ready to build image

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.github/workflows/deploy.yml

@@ -0,0 +1,88 @@
+name: Build
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+on: 
+  push:
+    branches:
+      - docker-container
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    outputs:
+      image_name: "${{ steps.meta.outputs.tags }}@${{ steps.build_push_action.outputs.digest }}"
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: build_push_action
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          push: true
+          provenance: false
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+#   scan:
+#       runs-on: ubuntu-latest
+#       needs: build-and-push-image
+#       steps:
+#         - uses: actions/checkout@v3
+#         - name: Scan image
+#           id: scan
+#           uses: anchore/[email protected]
+#           with:
+#             fail-build: false
+#             image: ${{needs.build-and-push-image.outputs.image_name}}
+#         - name: upload Anchore scan SARIF report
+#           uses: github/codeql-action/upload-sarif@v2
+#           with:
+#             sarif_file: ${{ steps.scan.outputs.sarif }}
+
+#  deploy:
+#    runs-on: ubuntu-latest
+#    needs: scan
+#  
+#    steps:
+#      - uses: actions/checkout@v3
+#        env:
+#          CG_USERNAME: ${{ secrets.CG_USERNAME }}
+#        if: ${{ env.CG_USERNAME }}
+#      - name: Deploy to cloud.gov
+#        uses: cloud-gov/cg-cli-tools@main
+#        env:
+#          CG_USERNAME: ${{ secrets.CG_USERNAME }}
+#        if: ${{ env.CG_USERNAME }}
+#        with: 
+#          cf_username: ${{ secrets.CG_USERNAME }}
+#          cf_password: ${{ secrets.CG_PASSWORD }}
+#          cf_org: ${{ secrets.CF_ORG }}
+#          cf_space: ${{ secrets.CF_SPACE }}
+#          command: cf delete Heat_CVD_UHI_Dashboard -f ; cf push -f manifest.yml

.github/workflows/deploy.yml.bak

@@ -0,0 +1,88 @@
+name: Build
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+on: 
+  push:
+    branches:
+      - docker-container
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    outputs:
+      image_name: "${{ steps.meta.outputs.tags }}@${{ steps.build_push_action.outputs.digest }}"
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: build_push_action
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          push: true
+          provenance: false
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+#   scan:
+#       runs-on: ubuntu-latest
+#       needs: build-and-push-image
+#       steps:
+#         - uses: actions/checkout@v3
+#         - name: Scan image
+#           id: scan
+#           uses: anchore/[email protected]
+#           with:
+#             fail-build: false
+#             image: ${{needs.build-and-push-image.outputs.image_name}}
+#         - name: upload Anchore scan SARIF report
+#           uses: github/codeql-action/upload-sarif@v2
+#           with:
+#             sarif_file: ${{ steps.scan.outputs.sarif }}
+
+#  deploy:
+#    runs-on: ubuntu-latest
+#    needs: scan
+#  
+#    steps:
+#      - uses: actions/checkout@v3
+#        env:
+#          CG_USERNAME: ${{ secrets.CG_USERNAME }}
+#        if: ${{ env.CG_USERNAME }}
+#      - name: Deploy to cloud.gov
+#        uses: cloud-gov/cg-cli-tools@main
+#        env:
+#          CG_USERNAME: ${{ secrets.CG_USERNAME }}
+#        if: ${{ env.CG_USERNAME }}
+#        with: 
+#          cf_username: ${{ secrets.CG_USERNAME }}
+#          cf_password: ${{ secrets.CG_PASSWORD }}
+#          cf_org: ${{ secrets.CF_ORG }}
+#          cf_space: ${{ secrets.CF_SPACE }}
+#          command: cf delete Heat_CVD_UHI_Dashboard -f ; cf push -f manifest.yml

.grype.yml

@@ -0,0 +1,3 @@
+ignore:
+  - package:
+      location: "/opt/shiny-server/node_modules/**"

