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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,37 @@ | ||
| // For format details, see https://aka.ms/devcontainer.json. For config options, see the README at: | ||
| // https://github.com/microsoft/vscode-dev-containers/tree/v0.224.2/containers/javascript-node-mongo | ||
| // Update the VARIANT arg in docker-compose.yml to pick a Node.js version | ||
| // For format details, see https://aka.ms/devcontainer.json. | ||
| // For config options, see the README at: | ||
| // https://github.com/devcontainers/templates/tree/main/src/javascript-node-mongo | ||
| { | ||
| "name": "Apollo", | ||
| "dockerComposeFile": "docker-compose.yml", | ||
| "service": "app", | ||
| "workspaceFolder": "/workspace", | ||
| "workspaceFolder": "/workspaces/${localWorkspaceFolderBasename}", | ||
|
|
||
| // Set *default* container specific settings.json values on container create. | ||
| "settings": {}, | ||
|
|
||
| // Add the IDs of extensions you want installed when the container is created. | ||
| "extensions": [ | ||
| "dbaeumer.vscode-eslint", | ||
| "mongodb.mongodb-vscode", | ||
| "arcanis.vscode-zipfs", | ||
| "eamodio.gitlens", | ||
| ], | ||
| // Features to add to the dev container. More info: https://containers.dev/features. | ||
| "features": { | ||
| "./git-autocomplete": "1.0.0", | ||
| }, | ||
| // Configure tool-specific properties. | ||
| "customizations": { | ||
| // Configure properties specific to VS Code. | ||
| "vscode": { | ||
| // Add the IDs of extensions you want installed when the container is created. | ||
| "extensions": [ | ||
| "dbaeumer.vscode-eslint", | ||
| "esbenp.prettier-vscode", | ||
| "mongodb.mongodb-vscode", | ||
| "arcanis.vscode-zipfs", | ||
| "eamodio.gitlens", | ||
| ], | ||
| }, | ||
| }, | ||
|
|
||
| // Use 'forwardPorts' to make a list of ports inside the container available locally. | ||
| "forwardPorts": [3999, 27017], | ||
|
|
||
| // Use 'postCreateCommand' to run commands after the container is created. | ||
| "postCreateCommand": "yarn install && mongosh --eval 'try {rs.initiate();} catch {}'", | ||
| "postCreateCommand": "yarn install --immutable && mongosh --eval 'try {rs.initiate();} catch {}'", | ||
|
|
||
| // Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root. | ||
| "remoteUser": "node" | ||
| // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root. | ||
| // "remoteUser": "root" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| { | ||
| "name": "Git Autocomplete", | ||
| "id": "git-autocomplete", | ||
| "version": "1.0.0", | ||
| "description": "Enable git autocomplete in the shell", | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,13 @@ | ||
| #!/usr/bin/env bash | ||
| UPDATE_RC="${UPDATE_RC:-"true"}" | ||
| AUTOCOMPLETE_SOURCE="source /usr/share/bash-completion/completions/git" | ||
|
|
||
| if [ "${UPDATE_RC}" = "true" ]; then | ||
| echo "Updating /etc/bash.bashrc and /etc/zsh/zshrc..." | ||
| if [[ "$(cat /etc/bash.bashrc)" != *"${AUTOCOMPLETE_SOURCE}"* ]]; then | ||
| echo -e "${AUTOCOMPLETE_SOURCE}" >> /etc/bash.bashrc | ||
| fi | ||
| if [ -f "/etc/zsh/zshrc" ] && [[ "$(cat /etc/zsh/zshrc)" != *"${AUTOCOMPLETE_SOURCE}"* ]]; then | ||
| echo -e "${AUTOCOMPLETE_SOURCE}" >> /etc/zsh/zshrc | ||
| fi | ||
| fi |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| name: Deploy to demo server | ||
|
|
||
| on: | ||
| workflow_call: | ||
| inputs: | ||
| environment: | ||
| required: true | ||
| type: string | ||
| workflow_dispatch: | ||
| inputs: | ||
| environment: | ||
| description: Environment to deploy | ||
| type: environment | ||
| required: true | ||
|
|
||
| jobs: | ||
| build: | ||
| name: Build and upload | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Check out | ||
| uses: actions/checkout@v4 | ||
| - name: Use Node.js 18.x | ||
