[WIP] Start of testing the shiny app

.github/workflows/build.yml

@@ -14,7 +14,7 @@ env:
   has_testthat: 'true'
 #  run_covr: 'true' # Disabled until later
   run_covr: 'false'
-#  run_pkgdown: 'true' # Disabled until later 
+#  run_pkgdown: 'true' # Disabled until later
   run_pkgdown: 'false'
   has_RUnit: 'false'
   has_BiocCheck: 'false'
@@ -26,17 +26,18 @@ jobs:
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
-    
+
     # Define the matrix for different configurations
     strategy:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+#          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
 # Disabling additional architectures until later
 #          - { os: macOS-latest, r: 'next', bioc: '3.18'}
 #          - { os: windows-latest, r: 'next', bioc: '3.18'}
-    
+
     # Define environment variables for the job
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -100,7 +101,7 @@ jobs:
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
         run: |
-          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
+          sysreqs=$(Rscript -e 'cat("apt-get update -y && ", paste(remotes::system_requirements("ubuntu", "20.04"), collapse = " && "))')
           echo $sysreqs
           sudo -s eval "$sysreqs"
 
@@ -275,7 +276,13 @@ jobs:
         if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
-      # Step 25: Deploy package
+      # Step 25: Test Shiny App in package
+      - name: Test Shiny App
+        uses: rstudio/shinytest2/actions/test-app@actions/v1
+        with:
+          app-dir: "inst/MetFamily"
+
+      # Step 26: Deploy package
       - name: Deploy package
         if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
@@ -289,7 +296,7 @@ jobs:
         ## branch (erasing anything you haven't version controlled!) and
         ## makes the git history recognizable by pkgdown.
 
-      # Step 26: Upload check results
+      # Step 27: Upload check results
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@master

DESCRIPTION

@@ -34,7 +34,8 @@ Depends:
 Remotes: decisionpatterns/searchable
 Suggests:
     knitr,
-    testthat
+    testthat,
+    shinytest2
 VignetteBuilder: knitr
 Maintainer: Hendrik Treutler<[email protected]>
 Description: We present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide.

README.md

@@ -1,49 +1,50 @@
+[![build](https://github.com/ipb-halle/MetFamily/workflows/build/badge.svg)](https://github.com/ipb-halle/MetFamily/actions?query=workflow%3Abuild)
+
 # MetFamily
 Understanding metabolism is fundamental in biomedical and plant research and the identification and quantification of thousands of metabolites by mass spectrometry in modern metabolomics is a prerequisite for elucidating this area. However, the identification of metabolites is a major bottleneck in traditional approaches hampering advances. Here, we present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide.  MetFamily is available under http://msbi.ipb-halle.de/MetFamily/.
 
 # Docker images
-The image `sneumann/metfamily-base` contains all dependencies 
+The image `sneumann/metfamily-base` contains all dependencies
 for the MetFamily web application.
 
 ## Building the container(s)
 Build via `docker build -t sneumann/metfamily-base -f Dockerfile-base . `
 
-The image `sneumann/metfamily` is built on top and contains 
-the actual MetFamily code and web application. 
+The image `sneumann/metfamily` is built on top and contains
+the actual MetFamily code and web application.
 
 Build via `docker build -t sneumann/metfamily . `
 
 The build of the metfamily-base image https://hub.docker.com/r/sneumann/metfamily-base is triggerd whenever in the `master` branch a tag `basechange-<date>` e.g. `basechange-20190804` is specified.
 
 ## Running from a container
 
-To run the resulting container, start with 
+To run the resulting container, start with
 `docker run --rm -p 3838:3838 sneumann/metfamily:latest`
 
 and point your browser to http://localhost:3838/
 
 ## Developing and debugging in a container
 
-If you want to develop and debug stuff, you can build a container 
-on top of `metfamily:latest` that has an added rstudio server. 
+If you want to develop and debug stuff, you can build a container
+on top of `metfamily:latest` that has an added rstudio server.
 First build using `docker build -t metfamily-rstudio -f Dockerfile-rstudio .`
 and then run via `docker run -it --rm -p 8787:8787 metfamily-rstudio:latest`.
 CAVEAT: the `Dockerfile-rstudio` specifies a fixed user/password combo
 of `rstudio:rstudio`. Do not use in Production !
 
-You can also pass a local directory with checked out MetFamily git tree 
+You can also pass a local directory with checked out MetFamily git tree
 via the `docker run -v` argument.
 
