From 1d9ed2c93c5185e66259356a75f30f8ce0a9876e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 12 Sep 2025 21:06:19 +0000
Subject: [PATCH 1/3] Initial plan


From 42e782964315e9230bf55ef2cbcfd6b5eac656c9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 12 Sep 2025 21:10:12 +0000
Subject: [PATCH 2/3] Initial analysis and plan for CONTRIBUTING.md creation

Co-authored-by: lbeckman314 <15309567+lbeckman314@users.noreply.github.com>
---
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 src/backup/__pycache__/options.cpython-312.pyc   | Bin 0 -> 3042 bytes
 .../grip/__pycache__/__init__.cpython-312.pyc    | Bin 0 -> 5441 bytes
 .../__pycache__/__init__.cpython-312.pyc         | Bin 0 -> 5634 bytes
 .../s3/__pycache__/__init__.cpython-312.pyc      | Bin 0 -> 3261 bytes
 .../conftest.cpython-312-pytest-8.4.2.pyc        | Bin 0 -> 2932 bytes
 .../test_backups.cpython-312-pytest-8.4.2.pyc    | Bin 0 -> 6124 bytes
 7 files changed, 0 insertions(+), 0 deletions(-)
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 create mode 100644 src/backup/__pycache__/options.cpython-312.pyc
 create mode 100644 src/backup/grip/__pycache__/__init__.cpython-312.pyc
 create mode 100644 src/backup/postgres/__pycache__/__init__.cpython-312.pyc
 create mode 100644 src/backup/s3/__pycache__/__init__.cpython-312.pyc
 create mode 100644 tests/__pycache__/conftest.cpython-312-pytest-8.4.2.pyc
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From 9d6762e218bd651fd6babcbb17cb90103b586a56 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 12 Sep 2025 21:13:41 +0000
Subject: [PATCH 3/3] Create comprehensive CONTRIBUTING.md with CLI, Helm, and
 S3 verification instructions

Co-authored-by: lbeckman314 <15309567+lbeckman314@users.noreply.github.com>
---
 .gitignore                                    |   5 +
 CONTRIBUTING.md                               | 477 ++++++++++++++++++
 src/backup/__pycache__/main.cpython-312.pyc   | Bin 7893 -> 0 bytes
 .../__pycache__/options.cpython-312.pyc       | Bin 3042 -> 0 bytes
 .../conftest.cpython-312-pytest-8.4.2.pyc     | Bin 2932 -> 0 bytes
 .../test_backups.cpython-312-pytest-8.4.2.pyc | Bin 6124 -> 0 bytes
 6 files changed, 482 insertions(+)
 create mode 100644 CONTRIBUTING.md
 delete mode 100644 src/backup/__pycache__/main.cpython-312.pyc
 delete mode 100644 src/backup/__pycache__/options.cpython-312.pyc
 delete mode 100644 tests/__pycache__/conftest.cpython-312-pytest-8.4.2.pyc
 delete mode 100644 tests/__pycache__/test_backups.cpython-312-pytest-8.4.2.pyc

diff --git a/.gitignore b/.gitignore
index 99dbb2e..1a7820e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -113,3 +113,8 @@ venv.bak/
 
