Merge pull request #610 from Sage-Bionetworks/FDS-2200-validation-error

Fds 2200 validation error

R/schematic_rest_api.R

@@ -216,7 +216,14 @@ manifest_validate <- function(url="http://localhost:3001/v1/model/validate",
   #     )
   #   )
   # }
-  httr2::resp_body_json(resp)
+  if (httr2::resp_is_error(resp)) {
+    list(list(
+      "errors" = list(
+        Row = NA, Column = NA, Value = NA,
+        Error = httr2::resp_body_string(resp)
+      )
+    ))
+  } else httr2::resp_body_json(resp)
 }
 
 

R/utils.R

@@ -11,4 +11,18 @@ parse_env_var <- function(x, el_delim=",", kv_delim=":"){
     kv <- stringr::str_split(y, kv_delim, n=2)
     setNames(kv[[1]][[2]], kv[[1]][[1]])
   }))
+}
+
+#' @title Truncate the results of schematic validation
+#' @param x Schematic validation result
+#' @param n Number of records to keep
+#' @export
+format_validation_response <- function(x, n = 50) {
+  if ("errors" %in% names(x) && length(x$errors) > n) {
+    x$errors <- x$errors[1:n]
+  }
+  if ("warnings" %in% names(x) && length(x$warnings) > n) {
+    x$warnings <- x$warnings[1:n]
+  }
+  x
 }

functions/schematic_rest_api.R

@@ -6,6 +6,11 @@ check_success <- function(x){
   if (tolower(status$category) == "success") {
     return()
   } else {
+    # Return content text for Data Type errors
+    if (grepl("LookupError: The DataType", httr::content(x, "text"))) {
+      stop(httr::content(x, "text"))
+    }
+
     stop(sprintf("Response from server: %s", status$reason))
   }
 }
@@ -211,7 +216,14 @@ manifest_validate <- function(url="http://localhost:3001/v1/model/validate",
   #     )
   #   )
   # }
-  httr2::resp_body_json(resp)
+  if (httr2::resp_is_error(resp)) {
+    list(list(
+      "errors" = list(
+        Row = NA, Column = NA, Value = NA,
+        Error = httr2::resp_body_string(resp)
+      )
+    ))
+  } else httr2::resp_body_json(resp)
 }
 
 
@@ -221,8 +233,18 @@ manifest_validate <- function(url="http://localhost:3001/v1/model/validate",
 #' @param schema_url URL to a schema jsonld 
 #' @param data_type Type of dataset
 #' @param dataset_id Synapse ID of existing manifest
-#' @param access_token Synapse login cookie, PAT, or API key.
-#' @param csv_file Filepath of csv to validate
+#' @param restrict_rules Default = FALSE
+#' @param access_token Synapse login cookie, PAT, or API key
+#' @param json_str Json string to submit
+#' @param asset_view Synapse fileview
+#' @param manifest_record_type Default = "table_and_file"
+#' @param file_name Name of file
+#' @param table_manipulation Default = "replace"
+#' @param hide_blanks Default = FALSE
+#' @param table_column_names Default = "class_and_label"
+#' @param annotation_keys Default = "class_and_label"
+#' @param data_model_labels Default = "class_and_label"
+#' @param upload_file_annotations Default = TRUE
 #' 
 #' @returns TRUE if successful upload or validate errors if not.
 #' @export
@@ -240,7 +262,8 @@ model_submit <- function(url="http://localhost:3001/v1/model/submit",
                          hide_blanks=FALSE,
                          table_column_names="class_label",
                          annotation_keys="class_label",
-                         data_model_labels="class_label") {
+                         data_model_labels="class_label",
+                         file_annotations_upload=TRUE) {
   req <- httr::POST(url,
                     httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
                     query=list(
@@ -255,7 +278,8 @@ model_submit <- function(url="http://localhost:3001/v1/model/submit",
                       table_column_names=table_column_names,
                       annotation_keys=annotation_keys,
                       data_model_labels=data_model_labels,
-                      hide_blanks=hide_blanks),
+                      hide_blanks=hide_blanks,
+                      file_annotations_upload=file_annotations_upload),
                     body=list(file_name=httr::upload_file(file_name))
                     #body=list(file_name=file_name)
   )
@@ -397,7 +421,7 @@ get_asset_view_table <- function(url="http://localhost:3001/v1/storage/assets/ta
 
   check_success(req)
   if (return_type=="json") {
-    return(list2DF(fromJSON(httr::content(req))))
+    return(list2DF(jsonlite::fromJSON(httr::content(req))))
   } else {
   csv <- readr::read_csv(httr::content(req), show_col_types = FALSE)
   return(csv)

server.R

@@ -846,6 +846,7 @@ shinyServer(function(input, output, session) {
       )
 
       # validation messages
+      annotation_status <- format_validation_response(annotation_status, 50)
       validationResult(annotation_status, .dd_template, .infile_data)
     }) %...>% validation_res()
   })
@@ -1067,7 +1068,7 @@ shinyServer(function(input, output, session) {
       .restrict_rules <- dcc_config_react()$schematic$model_validate$restrict_rules
       .hide_blanks <- dcc_config_react()$schematic$model_submit$hide_blanks
       .file_annotations_upload <- dcc_config_react()$schematic$model_submit$file_annotations_upload
-      
+
       # associates metadata with data and returns manifest id
       promises::future_promise({
         try(