fix tests and slack error

Author: alexvpickering

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dseqr
 Type: Package
 Title: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations
-Version: 0.36.0
+Version: 0.37.0
 Authors@R: person("Alex", "Pickering", email="[email protected]", role=c("cre", "aut"))
 BugReports: https://github.com/hms-dbmi/dseqr/issues
 URL: https://github.com/hms-dbmi/dseqr

NAMESPACE

@@ -28,6 +28,7 @@ export(run_dseqr)
 export(run_kb_scseq)
 export(scPage)
 export(scPageUI)
+export(send_slack_error)
 export(theme_dimgray)
 export(theme_no_xaxis)
 export(theme_no_yaxis)

R/recover_error.R

@@ -1,7 +1,14 @@
 
-send_slack_error <- function(project) {
+#' Send shiny errors to slack
+#'
+#' @param project The project that the error originated from
+#' @param user The user that the error originated from
+#'
+#' @return Generates an alert in browser
+#' @export
+#'
+send_slack_error <- function(project, user) {
 
-    user <- Sys.getenv('SHINYPROXY_USERNAME', 'localhost')
     project <- ifelse(project == user, 'private', project)
     error <- recover_error()
     slack <- readRDS(system.file('extdata/slack.rds', package = 'dseqr'))

R/run_dseqr.R

@@ -2,8 +2,8 @@
 #'
 #' Run dseqr application to explore single-cell and bulk RNA-seq datasets.
 #'
-#' @param user_name Name of user folder in \code{data_dir}. Will be created if doesn't exist.
-#' @param data_dir Directory containing user folders. By default also will contain folders
+#' @param app_name Name of user folder in \code{data_dir}. Will be created if doesn't exist.
+#' @param data_dir Directory containing app folders. By default also will contain folders
 #'  \code{.pert_query_dir}, \code{.pert_signature_dir}, and \code{.indices_dir}.
 #' @param tabs Character vector of tabs to include in order desired. Must be subset of 'Single Cell', 'Bulk Data', and 'Drugs'.
 #' @param pert_query_dir Path to directory where pert query results (using CMAP02/L1000 as query signature) will be downloaded as requested.
@@ -61,13 +61,9 @@ run_dseqr <- function(app_name,
     data_dir <- '/srv/dseqr'
   }
 
-
   # gather options
   opts <- list()
 
-  # on remote: send errors to slack
-  if (!is_local) opts$shiny.error <- function() send_slack_error(app_name)
-
   # allow up to 30GB uploads
   opts$shiny.maxRequestSize <- 30*1024*1024^2
 
@@ -91,14 +87,6 @@ run_dseqr <- function(app_name,
 
   if (missing(data_dir)) stop('data_dir not specified.')
 
-  # user_dir <- file.path(data_dir, app_name)
-  # if (!dir_exists(user_dir)) init_dseqr(app_name, data_dir)
-
-  # ensure various directories exist
-  # duplicated in server.R for tests
-  app_dirs <- c(pert_query_dir, pert_signature_dir, indices_dir, tx2gene_dir, gs_dir)
-  for (dir in app_dirs) dir.create(dir, showWarnings = FALSE)
-
   # pass arguments to app through options then run
   shiny::shinyOptions(
     data_dir = normalizePath(data_dir),

inst/app/server.R

@@ -66,13 +66,14 @@ get_num_bulk_datasets <- function(project, user_dir) {
 
 server <- function(input, output, session) {
 
+
   # get arguments from calling function
   # defaults for testing
   # shiny::shinyOptions don't make it through
 
   # base directory contains data_dir folder
   app_name <- getShinyOption('app_name', 'test_app')
-  data_dir <- getShinyOption('data_dir', 'tests/testthat/test_data_dir/')
+  data_dir <- getShinyOption('data_dir', 'tests/testthat/test_data_dir')
 
   # path where pert queries will be stored
   pert_query_dir <- getShinyOption('pert_query_dir', file.path(data_dir, '.pert_query_dir'))
@@ -92,11 +93,26 @@ server <- function(input, output, session) {
   is_example <- getShinyOption('is_example', FALSE)
   is_local <- getShinyOption('is_local', TRUE)
 
+  # reset testing data
+  if (isTRUE(getOption('shiny.testmode'))) {
+    unlink(data_dir, recursive = TRUE)
+    dir.create(data_dir, recursive = TRUE)
+  }
+
   # ensure various directories exist
-  # duplicated here and in run_dseqr for tests
   app_dirs <- c(pert_query_dir, pert_signature_dir, indices_dir, tx2gene_dir, gs_dir)
   for (dir in app_dirs) dir.create(dir, showWarnings = FALSE)
 
+  # on remote: send errors to slack
+  if (!is_local) {
+    options(shiny.error = function() {
+      observe({
+        user_name <- user_name()
+        send_slack_error(app_name, user_name)
+      })
+    })
+  }
+
 
   # hide tour button for docs page
   observe(shinyjs::toggleClass('start_tour', 'invisible', condition = input$tab == 'Docs'))
@@ -106,19 +122,13 @@ server <- function(input, output, session) {
 
     # app_name is 'private'
     user_name <- session$request$HTTP_X_SP_USERID
-    print('user_name!!!!')
-    print(user_name)
     return(user_name)
   })
 
   user_dir <- reactive({
     user_name <- user_name()
     user_dir <- file.path(data_dir, user_name)
 
-    # reset testing data
-    if (isTRUE(getOption('shiny.testmode')))
-      unlink(data_dir, recursive = TRUE)
-
     if (!dir_exists(user_dir))
       init_dseqr(user_name, data_dir)
 

inst/app/tests/testthat/test-shinytest2.R

@@ -46,8 +46,9 @@ test_that("{shinytest2} recording: Single-Cell Tab", {
       load_timeout = timeout)
   )
 
-  list_files <- function()
+  list_files <- function() {
     file.path(data_dir, list.files(data_dir, recursive = TRUE, all.files = TRUE, include.dirs = TRUE))
+  }
 
   # created expected files/folders
   init_files <- list_files()