Merge pull request #207 from Sage-Bionetworks/dev

Dev to staging v23.06.1
Sage-Bionetworks · Jun 20, 2023 · 48fcffb · 48fcffb
2 parents 8059ab1 + da1c15a
commit 48fcffb
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Showing 6 changed files with 135 additions and 34 deletions.
diff --git a/.github/workflows/shinyapps_deploy.yml b/.github/workflows/shinyapps_deploy.yml
@@ -22,6 +22,9 @@ jobs:
     runs-on: ubuntu-latest
     container: rocker/rstudio:4.1.2
     env:
+      SCHEMATIC_URL_DEV: https://schematic-dev.api.sagebionetworks.org
+      SCHEMATIC_URL_STAGING: https://schematic-staging.api.sagebionetworks.org
+      SCHEMATIC_URL_PROD: https://schematic.api.sagebionetworks.org
       # This should not be necessary for installing from public repo's however remotes::install_github() fails without it.
       GITHUB_PAT:  ${{ secrets.GITHUB_TOKEN }}
 
@@ -30,17 +33,15 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -y pip libcurl4-openssl-dev libpng-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libtiff-dev libxml2-dev
-        # this action checks out the $GITHUB_WORKSPACE repository so that the workflow can access it
+        
+      # this action checks out the $GITHUB_WORKSPACE repository so that the workflow can access it
       - uses: actions/checkout@v3
-        # this action sets up pandoc
+
+      # this action sets up pandoc
       - uses: r-lib/actions/setup-pandoc@v2
-        # this action activates renv
+
+      # this action activates renv
       - uses: r-lib/actions/setup-renv@v2
-        # Write synapse config (not sure if I even need this??)
-      - name: Set Configurations
-        shell: bash
-        run: |
-          echo "${{ secrets.SCHEMATIC_SYNAPSE_CONFIG }}" > .synapseConfig
         # deploy app using rsconnect
       - name: Authorize and deploy app
         run: |
@@ -51,19 +52,29 @@ jobs:
           repo <- Sys.getenv("GITHUB_REPOSITORY")
           appName <- strsplit(repo, "/")[[1]][2]
 
-          # if tag is v*.*.*, deploy to prod, if main to staging, otherwise to test
+          # if tag is v*.*.*, deploy to prod
+          # if main to staging
+          # otherwise to test
           if (grepl("v[0-9]+.[0-9]+.[0-9]+", refName)) {
-            message("Deploying release version of app")
+            message("Deploying release version of app using schematic API production instance")
+            renviron <- "DFA_SCHEMATIC_API_URL = '${{ env.SCHEMATIC_URL_PROD }}'"
           } else if (refName == "main") {
             appName <- paste(appName, "staging", sep = "-")
-            message("Deploying staging version of app")
+            renviron <- "DFA_SCHEMATIC_API_URL = '${{ env.SCHEMATIC_URL_STAGING }}'"
+            message("Deploying staging version of app using schematic API staging instance")
           } else {
             appName <- paste(appName, "testing", sep = "-")
-            message("Deploying testing version of app")
+            renviron <- "DFA_SCHEMATIC_API_URL = '${{ env.SCHEMATIC_URL_DEV }}'"
+            message("Deploying testing version of app using schematic API dev instance")
           }
 
+          # write .Renviron
+          writeLines(renviron, ".Renviron") 
+
+          # deploy
           message(sprintf("Deploying to %s instance.", appName))
 
+          # assign secrets to variables
           rsConnectUser <-"${{ secrets.RSCONNECT_USER }}"
           rsConnectToken <- "${{ secrets.RSCONNECT_TOKEN }}"
           rsConnectSecret <- "${{ secrets.RSCONNECT_SECRET }}"
@@ -74,15 +85,17 @@ jobs:
           appUrl<- sprintf("https://%s.shinyapps.io/%s", rsConnectUser, appName)
           config <- c(config, sprintf("app_url: %s", appUrl))
 
+          # write config file
           configFileConn<-file("oauth_config.yml")
           tryCatch(
              writeLines(config, configFileConn),
              finally=close(configFileConn)
           )
-          # FIXME ADD size parameter
+
+          # set account info
           rsconnect::setAccountInfo(rsConnectUser, rsConnectToken, rsConnectSecret)
 
