Set shinytest for MetaShARK.

earnaud · Aug 23, 2021 · 2d7e1a3 · 2d7e1a3
1 parent acd4349
commit 2d7e1a3
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Showing 13 changed files with 463 additions and 158 deletions.
diff --git a/R/app_header.R b/R/app_header.R
@@ -19,31 +19,51 @@
   assign("wip", .args$wip, main.env)
 
   # Paths ====
-  wwwPaths <- system.file("resources", package = "MetaShARK")
-  wwwPaths <- paste(wwwPaths, dir(wwwPaths), sep = "/") |>
+  wwwPaths <- system.file("resources", package = "MetaShARK") |>
+    dir(full.names = TRUE) |>
     as.list()
   names(wwwPaths) <- basename(unlist(wwwPaths))
+
+  HOME <- if(isTRUE(getOption("shiny.testmode")))
+    system.file("../tests/testthat/app/tests/shinytest/test_data_package/", package = "MetaShARK") else
+      "~/dataPackagesOutput/emlAssemblyLine"
   PATHS <- reactiveValues(
-    home = "~",
-    eal.dp = paste0("~/dataPackagesOutput/emlAssemblyLine/"),
-    eal.dp.index = paste0("~/dataPackagesOutput/emlAssemblyLine/index.txt"),
+    home = HOME,
+    eal.dp = sprintf(
+      "%s/",
+      HOME
+    ),
+    eal.dp.index =sprintf(
+      "%s/index.txt",
+      HOME
+    ),
     eal.tmp = tempdir(),
     resources = wwwPaths
   )
-  dir.create(isolate(PATHS$eal.dp), recursive = TRUE, showWarnings = FALSE)
+  if(!isTRUE(getOption("shiny.testmode")))
+    dir.create(isolate(PATHS$eal.dp), recursive = TRUE, showWarnings = FALSE)
   dir.create(isolate(PATHS$eal.tmp), recursive = TRUE, showWarnings = FALSE)
 
   assign("PATHS", PATHS, envir = main.env)
 
   # Sessionning ====
 
-  if (isTRUE(file.exists(isolate(PATHS$eal.dp.index)))) {
-    DP.LIST <- data.table::fread(isolate(PATHS$eal.dp.index), sep = "\t")
+  if(isTRUE(getOption("shiny.testmode"))) {
+    devmsg(tag = "test", "setting DP list")
+    DP.LIST <- data.frame(
+      creator = character(),
+      name = character(),
+      title = character(),
+      path = character(),
+      stringsAsFactors = FALSE
+    )
+  } else if (isTRUE(file.exists(isolate(PATHS$eal.dp.index)))) {
+    DP.LIST <- readDataTable(isolate(PATHS$eal.dp.index), sep = "\t")
     DP.LIST$path <- DP.LIST$path |>
       gsub(pattern = "//+", replacement = "/")
   } else {
     DP.LIST <- data.frame(
-      creator.orcid = character(),
+      creator = character(),
       name = character(),
       title = character(),
       path = character(),
@@ -56,8 +76,8 @@
       sapply(.files, function(.file) {
         .info <- jsonlite::read_json(
           sprintf(
-            "%s/%s.json", 
-            .file, 
+            "%s/%s.json",
+            .file,
             basename(.file) |>
               gsub(pattern = "_emldp$", replacement = "")
           )
@@ -81,18 +101,25 @@
     isolate(main.env$PATHS$eal.dp),
     pattern = "_emldp$",
     full.names = TRUE
-  ) |> gsub(pattern = "//+", replacement = "/")
+  ) |> 
+    gsub(pattern = "//+", replacement = "/")
   DP.LIST <- dplyr::filter(DP.LIST, path %in% .actual.index)
-
+  # save actual index
   data.table::fwrite(DP.LIST, isolate(PATHS$eal.dp.index), sep = "\t")
 
   assign("DP.LIST", DP.LIST, envir = main.env)
   makeReactiveBinding("DP.LIST", env = main.env)
 
   # Values ====
+  # DataONE nodes
+  .ENDPOINTS <- readDataTable(
+    wwwPaths$registeredEndpoints.txt
+  )
+
   assign(
     "VALUES",
     reactiveValues(
+      dataone.endpoints = .ENDPOINTS,
       thresholds = reactiveValues(
         files.size.max = 500000
       ),
@@ -101,8 +128,6 @@
     envir = main.env
   )
   # Formats ====
-  # DataONE nodes
-  .DATAONE.LIST <- data.table::fread(wwwPaths$dataoneCNodesList.txt)
 