 ## Running locally with MetFamily R Package
 
-After installing the `MetFamily` R package and its dependencies, you can 
+After installing the `MetFamily` R package and its dependencies, you can
 ```
 library(MetFamily)
 runApp(system.file("MetFamily", package="MetFamily"))
 ```
 
 ## Running through Kubernetes
 
-At IPB we are running MetFamily inside a Kubernetes cluster. 
+At IPB we are running MetFamily inside a Kubernetes cluster.
 Please contact us for questions.
-

inst/MetFamily/tests/testthat.R

@@ -0,0 +1 @@
+shinytest2::test_app()

inst/MetFamily/tests/testthat/_snaps/linux-4.3/shinytest2/MetFamilyLoadExample-002.json

@@ -0,0 +1,177 @@
+{
+  "input": {
+    "applyGlobalMS2filters": 0,
+    "applyHcaFilters": 0,
+    "applyPcaFilters": 0,
+    "applySearch": 0,
+    "changePlot": "Display HCA",
+    "changeSelection": "Selection by HCA/PCA",
+    "clearGlobalMS2filters": 0,
+    "clearHcaFilters": 0,
+    "clearPcaFilters": 0,
+    "clearSearch": 0,
+    "clearSelection": 0,
+    "confirmAnnotation": 0,
+    "displayImportParameters": false,
+    "doAnnotation": 0,
+    "doMs2PeakGroupDeisotoping": true,
+    "doMs2PeakGroupDeisotoping2": true,
+    "doPrecursorDeisotoping": true,
+    "doPrecursorDeisotoping2": true,
+    "downloadHcaImageType": "png",
+    "downloadPcaImageType": "png",
+    "drawHCAplots": 0,
+    "drawPCAplots": 0,
+    "fileInputSelection": "Example data",
+    "filterByPCAgroupSamples": false,
+    "globalFilter_ms2_masses1": "",
+    "globalFilter_ms2_masses2": "",
+    "globalFilter_ms2_masses3": "",
+    "globalFilter_ms2_ppm": "",
+    "hcaDistanceFunction": "Jaccard (intensity-weighted)",
+    "hcaFilterGroupOne": "",
+    "hcaFilterGroupTwo": "",
+    "hcaFilterIncludeIgnoredPrecursors": false,
+    "hcaFilter_average": "",
+    "hcaFilter_lfc": "",
+    "hcaPrecursorLabels": "m/z / RT",
+    "heatmapContent": "Log-fold-change",
+    "heatmapOrdering": "Specified order",
+    "importMs1Ms2Data": 0,
+    "importMs2Data": 0,
+    "importParameterFileInput": null,
+    "loadExampleData": 1,
+    "loadProjectData": 0,
+    "loadingsLabels": "None",
+    "matrixFile": null,
+    "maximumRtDifference": "0.05",
+    "maximumRtDifference2": "0.02",
+    "metaboliteFamilyComparisonClass": "[init]",
+    "minimumIntensityOfMaximalMS2peak": "2000",
+    "minimumIntensityOfMaximalMS2peak2": "2000",
+    "minimumProportionOfMS2peaks": "0.05",
+    "minimumProportionOfMS2peaks2": "0.05",
+    "ms1AnalysisMethod": "PCA (Principal Component Analysis)",
+    "ms1DataFile": null,
+    "ms2DataFile": null,
+    "mzDeviationAbsolute_grouping": "0.01",
+    "mzDeviationAbsolute_grouping2": "0.01",
+    "mzDeviationAbsolute_ms2PeakGroupDeisotoping": "0.01",
+    "mzDeviationAbsolute_ms2PeakGroupDeisotoping2": "0.01",
+    "mzDeviationAbsolute_precursorDeisotoping": "0.01",
+    "mzDeviationAbsolute_precursorDeisotoping2": "0.01",
+    "mzDeviationInPPM_grouping": "10",
+    "mzDeviationInPPM_grouping2": "10",
+    "mzDeviationInPPM_ms2PeakGroupDeisotoping": "10",
+    "mzDeviationInPPM_ms2PeakGroupDeisotoping2": "10",
+    "mzDeviationInPPM_precursorDeisotoping": "10",
+    "mzDeviationInPPM_precursorDeisotoping2": "10",
+    "neutralLossesFragmentsToFragments": false,
+    "neutralLossesFragmentsToFragments2": false,
+    "neutralLossesPrecursorToFragments": true,
+    "neutralLossesPrecursorToFragments2": true,
+    "newAnnotationColor": "#0000FF",
+    "newAnnotationColor2": "#0000FF",
+    "newAnnotationValue": "",
+    "newAnnotationValue2": "",
+    "pcaDimensionOne": "1",
+    "pcaDimensionTwo": "2",
+    "pcaFilterIncludeIgnoredPrecursors": false,
+    "pcaFilter_average": "",
+    "pcaFilter_lfc": "",
+    "pcaGroups": null,
+    "pcaLogTransform": false,
+    "pcaSamples": null,
+    "pcaScaling": "Pareto",
+    "precursorSelectionTabs": "Selection",
+    "prepareAllPrecursors": 0,
+    "presentAnnotationValue": "[init]",
+    "previousAnnotationValue": "Artifact",
+    "projectDescription": "",
+    "projectDescription2": "",
+    "projectName": "MetFamily project (created 2022-02-22_12.34.56.789)",
+    "projectName2": "",
+    "removeMetaboliteFamily": 0,
+    "removePresentAnnotation": 0,
+    "renameMetaboliteFamily": 0,
+    "runTabs": "Input",
+    "searchIncludeIgnoredPrecursors": false,
+    "searchMS1mass": "",
+    "searchMS1massPpm": "",
+    "searchMS1orMS2": "MS1 feature m/z",
+    "searchMS2massPpm": "",
+    "search_ms2_masses1": "",
+    "search_ms2_masses2": "",
+    "search_ms2_masses3": "",
+    "selectAllPCAGroups": 0,
+    "selectInvertedPCAGroups": 0,
+    "selectMetaboliteFamily": 0,
+    "selectNoPCAGroups": 0,
+    "selectedSpectrum": "",
+    "setPresentAnnotationPrimary": 0,
+    "showClusterLabels": true,
+    "showFragmentPlot": false,
+    "showHCAadvancedOptions": false,
+    "showHCAfilterOptions": true,
+    "showImportParameters": false,
+    "showImportParametersAdvanced": false,
+    "showLoadingsAbundance": false,
+    "showLoadingsFeatures": [
+      "Annotated",
+      "Not Annotated",
+      "Selected",
+      "Not Selected"
+    ],
+    "showPCAadvancedOptions": false,
+    "showPCAfilterOptions": true,
+    "showPlotControls": false,
+    "showScoresLabels": true,
+    "submitNewAnnotation": 0,
+    "submitPreviousAnnotation": 0,
+    "updateArtifactsFromCheckboxes": 0,
+    "updateProjectDescription": 0,
+    "updateSampleTable": 0
+  },
+  "output": {
+    "analysisType": "HCA",
+    "classifierClassMS1featureSelected": false,
+    "classifierClassSelected": false,
+    "classifierLoaded": false,
+    "fileInfo": "Please press 'Load example data' to load the full example data set",
+    "filterSearchActive": false,
+    "globalMS2filterValid": true,
+    "hcaFilterValid": true,
+    "metaboliteFamilySelected": false,
+    "pcaFilterValid": true,
+    "plotAnnotationShown": false,
+    "plotDendrogram_hover_info": null,
+    "plotHcaShown": false,
+    "plotHeatmap_hover_info": null,
+    "plotMS2_hover_info": null,
+    "plotPcaLoadings_hover_info": null,
+    "plotPcaScores_hover_info": null,
+    "plotPcaShown": false,
+    "precursorSetSelected": false,
+    "searchFilterValid": true,
+    "selectedSelection": null,
+    "selectionInfo": "Please select a cluster or MS¹ feature in the HCA plot",
+    "showAnnotationplotPanel": false,
+    "showGUI": true,
+    "showHCAplotPanel": false,
+    "showPCAplotPanel": false,
+    "showPutativeAnnotationsTableFromAnalysis": null,
+    "showSideBar": true,
+    "ui_plotAnnoLegendHCA": null,
+    "ui_plotAnnoLegendPCA": null,
+    "ui_plotHeatmap": {
+      "html": "<div class=\"shiny-plot-output html-fill-item\" data-hover-clip=\"TRUE\" data-hover-delay=\"50\" data-hover-delay-type=\"debounce\" data-hover-id=\"plotHeatmap_hover\" data-hover-null-outside=\"TRUE\" id=\"plotHeatmap\" style=\"width:100%;height:1px;\"><\/div>",
+      "deps": [
+
+      ]
+    },
+    "ui_plotScoresGroupsLegend": null
+  },
+  "export": {
+
+  }
+}

