change package names

CRI-iAtlas · Apr 13, 2022 · 0b8cdeb · 0b8cdeb
1 parent 4840ac7
commit 0b8cdeb
Show file tree

Hide file tree

Showing 18 changed files with 70 additions and 70 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -22,7 +22,7 @@ Imports:
     DT,
     dplyr (>= 1.0),
     forcats (>= 0.5),
-    iatlas.api.client,
+    iatlasGraphQLClient,
     iatlas.modules,
     magrittr (>= 2.0),
     plotly(>= 4.9),
@@ -42,7 +42,7 @@ Imports:
 URL: https://github.com/CRI-iAtlas/iatlas.modules2
 BugReports: https://github.com/CRI-iAtlas/iatlas.modules2/issues
 Remotes:
-    CRI-iAtlas/iatlas.api.client@main,
+    CRI-iAtlas/iatlasGraphQLClient@main,
     CRI-iAtlas/iatlas.modules@master
 Depends: 
     R (>= 2.10)
diff --git a/R/cohort.R b/R/cohort.R
@@ -40,11 +40,11 @@ Cohort <- R6::R6Class(
         tibble::deframe(.)
 
       dataset_displays <-
-        iatlas.api.client::query_datasets() %>%
+        iatlasGraphQLClient::query_datasets() %>%
         dplyr::filter(.data$name %in% dataset_names) %>%
         dplyr::pull("display")
 
-      feature_tbl <- iatlas.api.client::query_features(cohorts = cohort_names)
+      feature_tbl <- iatlasGraphQLClient::query_features(cohorts = cohort_names)
 
       # set values ----
 
@@ -91,7 +91,7 @@ Cohort <- R6::R6Class(
       features = NA, feature_classes = NA, groups = NA
     ){
       tbl <-
-        iatlas.api.client::query_feature_values(
+        iatlasGraphQLClient::query_feature_values(
           cohorts = self$cohort_names,
           features = features,
           feature_classes = feature_classes
@@ -117,7 +117,7 @@ Cohort <- R6::R6Class(
     },
 
     get_gene_values = function(entrez = NA, gene_types = NA){
-      iatlas.api.client::query_gene_expression(
+      iatlasGraphQLClient::query_gene_expression(
         cohorts = self$cohort_names,
         gene_types = gene_types,
         entrez = entrez
@@ -178,7 +178,7 @@ UploadCohort <- R6::R6Class(
         stop("group_name must be a column in upload_tbl")
       }
 
-      dataset_sample_tbl <- iatlas.api.client::query_dataset_samples(
+      dataset_sample_tbl <- iatlasGraphQLClient::query_dataset_samples(
         samples = upload_tbl$Sample
       )
 
@@ -222,7 +222,7 @@ UploadCohort <- R6::R6Class(
           "dataset_display"
         )
 
-      feature_tbl <- iatlas.api.client::query_features(
+      feature_tbl <- iatlasGraphQLClient::query_features(
         cohorts = dataset_tbl$dataset_name
       )
 
@@ -273,7 +273,7 @@ UploadCohort <- R6::R6Class(
       features = NA, feature_classes = NA, groups = NA
     ){
       tbl <-
-        iatlas.api.client::query_feature_values(
+        iatlasGraphQLClient::query_feature_values(
           cohorts = self$cohort_names,
           features = features,
           feature_classes = feature_classes
@@ -298,7 +298,7 @@ UploadCohort <- R6::R6Class(
       return(tbl)
     },
     get_gene_values = function(entrez = NA, gene_types = NA){
-      iatlas.api.client::query_gene_expression(
+      iatlasGraphQLClient::query_gene_expression(
         cohorts = self$cohort_names,
         gene_types = gene_types,
         entrez = entrez

diff --git a/R/cohort_dataset_selection_server.R b/R/cohort_dataset_selection_server.R
@@ -10,7 +10,7 @@ cohort_dataset_selection_server <- function(
       ns <- session$ns
 
