Merge pull request #19 from CRI-iAtlas/update_packages

Fix node queries

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: iatlasGraphQLClient
 Title: iatlas API Client
 Type: Package
-Version: 0.1.1
+Version: 0.2.2
 Author: Andrew Lamb
 Maintainer: Andrew Lamb <[email protected]>
 Description: This package is am R Client library for the iAtlas API.
@@ -20,8 +20,8 @@ Imports:
     ghql (>= 0.1),
     jsonlite (>= 1.7),
     magrittr (>= 2.0),
-    purrr (>= 0.3),
-    rlang (>= 0.4),
+    purrr (>= 1.0),
+    rlang (>= 1.0),
     snakecase,
     stringr (>= 1.0),
     tibble (>= 3.0),

R/api_functions.R

@@ -32,7 +32,7 @@ perform_api_query <- function(
   query_dir = system.file("queries", package = "iatlasGraphQLClient"),
   api_url = "https://api-staging.cri-iatlas.org/api"
 ){
-  if(!is.null(.GlobalEnv$API_URL)){
+  if (!is.null(.GlobalEnv$API_URL)) {
     api_url <- .GlobalEnv$API_URL
   }
   ghql_con <- ghql::GraphqlClient$new(api_url)
@@ -65,17 +65,18 @@ format_query_result <- function(
   select_cols = NULL,
   arrange_cols = NULL
 ){
-  if(!is.null(unnest_cols)) {
+  if (!is.null(unnest_cols)) {
     tbl <- tidyr::unnest(tbl, dplyr::all_of(unnest_cols), keep_empty = T)
   }
   tbl <- tbl %>%
+    as.data.frame() %>% 
     jsonlite::flatten(.) %>%
     dplyr::as_tibble()
 
-  if(!is.null(select_cols)) {
+  if (!is.null(select_cols)) {
     tbl <- dplyr::select(tbl, dplyr::any_of(select_cols))
   }
-  if(!is.null(arrange_cols)) {
+  if (!is.null(arrange_cols)) {
     tbl <- dplyr::arrange(tbl, !!!rlang::syms(arrange_cols))
   }
   return(tbl)
@@ -109,6 +110,12 @@ create_result_from_api_query <- function(
   if (is.null(tbl)) {
     return(default_tbl)
   }
+  if (length(tbl) == 0) {
+    return(default_tbl)
+  }
+  if (nrow(tbl) == 0) {
+    return(default_tbl)
+  }
   format_query_result(tbl, unnest_cols, select_cols, arrange_cols)
 }
 
@@ -135,7 +142,7 @@ create_result_from_cursor_paginated_api_query <- function(
   ...
 ){
   items_list <- do_cursor_paginated_api_query(query_args, query_file, ...)
-  if(length(items_list) == 0) return(default_tbl)
+  if (length(items_list) == 0) return(default_tbl)
   results <- items_list %>%
     rev() %>%
     purrr::map(
@@ -169,7 +176,7 @@ create_result_from_offset_paginated_api_query <- function(
   ...
 ){
   items_list <- do_offset_paginated_api_query(query_args, query_file, ...)
-  if(length(items_list) == 0) return(default_tbl)
+  if (length(items_list) == 0) return(default_tbl)
   results <- items_list %>%
     rev() %>%
     purrr::map(
@@ -204,8 +211,8 @@ do_cursor_paginated_api_query <- function(
   if (empty_result) {
     return(list())
   }
-  if(!is.null(paging$hasNextPage) && paging$hasNextPage){
-    if(length(query_args$paging) == 1 && is.na(query_args$paging)){
+  if (!is.null(paging$hasNextPage) && paging$hasNextPage) {
+    if (length(query_args$paging) == 1 && is.na(query_args$paging)) {
       new_paging <- list("after" = paging$endCursor)
     } else {
       new_paging <- query_args$paging
@@ -247,8 +254,8 @@ do_offset_paginated_api_query <- function(
     return(list())
   }
 
-  if(paging$page < paging$pages){
-    if(length(query_args$paging) == 1 && is.na(query_args$paging)){
+  if (paging$page < paging$pages) {
+    if (length(query_args$paging) == 1 && is.na(query_args$paging)) {
       new_paging <- list("page" = paging$page + 1)
     } else {
       new_paging <- query_args$paging

R/api_nodes_queries.R

@@ -21,27 +21,32 @@ query_nodes <- function(
   min_score = NA,
   parent_tags = NA,
   network = NA,
-  tags = NA,
+  tag1 = NA,
+  tag2 = NA,
   n_tags = NA,
   paging = NA,
   ...
 ){
   has_features <- !(length(features) == 1 && is.na(features))
   has_genes    <- !(length(entrez) == 1 && is.na(entrez))
 
