rjson::fromJSON can read URL, too. So implement reading URL schema in…

… the same function as reading a file.

R/get-template.R

@@ -86,12 +86,11 @@ get_template_keys_synID <- function(syn, synID, ...) {
 #' @export
 #' @inheritParams get_template
 #' @param id Registered synapse ID of schema.
-#' @param file Filepath to json schema.
-#' @param url URL to json schema.
-get_template_keys_schema <- function(syn, id = NA, file = NA, url = NA) {
+#' @param file Filepath or URL to json schema.
+get_template_keys_schema <- function(syn, id = NA, file = NA) {
 
-  if (sum(!is.na(id), !is.na(file), !is.na(url)) != 1){
-    stop("Specify only one of id, file, or url")
+  if (sum(!is.na(id), !is.na(file)) != 1){
+    stop("Specify only one of id, file")
   }
 
   if (!is.na(id)){
@@ -107,10 +106,6 @@ get_template_keys_schema <- function(syn, id = NA, file = NA, url = NA) {
   if (!is.na(file)) {
     schema <- get_file_schema(file = file)
   }
-  if (!is.na(url)) {
-    schema <- get_url_schema(url = url)
-  }
-
   return(names(schema$properties))
 }
 
@@ -204,8 +199,6 @@ rest_post <- function(syn, uri, body = NULL) {
 #' @param file Filepath of json schema.
 get_file_schema <- function(file) {
 
-  if (!file.exists(file)) stop(glue::glue("{file} does not exist."))
-  if (!tolower(tools::file_ext(file)) == "json") stop("File must be json.")
   schema <- fromJSON(file = file)
   return(schema)
 

tests/testthat/test-get-template.R

@@ -103,6 +103,11 @@ test_that("get_template can get a schema file", {
       "specimenID", "platform", "assay", "readLength", "dnaBatch", "Component", 
       "assayTarget", "libraryBatch"))
 
+  schema_url <- get_file_schema(file="https://raw.githubusercontent.com/afwillia/sysbioDCCjsonschemas/schematic_workflow/schema_metadata_templates/schematic_test/amp.ad.data.Assay16SrRNAseqMetadataTemplate.schema.json")
+  expect_equal(names(schema_url$properties),
+     c("dnaExtractionMethod", "runType", "libraryPrep", "sequencingBatch",
+       "specimenID", "platform", "assay", "readLength", "dnaBatch", "Component", 
+       "assayTarget", "libraryBatch"))
 })
 
 test_that("get_synapse_schema returns error if schema not returned", {