       choices <- shiny::reactive({
-        iatlas.api.client::query_datasets(types = dataset_type()) %>%
+        iatlasGraphQLClient::query_datasets(types = dataset_type()) %>%
           dplyr::select("display", "name") %>%
           tibble::deframe(.)
       })

diff --git a/R/cohort_filter_selection_server.R b/R/cohort_filter_selection_server.R
@@ -11,7 +11,7 @@ cohort_filter_selection_server <- function(
       # group filters -----------------------------------------------------------
       group_filter_list <- shiny::reactive({
         shiny::req(datasets())
-        iatlas.api.client::query_dataset_tags(dataset = datasets()) %>%
+        iatlasGraphQLClient::query_dataset_tags(dataset = datasets()) %>%
           dplyr::group_by(.data$tag_name) %>%
           dplyr::mutate(count = dplyr::n()) %>%
           dplyr::ungroup() %>%

diff --git a/R/cohort_filters.R b/R/cohort_filters.R
@@ -20,7 +20,7 @@ CohortFilters <- R6::R6Class("CohortFilters", list(
   },
   get_sample_tbl = function(cohorts){
     samples    <- self$get_samples(cohorts)
-    sample_tbl <- iatlas.api.client::query_cohort_samples(cohorts = cohorts)
+    sample_tbl <- iatlasGraphQLClient::query_cohort_samples(cohorts = cohorts)
     if(length(samples) > 0) {
       sample_tbl <- dplyr::filter(sample_tbl, .data$sample_name %in% samples)
     }
@@ -79,7 +79,7 @@ CohortNumericFilter <- R6::R6Class("CohortNumericFilter", list(
   },
   get_samples = function(cohorts){
     samples <-
-      iatlas.api.client::query_feature_values(
+      iatlasGraphQLClient::query_feature_values(
         cohorts = cohorts,
         features = self$name,
         max_value = self$max,
@@ -101,7 +101,7 @@ CohortGroupFilter <- R6::R6Class("CohortGroupFilter", list(
   },
   get_samples = function(cohorts){
     samples <-
-      iatlas.api.client::query_tag_samples(
+      iatlasGraphQLClient::query_tag_samples(
         cohorts = cohorts, tags = self$values
       ) %>%
       dplyr::pull("sample_name")

diff --git a/R/cohort_group_selection_functions.R b/R/cohort_group_selection_functions.R
@@ -1,5 +1,5 @@
 build_tag_group_tbl <- function(datasets){
-  tbl <- iatlas.api.client::query_cohorts(datasets = datasets)
+  tbl <- iatlasGraphQLClient::query_cohorts(datasets = datasets)
   if(!"tag_name" %in% names(tbl)) {
     return(dplyr::tibble("display" = character(), "name" = character()))
   }
@@ -24,7 +24,7 @@ build_custom_group_tbl <- function(datasets){
     ),
     dplyr::tibble(
       "name" = "Immune Feature Bins",
-      "dataset" = iatlas.api.client::query_datasets(types = "ici")$name
+      "dataset" = iatlasGraphQLClient::query_datasets(types = "ici")$name
     )
   ) %>%
     dplyr::filter(.data$dataset %in% datasets) %>%

diff --git a/R/cohort_group_selection_server.R b/R/cohort_group_selection_server.R
@@ -68,7 +68,7 @@ cohort_group_selection_server <- function(
       )
 
       mutation_tbl <- shiny::reactive({
-        iatlas.api.client::query_mutations(type = "driver_mutation")
+        iatlasGraphQLClient::query_mutations(type = "driver_mutation")
       })
 
       output$select_driver_mutation_group_ui <- shiny::renderUI({

diff --git a/R/cohort_manual_selection_server.R b/R/cohort_manual_selection_server.R
@@ -24,7 +24,7 @@ cohort_manual_selection_server <- function(
 