-  if(has_features & has_genes){
+  if (has_features & has_genes) {
     stop("Can not query for both entrez and features at a the same time")
-  } else if(has_features) {
+  } else if (has_features) {
     query_file <- "feature_nodes.txt"
     select_cols <- c(
-      get_node_json_names(),
+      get_node_json_names(), 
+      get_tag_one_json_names(),
+      get_tag_two_json_names(),
       "feature_name" = "feature.name",
       "feature_display" = "feature.display"
     )
-  } else if(has_genes) {
+  } else if (has_genes) {
     query_file <- "gene_nodes.txt"
     select_cols <- c(
-      get_node_json_names(),
+      get_node_json_names(), 
+      get_tag_one_json_names(),
+      get_tag_two_json_names(),
       "gene_entrez"  = "gene.entrez",
       "gene_hgnc"  = "gene.hgnc",
       "gene_friendly_name" = "gene.friendlyName"
@@ -55,8 +60,9 @@ query_nodes <- function(
     "minScore" = min_score,
     "related" = parent_tags,
     "network" = network,
-    "tag" = tags,
-    "nTags"= n_tags,
+    "tag1" = tag1,
+    "tag2" = tag2,
+    "nTags" = n_tags,
     "paging" = paging,
     "distinct" = F
   )
@@ -74,27 +80,22 @@ query_nodes <- function(
     )
   )
 
-  tbl <-create_result_from_cursor_paginated_api_query(
+  tbl <- create_result_from_cursor_paginated_api_query(
     query_args = query_args,
     query_file = query_file,
     default_tbl = default_tbl,
     select_cols = select_cols,
     ...
   )
-  if(nrow(tbl) == 0) return(tbl)
-  tbl %>%
-    dplyr::mutate("node_tags" = purrr::map(
-      .data$node_tags,
-      ~dplyr::select(.x, get_tag_json_names())
-    ))
-  if(!has_features){
+  if (nrow(tbl) == 0) return(tbl)
+  if (!has_features) {
     tbl <- tbl %>%
       dplyr::mutate(
         "feature_name" = NA_character_,
         "feature_display" = NA_character_,
       )
   }
-  if(!has_genes){
+  if (!has_genes) {
     tbl <- tbl %>%
       dplyr::mutate(
         "gene_entrez" = NA_integer_,
@@ -114,7 +115,6 @@ get_node_column_tbl <- function(prefix = "node_"){
     "label",           "label",           character(),
     "name",            "name",            character(),
     "score",           "score",           double(),
-    "tags",            "tags",            list(),
     "x",               "x",               character(),
     "y",               "y",               character()
 
@@ -141,3 +141,28 @@ get_node_field_names <- function(prefix = "node_"){
     get_node_column_tbl(prefix) %>%
     dplyr::pull("name")
 }
+
+get_tag_one_json_names <- function(){
+  c(
+    "tag_1_name" = "tag1.name",
+    "tag_1_characteristics" = "tag1.characteristics",
+    "tag_1_color" = "tag1.color",
+    "tag_1_long_display" = "tag1.longDisplay",
+    "tag_1_order" = "tag1.order",
+    "tag_1_short_display" = "tag1.shortDisplay",
+    "tag_1_type" = "tag1.type"
+  )
+}
+
+get_tag_two_json_names <- function(){
+  c(
+    "tag_2_name" = "tag2.name",
+    "tag_2_characteristics" = "tag2.characteristics",
+    "tag_2_color" = "tag2.color",
+    "tag_2_long_display" = "tag2.longDisplay",
+    "tag_2_order" = "tag2.order",
+    "tag_2_short_display" = "tag2.shortDisplay",
+    "tag_2_type" = "tag2.type"
+  )
+}
+

inst/queries/feature_nodes.txt

@@ -6,7 +6,8 @@ query FeatureNodes(
   $network: [String!]
   $nTags: Int
   $related: [String!]
-  $tag: [String!]
+  $tag1: [String!]
+  $tag2: [String!]
   $paging: PagingInput
   $distinct: Boolean
 ) {
@@ -18,7 +19,8 @@ query FeatureNodes(
     network: $network
     nTags: $nTags
     related: $related
-    tag: $tag
+    tag1: $tag1
+    tag2: $tag2
     paging: $paging
     distinct: $distinct
   ) {
@@ -28,7 +30,16 @@ query FeatureNodes(
       score
       x
       y
-      tags {
+      tag1 {
+        characteristics
+        color
+        name
+        longDisplay
+        order
+        shortDisplay
+        type
+      }
+      tag2 {
         characteristics
         color
         name

inst/queries/gene_nodes.txt

@@ -6,7 +6,8 @@ query GeneNodes(
   $network: [String!]
   $nTags: Int
   $related: [String!]
-  $tag: [String!]
+  $tag1: [String!]
+  $tag2: [String!]
   $paging: PagingInput
   $distinct: Boolean
 ) {
@@ -18,7 +19,8 @@ query GeneNodes(
     network: $network
     nTags: $nTags
     related: $related
-    tag: $tag
+    tag1: $tag1
+    tag2: $tag2
     paging: $paging
     distinct: $distinct
   ) {
@@ -28,7 +30,16 @@ query GeneNodes(
       score
       x
       y
-      tags {
+      tag1 {
+        characteristics
+        color
+        name
+        longDisplay
+        order
+        shortDisplay
+        type
+      }
+      tag2 {
         characteristics
         color
         name