Codex/sidebar nav prototype

.github/workflows/docker-image.yml

@@ -7,27 +7,58 @@ on:
     branches: [ "main", "master" ]
 
 jobs:
-  build:
+  build-and-push:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - image_repo: sigrepo-mysql
+            context: mysql
+            dockerfile: mysql/Dockerfile
+            build_args: |
+              mysql_image=mysql:8.0-bookworm
+            tags_extra: ""
+          - image_repo: sigrepo-api
+            context: .
+            dockerfile: Dockerfile
+            build_args: |
+              R_VERSION=4.4.3
+              SIGREPO_BRANCH=master
+            tags_extra: |
+              ${{ secrets.DOCKERHUB_USERNAME }}/sigrepo-shiny:latest
+              ${{ secrets.DOCKERHUB_USERNAME }}/sigrepo-shiny:${{ github.sha }}
+              ${{ secrets.DOCKERHUB_USERNAME }}/sigrepo:latest
+              ${{ secrets.DOCKERHUB_USERNAME }}/sigrepo:${{ github.sha }}
 
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
 
       - name: Log in to Docker Hub
+        if: github.event_name == 'push'
         uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
-      - name: Build and push Docker image
+      - name: Build and push ${{ matrix.image_repo }}
         uses: docker/build-push-action@v5
         with:
-          context: .
-          push: true
+          context: ${{ matrix.context }}
+          file: ${{ matrix.dockerfile }}
+          build-args: ${{ matrix.build_args }}
+          platforms: linux/amd64,linux/arm64
+          push: ${{ github.event_name == 'push' }}
           tags: |
-            ${{ secrets.DOCKERHUB_USERNAME }}/sigrepo:latest
-            ${{ secrets.DOCKERHUB_USERNAME }}/sigrepo:${{ github.sha }}
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ matrix.image_repo }}:latest
+            ${{ secrets.DOCKERHUB_USERNAME }}/${{ matrix.image_repo }}:${{ github.sha }}
+            ${{ matrix.tags_extra }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

Dockerfile

@@ -1,11 +1,11 @@
 # Build according to a specified version of R
 ARG R_VERSION
-ARG R_VERSION=${R_VERSION:-4.5.0}
+ARG R_VERSION=${R_VERSION:-4.4.3}
 
 ############# Build Stage ##################
 
-# Get shiny+tidyverse+devtools packages from rocker image
-FROM rocker/shiny-verse:${R_VERSION} AS base
+# Use a multi-arch Rocker base.
+FROM rocker/r-ver:${R_VERSION} AS base
 
 # Build according to a specified version of R
 ARG SIGREPO_BRANCH
@@ -22,6 +22,12 @@ ARG DEBIAN_FRONTEND=noninteractive
 # Install system libraries of general use
 RUN apt-get update --allow-releaseinfo-change --fix-missing \
   && apt-get -y --no-install-recommends install \
+  build-essential \
+  pkg-config \
+  libcurl4-openssl-dev \
+  libssl-dev \
+  libxml2-dev \
+  default-libmysqlclient-dev \
   librsvg2-dev \
   libudunits2-dev \
   libv8-dev \
@@ -90,16 +96,16 @@ RUN Rscript "${SIGREPO_SERVER_DIR}/install_r_packages.R"
 RUN R -e "BiocManager::install('limma')"
 
 # Install OmicSignature 
-RUN R -e "devtools::install_github(repo = 'montilab/OmicSignature', dependencies = TRUE)"
+RUN R -e "remotes::install_github(repo = 'montilab/OmicSignature', dependencies = c('Depends','Imports','LinkingTo'))"
 
 # Install dependencies for OmicSignature 
 RUN R -e "BiocManager::install('biomaRt')"
 
 # Install SigRepo 
-RUN R -e "branch <- base::Sys.getenv('SIGREPO_BRANCH'); devtools::install_github(repo = 'montilab/SigRepo', ref = branch, dependencies = TRUE)"
+RUN R -e "branch <- base::Sys.getenv('SIGREPO_BRANCH'); remotes::install_github(repo = 'montilab/SigRepo', ref = branch, dependencies = c('Depends','Imports','LinkingTo'))"
 
