Merge pull request #9 from CRI-iAtlas/new_api

updated to use new api

NAMESPACE

@@ -33,6 +33,7 @@ export(query_immunomodulators)
 export(query_io_targets)
 export(query_mutation_statuses)
 export(query_mutations)
+export(query_neoantigens)
 export(query_nodes)
 export(query_patient_slides)
 export(query_patients)

R/api_cohorts_queries.R

@@ -72,7 +72,7 @@ query_cohort_features <- function(
     ),
     ...
   )
-  if(nrow(tbl) == 0) return(tbl)
+  if (nrow(tbl) == 0) return(tbl)
   else {
     tbl <- tbl %>%
       tidyr::unnest(cols = "features", keep_empty = T) %>%

R/api_functions.R

@@ -35,6 +35,7 @@ perform_api_query <- function(
   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)

R/api_genes_queries.R

@@ -264,7 +264,7 @@ query_gene_nanostring_expression <- function(
         ),
         ...
     )
-    if(nrow(tbl) == 0) return(tbl)
+    if (nrow(tbl) == 0) return(tbl)
     else {
         tbl %>%
             tidyr::unnest(cols = "samples", keep_empty = T) %>%

R/api_neoantigens_queries.R

@@ -0,0 +1,44 @@
+#' Query Neoantigens
+#'
+#' @param pmhcs A vector of strings
+#' @param entrez A vector of integers
+#' @param patients A vector of strings
+#' @param paging A named list
+#' @param ... Arguments to create_result_from_api_query
+#'
+#' @export
+query_neoantigens <- function(
+    pmhcs = NA,
+    entrez = NA,
+    patients = NA,
+    paging = NA,
+    ...
+){
+  create_result_from_cursor_paginated_api_query(
+    query_args =  list(
+      "pmhc" = pmhcs,
+      "entrez" = entrez,
+      "patient" = patients,
+      "paging" = paging,
+      "distinct" = F
+    ),
+    query_file = "neoantigens.txt",
+    default_tbl = dplyr::tibble(
+      "tpm" = double(),
+      "pmhc" = character(),
+      "freq_pmhc" = integer(),
+      "patient" =  character(),
+      "gene_entrez" = integer(),
+      "gene_hgnc" = character(),
+    ),
+    select_cols = c(
+      "tpm" = "tpm",
+      "pmhc" = "pmhc",
+      "freq_pmhc" = "freqPmhc",
+      "patient" = "patient.barcode",
+      "gene_entrez" = "gene.entrez",
+      "gene_hgnc" = "gene.hgnc"
+    ),
+    ...
+  )
+}

inst/queries/neoantigens.txt

@@ -0,0 +1,38 @@
+query Neoantigens(
+  $paging: PagingInput
+  $distinct:Boolean
+  $entrez: [Int!]
+  $patient: [String!]
+  $pmhc: [String!]
+){
+  neoantigens(
+    paging: $paging
+    distinct: $distinct
+    entrez: $entrez
+    patient: $patient
+    pmhc: $pmhc
+  ){
+    items {
+      tpm
+      pmhc
+      freqPmhc
+      patient { barcode }
+      gene {
+        entrez
+        hgnc
+      }
+    }
+    paging{
+      type
+      pages
+      total
+      page
+      limit
+      hasNextPage
+      hasPreviousPage
+      startCursor
+      endCursor
+    }
+    error
+  }
+}

tests/testthat/helper-globals.R

@@ -1,3 +1,4 @@
 query_dir  <- system.file("queries", package = "iatlasGraphQLClient")
 api_url <- "https://api.cri-iatlas.org/api"
 test_api_url <- "https://api-staging.cri-iatlas.org/api"
+local_api_url <- "http://localhost:5000/graphiql"

tests/testthat/test-api_cohorts_queries.R

@@ -22,29 +22,22 @@ test_that("query_cohorts", {
   expect_named(result1, expected_columns1)
   expect_equal(nrow(result1), 1)
 