inst/MetFamily/tests/testthat/setup-shinytest2.R

@@ -0,0 +1,2 @@
+# Load application support files into testing environment
+shinytest2::load_app_env()

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

@@ -0,0 +1,10 @@
+library(shinytest2)
+
+test_that("{shinytest2} recording: MetFamilyLoadExample", {
+  app <- AppDriver$new(variant = platform_variant(), name = "MetFamilyLoadExample",
+      height = 1113, width = 1549)
+  #app$expect_screenshot()
+  app$set_inputs(fileInputSelection = "Example data")
+  app$click("loadExampleData")
+  app$expect_values(screenshot_args = FALSE)
+})

inst/MetFamily/ui.R

@@ -130,7 +130,11 @@ shinyUI(
                 conditionalPanel(
                   condition = 'input.fileInputSelection == "Import data"',
                   bsTooltip(id = "projectName", title = "Please type the name of the project", placement = "bottom", trigger = "hover"),
-                  textInput(inputId = "projectName", label = "Project name", value = paste("MetFamily project (created ", gsub(" ", "_", gsub(":", ".", Sys.time())), ")", sep = "")),
+                  # Temporarily use const date under testing, see https://github.com/rstudio/shinytest2/issues/300#issuecomment-1908500601
+                  textInput(inputId = "projectName", label = "Project name", 
+                            value = paste("MetFamily project (created ", gsub(" ", "_", gsub(":", ".", 
+                                                                                             ifelse(isFALSE(getOption("shiny.testmode")), Sys.time(), "2022-02-22_12.34.56.789")
+                                                                                             )), ")", sep = "")),
                   bsTooltip(id = "projectDescription", title = "Please type a description of this project as free text", placement = "bottom", trigger = "hover"),
                   tags$style(type="text/css", "textarea {width:100%}"),
                   tags$textarea(id = 'projectDescription', placeholder = 'Comments here', rows = 3, ""),