   # Taxa authorities
   .TAXA.AUTHORITIES <- data.table::fread(wwwPaths$taxaAuthorities.txt)
@@ -142,7 +167,6 @@
         "hh:mm:ss", "hh:mm", "mm:ss", "hh"
       ),
       units = .units,
-      dataone.list = .DATAONE.LIST,
       taxa.authorities = .TAXA.AUTHORITIES
     ),
     envir = main.env

diff --git a/R/app_server.R b/R/app_server.R
@@ -8,6 +8,7 @@ server <- function(input, output, session) {
   # get variables
   args <- get("metashark.args", envir = .GlobalEnv)
   main.env <- .globalScript(.args = args, envir = session$userData)
+  addResourcePath("media", system.file("media/", package = "MetaShARK"))
 
   # Set user-specific data
   assign(
@@ -61,17 +62,6 @@ server <- function(input, output, session) {
 
   # Update values ====
   invisible({
-    # DataONE nodes
-    .DATAONE.LIST <- if(!main.env$dev) 
-      try(dataone::listFormats(dataone::CNode())) else
-        try(silent = TRUE)
-    if (class(.DATAONE.LIST) != "try-error") {
-      .DATAONE.LIST <- readDataTable(
-        isolate(main.env$PATHS$resources$dataoneCNodesList.txt)
-      )
-      isolate(main.env$dataone.list <- .DATAONE.LIST)
-    }
-
     # Taxa authorities
     .TAXA.AUTHORITIES <- if(!main.env$dev)
       try(taxonomyCleanr::view_taxa_authorities()) else

diff --git a/R/app_ui.R b/R/app_ui.R
@@ -10,6 +10,8 @@ ui <- function() {
   # get app arguments
   # main.env <- get("main.env", options()$metashark.env)
 
+  addResourcePath("media", system.file("media/", package = "MetaShARK"))
+
   # prepare variable
   .menu.width <- "250px"
   # ShinyJS extension -- unused
@@ -46,7 +48,7 @@ ui <- function() {
       h2("Loading..."),
       shinydashboardPlus::loadingState(),
       tags$img(
-        src = "media/sea_shark.png",
+        src = "media/sea_shark.png", 
         width = "473px",
         height = "235px"
       )

diff --git a/R/eal_1_SelectDP.R b/R/eal_1_SelectDP.R
@@ -97,7 +97,7 @@ SelectDPUI <- function(id) {
           textInput(
             NS(id, "dp_name"),
             "Data package name",
-            placeholder = paste0(Sys.Date(), "_project")
+            placeholder = "my_project"
           ),
           textInput(
             NS(id, "dp_title"),
@@ -304,8 +304,10 @@ SelectDP <- function(id, main.env) {
     )
 
     observeEvent(input$quick, {
-      req(input$dp_name %in% c("", paste0(Sys.Date(), "_project"))) # Do not change a yet changed name
-      if (input$quick) {
+      req(input$dp_name %in% c("", "my_project", paste0(Sys.Date(), "_project"))) # Do not change a yet changed name
+      if(isTRUE(getOption("shiny.testmode"))) {
+        updateTextInput(session, "dp_name", value = "my_project")
+      } else if (input$quick) {
         updateTextInput(session, "dp_name", value = paste0(Sys.Date(), "_project"))
       } else {
         updateTextInput(session, "dp_name", placeholder = paste0(Sys.Date(), "_project"))

diff --git a/R/runMetashark.R b/R/runMetashark.R
@@ -96,6 +96,7 @@ runMetashark <- function(...) {
       )
     })
   } else if(isTRUE(args$use.test)) {
+    options("shiny.testmode" = TRUE)
     shinyApp(ui = ui, server = server)
   } else {
     runApp(

diff --git a/...hinytest/test_metashark-expected/001.json → .../shinytest/app_launches-expected/001.json b/...hinytest/test_metashark-expected/001.json → .../shinytest/app_launches-expected/001.json
@@ -26,7 +26,6 @@
     "fill-Miscellaneous-additional.information-file": null,
     "fill-Miscellaneous-methods-content": "<p><br><\/p>",
     "fill-Miscellaneous-methods-file": null,
-    "fill-Miscellaneous-Miscs": null,
     "fill-Miscellaneous-temporal_coverage": [
       null,
       null
@@ -38,7 +37,7 @@
     "fill-SelectDP-dp_delete": 0,
     "fill-SelectDP-dp_list": "",
     "fill-SelectDP-dp_load": 0,
-    "fill-SelectDP-dp_name": "2021-08-16_project",
+    "fill-SelectDP-dp_name": "my_project",
     "fill-SelectDP-dp_title": "",
     "fill-SelectDP-license": "CCBY",
     "fill-SelectDP-quick": true,
@@ -67,15 +66,13 @@
     "settings-help-metacat-link": 0,
     "settings-metacat_token": "",
     "settings-orcid-help-link": 0,
-    "sidemenu": "upload",
     "sn-checkbox-open-in-new-window": true,
     "test_end": 0,
     "upload": "upload",
     "upload-action": "upload",
     "upload-data": null,
-    "upload-dev": 0,
     "upload-DP": "---",
-    "upload-endpoint": "PNDB (dev)",
+    "upload-endpoint": "cn",
     "upload-metadata": null,
     "upload-online_dp": "",
     "upload-process": 0,