       dataset_feature_tbl <- shiny::reactive({
         shiny::req(datasets())
-        iatlas.api.client::query_features(cohorts = datasets())
+        iatlasGraphQLClient::query_features(cohorts = datasets())
       })
 
       group_object <- cohort_group_selection_server(

diff --git a/R/driver_associations_multivariate_functions.R b/R/driver_associations_multivariate_functions.R
@@ -4,7 +4,7 @@ build_md_tag_covariate_tbl <- function(cohort_obj, cov_obj){
   tbl <-
     purrr::map(
       parent_tags,
-      ~iatlas.api.client::query_tag_samples(
+      ~iatlasGraphQLClient::query_tag_samples(
         cohorts = cohort_obj$dataset_names,
         parent_tags = .x
       )

diff --git a/R/driver_associations_multivariate_server.R b/R/driver_associations_multivariate_server.R
@@ -76,7 +76,7 @@ multivariate_driver_server <- function(id, cohort_obj) {
       })
 
       status_tbl <- shiny::reactive({
-        iatlas.api.client::query_mutation_statuses(
+        iatlasGraphQLClient::query_mutation_statuses(
           samples = cohort_obj()$sample_tbl$sample
         ) %>%
           dplyr::select(
@@ -128,7 +128,7 @@ multivariate_driver_server <- function(id, cohort_obj) {
 
       total_associations <- shiny::reactive({
         n_mutations <-
-          iatlas.api.client::query_mutations(
+          iatlasGraphQLClient::query_mutations(
             datasets = "TCGA", types = "driver_mutation"
           ) %>%
           nrow()

diff --git a/R/driver_associations_univariate_server.R b/R/driver_associations_univariate_server.R
@@ -49,7 +49,7 @@ univariate_driver_server <- function(id, cohort_obj) {
           length(cohort_obj()$group_name) == 1,
         )
 
-        iatlas.api.client::query_tags(
+        iatlasGraphQLClient::query_tags(
           cohorts = cohort_obj()$dataset_names,
           parent_tags = cohort_obj()$group_name
         ) %>%
@@ -65,7 +65,7 @@ univariate_driver_server <- function(id, cohort_obj) {
         )
 
         tbl <-
-          iatlas.api.client::query_driver_results(
+          iatlasGraphQLClient::query_driver_results(
             datasets = cohort_obj()$dataset_names,
             tags = tags(),
             features = input$response_choice,
@@ -88,7 +88,7 @@ univariate_driver_server <- function(id, cohort_obj) {
 
       total_associations <- shiny::reactive({
         n_mutations <-
-          iatlas.api.client::query_cohort_mutations(
+          iatlasGraphQLClient::query_cohort_mutations(
             cohorts = cohort_obj()$dataset_names
           ) %>%
           nrow()
@@ -200,7 +200,7 @@ univariate_driver_server <- function(id, cohort_obj) {
           dplyr::select("sample_name", "feature_value", "group_short_name")
 
         status_tbl <-
-          iatlas.api.client::query_mutation_statuses(
+          iatlasGraphQLClient::query_mutation_statuses(
             entrez = selected_volcano_result()$entrez,
             codes = selected_volcano_result()$mutation_code,
             types = "driver_mutation",

diff --git a/R/elements_functions.R b/R/elements_functions.R
@@ -1,6 +1,6 @@
 
 build_tag_filter_list <- function(parent_tag_name, datasets){
-  iatlas.api.client::query_tags(
+  iatlasGraphQLClient::query_tags(
     cohorts = datasets,
     parent_tags = parent_tag_name
   ) %>%

diff --git a/R/elements_server.R b/R/elements_server.R
@@ -36,7 +36,7 @@ numeric_filter_element_server <- function(
       features_tbl <- shiny::reactive({
         shiny::req(datasets(), input$numeric_choice)
         tbl <-
-          iatlas.api.client::query_features_range(
+          iatlasGraphQLClient::query_features_range(
             cohorts = datasets(),
             features = input$numeric_choice
           ) %>%

