Add CI/CD Pipeline (#1)

* feat: docker build (#1) * fix: switch branch to master * fix: add renv lock * fix: udpate the docker file * functional shiny app (#2) Co-authored-by: zoey-rw <[email protected]> * fix: update packages * fix: update dependencies * fix: downgrade shiny * fix: add conflict management * fix: add conflict package * fix: update conflicted * feat: test this app.R file * fix: use older app file * feat: add docker compose * added docker compose. need to run python clean scripts before running init.sql * updated init file * delete node files * feat: add production docker compose * fix: remove DS Store file * fix: remove DS store file * feat: add deployment hook --------- Co-authored-by: zoey-rw <[email protected]> Co-authored-by: Asad <[email protected]>
hicsail · Nov 25, 2024 · 2e071bd · 2e071bd
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -0,0 +1,74 @@
+name: Build & Deploy
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - comets_shinyapp_example/**
+    branches:
+      - master
+  pull_request:
+    paths:
+      - comets_shinyapp_example/**
+    branches:
+      - master
+
+jobs:
+  build:
+    permissions:
+      pages: write
+      id-token: write
+      contents: read
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: comets_shinyapp_example
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Login to Docker
+        uses: docker/login-action@v3
+        if: github.event_name != 'pull_request'
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Cache Docker layers
+        uses: actions/cache@v4
+        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@v5
+        with:
+          images: hicsail/comets_shinyapp
+          tags: |
+            type=ref,event=branch
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v6
+        with:
+          context: ./comets_shinyapp_example
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Push to Production
+        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+        uses: fjogeleit/http-request-action@v1
+        with:
+          method: "POST"
+          url: ${{ secrets.PORTAINER_WEBHOOK }}
+          preventFailureOnNoResponse: true
diff --git a/comets_shinyapp_example/Dockerfile b/comets_shinyapp_example/Dockerfile
@@ -0,0 +1,58 @@
+# Use the official R image as a base
+FROM rocker/shiny:4
+
+# Set environment variables to reduce interactive prompts during installation
+ENV DEBIAN_FRONTEND=noninteractive
+
+# system libraries of general use
+## install debian packages
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+    libxml2-dev \
+    libcairo2-dev \
+    libsqlite3-dev \
+    libmariadbd-dev \
+    libpq-dev \
+    libssh2-1-dev \
+    unixodbc-dev \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libfreetype6-dev \
+    libpng-dev \
+    libtiff5-dev \
+    libjpeg-dev
+
+
+## update system libraries
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get clean
+
+
+# Install necessary R packages
+COPY ./renv.lock /renv.lock
+
+RUN Rscript -e 'install.packages("renv")'
+RUN Rscript -e 'renv::restore()'
+
+
+# Copy the app files into the image
+COPY ./app.R /srv/shiny-server/app.R
+COPY ./species_abundance_filt.csv /srv/shiny-server/species_abundance_filt.csv
+COPY ./organism_data_to_subset.csv /srv/shiny-server/organism_data_to_subset.csv
+COPY ./organism_data_to_print.csv /srv/shiny-server/organism_data_to_print.csv
+COPY ./nlcd_key.csv /srv/shiny-server/nlcd_key.csv
+COPY ./organism_taxonomy.csv /srv/shiny-server/organism_taxonomy.csv
+
+# Set permissions for the shiny-server directory
+RUN chown -R shiny:shiny /srv/shiny-server
+
+# Expose the Shiny app port
+EXPOSE 3838
+
+# Switch to the 'shiny' user to improve security
+USER shiny
+
+# Run the Shiny app
+CMD ["R", "-e", "shiny::runApp('/srv/shiny-server', host = '0.0.0.0', port = 3838)"]
diff --git a/comets_shinyapp_example/docker-compose-production.yml b/comets_shinyapp_example/docker-compose-production.yml
@@ -0,0 +1,21 @@
+version: '3.9'
+
+services:
+  shiny:
+    image: hicsail/comets_shinyapp:master
+    container_name: soil_shiny_app
+    ports:
+      - "3838:3838"
+    restart: unless-stopped
+  postgres:
+    image: postgres:13
+    container_name: soil_db
+    env_file: ../stack.env
+    ports:
+      - "3839:5432"
+    restart: unless-stopped
+    volumes:
+      - soil-volume:/var/lib/postgresql/data
+
+volumes:
+  soil-volume: ~
diff --git a/comets_shinyapp_example/docker-compose.yml b/comets_shinyapp_example/docker-compose.yml
@@ -0,0 +1,20 @@
+version: '3.9'
+
+services:
+  shiny:
+    build: .
