shiny-cromwell v1.2.0 Updates

.gitlab-ci.yml

@@ -18,13 +18,14 @@ stages:
   - build
   - test
   - deploy
+
 
 build:
   stage: build
   script: |
     python3 build_helper.py docker-compose.yml --fluentd-logging > /dev/null
     echo $DB_CONFIG | base64 -d > .my.cnf
-    docker build --no-cache \
+    docker build \
       -t sc-registry.fredhutch.org/shiny-cromwell:test \
       --build-arg CI_COMMIT_BRANCH=${CI_COMMIT_BRANCH} \
       --build-arg CI_COMMIT_SHA=${CI_COMMIT_SHA} \
@@ -48,18 +49,8 @@ test:
     # env
     # curl -si http://shiny-cromwell:3838/
     # docker logs $CONTAINER_ID
-    curl -sI http://shiny-cromwell:3838 | head -1 | grep -q "200 OK"
     docker run -w /srv/shiny-server --rm sc-registry.fredhutch.org/shiny-cromwell:test R -q -e 'testthat::test_dir("tests")'
-
-deploy_review_image:
-  stage: deploy
-  except:
-    refs:
-      - main
-      - dev
-  script:
-    - docker tag sc-registry.fredhutch.org/shiny-cromwell:test nexus-registry.fredhutch.org/scicomp-nexus/${CI_PROJECT_NAME}:${CI_COMMIT_BRANCH}
-    - docker push nexus-registry.fredhutch.org/scicomp-nexus/${CI_PROJECT_NAME}:${CI_COMMIT_BRANCH}
+    curl -sI http://shiny-cromwell:3838 | head -1 | grep -q "200 OK"
 
 deploy_review_image:
   stage: deploy

Dockerfile

@@ -1,15 +1,17 @@
-FROM fredhutch/r-shiny-server-base:4.3.2
+FROM fredhutch/r-shiny-server-base:4.4.1
 
 RUN apt-get update -y && apt-get install -y libssh-dev python3-pip git libmariadb-dev
 
 RUN R -q -e 'install.packages(c("ellipsis"), repos="https://cran.rstudio.com/")'
 RUN R -q -e 'install.packages(c("shiny"), repos="https://cran.rstudio.com/")'
-RUN R -q -e 'install.packages(c("shinyFeedback", "shinyWidgets", "shinydashboard", "shinydashboardPlus", "ssh", "remotes", "markdown", "lubridate", "jsonlite", "dplyr", "DT", "glue", "httr", "purrr", "RColorBrewer", "rlang", "shinyBS", "shinyjs", "tidyverse", "uuid", "memoise", "rclipboard", "shinyvalidate", "shinylogs", "testhat", "bsicons", "listviewer", "cookies", "RMariaDB", "DBI"), repos="https://cran.r-project.org")'
+RUN R -q -e 'install.packages(c("shinyFeedback", "shinyWidgets", "shinydashboard", "shinydashboardPlus", "ssh", "remotes", "markdown", "lubridate", "jsonlite", "dplyr", "DT", "glue", "httr", "purrr", "RColorBrewer", "rlang", "shinyBS", "shinyjs", "tidyverse", "uuid", "memoise", "rclipboard", "shinyvalidate", "shinylogs", "testhat", "bsicons", "listviewer", "htmltools", "cookies", "RMariaDB", "DBI", "parsedate", "testthat", "shinylogs", "ids", "shinycssloaders"), repos="https://cran.r-project.org")'
 
 RUN R -q -e "remotes::install_github('getwilds/[email protected]')"
 
 RUN R -q -e "remotes::install_github('getwilds/[email protected]')"
 
+RUN R -q -e "remotes::install_github('rstudio/bslib')"
+
 ADD .my.cnf /root/
 
 # python wdl2mermaid setup:

Makefile

@@ -4,7 +4,7 @@ DEPS := $(shell ${RSCRIPT} -e 'invisible(lapply(c("glue", "cli"), require, chara
 
 run:
 	${RSCRIPT} -e "options(shiny.autoreload = TRUE)" \
-		-e "shiny::runApp(\"app\", launch.browser = TRUE)"
+		-e "shiny::runApp(\"app\", launch.browser = TRUE, port = 4026)"
 
 run_docker:
 	docker build --platform linux/amd64 -t shiny-cromwell:app .