 # SQL files
 .sql
+
+# Python cache files
+__pycache__/
+*.pyc
+*.pyo
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..082559b
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,477 @@
+# Contributing to Backup Service
+
+Welcome to the backup-service project! This guide will help you get started with installing, running, and deploying the backup service for CALYPR systems. 🔄
+
+## Table of Contents
+
+- [Manual Installation & CLI Usage](#manual-installation--cli-usage)
+- [Kubernetes Deployment with Helm](#kubernetes-deployment-with-helm)
+- [Verifying S3 Backups](#verifying-s3-backups)
+- [Development Setup](#development-setup)
+- [Contributing Guidelines](#contributing-guidelines)
+
+## Manual Installation & CLI Usage
+
+### Prerequisites
+
+- **Python 3.12+** is required
+- **PostgreSQL client tools** (for database operations)
+- **Docker** (optional, for containerized usage)
+
+### Installation Steps
+
+1. **Clone the repository:**
+   ```bash
+   git clone https://github.com/calypr/backup-service.git
+   cd backup-service
+   ```
+
+2. **Create and activate a virtual environment:**
+   ```bash
+   python3 -m venv venv
+   source venv/bin/activate  # On Windows: venv\Scripts\activate
+   ```
+
+3. **Install dependencies:**
+   ```bash
+   pip install --upgrade pip
+   pip install -r requirements.txt
+   ```
+
+4. **Install the backup service:**
+   ```bash
+   pip install -e .
+   ```
+
+5. **Verify installation:**
+   ```bash
+   bak --help
+   ```
+
+### CLI Usage Examples
+
+#### PostgreSQL Operations
+
+**List databases:**
+```bash
+bak pg ls \
+  --host localhost \
+  --port 5432 \
+  --user postgres \
+  --password your_password
+```
+
+**Dump all databases to local directory:**
+```bash
+bak pg dump \
+  --host localhost \
+  --port 5432 \
+  --user postgres \
+  --password your_password \
+  --dir /path/to/backup/directory
+```
+
+**Restore databases from local directory:**
+```bash
+bak pg restore \
+  --host localhost \
+  --port 5432 \
+  --user postgres \
+  --password your_password \
+  --dir /path/to/backup/directory
+```
+
+#### S3 Operations
+
+**Upload backups to S3:**
+```bash
+bak s3 upload \
+  --endpoint https://s3.amazonaws.com \
+  --bucket your-backup-bucket \
+  --key your-access-key \
+  --secret your-secret-key \
+  --dir /path/to/backup/directory
+```
+
+**Download backups from S3:**
+```bash
+bak s3 download \
+  --endpoint https://s3.amazonaws.com \
+  --bucket your-backup-bucket \
+  --key your-access-key \
+  --secret your-secret-key \
+  --dir /path/to/restore/directory
+```
+
+#### GRIP Operations
+
+**Backup GRIP database:**
+```bash
+bak grip backup \
+  --host localhost \
+  --port 8201 \
+  --graph your-graph-name \
+  --dir /path/to/backup/directory \
+  --vertices \
+  --edges
+```
+
+**Restore GRIP database:**
+```bash
+bak grip restore \
+  --host localhost \
+  --port 8201 \
+  --graph your-graph-name \
+  --dir /path/to/backup/directory
+```
+
+### Docker Usage
+
+You can also run the backup service using Docker:
+
+```bash
+# Build the Docker image
+docker build -t backup-service .
+
+# Run a backup operation
+docker run --rm \
+  -v /host/backup/path:/backups \
+  backup-service bak pg dump \
+  --host database-host \
+  --port 5432 \
+  --user postgres \
+  --password password \
+  --dir /backups
+```
+
+## Kubernetes Deployment with Helm
+
+### Prerequisites
+
+- **kubectl** configured with access to your Kubernetes cluster
+- **Helm 3.x** installed
+- Access to the **ohsu-comp-bio/helm-charts** repository
+
+### Helm Installation Steps
+
+1. **Add the Helm repository:**
+   ```bash
+   helm repo add ohsu-comp-bio https://ohsu-comp-bio.github.io/helm-charts
+   helm repo update
+   ```
+
+2. **Create a values file for your deployment:**
+   ```bash
+   cat > backup-values.yaml << EOF
+   image:
+     repository: quay.io/ohsu-comp-bio/backup-service
+     tag: "latest"
+     pullPolicy: Always
+
+   # Configure backup schedule as a CronJob
+   schedule: "0 2 * * *"  # Daily at 2 AM
+