diff --git a/...shinytest/test_metashark-expected/001.png → ...s/shinytest/app_launches-expected/001.png b/...shinytest/test_metashark-expected/001.png → ...s/shinytest/app_launches-expected/001.png
diff --git a/tests/testthat/app/tests/shinytest/app_launches.R b/tests/testthat/app/tests/shinytest/app_launches.R
@@ -0,0 +1,4 @@
+app <- ShinyDriver$new("../../")
+app$snapshotInit("app_launches")
+
+app$snapshot()
diff --git a/tests/testthat/app/tests/shinytest/datafile_1.tsv b/tests/testthat/app/tests/shinytest/datafile_1.tsv
@@ -0,0 +1,113 @@
+Id	density_boats	distance_coast	percentage_turbidity	nb_individual	recorder	min_t	max_wind
+ID1	0	7.083851986	1	1	13740	9	13
+ID2	0	5.057419245	1	1	3760	11.7	15
+ID3	0	14.81271925	1	1	17598	9	13
+ID4	23.38130966	17.39474876	0	1	17607	12.8	24
+ID5	0	13.8788222	1	1	17608	14.3	17
+ID6	0	20.55593297	1	1	13733	20	17
+ID7	0	5.228906117	1	1	10250	14.3	30
+ID8	0	8.18336163	0.963336783	2	13740	11.7	15
+ID9	0	14.77478497	1	1	13733	11.7	15
+ID10	0	18.23789045	1	1	17573	9	13
+ID11	0	30.97770737	0.934057759	2	17608	8.1	13
+ID12	0	14.72135785	0	2	13733	8.1	13
+ID13	0	26.97792869	1	1	17578	8.1	13
+ID14	0	8.63834361	1	1	17329	11.7	15
+ID15	23.42372625	2.371250707	0.611485317	2	17232	14.3	30
+ID16	0	2.058590657	1	1	NA	11.7	15
+ID17	0	14.5557442	1	1	11693	14.3	17
+ID18	0	15.31628381	0.484376584	2	10250	14.2	9
+ID19	22.68310089	18.12266606	1	1	13733	16.9	13
+ID20	0	10.71630644	0.946424061	2	17608	NA	NA
+ID21	0	7.492501839	1	1	17608	14.3	30
+ID22	0	2.455167732	1	1	17578	8.1	13
+ID23	0	0.215005092	0.619357094	2	17608	13.3	0
+ID24	0	20.5942275	0.530977409	2	17573	12.8	24
+ID25	0	0.00565931	1	1	10250	9	13
+ID26	0	4.61669024	1	1	3760	8.1	13
+ID27	0	0.650746944	1	1	13289	NA	NA
+ID28	11.55094443	4.256523462	0.534748923	2	17608	17.4	15
+ID29	25.29249263	0.333785924	0	3	11693	16.9	13
+ID30	5.659985665	3.927116342	1	1	17578	16.9	13
+ID31	0	0.011314137	0	2	13740	20	17
+ID32	0	6.724401426	0.262229612	3	17578	8.5	7
+ID33	0	10.20546782	0.456408314	2	13676	17.8	13
+ID34	0	0.005662514	1	1	13289	9	13
+ID35	0	12.50424544	1	1	13733	13.3	0
+ID36	41.24173899	0.028288543	0	2	17607	NA	NA
+ID37	0	0.707453733	0	2	13733	17.8	13
+ID38	7.278017273	8.411585021	0.521433594	2	17601	17.4	15
+ID39	26.46665163	3.174693	1	1	17598	11.7	15
+ID40	21.65723654	8.846001472	0.672489759	2	17232	9	13
+ID41	0	7.296088753	0.033790965	2	17601	9	13
+ID42	0	0.848848396	0	3	17608	17.4	14
+ID43	0	17.47693701	1	1	NA	8.1	13
+ID44	0	8.040770102	1	1	17329	8.1	13
+ID45	0	9.227200724	1	1	17607	8.1	13
+ID46	0	4.089829166	0	1	17607	17.4	15
+ID47	16.24258106	12.9081546	0.519677866	2	17232	14.3	17
+ID48	0	28.17682685	0	3	13733	14.2	9
+ID49	0	11.13752122	0.568145458	2	17329	12.8	24