 # Install hypeR 
-RUN R -e "devtools::install_github(repo = 'montilab/hypeR', dependencies = TRUE)"
+RUN R -e "remotes::install_github(repo = 'montilab/hypeR', dependencies = c('Depends','Imports','LinkingTo'))"
 
 # Expose app at port 3838
 EXPOSE 3838
@@ -121,5 +127,3 @@ RUN dos2unix ${SIGREPO_SERVER_DIR}/api/api-server.sh
 
 # Allow permissions to execute the bash script
 RUN chmod a+x ${SIGREPO_SERVER_DIR}/api/api-server.sh
-
-

docker-compose-build-version.yml

@@ -1,37 +1,37 @@
 x-sql-volume:
   &sql-volume
   type: bind
-  source: /Users/reinachau/mysql/database
+  source: /Users/cameronvicnaire/mysql/database
   target: /var/lib/mysql
 
 x-difexp-volume:
   &difexp-volume
   type: bind
-  source: /Users/reinachau/mysql/difexp
+  source: /Users/cameronvicnaire/mysql/difexp
   target: /difexp
 
 x-omic-signature-volume:
   &omic-signature-volume
   type: bind
-  source: /Users/reinachau/OmicSignature
+  source: /Users/cameronvicnaire/Documents/GitHub/OmicSignature
   target: /OmicSignature
 
 x-hyper-volume:
   &hyper-volume
   type: bind
-  source: /Users/reinachau/hypeR
+  source: /Users/cameronvicnaire/Documents/GitHub/hypeR
   target: /hypeR
 
 x-sigrepo-volume:
   &sigrepo-volume
   type: bind
-  source: /Users/reinachau/SigRepo
+  source: /Users/cameronvicnaire/Documents/GitHub/SigRepo
   target: /SigRepo  
 
 x-sigrepo-server-volume:
   &sigrepo-server-volume
   type: bind
-  source: /Users/reinachau/SigRepo_Server
+  source: /Users/cameronvicnaire/Documents/GitHub/SigRepo_Server
   target: /SigRepo_Server
 
 services:

