Merge pull request #101 from FredHutch/dev

Adding server start time, table abbreviations, documentation links, and replica/stickiness fix

README.md

@@ -15,7 +15,7 @@ You can run this Shiny app locally. First you'll need to install required packag
 (note: run `make pkg_deps_cmd` to update the below code block)
 
 ```r
-pak::pak(c("getwilds/[email protected]", "getwilds/[email protected]", "base64enc", "cookies", "DBI", "dplyr", "DT", "ggplot2", "glue", "jsonlite", "lubridate", "magrittr", "purrr", "RColorBrewer", "rlang", "RSQLite", "shiny", "shinyBS", "shinydashboard", "shinydashboardPlus", "shinyFeedback", "shinyjs", "shinyWidgets", "tibble", "uuid"))
+pak::pak(c("getwilds/[email protected]", "getwilds/[email protected]", "dplyr", "DT", "ggplot2", "glue", "httr", "jsonlite", "lubridate", "magrittr", "memoise", "purrr", "rclipboard", "RColorBrewer", "rlang", "shiny", "shinyBS", "shinydashboard", "shinydashboardPlus", "shinyFeedback", "shinyjs", "shinylogs", "shinyvalidate", "shinyWidgets", "testthat", "tibble", "uuid"))
 ```
 
 And the above yourself in R. 

app/about.md

@@ -4,6 +4,7 @@ This is a [Shiny](https://shiny.posit.co/) app being developed by the [Fred Hutc
 At Fred Hutch, we offer a service for supporting the use of our on-premise HPC cluster to run WDL workflows called PROOF.  To use this app at Fred Hutch, choose the "PROOF Login" button at the top of the page and enter your Fred Hutch credentials to get started. 
 
 ### Resources
+- Get started with PROOF [How-To documentation](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) and [troubleshooting tips](https://sciwiki.fredhutch.org/dasldemos/proof-troubleshooting/)
 - Find curated WDL workflow repositories and containers in Fred Hutch [DaSL's getWILDS GitHub organization](https://github.com/orgs/getwilds/repositories?q=wdl).
 - Find Cromwell and WDL Resources in [Fred Hutch's GitHub organization](https://github.com/FredHutch?utf8=%E2%9C%93&q=wdl+OR+cromwell&type=&language=).
 - Learn about Cromwell and WDL on the [Fred Hutch Biomedical Data Science Wiki](https://sciwiki.fredhutch.org/compdemos/Cromwell/).

app/server.R

@@ -329,6 +329,7 @@ server <- function(input, output, session) {
   output$proofStatusServerTime <- proofStatusTextGenerator("Server time", "SERVERTIME", "PROOF server job lifetime")
   output$proofStatusUseAWS <- proofStatusTextGenerator("Use AWS?", "USE_AWS", "AWS credentials found?")
   output$proofStatusSlurmJobAccount <- proofStatusTextGenerator("Slurm job account", "SLURM_JOB_ACCOUNT", "Designated Gizmo PI account")
+  output$proofStatusServerStartTime <- proofStatusTextGenerator("PROOF Server Start Time", "jobStartTime")
 
   ###### Cromwell Validate tab ######
   ## Validate a possible workflow
@@ -813,13 +814,36 @@ server <- function(input, output, session) {
     )
   })
   ## Jobs Lists
-  output$tasklistBatch <- renderDT(
-    dplyr::mutate(callsUpdate(), dplyr::across(matches(c("start", "end")), as_pt)),
-    class = "compact",
-    filter = "top",
-    options = list(scrollX = TRUE),
-    rownames = FALSE
-  )
+  output$tasklistBatch <- renderDT({
+    datatable(
+      {
+        callsUpdate() %>%
+          dplyr::mutate(dplyr::across(matches(c("start", "end")), as_pt))
+      },
+      escape = FALSE,
+      selection = "single",
+      rownames = FALSE,
+      filter = "top",
+      options = list(
+        scrollX = TRUE,
+        columnDefs = list(
+          list(
+            targets = "_all",
+            render = JS(
+              "function(data, type, row, meta) {",
+                "if (data === null) {",
+                "return data;",
+                "} else {",
+                "return type === 'display' && data.length > 150 ?",
+                "'<span title=\"' + data + '\">' + data.substr(0, 150) + '...</span>' : data;",
+                "}",
+              "}"
+            )
+          )
+        )
+      )
+    )
+  })
 
   output$downloadJobs <- downloadHandler(
     filename = function() {

app/tab-servers.R

@@ -21,6 +21,7 @@ tab_servers <- tabItem(
       br(),
       br(),
       h5("Current PROOF server information (if live)"),
+      uiOutput("proofStatusServerStartTime"),
       uiOutput("proofStatusWorkflowLogDir"),
       uiOutput("proofStatusScratchDir"),
       uiOutput("proofStatusServerTime"),

app/ui.R

@@ -39,6 +39,8 @@ ui <- dashboardPage(
     sidebarMenuOutput("uiSideBar")
   ),
   dashboardBody(
+    tags$head(tags$title("PROOF")),
+    tags$script("document.title = 'PROOF';"),
     shinyjs::useShinyjs(),
     rclipboard::rclipboardSetup(),
     enter_to_click,

app/utils.R

@@ -65,3 +65,8 @@ make_copybtn <- function(x, clip_prefix, tooltip) {
     )
   )
 }
+
+abbreviate <- function(x, last = 100) {
+  if (nchar(x) < 100) return(x)
+  paste0(substring(x, 1, last), " ...")
+}

docker-compose-preview.yml

@@ -5,6 +5,7 @@ services:
       - proxy
     image: sc-registry.fredhutch.org/shiny-cromwell-preview:latest
     deploy:
+      replicas: 4
       restart_policy:
         condition: on-failure
       labels:
@@ -14,6 +15,8 @@ services:
         - "traefik.http.routers.shiny-cromwell-preview.entrypoints=web,web-secured"
         - "traefik.http.services.shiny-cromwell-preview.loadbalancer.server.port=3838" # it seems you always need to give traefik a port so it 'notices' the service
         - "traefik.http.routers.shiny-cromwell-preview.tls=true"
+        - "traefik.http.services.shiny-cromwell-preview.loadbalancer.sticky.cookie=true"
+        - "traefik.http.services.shiny-cromwell-preview.loadbalancer.sticky.cookie.name=my_sticky_cookie"
 
 
 networks:

docker-compose.yml

@@ -15,6 +15,8 @@ services:
         - "traefik.http.routers.shiny-cromwell.entrypoints=web,web-secured"
         - "traefik.http.services.shiny-cromwell.loadbalancer.server.port=3838" # it seems you always need to give traefik a port so it 'notices' the service
         - "traefik.http.routers.shiny-cromwell.tls=true"
+        - "traefik.http.services.shiny-cromwell.loadbalancer.sticky.cookie=true"
+        - "traefik.http.services.shiny-cromwell.loadbalancer.sticky.cookie.name=my_sticky_cookie"
 
 
   shiny-cromwell-redirect: