Merge pull request #378 from MEDomics-UdeS/scalability

THE V1 MERGE

.eslintignore

@@ -0,0 +1,16 @@
+.vscode/*
+app/*
+flask_server/*
+main/*
+node_modules/*
+WorkspaceTemplate/*
+ressources/*
+*.md
+*.json
+*.yml
+*.cmd
+*.sh
+.eslintrc.js
+next.config.js
+*/utilities/fileManagementUtils.js
+

.eslintrc.js

@@ -0,0 +1,25 @@
+module.exports = {
+  env: {
+    browser: true,
+    es2021: true
+  },
+  extends: ["eslint:recommended", "plugin:react/recommended", "next"],
+  parserOptions: {
+    ecmaVersion: "latest",
+    sourceType: "module"
+  },
+  plugins: ["react"],
+  rules: {
+    camelcase: ["error"],
+    "quote-props": ["error", "consistent"],
+    "react/prop-types": ["off"],
+    "no-mixed-spaces-and-tabs": ["error", "smart-tabs"],
+    "react/no-unescaped-entities": "off",
+    "@next/next/no-page-custom-font": "off",
+    "react-hooks/exhaustive-deps": "off",
+    "@next/next/no-img-element": "off",
+    "jsx-a11y/role-supports-aria-props": "off",
+    "@next/next/no-img-element": "off",
+    "react/no-direct-mutation-state": "off",
+  },
+}