install_r_packages.R

@@ -1,49 +1,55 @@
-
-# Create a list of start-up packages 
-startup_packages <- c("BiocManager", "dplyr", "rvest", "xml2", "yaml")
-
-# Select only the packages that aren't currently installed in the system
-install_startup_packages <- startup_packages[base::which(!startup_packages %in% utils::installed.packages())]
-
-# And finally we install the required packages
-for(pkg in install_startup_packages) utils::install.packages(pkg, dependencies=TRUE, repos='http://cran.rstudio.com/')
-
-# Load packages
-library(BiocManager)
-library(dplyr)
-library(rvest)
-library(xml2)
-library(yaml)
-
-# Get all available Bioconductor packages
-url <- 'https://www.bioconductor.org/packages/release/bioc/'
-biocPackages <- url |> 
-  xml2::read_html() |> 
-  rvest::html_table() |>
-  base::lapply(`[[`, "Package") |>
-  base::unlist()
-
-# Read in package dependencies in DESCRIPTION
-DESCRIPTION <- yaml::read_yaml("DESCRIPTION")
-
-# Extract all imports packages
-required_pkgs <- base::trimws(base::strsplit(DESCRIPTION$Imports, ",", fixed=TRUE)[[1]])
-
-# Extract all required bioconductor packages
-bioconductor_pkgs <- required_pkgs[base::which(required_pkgs %in% biocPackages)]
-
-# Select only the packages that aren't currently installed in the system
-install_bioconductor_pkgs <- bioconductor_pkgs[base::which(!bioconductor_pkgs %in% utils::installed.packages())]
-
-# And finally we install the required Bioconductor packages
-for(pkg in install_bioconductor_pkgs) BiocManager::install(pkg)
-
-# Extract all required CRAN packages
-cran_pkgs <- required_pkgs[base::which(!required_pkgs %in% bioconductor_pkgs)]
-
-# Select only the packages that aren't currently installed in the system
-install_cran_pkgs <- cran_pkgs[base::which(!cran_pkgs %in% utils::installed.packages())]
-
-# And finally we install the required packages including their dependencies
-for(pkg in install_cran_pkgs) utils::install.packages(pkg, dependencies = TRUE, repos='http://cran.rstudio.com/')
-
+repos <- "https://cloud.r-project.org"
+options(repos = c(CRAN = repos))
+
+install_if_missing <- function(pkgs) {
+  installed <- rownames(utils::installed.packages())
+  to_install <- setdiff(pkgs, installed)
+  if (length(to_install) > 0) {
+    utils::install.packages(
+      to_install,
+      dependencies = c("Depends", "Imports", "LinkingTo"),
+      repos = repos
+    )
+  }
+}
+
+# Minimal bootstrap only.
+bootstrap_pkgs <- c("BiocManager", "remotes", "yaml")
+install_if_missing(bootstrap_pkgs)
+
+# Parse DESCRIPTION (DCF format)
+desc <- read.dcf("DESCRIPTION")
+imports_field <- if ("Imports" %in% colnames(desc)) desc[1, "Imports"] else ""
+
+parse_pkg_names <- function(field) {
+  if (!nzchar(field)) return(character(0))
+  x <- unlist(strsplit(field, ",", fixed = TRUE), use.names = FALSE)
+  x <- trimws(gsub("\\s*\\(.*\\)", "", x))
+  x[x != ""]
+}
+
+required_pkgs <- unique(parse_pkg_names(imports_field))
+
+bioc_available <- tryCatch(BiocManager::available(), error = function(e) character(0))
+bioc_pkgs <- intersect(required_pkgs, bioc_available)
+cran_pkgs <- setdiff(required_pkgs, bioc_pkgs)
+
+if (length(cran_pkgs) > 0) {
+  install_if_missing(cran_pkgs)
+}
+
+if (length(bioc_pkgs) > 0) {
+  installed <- rownames(utils::installed.packages())
+  bioc_to_install <- setdiff(bioc_pkgs, installed)
+  if (length(bioc_to_install) > 0) {
+    BiocManager::install(bioc_to_install, ask = FALSE, update = FALSE)
+  }
+}
+
+installed <- rownames(utils::installed.packages())
+missing <- setdiff(required_pkgs, installed)
+if (length(missing) > 0) {
+  stop(sprintf("Failed to install required packages: %s", paste(missing, collapse = ", ")))
+}
+
+cat("Dependency install complete.\n")

mysql/Dockerfile

@@ -5,14 +5,23 @@ ARG mysql_image=${mysql_image:-mysql:8.0-bookworm}
 ############# Build Stage ##################
 FROM ${mysql_image} AS base
 
-# Install system libraries of general use
-RUN apt-get update --allow-releaseinfo-change --fix-missing \
-  && apt-get -y --no-install-recommends install \
-  vim \
-  curl \
-  && apt clean autoclean \
-  && apt autoremove --yes \
-	&& rm -rf /var/lib/{apt,dpkg,cache,log}/
+# Install small debug tools across distro variants used by mysql base images.
+RUN set -eux; \
+  if command -v apt-get >/dev/null 2>&1; then \
+    apt-get update --allow-releaseinfo-change --fix-missing; \
+    apt-get -y --no-install-recommends install vim curl; \
+    apt-get clean; \
+    rm -rf /var/lib/apt/lists/*; \
+  elif command -v microdnf >/dev/null 2>&1; then \
+    microdnf install -y vim-minimal curl; \
+    microdnf clean all; \
+  elif command -v yum >/dev/null 2>&1; then \
+    yum install -y vim-minimal curl; \
+    yum clean all; \
+  else \
+    echo "No supported package manager found in base image"; \
+    exit 1; \
+  fi
 
 # Expose mysql to host
-EXPOSE 3306 33060
+EXPOSE 3306 33060