+
   result2 <- query_cohorts(
-    cohort = "TCGA_Gender",
+    cohort = "TCGA",
     query_dir = query_dir
   )
 
-  expect_named(result2, expected_columns1)
+  expect_named(result2, expected_columns2)
   expect_equal(nrow(result2), 1)
 
   result3 <- query_cohorts(
-    cohort = "TCGA",
-    query_dir = query_dir
-  )
-
-  expect_named(result3, expected_columns2)
-  expect_equal(nrow(result3), 1)
-
-  result4 <- query_cohorts(
     cohort = "not_a_cohort",
     query_dir = query_dir
   )
 
-  expect_named(result4, c('name'))
-  expect_equal(nrow(result4), 0)
+  expect_named(result3, c('name'))
+  expect_equal(nrow(result3), 0)
 })
 
 test_that("query_cohort_features", {
@@ -62,16 +55,8 @@ test_that("query_cohort_features", {
   expect_named(result1, expected_columns)
   expect_true(nrow(result1) > 1)
 
-  result2 <- query_cohort_features(
-    cohorts = "PCAWG_Gender",
-    query_dir = query_dir
-  )
-
-  expect_named(result2, expected_columns)
-  expect_true(nrow(result2) > 1)
-
   result3 <- query_cohort_features(
-    cohort = "PCAWG",
+    cohort = "TCGA",
     query_dir = query_dir
   )
 
@@ -102,14 +87,6 @@ test_that("query_cohort_genes", {
   expect_named(result1, expected_columns)
   expect_true(nrow(result1) > 1)
 
-  result2 <- query_cohort_genes(
-    cohorts = "TCGA_Gender",
-    query_dir = query_dir
-  )
-
-  expect_named(result2, expected_columns)
-  expect_true(nrow(result2) > 1)
-
   result3 <- query_cohort_genes(
     cohort = "TCGA",
     query_dir = query_dir
@@ -149,14 +126,6 @@ test_that("query_cohort_mutations", {
   expect_named(result1, expected_columns1)
   expect_true(nrow(result1) > 1)
 
-  result2 <- query_cohort_mutations(
-    cohorts = "TCGA_Gender",
-    query_dir = query_dir
-  )
-
-  expect_named(result2, expected_columns1)
-  expect_true(nrow(result2) > 1)
-
   result3 <- query_cohort_mutations(
     cohort = "TCGA",
     query_dir = query_dir
@@ -197,23 +166,15 @@ test_that("query_cohort_samples", {
   )
 
   result1 <- query_cohort_samples(
-    cohorts = "PCAWG_Immune_Subtype",
+    cohorts = "TCGA_Immune_Subtype",
     query_dir = query_dir
   )
 
   expect_named(result1, expected_columns1)
   expect_true(nrow(result1) > 1)
 
-  result2 <- query_cohort_samples(
-    cohorts = "PCAWG_Gender",
-    query_dir = query_dir
-  )
-
-  expect_named(result2, expected_columns1)
-  expect_true(nrow(result2) > 1)
-
   result3 <- query_cohort_samples(
-    cohort = "PCAWG",
+    cohort = "TCGA",
     query_dir = query_dir
   )
 

tests/testthat/test-api_copy_number_result_queries.R

@@ -21,7 +21,6 @@ test_that("query_copy_number_results",{
     datasets = "TCGA",
     tags = "C1",
     max_p_value = 0.000000000000000000000000000000000000000000000001,
-    entrez =  1,
     query_dir = query_dir
   )
   expect_named(result1, expected_columns)

tests/testthat/test-api_datasets_queries.R

@@ -36,7 +36,7 @@ test_that("query_dataset_tags", {
     "dataset_type"
   )
 