+ID50	0	12.15482119	0.744442086	2	13676	17.4	14
+ID51	0	1.075147125	0.126547756	2	17329	17.8	13
+ID52	0	0.639429606	0.318501019	3	17573	17.8	13
+ID53	0	11.34563151	1	1	13289	9	13
+ID54	0	6.070721358	1	1	11693	8.1	13
+ID55	0	2.534940304	1	1	3760	NA	NA
+ID56	0	0	1	1	17608	14.9	13
+ID57	23.6734518	9.73526417	1	1	13733	14.9	13
+ID58	22.77461434	2.30834512	0	2	3760	17.4	15
+ID59	0	9.034849513	1	1	NA	14.3	30
+ID60	0	1.61299451	1	1	17598	8.1	13
+ID61	0	1.550212164	1	1	17601	8.1	13
+ID62	16.6417688	0.198064626	1	1	13676	13.3	0
+ID63	0	0.147167035	0.503759276	2	13740	14.9	13
+ID64	0	1.126075147	1	1	17329	14.2	9
+ID65	0	1.166213768	0.486555056	2	10250	17.4	14
+ID66	0	37.17890687	0.241246715	3	11693	12.3	11
+ID67	0	1.01318843	1	1	NA	11.7	15
+ID68	0	14.97426034	0.513275979	3	17578	8.5	7
+ID69	0	0.050933786	1	1	10250	13.3	0
+ID70	0	1.60733488	1	1	11693	13.3	0
+ID71	0	0.15274085	0.616607437	2	11693	14.9	13
+ID72	0	4.745186863	0.427826338	3	17578	14.9	13
+ID73	0	0.005658029	1	1	13289	17.4	15
+ID74	20.10097018	1.120479882	1	1	17329	9	13
+ID75	0	1.833512535	1	1	11693	9	13
+ID76	0	1.964892412	1	1	3760	14.9	13
+ID77	0	1.024508972	1	1	17598	13.3	0
+ID78	13.02008677	2.446206116	0	2	17601	17.8	13
+ID79	0	5.849408836	0.506514891	2	17601	12.3	11
+ID80	0	0.82602546	1	1	17607	20	17
+ID81	0	6.632335465	1	1	13733	17.8	13
+ID82	9.774097667	2.083923212	0.147137616	2	17329	17.4	14
+ID83	0	0.843046283	1	1	17598	11.7	15
+ID84	0	17.16743054	1	1	3760	9	13
+ID85	0	2.347816248	1	1	17607	13.3	0
+ID86	0	2.089467724	1	1	17608	8.1	13
+ID87	14.70497236	1.782279054	1	1	17329	8.1	13
+ID88	0	1.828267391	1	1	10250	8.1	13
+ID89	19.54258479	2.829334541	1	1	3760	14.3	30
+ID90	22.89867383	0.50376408	1	1	17573	14.3	30
+ID91	0	7.486419194	1	1	13676	14.2	9
+ID92	0	4.612337295	1	1	17601	11.7	15
+ID93	0	20.34521788	1	1	17232	11.7	15
+ID94	0	13.69731259	0.558754442	2	13289	14.3	17
+ID95	0	0.481041313	0.601822162	2	17607	14.3	17
+ID96	0	19.55721647	0.856473518	3	17232	16.9	13
+ID97	0	9.467489106	1	1	10250	17.4	15
+ID98	0	22.78746039	0.460271388	3	11693	14.3	30
+ID99	0	8.380520951	0.769578171	2	17607	9	13
+ID100	32.43763517	0.486507892	0.297384797	4	17573	12.3	11
+ID101	39.87341993	18.47598574	0.377696294	3	17329	NA	NA
+ID102	0	1.482655198	0.420523151	2	17598	NA	NA
+ID103	0	1.188455008	1	1	13289	8.1	13
+ID104	0	2.981949867	1	1	17232	13.3	0
+ID105	6.048310547	0.06224536	1	1	17578	17.4	14
+ID106	0	0.067957866	1	1	17232	17.4	14
+ID107	0	0.305516266	0	1	17598	17.4	14
+ID108	0	1.375212224	0.512278187	2	17601	20	17
+ID109	23.18323585	0.045282164	0.355925541	2	13676	17.4	14
+ID110	0	0	0.599181014	2	17232	13.3	0
+ID111	0	0.050922259	1	1	17329	14.9	13
+ID112	0	0.763920326	1	1	13740	13.3	0