+    #image: hicsail/comets_shinyapp:master
+    container_name: shiny_app
+    ports:
+      - "3838:3838"
+    restart: unless-stopped
+  postgres:
+    image: postgres:13
+    container_name: postgres
+    environment:
+      POSTGRES_USER: shiny
+      POSTGRES_PASSWORD: password
+      POSTGRES_DB: shiny
+    ports:
+      - "5432:5432"
+    restart: unless-stopped
diff --git a/comets_shinyapp_example/renv.lock b/comets_shinyapp_example/renv.lock
@@ -0,0 +1,67 @@
+{
+  "R": {
+    "Version": "4.4.1",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://mirror.las.iastate.edu/CRAN"
+      }
+    ]
+  },
+  "Packages": {
+    "shiny": {
+      "Package": "shiny",
+      "Version": "1.8.1.1",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "data.table": {
+      "Package": "data.table",
+      "Version": "1.16.2",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "tidyverse": {
+      "Package": "tidyverse",
+      "Version": "2.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "DT": {
+      "Package": "DT",
+      "Version": "0.33",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "renv": {
+      "Package": "renv",
+      "Version": "1.0.11",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "ggplot2": {
+      "Package": "ggplot2",
+      "Version": "3.5.1",
+      "Source": "Repository",
+      "Repository": "CRAN"
+    },
+    "shinydashboard": {
+        "Package": "shinydashboard",
+        "Version": "0.7.2",
+        "Source": "Repository",
+        "Repository": "CRAN"
+    },
+    "shinyhelper": {
+        "Package": "shinyhelper",
+        "Version": "0.3.2",
+        "Source": "Repository",
+        "Repository": "CRAN"
+    },
+    "conflicted": {
+        "Package": "conflicted",
+        "Version": "0.1.2",
+        "Source": "Repository",
+        "Repository": "CRAN"
+    }
+  }
+}
diff --git a/microbe-sql-compose/data/clean_organism_taxonomy.py b/microbe-sql-compose/data/clean_organism_taxonomy.py
@@ -0,0 +1,16 @@
+import pandas as pd
+
+# Load the CSV file
+input_file = "organism_taxonomy.csv"
+output_file = "cleaned_organism_taxonomy.csv"
+
+# Read the CSV into a DataFrame
+df = pd.read_csv(input_file)
+
+# Replace "NA" with None (interpreted as NULL in PostgreSQL)
+df.replace("NA", None, inplace=True)
+
+# Save the cleaned DataFrame to a new CSV file
+df.to_csv(output_file, index=False)
+
+print(f"Cleaned CSV saved to {output_file}")
diff --git a/microbe-sql-compose/data/clean_species_abundance_filt.py b/microbe-sql-compose/data/clean_species_abundance_filt.py
@@ -0,0 +1,16 @@
+import pandas as pd
+
+# Input and output file paths
+input_file = "species_abundance_filt.csv"
+output_file = "cleaned_species_abundance_filt.csv"
+
+# Load the CSV into a pandas DataFrame
+df = pd.read_csv(input_file)
+
+# Replace "NA" or any invalid placeholder with None (interpreted as NULL in PostgreSQL)
+df.replace("NA", None, inplace=True)
+
+# Save the cleaned DataFrame to a new CSV file
+df.to_csv(output_file, index=False)
+
+print(f"Cleaned CSV saved to {output_file}")