declare yaml package, add comment

DESCRIPTION

@@ -27,7 +27,8 @@ Imports:
     redoc,
     rlang,
     stringr,
-    tibble
+    tibble,
+    yaml
 Remotes:
     hillalex/porcelain@i39,
 Suggests:

R/api.R

@@ -194,8 +194,6 @@ target_get_individual <- function(req,
                                     color = NULL,
                                     linetype = NULL,
                                     page = 1) {
-  .data <- value <- NULL
-
   data <- read_dataset(req, name, scale)
   dat <- data$data
   xcol <- data$xcol
@@ -244,6 +242,7 @@ get_paged_ids <- function(ids, current_page, page_length) {
 }
 
 get_aes <- function(color, linetype, xcol) {
+  .data <- value <- NULL
   if (is.null(color)) {
     if (is.null(linetype)) {
       aes <- ggplot2::aes(x = .data[[xcol]], y = value)
@@ -347,12 +346,6 @@ apply_filter <- function(filter, dat, cols) {
   dat[dat[filter_var] == filter_level, ]
 }
 
-bad_request_response <- function(msg) {
-  error <- list(error = "BAD_REQUEST",
-                detail = msg)
-  return(list(status = "failure", errors = list(error), data = NULL))
-}
-
 get_or_create_session_id <- function(req) {
   if (is.null(req$session$id)) {
     logger::log_info("Creating new session id")

R/dataset-validation.R

@@ -1,3 +1,12 @@
+# The POST /dataset endpoint isn't using Porcelain, so we can't use
+# porcelain::porcelain_stop when something goes wrong. Instead we have
+# to manually return failure responses with the desired error messages
+bad_request_response <- function(msg) {
+  error <- list(error = "BAD_REQUEST",
+                detail = msg)
+  return(list(status = "failure", errors = list(error), data = NULL))
+}
+
 invalid_file_type <- function(res) {
   res$status <- 400L
   msg <- "Invalid file type; please upload file of type text/csv."

docker/Dockerfile

@@ -27,7 +27,8 @@ RUN install_packages --repo=https://mrc-ide.r-universe.dev \
         remotes \
         Rook \
         stringr \
-        tibble
+        tibble \
+        yaml
 
 RUN Rscript -e "install.packages('remotes')"
 RUN Rscript -e 'remotes::install_github("hillalex/porcelain@i39")'