Merge pull request #38 from nmfs-fish-tools/37-use-json-schema-to-val…

…idate-terms-in-the-dictionary

37 use json schema to validate terms in the dictionary

.github/workflows/call-r-cmd-check.yml

@@ -0,0 +1,12 @@
+# Run r cmd check
+name: call-r-cmd-check
+# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+# The default build trigger is to run the action on every push and pull request, for any branch
+  push:
+  # To run the default repository branch weekly on sunday, uncomment the following 2 lines
+  #schedule:
+    #- cron: '0 0 * * 0'
+jobs:
+  call-workflow:
+    uses: nmfs-fish-tools/ghactions4r/.github/workflows/r-cmd-check.yml@main

DESCRIPTION

@@ -9,6 +9,11 @@ License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
     license
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.0.9000
+RoxygenNote: 7.2.1
 Imports: 
-    mvbutils
+    mvbutils,
+    tools
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3
+Config/testthat/parallel: true

NAMESPACE

@@ -7,3 +7,5 @@ export(Weight)
 export(add_object)
 export(read_in)
 export(shiny_dd)
+export(validate_Rd)
+import(tools)

R/validate_Rd.R

@@ -0,0 +1,72 @@
+#' Function to validate terms in the dictionary.
+#'
+#' The dictionary terms are written in R documentation (Rd) format.
+#' This function reads the Rd file using the `tools::parse_Rd` function
+#' validate the information in each section (e.g., examples, rationale,
+#' range of possible values, etc.).
+#'
+#' @param Rd_file a Rd filename to use as input.
+#' @return a message if the term passes all validations.
+#' @import tools
+#' @export
+validate_Rd <- function(Rd_file) {
+  if (is.null(Rd_file)) stop("Please provide the path to the R documentation (Rd) file.")
+
+  Rd <- tools::parse_Rd(Rd_file)
+  tags <- tools:::RdTags(Rd)
+
+  # Validate name
+  name <- Rd[[which(tags == "\\name")]]
+  if (is.null(name[[1]][1])) stop("Name is not provided. This should be the basename of the Rd file.")
+
+  # Validate title
+  title <- Rd[[which(tags == "\\title")]]
+  if (is.null(title[[1]][1])) stop("Title is not provided. Title should be capitalized and not end in a period.")
+
+  # Validate description
+  description <- Rd[[which(tags == "\\description")]]
+  if (gsub("[\r\n]", "", description[[2]][1]) == title[[1]][1] |
+    is.null(description[[1]][1])) {
+    stop("Description is not provided. This should be capitalized and not end in a period.")
+  }
+
+  # Extract format section for validating examples, rationale, alternatives, range of possible values, and units
+  format <- Rd[[which(tags == "\\format")]][[2]]
+  items <- c("Examples", "Rationale", "Alternatives", "Range of possible values", "Units")
+  missing_items <- items[!is.element(items, unlist(format))]
+  if (any(!is.element(items, unlist(format)))) stop(paste("Missing", paste(missing_items, collapse = ", ")))
+
+  # Validate examples
+  if (format[[2]][[1]][[1]][1] == "Examples" &
+    length(format[[2]][[2]]) == 0) {
+    stop("Examples are not provided. Use NA if there is no input for examples.")
+  }
+
+  # Validate rationale
+  if (format[[4]][[1]][[1]][1] == "Rationale" &
+    length(format[[4]][[2]]) == 0) {
+    stop("Rationale is not provided.")
+  }
+
+  # Validate alternatives
+  if (format[[6]][[1]][[1]][1] == "Alternatives" &
+    length(format[[6]][[2]]) == 0) {
+    stop("Alternatives are not provided. Use NA if there is no input for alternatives.")
+  }
+
+  # Validate range of possible values
+  if (format[[8]][[1]][[1]][1] == "Range of possible values" &
+    length(format[[8]][[2]]) == 0) {
+    stop("Range of possible values is not provided. Use NA if there is no input for range of possible values.")
+  }
+
+  # Validate range of possible values
+  if (format[[10]][[1]][[1]][1] == "Units" &
+    length(format[[10]][[2]]) == 0) {
+    stop("Units are not provided. Use NA if there is no input for units.")
+  }
+
+
+  # Return a message if the term passes all validations
+  message(paste("Term", name[[1]][1], "has passed all validations!"))
+}