Dockerfile

@@ -0,0 +1,47 @@
+# The image is based off of the rocker base image, which you can learn about here:
+# https://rocker-project.org/
+# The image is based off of ubuntu, but then runs a few scripts to install R and R shiny
+FROM rocker/shiny:latest
+
+# I added this label, though it doesn't do anything
+LABEL name=CBCS
+
+# I reset the ubuntu package mirror to the Oregon State open source lab, because at some point while I was working on this
+# the official ubuntu package mirror went offline, but this can probably be removed
+RUN sed -i -e 's/http:\/\/archive\.ubuntu\.com\/ubuntu\//http:\/\/ubuntu\.osuosl\.org\/ubuntu/' /etc/apt/sources.list
+
+# This part is the part that installs the system packages, usually needed for use in compiling some R package.
+# I just added packages to this list as I got errors
+RUN apt-get update && apt-get install -y \
+    libssl-dev \
+    libxml2-dev \
+    libgit2-dev \
+    default-jdk \
+    r-cran-rjava \
+    r-base-dev dh-r automake \
+    libharfbuzz-dev  libfribidi-dev \
+    libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
+    libgdal-dev \
+    libudunits2-dev \
+    cmake \
+    && apt-get clean
+
+# This sets the main path in the docker image to /app, which is a standard practice.
+WORKDIR /app
+
+# This is part copies in the renv dependency list
+# The reason this is copied in seperately is for caching. Docker if it sees the dependencies haven't changed doesn't have to spend
+# the time re-compiling everything
+COPY renv.lock renv.lock
+RUN mkdir -p renv
+COPY .Rprofile .Rprofile
+COPY renv/activate.R renv/activate.R
+COPY renv/settings.dcf renv/settings.dcf
+RUN Rscript -e 'install.packages("renv")'
+RUN Rscript -e 'renv::restore()'
+
+# This part copies in the rest of the project
+COPY . /app
+
+# This sets what is run when the docker image is run
+CMD ["Rscript", "run.R"]

Dockerfile.bak

@@ -0,0 +1,47 @@
+# The image is based off of the rocker base image, which you can learn about here:
+# https://rocker-project.org/
+# The image is based off of ubuntu, but then runs a few scripts to install R and R shiny
+FROM rocker/shiny:latest
+
+# I added this label, though it doesn't do anything
+LABEL name=MyPracticeApp1
+
+# I reset the ubuntu package mirror to the Oregon State open source lab, because at some point while I was working on this
+# the official ubuntu package mirror went offline, but this can probably be removed
+RUN sed -i -e 's/http:\/\/archive\.ubuntu\.com\/ubuntu\//http:\/\/ubuntu\.osuosl\.org\/ubuntu/' /etc/apt/sources.list
+
+# This part is the part that installs the system packages, usually needed for use in compiling some R package.
+# I just added packages to this list as I got errors
+RUN apt-get update && apt-get install -y \
+    libssl-dev \
+    libxml2-dev \
+    libgit2-dev \
+    default-jdk \
+    r-cran-rjava \
+    r-base-dev dh-r automake \
+    libharfbuzz-dev  libfribidi-dev \
+    libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
+    libgdal-dev \
+    libudunits2-dev \
+    cmake \
+    && apt-get clean
+
+# This sets the main path in the docker image to /app, which is a standard practice.
+WORKDIR /app
+
+# This is part copies in the renv dependency list
+# The reason this is copied in seperately is for caching. Docker if it sees the dependencies haven't changed doesn't have to spend
+# the time re-compiling everything
+COPY renv.lock renv.lock
+RUN mkdir -p renv
+COPY .Rprofile .Rprofile
+COPY renv/activate.R renv/activate.R
+COPY renv/settings.dcf renv/settings.dcf
+RUN Rscript -e 'install.packages("renv")'
+RUN Rscript -e 'renv::restore()'
+
+# This part copies in the rest of the project
+COPY . /app
+
+# This sets what is run when the docker image is run
+CMD ["Rscript", "run.R"]

app.R

@@ -3,7 +3,6 @@ library(deSolve)
 library(ggplot2)
 library(reshape2)
 library(scales)
-library(shiny)
 library(shinyBS)
 library(shinythemes)