| uses: actions/setup-node@v4 | ||
| with: | ||
| node-version: 18 | ||
| cache: yarn | ||
| - name: Install | ||
| run: yarn --immutable | ||
| - name: Build plugin | ||
| run: yarn build | ||
| working-directory: packages/jbrowse-plugin-apollo | ||
| - name: Upload built plugin files | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: plugin | ||
| path: | | ||
| packages/jbrowse-plugin-apollo/dist/jbrowse-plugin-apollo.umd.development.js | ||
| packages/jbrowse-plugin-apollo/dist/jbrowse-plugin-apollo.umd.production.min.js | ||
| deploy: | ||
| name: Deploy to ${{ inputs.environment }} demo server | ||
| runs-on: ubuntu-latest | ||
| environment: ${{ inputs.environment }} | ||
| needs: [build] | ||
| steps: | ||
| - name: Check out | ||
| uses: actions/checkout@v4 | ||
| - name: Download built plugin files | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: plugin | ||
| path: .github/workflows/deploy/ | ||
| - name: Configure AWS credentials | ||
| uses: aws-actions/configure-aws-credentials@v4 | ||
| with: | ||
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | ||
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | ||
| aws-region: us-east-1 | ||
| - name: Get instance address | ||
| id: ec2-describe-instances | ||
| run: | | ||
| INSTANCE_ADDRESS=$(aws ec2 describe-instances \ | ||
| --instance-ids ${{ vars.INSTANCE_ID }} \ | ||
| --query "Reservations[*].Instances[*].[PublicDnsName]" \ | ||
| --output text) | ||
| echo "INSTANCE_ADDRESS=$INSTANCE_ADDRESS" >> "$GITHUB_OUTPUT" | ||
| - name: Set up SSH | ||
| run: | | ||
| mkdir --parents ~/.ssh | ||
| echo "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/staging | ||
| chmod 600 ~/.ssh/staging | ||
| cat >>~/.ssh/config <<END | ||
| Host staging | ||
| HostName ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }} | ||
| User ec2-user | ||
| IdentityFile ~/.ssh/staging | ||
| END | ||
| ssh-keyscan -H ${{ steps.ec2-describe-instances.outputs.INSTANCE_ADDRESS }} >> ~/.ssh/known_hosts | ||
| - name: Create Docker context | ||
| run: | | ||
| docker context create staging \ | ||
| --docker host=ssh://staging \ | ||
| --description "Staging server" | ||
| - name: Log in to the GitHub Container Registry | ||
| uses: docker/login-action@v3 | ||
| with: | ||
| registry: ghcr.io | ||
| username: ${{ github.repository_owner }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
| - name: Deploy | ||
| env: | ||
| JWT_SECRET: ${{ secrets.JWT_SECRET }} | ||
| SESSION_SECRET: ${{ secrets.SESSION_SECRET }} | ||
| GOOGLE_CLIENT_ID: ${{ secrets.GOOGLE_CLIENT_ID }} | ||
| GOOGLE_CLIENT_SECRET: ${{ secrets.GOOGLE_CLIENT_SECRET }} | ||
| ROOT_USER_NAME: ${{ secrets.ROOT_USER_NAME }} | ||
| ROOT_USER_PASSWORD: ${{ secrets.ROOT_USER_PASSWORD }} | ||
| URL: ${{ vars.URL }} | ||
| DOCKER_TAG: ${{ vars.DOCKER_TAG }} | ||
| working-directory: .github/workflows/deploy | ||
| run: | | ||
| docker --context staging compose down | ||
| docker --context staging compose pull | ||
| docker --context staging compose up --build --detach |
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| FROM httpd:alpine | ||
| ARG JBROWSE_VERSION | ||
| COPY ./httpd.conf /usr/local/apache2/conf/httpd.conf | ||
| COPY ./jbrowse-plugin-apollo.umd.development.js /usr/local/apache2/htdocs/ | ||
| COPY ./jbrowse-plugin-apollo.umd.production.min.js /usr/local/apache2/htdocs/ | ||
| COPY ./jbrowse-plugin-apollo.umd.production.min.js /usr/local/apache2/htdocs/apollo.js | ||
| WORKDIR /usr/local/apache2/htdocs/ | ||
| RUN <<EOF | ||
| set -o errexit | ||
| set -o nounset | ||
| set -o pipefail | ||
| wget https://github.com/GMOD/jbrowse-components/releases/download/v$JBROWSE_VERSION/jbrowse-web-v$JBROWSE_VERSION.zip | ||
| unzip -o jbrowse-web-v$JBROWSE_VERSION.zip | ||
| rm jbrowse-web-v$JBROWSE_VERSION.zip | ||
| EOF |
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