-          # Get app names. If app exists, configure then deploy. Otherwise
+          # get app names. If app exists, configure then deploy. Otherwise
           # deploy then configure.
           apps <- rsconnect::applications()$name
           if (appName %in% apps) {
@@ -92,4 +105,4 @@ jobs:
             rsconnect::deployApp(appName = appName)
             rsconnect::configureApp(appName = appName, size = "xxxlarge", logLevel = "verbose")
           }
-        shell: Rscript {0}
+        shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: dataflow
 Title: Data Flow App Demo
-Version: 0.0.0.9000
+Version: 23.06.1
 Authors@R: person('L', 'Wolfe', email = '[email protected]', 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
@@ -9,8 +9,7 @@
 app_server <- function( input, output, session ) {
   # Your application server logic
   options(shiny.reactlog = TRUE)
-
-
+
   # AUTHENTICATION
   params <- parseQueryString(isolate(session$clientData$url_search))
   if (!has_auth_code(params)) {
@@ -35,10 +34,6 @@ app_server <- function( input, output, session ) {
   access_token <- token_response$access_token
 
   session$userData$access_token <- access_token
-  # DEV STUFF ###########################################################################
-
-  # read in configs
-  global_config <- jsonlite::read_json("inst/global.json")
 
   # generate dashboard configuration from dataFlow schema
   dash_config <- dfamodules::generate_dashboard_config(schema_url = global_config$schema_url,
@@ -58,13 +53,13 @@ app_server <- function( input, output, session ) {
                                                                          release_scheduled = "Not Scheduled",
                                                                          embargo = "No Embargo",
                                                                          dataset = "No Manifest"),
-                                                       base_url = global_config$api_base_url)
+                                                       base_url = schematic_api_url)
 
   # download data flow status manifest
   manifest_obj <- dfamodules::dataset_manifest_download(asset_view = global_config$asset_view,
                                                         dataset_id = global_config$manifest_dataset_id,
                                                         access_token = access_token,
-                                                        base_url = global_config$api_base_url)
+                                                        base_url = schematic_api_url)
 
   manifest_dfa <- dfamodules::prep_manifest_dfa(manifest = manifest_obj$content,
                                                 config = dash_config)
@@ -246,15 +241,15 @@ app_server <- function( input, output, session ) {
   select_storage_project_out <- dfamodules::mod_select_storage_project_server(id = "select_storage_project_1",
                                                                               asset_view = global_config$asset_view,
                                                                               access_token = access_token,
-                                                                              base_url = global_config$api_base_url)
+                                                                              base_url = schematic_api_url)
 
   # DATASET SELECTION
 
   dataset_selection <- dfamodules::mod_dataset_selection_server(id = "dataset_selection_1",
                                                                 storage_project_df = select_storage_project_out,
                                                                 asset_view = global_config$asset_view,
                                                                 access_token = access_token,
-                                                                base_url = global_config$api_base_url)
+                                                                base_url = schematic_api_url)
 
   # UPDATE DATA FLOW STATUS SELECTIONS 
   updated_data_flow_status <- dfamodules::mod_update_data_flow_status_server("update_data_flow_status_1")
@@ -320,7 +315,7 @@ app_server <- function( input, output, session ) {
                                       dataset_id = global_config$manifest_dataset_id,
                                       manifest_dir = "./manifest",
                                       access_token = access_token,
-                                      base_url = global_config$api_base_url,
+                                      base_url = schematic_api_url,
                                       schema_url = global_config$schema_url)
 
 }
diff --git a/R/global.R b/R/global.R
@@ -1,4 +1,22 @@
-library(yaml)
+# READ IN CONFIG
+global_config <- jsonlite::read_json("inst/global.json")
+
+# GET SCHEMATIC API URL
+# If there is a config file, use that
+# Else use environment variables
+if ("schematic_api_url" %in% names(global_config)) {
+  schematic_api_url <- global_config$schematic_api_url
+} else {
+  schematic_api_url <- Sys.getenv("DFA_SCHEMATIC_API_URL")
+}
+
+# check that all variables are present
+if (is.null(schematic_api_url) || nchar(schematic_api_url) == 0) stop("missing DFA_SCHEMATIC_API_URL environmental variable")
+if (is.null(global_config$asset_view) || nchar(global_config$asset_view) == 0) stop("asset_view is missing from global.json")
+if (is.null(global_config$manifest_dataset_id) || nchar(global_config$manifest_dataset_id) == 0) stop("manifest_dataset_id is missing from global.json")
+if (is.null(global_config$schema_url) || nchar(global_config$schema_url) == 0) stop("schema_url is missing from global.json")
+
+message("DFA is using ", schematic_api_url)
 
