Merge pull request #236 from Sage-Bionetworks/fds-1615-json-config

FDS-1615: Refactor to handle JSON configuration
Sage-Bionetworks · Feb 23, 2024 · 889fdde · 889fdde
2 parents fb7bfd1 + ca89f0a
commit 889fdde
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dataflow
 Title: Data Flow App Demo
-Version: 23.10.1
+Version: 24.2.1
 Authors@R: person('L', 'Wolfe', email = 'loren.wolfe@sagebase.org', role = c('cre', 'aut'))
 Description: A data flow package.
 License: MIT + file LICENSE

diff --git a/R/app_server.R b/R/app_server.R
@@ -23,11 +23,13 @@ app_server <- function( input, output, session ) {
   )
 
   # get the access_token and userinfo token
-  req <- httr::POST(redirect_url, 
-                    encode = "form", 
-                    body = "", 
-                    httr::authenticate(app$key, app$secret, type = "basic"), 
-                    config = list())
+  req <- httr::POST(
+    redirect_url,
+    encode = "form",
+    body = "",
+    httr::authenticate(app$key, app$secret, type = "basic"),
+    config = list()
+    )
   # Stop the code if anything other than 2XX status code is returned
 
   httr::stop_for_status(req, task = "get an access token")
@@ -61,17 +63,21 @@ app_server <- function( input, output, session ) {
 
 
   # SELECT A DCC  #############################################################
-  mod_select_dcc_out <- dfamodules::mod_select_dcc_server("select_dcc",
-                                                          dcc_config,
-                                                          access_token)
+  mod_select_dcc_out <- dfamodules::mod_select_dcc_server(
+    id = "select_dcc",
+    tenants_config_path = tenants_config_path ,
+    access_token = access_token
+    )
 
   # CONFIGURE APP ############################################################
   observeEvent(mod_select_dcc_out()$btn_click, {
-    
+
     # move to dashboard page
-    shinydashboard::updateTabItems(session = session,
-                                   inputId = "tabs",
-                                   selected = "tab_dashboard")
+    shinydashboard::updateTabItems(
+      session = session,
+      inputId = "tabs",
+      selected = "tab_dashboard"
+    )
 
     # show waiter on button click
     waiter::waiter_show(
@@ -85,12 +91,23 @@ app_server <- function( input, output, session ) {
     shinyjs::show(selector = ".sidebar-menu")
 
     # update reactiveVals
-    selected_dcc_config_list$synapse_asset_view(mod_select_dcc_out()$selected_dcc_config$synapse_asset_view)
-    selected_dcc_config_list$manifest_dataset_id(mod_select_dcc_out()$selected_dcc_config$manifest_dataset_id)
-    selected_dcc_config_list$project_name(mod_select_dcc_out()$selected_dcc_config$project_name)
-    selected_dcc_config_list$schema_url(mod_select_dcc_out()$selected_dcc_config$schema_url)
-    selected_dcc_config_list$icon(mod_select_dcc_out()$selected_dcc_config$icon)
+    selected_dcc_config_list$synapse_asset_view(
+      mod_select_dcc_out()$selected_dcc_config$dcc$synapse_asset_view
+    )
+    selected_dcc_config_list$manifest_dataset_id(
+      mod_select_dcc_out()$selected_dcc_config$dcc$manifest_dataset_id
+      )
+    selected_dcc_config_list$project_name(
+      mod_select_dcc_out()$selected_dcc_config$dcc$name
+      )
+    selected_dcc_config_list$schema_url(
+      mod_select_dcc_out()$selected_dcc_config$dcc$data_model_url
+      )
+    selected_dcc_config_list$icon(
+      mod_select_dcc_out()$selected_dcc_config$dfa_dashboard$icon
+      )
 
