From 7a79d42590f52587bc6dc4c63e72ed412b888aac Mon Sep 17 00:00:00 2001
From: andrewelamb <andrewelamb@gmail.com>
Date: Mon, 14 Aug 2023 09:37:20 -0700
Subject: [PATCH 1/2] fix bug

---
 R/api_cohorts_queries.R |  2 ++
 R/api_functions.R       |  3 +--
 R/api_tags_queries.R    | 60 ++++++++++++++++++++---------------------
 3 files changed, 33 insertions(+), 32 deletions(-)

diff --git a/R/api_cohorts_queries.R b/R/api_cohorts_queries.R
index 0799888..580aa01 100644
--- a/R/api_cohorts_queries.R
+++ b/R/api_cohorts_queries.R
@@ -229,7 +229,9 @@ query_cohort_samples <- function(
   if(nrow(tbl) == 0) return(tbl)
   else {
     tbl <- tbl %>%
+      print() %>% 
       tidyr::unnest(cols = "samples", keep_empty = T) %>%
+      print() %>% 
       dplyr::select(
         "cohort_name",
         "sample_name" = "name",
diff --git a/R/api_functions.R b/R/api_functions.R
index a90821a..ea854c6 100644
--- a/R/api_functions.R
+++ b/R/api_functions.R
@@ -30,12 +30,11 @@ perform_api_query <- function(
   variables,
   query_file,
   query_dir = system.file("queries", package = "iatlasGraphQLClient"),
-  api_url = "https://api.cri-iatlas.org/api"
+  api_url = "https://api-staging.cri-iatlas.org/api"
 ){
   if(!is.null(.GlobalEnv$API_URL)){
     api_url <- .GlobalEnv$API_URL
   }
-  api_url <- "https://api-staging.cri-iatlas.org/api"
   ghql_con <- ghql::GraphqlClient$new(api_url)
   ghql_query_obj <- ghql::Query$new()
   query_path <- file.path(query_dir, query_file)
diff --git a/R/api_tags_queries.R b/R/api_tags_queries.R
index 1506a39..7a5e119 100644
--- a/R/api_tags_queries.R
+++ b/R/api_tags_queries.R
@@ -61,12 +61,12 @@ query_tags <- function(
 #' @export
 #' @importFrom magrittr %>%
 query_tag_samples <- function(
-  cohorts = NA,
-  samples = NA,
-  datasets = NA,
-  parent_tags = NA,
-  tags = NA,
-  type = NA,
+  cohorts = NA_character_,
+  samples = NA_character_,
+  datasets = NA_character_,
+  parent_tags = NA_character_,
+  tags = NA_character_,
+  type = NA_character_,
   paging = NA,
   ...
 ){
@@ -122,12 +122,12 @@ query_tag_samples <- function(
 #' @export
 #' @importFrom magrittr %>%
 query_tag_samples_parents <- function(
-  cohorts = NA,
-  samples = NA,
-  datasets = NA,
-  parent_tags = NA,
-  tags = NA,
-  type = NA,
+  cohorts = NA_character_,
+  samples = NA_character_,
+  datasets = NA_character_,
+  parent_tags = NA_character_,
+  tags = NA_character_,
+  type = NA_character_,
   paging = NA,
   ...
 ){
@@ -191,12 +191,12 @@ query_tag_samples_parents <- function(
 #' @export
 #' @importFrom magrittr %>%
 query_tag_sample_count <- function(
-  cohorts = NA,
-  samples = NA,
-  datasets = NA,
-  parent_tags = NA,
-  tags = NA,
-  type = NA,
+  cohorts = NA_character_,
+  samples = NA_character_,
+  datasets = NA_character_,
+  parent_tags = NA_character_,
+  tags = NA_character_,
+  type = NA_character_,
   paging = NA,
   ...
 ){
@@ -243,12 +243,12 @@ query_tag_sample_count <- function(
 #' @export
 #' @importFrom magrittr %>%
 query_tag_publications <- function(
-  cohorts = NA,
-  samples = NA,
-  datasets = NA,
-  parent_tags = NA,
-  tags = NA,
-  type = NA,
+  cohorts = NA_character_,
+  samples = NA_character_,
+  datasets = NA_character_,
+  parent_tags = NA_character_,
+  tags = NA_character_,
+  type = NA_character_,
   paging = NA,
   ...
 ){
@@ -316,12 +316,12 @@ query_tag_publications <- function(
 #' @export
 #' @importFrom magrittr %>%
 query_tags_with_parent_tags <- function(
-  cohorts = NA,
-  samples = NA,
-  datasets = NA,
-  parent_tags = NA,
-  tags = NA,
-  type = NA,
+  cohorts = NA_character_,
+  samples = NA_character_,
+  datasets = NA_character_,
+  parent_tags = NA_character_,
+  tags = NA_character_,
+  type = NA_character_,
   paging = NA,
   ...
 ){

From 09ccaf1c43c75daf85aa373df2b007127a7c6600 Mon Sep 17 00:00:00 2001
From: andrewelamb <andrewelamb@gmail.com>
Date: Mon, 14 Aug 2023 09:43:28 -0700
Subject: [PATCH 2/2] remove print statements

---
 R/api_cohorts_queries.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/R/api_cohorts_queries.R b/R/api_cohorts_queries.R
index 580aa01..0799888 100644
--- a/R/api_cohorts_queries.R
+++ b/R/api_cohorts_queries.R
@@ -229,9 +229,7 @@ query_cohort_samples <- function(
   if(nrow(tbl) == 0) return(tbl)
   else {
     tbl <- tbl %>%
-      print() %>% 
       tidyr::unnest(cols = "samples", keep_empty = T) %>%
-      print() %>% 
       dplyr::select(
         "cohort_name",
         "sample_name" = "name",