-  result1 <- query_dataset_tags(datasets = "PCAWG", query_dir = query_dir)
+  result1 <- query_dataset_tags(datasets = "TCGA", query_dir = query_dir)
   expect_named(result1, expected_names)
   expect_true(nrow(result1) > 0)
 

tests/testthat/test-api_features_queries.R

@@ -54,7 +54,7 @@ test_that("query_feature_values", {
 test_that("query_features_range", {
   expected_columns <- c("name", "display", "value_min", "value_max")
   result1 <- query_features_range(
-    cohorts = "PCAWG_Gender",
+    cohorts = "TCGA_Immune_Subtype",
     features = "Lymphocytes_Aggregate1",
     query_dir = query_dir
   )
@@ -63,7 +63,7 @@ test_that("query_features_range", {
   expect_true(result1$value_min <= result1$value_max)
 
   result2 <- query_features_range(
-    cohorts = "PCAWG_Gender",
+    cohorts = "TCGA_Immune_Subtype",
     features = "not_a_feature",
     query_dir = query_dir
   )

tests/testthat/test-api_functions.R

@@ -248,19 +248,6 @@ test_that("do_cursor_paginated_api_query", {
 
 test_that("do_offset_paginated_api_query", {
 
-  result1 <- do_offset_paginated_api_query(
-    query_args = list(
-      paging = list("limit" = 10),
-      feature = "frac_altered",
-      maxPValue = 0.1e-170,
-      distinct = T
-    ),
-    query_file = "pagination_test.txt",
-    query_dir = query_dir
-  )
-  expect_type(result1, "list")
-  expect_true(length(result1) > 1)
-
   result2 <- do_offset_paginated_api_query(
     query_args = list(
       paging = list("first" = 10),

tests/testthat/test-api_genes_queries.R

@@ -86,8 +86,8 @@ test_that("query_gene_nanostring_expression", {
         "nanostring_expr"
     )
     result1 <- query_gene_nanostring_expression(
-        entrez = 259L,
-        samples = "Prins_GBM_2019-SK08-ar-A07",
+        entrez = 4282L,
+        samples = "Chen_CanDisc_2016-c25-ar-c25_pre",
         query_dir = query_dir
     )
     expect_named(result1, expected_columns)

tests/testthat/test-api_germline_gwas_results_queries.R

@@ -16,8 +16,8 @@ test_that("query_germline_gwas_results",{
   )
   result1 <- query_germline_gwas_results(
     datasets = "TCGA",
-    feature = "Attractors_G_SIGLEC9",
-    snps = "2:206655924:C:T",
+    feature = "Module3_IFN_score",
+    snps = "3:133016759:C:G",
     query_dir = query_dir
   )
 
@@ -27,14 +27,14 @@ test_that("query_germline_gwas_results",{
 
   result2 <- query_germline_gwas_results(
     datasets = "TCGA",
-    min_p_value = 4.24e-25,
-    max_p_value = 5.25e-25,
+    min_p_value = 1.0e-07,
+    max_p_value = 9.9e-07,
     query_dir = query_dir
   )
   expect_named(result2, expected_columns)
   expect_true(nrow(result2) > 0)
-  expect_true(all(result2$p_value >= 4.24e-25))
-  expect_true(all(result2$p_value <= 5.25e-25))
+  expect_true(all(result2$p_value >= 1.0e-07))
+  expect_true(all(result2$p_value <= 9.9e-07))
 
   result3 <- query_germline_gwas_results(
     datasets = "TCGA",

tests/testthat/test-api_neoantigens.R

@@ -0,0 +1,24 @@
+
+test_that("query_neoantigens",{
+  expected_columns <- c(
+    "tpm",
+    "pmhc",
+    "freq_pmhc",
+    "patient",
+    "gene_entrez",
+    "gene_hgnc"
+  )
+  result1 <- query_neoantigens(
+    pmhcs = list("RLMELQEAV HLA_A*02:01 SPAG9"),
+    patients = list("VanAllen_antiCTLA4_2015-p126"),
+    query_dir = query_dir
+  )
+  result2 <- query_neoantigens(
+    pmhcs = list("xxx"),
+    query_dir = query_dir
+  )
+  expect_named(result1, expected_columns)
+  expect_named(result2, expected_columns)
+  expect_true(nrow(result1) > 0)
+  expect_equal(nrow(result2), 0)
+})