+    # Check that user has appropriate permissions to use DFA
     # User must have DOWNLOAD access to the DFA manifest.
     manifest_perm <- dfamodules::synapse_access(
       id = selected_dcc_config_list$manifest_dataset_id(),
@@ -114,10 +131,12 @@ app_server <- function( input, output, session ) {
       waiter::waiter_hide()
     }
 
+    # generate dashboard config file
     dash_config <- dfamodules::generate_dashboard_config(
       schema_url = selected_dcc_config_list$schema_url(),
       icon = selected_dcc_config_list$icon(),
-      base_url = schematic_api_url)
+      base_url = schematic_api_url
+      )
 
     # download manifest
     manifest_obj <- dfamodules::dataset_manifest_download(
@@ -126,36 +145,36 @@ app_server <- function( input, output, session ) {
       access_token = access_token,
       base_url = schematic_api_url
       )
-
+    
     # prep manifest for app
     prepped_manifest <- dfamodules::prep_manifest_dfa(
       manifest = manifest_obj$content,
       config = dash_config
     )
-    
+
     # update reactiveVals
     original_manifest(prepped_manifest)
     admin_manifest(prepped_manifest)
-    
+
     dash_config_react(dash_config)
-    
+
     # FILTER MANIFEST FOR DASH  ###############################################
 
     filtered_manifest <- dfamodules::mod_datatable_filters_server(
       "datatable_filters_1",
       original_manifest
       )
-    
+
     # DATASET DASH  ###########################################################
 
     dfamodules::mod_datatable_dashboard_server(
       "dashboard_1",
       filtered_manifest,
       dash_config_react
       )
-    
+
     # DATASET DASH VIZ : DISTRIBUTIONS ########################################
-    
+
     dfamodules::mod_distribution_server(
       id = "distribution_contributor",
       df = filtered_manifest,
@@ -165,7 +184,7 @@ app_server <- function( input, output, session ) {
       y_lab = "Number of Datasets",
       fill = "#0d1c38"
     )
-    
+
     dfamodules::mod_distribution_server(
       id = "distribution_datatype",
       df = filtered_manifest,
@@ -175,7 +194,7 @@ app_server <- function( input, output, session ) {
       y_lab = "Number of Datasets",
       fill = "#0d1c38"
     )
-    
+
    # hide waiter
     waiter::waiter_hide()
 
@@ -212,7 +231,9 @@ app_server <- function( input, output, session ) {
 
   # COLLECT WIDGET SELECTIONS  ################################################
 
-  mod_administrator_widgets_out <- dfamodules::mod_administrator_widgets_server("update_data_flow_status_1")
+  mod_administrator_widgets_out <- dfamodules::mod_administrator_widgets_server(
+    id = "update_data_flow_status_1"
+    )
 
   # MAKE UPDATES TO MANIFEST  #################################################
 
@@ -232,10 +253,10 @@ app_server <- function( input, output, session ) {
   })
 
   dfamodules::mod_manifest_preview_server(
-    "highlight_datatable_1",
-    updated_manifest,
-    selected_rows,
-    "dataset_id"
+    id = "highlight_datatable_1",
+    df = updated_manifest,
+    selection = selected_rows,
+    df_match_colname = "dataset_id"
   )
 
   # BUTTON CLICK ACTIONS  #####################################################
@@ -260,8 +281,9 @@ app_server <- function( input, output, session ) {
     req(updated_manifest())
 
     dfamodules::prep_manifest_submit(
-      updated_manifest(),
-      dash_config_react()
+      manifest = updated_manifest(),
+      config = dash_config_react(),
+      na_replace = ""
     )
   })
 

diff --git a/R/app_ui.R b/R/app_ui.R
@@ -79,8 +79,7 @@ app_ui <- function() {
             tabName = "tab_select_dcc",
             shiny::fluidRow(
               dfamodules::mod_select_dcc_ui(
-                "select_dcc",
-                dcc_config
+                "select_dcc"
               )
             )
           ),