diff --git a/R/group.R b/R/group.R
@@ -21,15 +21,15 @@ TagGroup <- R6::R6Class(
       }
 
       group_display <- group_name %>%
-        iatlas.api.client::query_tags(tags = .) %>%
+        iatlasGraphQLClient::query_tags(tags = .) %>%
         dplyr::pull("tag_short_display")
 
       if(length(group_display) == 0) {
         stop("group_name not found in database")
       }
 
       cohort_names <-
-        iatlas.api.client::query_cohorts(
+        iatlasGraphQLClient::query_cohorts(
           datasets = dataset_names,
           tags = group_name
         ) %>%
@@ -98,7 +98,7 @@ FeatureBinGroup <- R6::R6Class(
     initialize = function(dataset_names, feature_name, feature_bins){
 
       feature_display <-
-        iatlas.api.client::query_features(features = feature_name) %>%
+        iatlasGraphQLClient::query_features(features = feature_name) %>%
         dplyr::pull("display")
 
       group_name  = stringr::str_c("Immune Feature Bins: ", feature_display)
@@ -113,7 +113,7 @@ FeatureBinGroup <- R6::R6Class(
     },
     get_tables = function(sample_tbl){
 
-      sample_tbl <- iatlas.api.client::query_feature_values(
+      sample_tbl <- iatlasGraphQLClient::query_feature_values(
         features = self$feature_name, cohorts = self$dataset_names
       ) %>%
         dplyr::mutate("group_name" = as.character(cut(.data$feature_value, self$feature_bins))) %>%
@@ -172,7 +172,7 @@ MutationStatusGroup <- R6::R6Class(
     get_tables = function(sample_tbl){
 
       sample_tbl <-
-        iatlas.api.client::query_mutation_statuses(
+        iatlasGraphQLClient::query_mutation_statuses(
           mutations = self$mutation_name,
           cohorts = self$cohort_names
         ) %>%

diff --git a/renv.lock b/renv.lock
@@ -637,31 +637,6 @@
         "openssl"
       ]
     },
-    "iatlas.api.client": {
-      "Package": "iatlas.api.client",
-      "Version": "0.29.0",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteUsername": "CRI-iAtlas",
-      "RemoteRepo": "iatlas.api.client",
-      "RemoteRef": "main",
-      "RemoteSha": "3a919b12e4afbd41ae6b23f756c8aebd2ce76d29",
-      "RemoteHost": "api.github.com",
-      "Hash": "fe91864da09cdacdb3cbac7617b9f4e1",
-      "Requirements": [
-        "assertthat",
-        "dplyr",
-        "ghql",
-        "jsonlite",
-        "magrittr",
-        "purrr",
-        "rlang",
-        "snakecase",
-        "stringr",
-        "tibble",
-        "tidyr"
-      ]
-    },
     "iatlas.modules": {
       "Package": "iatlas.modules",
       "Version": "0.9.0",
@@ -696,6 +671,31 @@
         "viridis"
       ]
     },
+    "iatlasGraphQLClient": {
+      "Package": "iatlasGraphQLClient",
+      "Version": "0.1.0",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteUsername": "CRI-iAtlas",
+      "RemoteRepo": "iatlasGraphQLClient",
+      "RemoteRef": "main",
+      "RemoteSha": "d97a8b7c4162ee0f31f717ff4b2e7c61ae77edca",
+      "Hash": "92d3a568c2fbd8b97267dc67a5f4a9c1",
+      "Requirements": [
+        "assertthat",
+        "dplyr",
+        "ghql",
+        "jsonlite",
+        "magrittr",
+        "purrr",
+        "rlang",
+        "snakecase",
+        "stringr",
+        "tibble",
+        "tidyr"
+      ]
+    },
     "ini": {
       "Package": "ini",
       "Version": "0.3.1",