Add tests before Docker builds, general clean up (#2)

* clean up requirements * clean up lasso experiment remnants * sync package loading with req.txt file * fix checkInstalledPackages * clean up redundant code to check and install packages * clean up server.R * cleaned req.txt * clean up main directory * set up tests for mzML and Bruker file loading * add test that checks if processing was successful * activate GHA caching * update GHA to use versions instead of hashes * removed more left overs from LASSO experiment * remove library() calls from individual functions
CeMOS-Mannheim · May 28, 2024 · 4c26569 · 4c26569
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1 @@
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
@@ -1,28 +1,20 @@
 name: Docker
 
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-
 on:
   push:
-    branches: 
+    branches:
       - main
       - dev
-    # Publish semver tags as releases.
     tags: [ 'v*.*.*' ]
   pull_request:
-    branches: 
+    branches:
       - main
       - dev
 
 env:
-  # Use docker.io for Docker Hub if empty
   REGISTRY: docker.io
-  # github.repository as <account>/<repo>
   IMAGE_NAME: thomasenzlein/m2ara
-
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
 jobs:
   build:
@@ -31,51 +23,73 @@ jobs:
     permissions:
       contents: read
       packages: write
-      # This is used to complete the identity challenge
-      # with sigstore/fulcio when running outside of PRs.
       id-token: write
 
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      # Install the cosign tool except on PR
-      # https://github.com/sigstore/cosign-installer
-      - name: Install cosign
-        if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@6e04d228eb30da1757ee4e1dd75a0ec73a653e06 #v3.1.1
+      # Set up R environment
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
         with:
-          cosign-release: 'v2.1.1'
+          r-version: '4.4.0'
+
+      # Install system dependencies for R packages
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get -y install libcurl4-openssl-dev libssl-dev libxml2-dev build-essential libxml2-dev libgit2-dev libudunits2-dev librsvg2-dev tk libharfbuzz-dev libfribidi-dev
+
+      # Install R package dependencies from req.txt
+      - name: Install R packages from req.txt
+        run: |
+          R -e "install.packages('devtools')"
+          R -e "devtools::install_github('CeMOS-Mannheim/MALDIcellassay')"
+          R -e "packages <- readLines('req.txt'); install.packages(packages)"
 
-      # Set up BuildKit Docker container builder to be able to build
-      # multi-platform images and export cache
-      # https://github.com/docker/setup-buildx-action
+      # Install testthat if it's not listed in req.txt
+      - name: Install testthat
+        run: R -e "if (!require('testthat')) install.packages('testthat')"
+
+      # Run tests
+      - name: Run tests
+        run: R -e "source('tests/testthat.R')"
+
+      # This step will be skipped if the tests fail
+      # Set up Docker Buildx
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+        uses: docker/setup-buildx-action@v3.3.0
 
-      # Login against a Docker registry except on PR
-      # https://github.com/docker/login-action
       - name: Log into registry ${{ env.REGISTRY }}
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        uses: docker/login-action@v3.1.0
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ secrets.dockeriouser }}
           password: ${{ secrets.dockeriopwd }}
 
-      # Extract metadata (tags, labels) for Docker
-      # https://github.com/docker/metadata-action
+      - name: Create cache directory
+        run: mkdir -p /tmp/.buildx-cache
+
+      - name: Cache Docker layers
+        id: cache-docker-layers
+        uses: actions/cache@v4.0.2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+           ${{ runner.os }}-buildx-
+
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        uses: docker/metadata-action@v5.5.1
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
-      # Build and push Docker image with Buildx (don't push on PR)
-      # https://github.com/docker/build-push-action
       - name: Build and push Docker image
         id: build-and-push
-        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        uses: docker/build-push-action@v5.3.0
         with:
           context: .
           push: ${{ github.event_name != 'pull_request' }}

diff --git a/Dockerfile b/Dockerfile
@@ -1,25 +1,23 @@
 # Base image https://hub.docker.com/u/rocker/
 FROM rocker/shiny-verse:latest
 
-# copy necessary files
-## renv.lock file
-#COPY ./renv.lock ./renv.lock
-## app folder
-COPY ./ ./app
+RUN apt-get update && apt-get install -y \
+    sudo \
+    libudunits2-dev \
+    librsvg2-dev \
+    tk
 
-# install renv
-#RUN Rscript -e 'install.packages("renv")'
+# Copy the req.txt file to the Docker image
+COPY req.txt /req.txt
 
-# set renv library path
-#ENV RENV_PATHS_LIBRARY renv/library
+# Install R packages from req.txt
+RUN R -e "packages <- readLines('/req.txt'); install.packages(packages)"
 
-# restore packages
-#RUN Rscript -e 'renv::restore()'
+# Install the MALDIcellassay from GitHub
+RUN R -e "devtools::install_github('CeMOS-Mannheim/MALDIcellassay')"
 
-# install main package
-RUN Rscript -e 'install.packages("devtools")'
-RUN Rscript -e 'devtools::install_github("CeMOS-Mannheim/MALDIcellassay")'
-RUN Rscript -e 'source("/app/install_packages.R")'
+## copy app folder into container
+COPY ./ ./app
 
 # expose port
 EXPOSE 3838

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-<img src="M2ara_Logo.png" alt="M²ara overview" width="100" height="100">
+<img src="figures/M2ara_Logo.png" alt="M²ara overview" width="100" height="100">
 
 # M²ara - MALDI MS Bioassays Evaluation and Classification App
 

diff --git a/Workflow_figure.png b/Workflow_figure.png
diff --git a/app.R b/app.R
@@ -1,48 +1,6 @@
-(function(req_file, install = T, update = F, silent = F) {
-
-  # Read text file containing required packages
-  if(!file.exists("req.txt")) {
-    warning("req.txt was not found. No packages installed or checked.")
-    return()
-  }
-
-  req <- scan(req_file, character(), quiet = T)
-
-  # Update packages
-  if (update) {
-    update.packages(repos = "https://cloud.r-project.org", ask = F)
-  }
-
-  # Install missing packages
-  if (length(req) > 0 & install) {
-    missing_packages <- req[!(req %in% installed.packages()[,"Package"])]
-    if (length(missing_packages) > 0) {
-      install.packages(
-        missing_packages,
-        repos = "https://cloud.r-project.org",
-        dependencies = T,
-        clean = T
-      )
-    }
-  }
-
-
-
-  # Load packages
-  if (silent) {
-    suppressPackageStartupMessages(invisible(lapply(req, library, character.only = T)))
-  } else {
-    lapply(req, library, character.only = T)
-  }
-
-
-})("req.txt", silent = F)
-
-
 # check if all required packages are installed
-
 source("functions/checkInstalledPackages.R")
-checkInstalledPackages()
+checkInstalledPackages(req_file = "req.txt")
 
 knit("manual.Rmd", quiet = TRUE)
 

diff --git a/components/lassoTab.R b/components/lassoTab.R
diff --git a/components/mainpanel.R b/components/mainpanel.R
@@ -1,7 +1,6 @@
 source("components/mainTab.R")
 source("components/qcTab.R")
 source("components/pcaTab.R")
-source("components/lassoTab.R")
 source("components/hcTab.R")
 
 appMainPanel <- function(defaults) {

diff --git a/components/qcTab.R b/components/qcTab.R
@@ -18,7 +18,6 @@ qcTab <- function() {
                                             "Selected-mz",
                                             "PC-x",
                                             "PC-y",
-                                            "LASSO-error",
                                             "Outlier-mz",
                                             "Outlier-all"),
                                 multiple = FALSE,