diff --git a/R/global.R b/R/global.R
@@ -1,16 +1,12 @@
-# READ IN CONFIG
-dcc_config <- Sys.getenv("DFA_DCC_CONFIG")
-if (is.null(dcc_config) || nchar(dcc_config) == 0) stop("missing DFA_DCC_CONFIG environmental variable")
-
-dcc_config <- readr::read_csv(dcc_config,
-                              show_col_types = FALSE)
+# READ IN TENANTS.JSON
+tenants_config_path <- Sys.getenv("DFA_DCC_CONFIG")
+if (is.null(tenants_config_path) || nchar(tenants_config_path) == 0) stop("missing DFA_DCC_CONFIG environmental variable")
 
 # GET SCHEMATIC API URL
 schematic_api_url <- Sys.getenv("DFA_SCHEMATIC_API_URL")
 message("DFA is using ", schematic_api_url)
 
 # SET UP OAUTH
-
 client_id <- Sys.getenv("DFA_CLIENT_ID")
 client_secret <- Sys.getenv("DFA_CLIENT_SECRET")
 app_url <- Sys.getenv("DFA_APP_URL")

diff --git a/renv.lock b/renv.lock
@@ -416,14 +416,14 @@
     },
     "dfamodules": {
       "Package": "dfamodules",
-      "Version": "23.12.1",
+      "Version": "24.2.1",
       "Source": "GitHub",
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteUsername": "Sage-Bionetworks",
       "RemoteRepo": "dfamodules",
-      "RemoteRef": "main",
-      "RemoteSha": "186060a0107db12255b1c65275e9dfc3e77be53e",
+      "RemoteRef": "dev",
+      "RemoteSha": "b195b41b40453b98bbc09ae81cf21155fb2a6745",
       "Requirements": [
         "DT",
         "dplyr",
@@ -442,7 +442,7 @@
         "shinyjs",
         "waiter"
       ],
-      "Hash": "05924f504f548e7b17adb4bb6fce1c37"
+      "Hash": "8e16a925b17b61a27fc8c3ae2273c669"
     },
     "diffobj": {
       "Package": "diffobj",
@@ -492,9 +492,9 @@
     },
     "dplyr": {
       "Package": "dplyr",
-      "Version": "1.1.3",
+      "Version": "1.1.4",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "R6",
@@ -511,7 +511,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949"
+      "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
     },
     "ellipsis": {
       "Package": "ellipsis",
@@ -888,13 +888,13 @@
     },
     "jsonlite": {
       "Package": "jsonlite",
-      "Version": "1.8.7",
+      "Version": "1.8.8",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "methods"
       ],
-      "Hash": "266a20443ca13c65688b2116d5220f76"
+      "Hash": "e1b9c55281c5adc4dd113652d9e26768"
     },
     "knitr": {
       "Package": "knitr",
@@ -1627,7 +1627,14 @@
       "RemoteUsername": "dreamRs",
       "RemoteRepo": "shinypop",
       "RemoteRef": "master",
-      "RemoteSha": "7745a0b1ecf31f783fa59603f3c5cede0c948118"
+      "RemoteSha": "7745a0b1ecf31f783fa59603f3c5cede0c948118",
+      "Requirements": [
+        "R",
+        "htmltools",
+        "jsonlite",
+        "shiny"
+      ],
+      "Hash": "ee29555190ce6a726046a5909cc91d9b"
     },
     "sourcetools": {
       "Package": "sourcetools",
@@ -1866,17 +1873,17 @@
     },
     "vctrs": {
       "Package": "vctrs",
-      "Version": "0.6.2",
+      "Version": "0.6.5",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "cli",
         "glue",
         "lifecycle",
         "rlang"
       ],
-      "Hash": "a745bda7aff4734c17294bb41d4e4607"
+      "Hash": "c03fa420630029418f7e6da3667aac4a"
     },
     "viridisLite": {
       "Package": "viridisLite",