.github/workflows/automaticBuilding.yml

@@ -0,0 +1,352 @@
+name: Full build and publish with versioning
+on:
+  push:
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+permissions:
+  contents: write
+jobs:
+  build-windows:
+    runs-on: windows-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0 # Fetch full history for branches
+
+      - name: Checking out the correct branches for submodules
+        run: |
+          git submodule foreach '
+          if [ "$name" = "pythonCode/submodules/MEDimage" ]; then
+            git fetch origin && git checkout -B dev_lab origin/dev_lab && git pull origin dev_lab
+          elif [ "$name" = "pythonCode/submodules/MEDprofiles" ]; then
+            git fetch origin && git checkout -B fusion_MEDomicsLab origin/fusion_MEDomicsLab && git pull origin fusion_MEDomicsLab
+          else
+            echo "No branch specified for $name"
+          fi
+          '
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: 18.13
+
+      - name: Get tag name
+        shell: bash
+        run: |
+          VERSION=${GITHUB_REF/refs\/tags\//} # Remove "refs/tags/" from the beginning of the tag name 
+          NEW_VERSION="${VERSION}"
+          node -p "let pkg=require('./package.json'); pkg.version='$NEW_VERSION'; require('fs').writeFileSync('package.json', JSON.stringify(pkg, null, 2));"
+
+      - name: Print package.json
+        run: Get-Content package.json
+
+      - name: Install dependencies
+        run: npm install
+
+      - name: Setup Go
+        uses: actions/setup-go@v4
+        with:
+          go-version: 1.21
+
+      - name: Build go
+        run: |
+          cd go_server
+          go build main.go 
+          cd ..
+
+      - name: Prebuild libmongocrypt
+        run: bash ./utilScripts/libmongocrypt_prebuild.sh
+
+      - name: Build for Windows
+        run: npm run build:win
+
+      - name: Get tag name
+        id: get-tag
+        shell: bash
+        run: |
+          VERSION=${GITHUB_REF/refs\/tags\//}
+          echo "::set-output name=VERSION::${VERSION#v}"
+
+      - name: Archive Windows
+        uses: actions/upload-artifact@v3
+        with:
+          name: windows-built
+          path: ./build/dist/MEDomicsLab-${{ env.VERSION }}-win.exe
+        env:
+          VERSION: ${{ steps.get-tag.outputs.VERSION }}
+
+  build-linux-ubuntu:
+    runs-on: ubuntu-20.04
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0 # Fetch full history for branches
+
+      - name: Checking out the correct branches for submodules
+        run: |
+          git submodule foreach '
+          if [ "$name" = "pythonCode/submodules/MEDimage" ]; then
+            git fetch origin && git checkout -B dev_lab origin/dev_lab && git pull origin dev_lab
+          elif [ "$name" = "pythonCode/submodules/MEDprofiles" ]; then
+            git fetch origin && git checkout -B fusion_MEDomicsLab origin/fusion_MEDomicsLab && git pull origin fusion_MEDomicsLab
+          else
+            echo "No branch specified for $name"
+          fi
+          '
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: 18.13
+
+      - name: Get tag name
+        run: |
+          VERSION=${GITHUB_REF/refs\/tags\//}
+          NEW_VERSION="${VERSION}"
+          node -p "let pkg=require('./package.json'); pkg.version='$NEW_VERSION'; require('fs').writeFileSync('package.json', JSON.stringify(pkg, null, 2));"
+
+      - name: Print package.json
+        run: cat package.json
+
+      - name: Install dependencies
+        run: npm install
+
+      - name: Setup Go
+        uses: actions/setup-go@v4
+        with:
+          go-version: 1.21
+
+      - name: Build go
+        run: |
+          cd go_server
+          go build main.go 
+          cd ..
+
+      - name: Prebuild libmongocrypt
+        run: bash ./utilScripts/libmongocrypt_prebuild.sh
+
+      - name: Build for Linux
+        run: npm run build:linux
+
+      - name: Get tag name
+        id: get-tag
+        run: |
+          VERSION=${GITHUB_REF/refs\/tags\//}
+          echo "::set-output name=VERSION::${VERSION#v}"
+
+      - name: Rename Linux
+        run: mv ./build/dist/MEDomicsLab-${{ env.VERSION }}-linux.deb ./build/dist/MEDomicsLab-${{ env.VERSION }}-ubuntu.deb
+        env:
+          VERSION: ${{ steps.get-tag.outputs.VERSION }}
+
+      - name: Archive Linux
+        uses: actions/upload-artifact@v3
+        with:
+          name: linux-built-ubuntu
+          path: ./build/dist/MEDomicsLab-${{ env.VERSION }}-ubuntu.deb
+        env:
+          VERSION: ${{ steps.get-tag.outputs.VERSION }}
+
+  build-mac:
+    runs-on: macos-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0 # Fetch full history for branches
+
+      - name: Checking out the correct branches for submodules
+        run: |
+          git submodule foreach '
+          if [ "$name" = "pythonCode/submodules/MEDimage" ]; then
+            git fetch origin && git checkout -B dev_lab origin/dev_lab && git pull origin dev_lab
+          elif [ "$name" = "pythonCode/submodules/MEDprofiles" ]; then
+            git fetch origin && git checkout -B fusion_MEDomicsLab origin/fusion_MEDomicsLab && git pull origin fusion_MEDomicsLab
+          else
+            echo "No branch specified for $name"
+          fi
+          '
+          
+      - name: Setup Go
+        uses: actions/setup-go@v4
+        with:
+          go-version: 1.21
+
+      - name: Build go
+        run: |
+          cd go_server