app/about.md

@@ -1,21 +1,18 @@
-This is a [Shiny](https://shiny.posit.co/) app being developed by the [Fred Hutch Data Science Lab, DaSL](https://hutchdatascience.org/) that simplifies user interactions with a [Cromwell](https://cromwell.readthedocs.io/en/stable/) server, an open source [WDL](https://openwdl.org/) workflow engine that can be used with a range of HPC backends. We are developing this application alongside Fred Hutch oriented infrastructure with the intention to develop open source resources to enable others to do the same. 
-
-## Fred Hutch Users
-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
+### Getting Help with PROOF and WDL at Fred Hutch
 - 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/)
+- Ask a question about or report a problem with PROOF in our [GitHub repository](https://github.com/getwilds/proof/issues/new?template=Blank+issue)
+- Email us at [[email protected]](mailto:[email protected])
 - 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/).
 - Join the community in the [#workflow-managers FH-Data Slack channel](https://fhdata.slack.com/archives/CJFP1NYSZ), (open to all Fred Hutch, UW and Seattle Children's staff using their work emails).
-- Get Help from Fred Hutch DaSL staff through [Data House Calls](https://hutchdatascience.org/datahousecalls/).
+- Get Help from Fred Hutch DaSL staff through [Data House Calls](https://calendly.com/data-house-calls/resources).
 
 
 ## Users Elsewhere
 This Shiny app and the R packages it relies on are all open source.  Thus, if you are at a different institution and want to use this application to support your work or your users, we encourage you to look through our resources and fork our repositories.  Feel free to contact DaSL developers by filing issues or emailing `[email protected]`. For this use case, we have provided the more general "DIY Cromwell" login button at the top. 
 
-### Resources
+### Some Resources for Using Cromwell
   - DIY: Get a Cromwell server running by yourself (does not require logging in). To learn more about how to get your Cromwell server running, read through the instructions in the GitHub repo [FredHutch/diy-cromwell-server](https://github.com/FredHutch/diy-cromwell-server)
 - `rcromwell`:  An [R package](https://github.com/getwilds/rcromwell) that makes interacting with the Cromwell API easier. 
 - `shiny-cromwell`:  This app's [GitHub repo](https://github.com/FredHutch/shiny-cromwell) contains information on how to set started with this application.  

app/buttons.R

@@ -2,14 +2,16 @@ logInButton <-
   actionButton(
     inputId = "proofAuth",
     label = "PROOF Login",
+    class = "btn-success btn-sm",
+    style = "color: white;",
     icon = icon("truck-fast")
 
   )
 logOutButton <-
   actionButton(
     inputId = "proofAuthLogout",
     label = "PROOF Logout",
-    class = "btn-danger",
+    class = "btn-danger btn-sm",
     style = "color: white;",
     icon = icon("arrow-right-to-bracket")
   )
@@ -18,13 +20,15 @@ logInCromwellButton <-
   actionButton(
     inputId = "ownCrom",
     label = "DIY Cromwell",
+    class = "btn-sm",
+    style = "color: white;",
     icon = icon("plug-circle-xmark")
   )
 logOutCromwellButton <-
   actionButton(
     inputId = "proofCromwellLogout",
     label = " Exit",
-    class = "btn-danger",
+    class = "btn-danger btn-sm",
     style = "color: white;",
     icon = icon("arrow-right-to-bracket")
   )

app/constants.R

@@ -0,0 +1 @@
+DAYS_WORKFLOW_HISTORY <- 120

app/modals.R

@@ -13,7 +13,11 @@ loginModal <- function(failed = FALSE, error = "Invalid username or password") {
     },
     footer = tagList(
       modalButton("Cancel"),
-      actionButton("submit", "Submit")
+      shinyFeedback::loadingButton(
+        inputId = "submit",
+        label = "Submit",
+        class = "btn btn-default"
+      )
     ),
     easyClose = TRUE
   )
@@ -67,21 +71,15 @@ verifyCromwellDeleteModal <- function(failed = FALSE, error = "Woops, an error!
     "Stop your PROOF server. Although you can't undo this action, you can start up another one anytime!",
     br(),
     br(),
-    textInput(
-      inputId = "stopCromwell",
-      label = div(HTML("To stop your server, confirm by typing<br> <em>delete me</em> into the field."))
-    ),
     if (failed) {
       div(tags$b(error, style = "color: red;"))
     },
     footer = tagList(
       modalButton("Cancel"),
-      shinyjs::disabled(
-        shinyFeedback::loadingButton(
-          inputId = "deleteCromwell",
-          label = "Stop Server",
-          class = "btn btn-warning"
-        )
+      shinyFeedback::loadingButton(
+        inputId = "deleteCromwell",
+        label = "Stop Server",
+        class = "btn btn-warning"
       )
     ),
     easyClose = TRUE