonname = handle_multiple(null2na(x$commonname)),
+        taxonid = handle_multiple(null2na(x$taxonId$taxonId)),
+        taxonidprovider = handle_multiple(null2na(x$taxonId$provider))
+      )
+    j <- j + 1
+    a <- handle_one(x$taxonomicClassification)
+    t[[j]] <- data.table::rbindlist(lapply(seq_along(a), function(x) parse_taxonomic_classification(a[[x]], i = i, j = j)), fill = TRUE)
+  } else {
+      t[[j]] <-
+      data.frame(
+        taxonrecordid = i,
+        parenttaxonid = j,
+        taxonrankname = null2na(x$taxonRankName),
+        taxonrankvalue = null2na(x$taxonRankValue),
+        commonname = handle_multiple(null2na(x$commonname)),
+        taxonid = handle_multiple(null2na(x$taxonId$taxonId)),
+        taxonidprovider = handle_multiple(null2na(x$taxonId$provider)))
+  }
+  return(data.table::rbindlist(t, fill = TRUE))
+}