From 1c131a024b2a6162c19fb013013e0746e99a4b57 Mon Sep 17 00:00:00 2001
From: Anthony Williams <anthony.williams@sagebase.org>
Date: Thu, 24 Aug 2023 14:22:55 -0700
Subject: [PATCH] Add strict_validation argument to manifest_generate. (#561)

---
 R/schematic_rest_api.R         |  6 ++++--
 functions/schematic_rest_api.R | 11 +++++++----
 server.R                       |  3 ++-
 3 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/R/schematic_rest_api.R b/R/schematic_rest_api.R
index 8128da74..c2db54ad 100644
--- a/R/schematic_rest_api.R
+++ b/R/schematic_rest_api.R
@@ -57,7 +57,8 @@ manifest_generate <- function(url="http://localhost:3001/v1/manifest/generate",
                               schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", #nolint
                               title, data_type,
                               use_annotations="false", dataset_id=NULL,
-                              asset_view, output_format, access_token = NULL) {
+                              asset_view, output_format, access_token = NULL,
+                              strict_validation = FALSE) {
   
   req <- httr::GET(url,
                    query = list(
@@ -68,7 +69,8 @@ manifest_generate <- function(url="http://localhost:3001/v1/manifest/generate",
                      dataset_id=dataset_id,
                      asset_view=asset_view,
                      output_format=output_format,
-                     access_token = access_token
+                     access_token = access_token,
+                     strict_validation = strict_validation
                    ))
   
   check_success(req)
diff --git a/functions/schematic_rest_api.R b/functions/schematic_rest_api.R
index d498fe3a..c2db54ad 100644
--- a/functions/schematic_rest_api.R
+++ b/functions/schematic_rest_api.R
@@ -57,7 +57,8 @@ manifest_generate <- function(url="http://localhost:3001/v1/manifest/generate",
                               schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", #nolint
                               title, data_type,
                               use_annotations="false", dataset_id=NULL,
-                              asset_view, output_format, access_token = NULL) {
+                              asset_view, output_format, access_token = NULL,
+                              strict_validation = FALSE) {
   
   req <- httr::GET(url,
                    query = list(
@@ -68,7 +69,8 @@ manifest_generate <- function(url="http://localhost:3001/v1/manifest/generate",
                      dataset_id=dataset_id,
                      asset_view=asset_view,
                      output_format=output_format,
-                     access_token = access_token
+                     access_token = access_token,
+                     strict_validation = strict_validation
                    ))
   
   check_success(req)
@@ -157,7 +159,7 @@ model_submit <- function(url="http://localhost:3001/v1/model/submit",
                          schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", #notlint
                          data_type, dataset_id, restrict_rules=FALSE, access_token, json_str=NULL, asset_view,
                          use_schema_label=TRUE, manifest_record_type="table_and_file", file_name,
-                         table_manipulation="replace") {
+                         table_manipulation="replace", hide_blanks=FALSE) {
   req <- httr::POST(url,
                     #add_headers(Authorization=paste0("Bearer ", pat)),
                     query=list(
@@ -170,7 +172,8 @@ model_submit <- function(url="http://localhost:3001/v1/model/submit",
                       asset_view=asset_view,
                       use_schema_label=use_schema_label,
                       manifest_record_type=manifest_record_type,
-                      table_manipulation=table_manipulation),
+                      table_manipulation=table_manipulation,
+                      hide_blanks=hide_blanks),
                     body=list(file_name=httr::upload_file(file_name))
                     #body=list(file_name=file_name)
   )
diff --git a/server.R b/server.R
index efd2f213..5a7a70d0 100644
--- a/server.R
+++ b/server.R
@@ -585,7 +585,8 @@ shinyServer(function(input, output, session) {
           asset_view = .asset_view,
           use_annotations = .use_annotations,
           output_format = .output_format,
-          access_token=access_token
+          access_token=access_token,
+          strict_validation = FALSE
         ),
         {
           message("Downloading offline manifest")