 # SET UP OAUTH
 oauth_client <- yaml::yaml.load_file("oauth_config.yml")

diff --git a/inst/global.json b/inst/global.json
@@ -1,6 +1,5 @@
 {
     "asset_view": "syn50896957",
     "manifest_dataset_id": "syn50900267",
-    "schema_url": "https://raw.githubusercontent.com/Sage-Bionetworks/data_flow/main/inst/data_model/dataflow_component.jsonld",
-    "api_base_url": "https://schematic-staging.api.sagebionetworks.org"
+    "schema_url": "https://raw.githubusercontent.com/Sage-Bionetworks/data_flow/main/inst/data_model/dataflow_component.jsonld"
 }
diff --git a/renv.lock b/renv.lock
@@ -111,6 +111,16 @@
       ],
       "Hash": "e8a22846fff485f0be3770c2da758713"
     },
+    "assertthat": {
+      "Package": "assertthat",
+      "Version": "0.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "tools"
+      ],
+      "Hash": "50c838a310445e954bc13f26f26a6ecf"
+    },
     "attempt": {
       "Package": "attempt",
       "Version": "0.3.1",
@@ -415,14 +425,14 @@
     },
     "dfamodules": {
       "Package": "dfamodules",
-      "Version": "23.05.4",
+      "Version": "23.06.1",
       "Source": "GitHub",
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteUsername": "Sage-Bionetworks",
       "RemoteRepo": "dfamodules",
-      "RemoteRef": "main",
-      "RemoteSha": "f752696c312c55213847b6f355e8e71a1a5ab33f",
+      "RemoteRef": "v23.06.1",
+      "RemoteSha": "b9aae411037b6c367c3147648397672b53dc8e46",
       "Requirements": [
         "DT",
         "dplyr",
@@ -439,7 +449,7 @@
         "shinyjs",
         "waiter"
       ],
-      "Hash": "c731727e2e4c768b015ffe9eb465f2aa"
+      "Hash": "7fa1b0d1960ea992c07eed141875d46f"
     },
     "diffobj": {
       "Package": "diffobj",
@@ -1064,6 +1074,13 @@
       ],
       "Hash": "0f7cd2962e3044bb940cca4f4b5cecbe"
     },
+    "parsedate": {
+      "Package": "parsedate",
+      "Version": "1.3.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "7f5024cc7af45eeecef657fa62beb568"
+    },
     "patchwork": {
       "Package": "patchwork",
       "Version": "1.1.2",
@@ -1345,6 +1362,13 @@
       ],
       "Hash": "b5047343b3825f37ad9d3b5d89aa1078"
     },
+    "rematch": {
+      "Package": "rematch",
+      "Version": "1.0.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "c66b930d20bb6d858cd18e1cebcfae5c"
+    },
     "rematch2": {
       "Package": "rematch2",
       "Version": "2.1.2",
@@ -1379,6 +1403,36 @@
       ],
       "Hash": "4543b8cd233ae25c6aba8548be9e747e"
     },
+    "rhub": {
+      "Package": "rhub",
+      "Version": "1.1.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R6",
+        "assertthat",
+        "callr",
+        "cli",
+        "crayon",
+        "desc",
+        "digest",
+        "httr",
+        "jsonlite",
+        "parsedate",
+        "pillar",
+        "prettyunits",
+        "processx",
+        "rappdirs",
+        "rcmdcheck",
+        "rematch",
+        "tibble",
+        "utils",
+        "uuid",
+        "whoami",
+        "withr"
+      ],
+      "Hash": "e0880f6783f720d136755fb92d63c78b"
+    },
     "rlang": {
       "Package": "rlang",
       "Version": "1.1.1",
@@ -1821,6 +1875,16 @@
       ],
       "Hash": "1fe17157424bb09c48a8b3b550c753bc"
     },
+    "uuid": {
+      "Package": "uuid",
+      "Version": "1.1-0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "f1cb46c157d080b729159d407be83496"
+    },
     "vctrs": {
       "Package": "vctrs",
       "Version": "0.6.2",
@@ -1907,6 +1971,18 @@
       "Repository": "CRAN",
       "Hash": "c6abfa47a46d281a7d5159d0a8891e88"
     },
+    "whoami": {
+      "Package": "whoami",
+      "Version": "1.3.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "httr",
+        "jsonlite",
+        "utils"
+      ],
+      "Hash": "ef0f4d9b8f2cc2ebeccae1d725b8a023"
+    },
     "withr": {
       "Package": "withr",
       "Version": "2.5.0",