+          go build main.go 
+          cd ..
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: 18.13
+
+      - name: Mac OS X with M1 chip
+        run: uname -m
+
+      - name: Install Python 2.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - name: Bash python 1st try
+        run: |
+          echo $PATH
+          python --version
+          which python
+      - name: Bash python 2nd try
+        run: |
+          echo $PATH
+          python --version
+          which python
+        shell: bash {0}
+      - name: Bash python 3rd try
+        run: |
+          echo $PATH
+          python --version
+          which python
+        shell: bash -l {0}
+
+      - name: Check if Python2.7 is installed
+        run: |
+          if ! which python2.7 > /dev/null; then
+            curl -O https://www.python.org/ftp/python/2.7.18/python-2.7.18-macosx10.9.pkg
+            sudo installer -pkg python-2.7.18-macosx10.9.pkg -target /
+          else
+            echo "Python 2.7 is already installed"
+          fi
+
+      - name: Install dependencies
+        run: npm install
+
+      - uses: actions/checkout@v4
+
+      - name: Cache node modules
+        id: cache-npm
+        uses: actions/cache@v3
+        env:
+          cache-name: cache-node-modules
+        with:
+          # npm cache files are stored in `~/.npm` on Linux/macOS
+          path: ~/.npm
+          key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/package-lock.json') }}
+          restore-keys: |
+            ${{ runner.os }}-build-${{ env.cache-name }}-
+            ${{ runner.os }}-build-
+            ${{ runner.os }}-
+
+      - if: ${{ steps.cache-npm.outputs.cache-hit != 'true' }}
+        name: List the state of node modules
+        continue-on-error: true
+        run: npm list
+
+      - name: Install dependencies
+        run: npm install
+
+      - name: Prebuild libmongocrypt
+        run: bash ./utilScripts/libmongocrypt_prebuild.sh
+
+      - name: Update version
+        run: |
+          node -p "let pkg=require('./package.json'); pkg.version='${GITHUB_REF/refs\/tags\//}'; require('fs').writeFileSync('package.json', JSON.stringify(pkg, null, 2));"
+          echo "Version updated to ${GITHUB_REF/refs\/tags\//}"
+
+      # Before building the app, allocate more memory to the shell
+      - name: Allocate more memory
+        run: export NODE_OPTIONS=--max-old-space-size=8192
+
+      - name: Build for Mac
+        run: npm run build:mac
+
+      - name: Get tag name
+        id: get-tag
+        run: |
+          VERSION=${GITHUB_REF/refs\/tags\//}
+          echo "::set-output name=VERSION::${VERSION#v}"
+
+      - name: Archive Mac
+        uses: actions/upload-artifact@v3
+        with:
+          name: mac-built
+          path: ./build/dist/MEDomicsLab-${{ env.VERSION }}-mac.pkg
+        env:
+          VERSION: ${{ steps.get-tag.outputs.VERSION }}
+
+  # Publish to GitHub
+  publish:
+    needs: [build-windows, build-linux-ubuntu, build-mac]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Download Windows
+        uses: actions/download-artifact@v3
+        with:
+          name: windows-built
+
+      - name: Download Linux Ubuntu
+        uses: actions/download-artifact@v3
+        with:
+          name: linux-built-ubuntu
+
+      - name: Download Mac
+        uses: actions/download-artifact@v3
+        with:
+          name: mac-built
+
+      - name: Install zip
+        run: sudo apt-get install zip
+
+      - name: Move files out of pythonEnv - to root
+        run: |
+          mv ./pythonEnv/requirements.txt ./requirements.txt
+          mv ./pythonEnv/requirements_mac.txt ./requirements_mac.txt
+          mv ./pythonEnv/conda_env_osx64.yml ./conda_env_osx64.yml
+          mv ./pythonEnv/create_conda_env_win.bat ./create_conda_env_win.bat
+          mv ./pythonEnv/create_conda_env_linux.sh ./create_conda_env_linux.sh
+          mv ./pythonEnv/create_conda_env_mac_yml.sh ./create_conda_env_mac_yml.sh
+          mv ./pythonEnv/create_conda_env_mac.sh ./create_conda_env_mac.sh
+          ls -R
+
+      - name: zip Windows
+        run: zip -r MEDomicsLab-PythonEnv-win.zip ./requirements.txt ./create_conda_env_win.bat
+
+      - name: zip Linux
+        run: zip -r MEDomicsLab-PythonEnv-linux.zip ./requirements.txt ./create_conda_env_linux.sh
+
+      - name: zip Mac
+        run: zip -r MEDomicsLab-PythonEnv-mac.zip ./create_conda_env_mac.sh ./requirements_mac.txt
+      - name: Get tag name
+        id: get-tag
+        run: |
+          VERSION=${GITHUB_REF/refs\/tags\//}
+          echo "::set-output name=VERSION::${VERSION#v}"
+
+      - name: Publish to GitHub
+        uses: softprops/action-gh-release@v1
+        with:
+          files: |
+            ./MEDomicsLab-${{ env.VERSION }}-win.exe
+            ./MEDomicsLab-${{ env.VERSION }}-ubuntu.deb
+            ./MEDomicsLab-${{ env.VERSION }}-mac.pkg
+          name: MEDomicsLab-${{ env.VERSION }}
+          body: |
+            MEDomicsLab-${{ env.VERSION }}
+            This is a full release of MEDomicsLab. This release includes the MEDomicsLab application and the Python environment.
+            Refer to the [Documentation](https://medomics-udes.gitbook.io/medomicslab-docs/)
+            ${{ github.ref }}
+          draft: true
+          prerelease: false
+          token: ${{ secrets.GITHUB_TOKEN }}
+        env:
+          VERSION: ${{ steps.get-tag.outputs.VERSION }}