+   # Environment variables for database connection
+   env:
+     - name: POSTGRES_HOST
+       value: "postgres-service.default.svc.cluster.local"
+     - name: POSTGRES_PORT
+       value: "5432"
+     - name: POSTGRES_USER
+       valueFrom:
+         secretKeyRef:
+           name: postgres-secret
+           key: username
+     - name: POSTGRES_PASSWORD
+       valueFrom:
+         secretKeyRef:
+           name: postgres-secret
+           key: password
+
+   # S3 configuration
+     - name: S3_ENDPOINT
+       value: "s3.amazonaws.com"
+     - name: S3_BUCKET
+       value: "your-backup-bucket"
+     - name: AWS_ACCESS_KEY_ID
+       valueFrom:
+         secretKeyRef:
+           name: s3-secret
+           key: access-key
+     - name: AWS_SECRET_ACCESS_KEY
+       valueFrom:
+         secretKeyRef:
+           name: s3-secret
+           key: secret-key
+
+   # Resource limits
+   resources:
+     limits:
+       cpu: 500m
+       memory: 512Mi
+     requests:
+       cpu: 100m
+       memory: 128Mi
+
+   # Persistent volume for temporary backup storage
+   persistence:
+     enabled: true
+     size: 10Gi
+     storageClass: "standard"
+   EOF
+   ```
+
+3. **Create necessary secrets:**
+   ```bash
+   # PostgreSQL credentials
+   kubectl create secret generic postgres-secret \
+     --from-literal=username=postgres \
+     --from-literal=password=your-postgres-password
+
+   # S3 credentials
+   kubectl create secret generic s3-secret \
+     --from-literal=access-key=your-access-key \
+     --from-literal=secret-key=your-secret-key
+   ```
+
+4. **Install the Helm chart:**
+   ```bash
+   helm install backup-service ohsu-comp-bio/backups \
+     --values backup-values.yaml \
+     --namespace backup-system \
+     --create-namespace
+   ```
+
+5. **Verify the deployment:**
+   ```bash
+   kubectl get pods -n backup-system
+   kubectl get cronjobs -n backup-system
+   kubectl logs -n backup-system deployment/backup-service
+   ```
+
+### Helm Chart Configuration
+
+The backup service Helm chart supports the following key configurations:
+
+- **Schedule**: Configure CronJob schedule for automated backups
+- **Image**: Specify the backup service container image
+- **Environment**: Database and S3 connection parameters
+- **Resources**: CPU and memory limits/requests
+- **Persistence**: Temporary storage for backup files
+- **Security**: Pod security context and service account configuration
+
+For complete configuration options, see: https://github.com/ohsu-comp-bio/helm-charts/tree/main/charts/backups
+
+## Verifying S3 Backups
+
+### Using AWS CLI
+
+1. **Install AWS CLI:**
+   ```bash
+   pip install awscli
+   ```
+
+2. **Configure AWS credentials:**
+   ```bash
+   aws configure
+   # Enter your Access Key ID, Secret Access Key, region, and output format
+   ```
+
+3. **List backup files:**
+   ```bash
+   # List all backups in your bucket
+   aws s3 ls s3://your-backup-bucket/
+
+   # List backups with timestamps
+   aws s3 ls s3://your-backup-bucket/ --recursive --human-readable
+
+   # List specific database backups
+   aws s3 ls s3://your-backup-bucket/postgres/ --recursive
+   ```
+
+4. **Download and verify backup content:**
+   ```bash
+   # Download a specific backup
+   aws s3 cp s3://your-backup-bucket/postgres/database-2024-01-15.sql.gz ./
+
+   # Verify the backup file
+   gunzip database-2024-01-15.sql.gz
+   head -50 database-2024-01-15.sql  # Check backup contents
+   ```
+
+5. **Check backup sizes and dates:**
+   ```bash
+   # Get detailed information about backups
+   aws s3api list-objects-v2 \
+     --bucket your-backup-bucket \
+     --prefix postgres/ \
+     --query 'Contents[?Size>`1000000`].[Key,Size,LastModified]' \
+     --output table
+   ```
+
+### Using MinIO Client (mc)
+
+1. **Install MinIO client:**
+   ```bash
+   # Linux/macOS
+   curl https://dl.min.io/client/mc/release/linux-amd64/mc \
+     --create-dirs -o ~/bin/mc
+   chmod +x ~/bin/mc
+
+   # Or via package manager
+   brew install minio/stable/mc  # macOS
+   ```
+
+2. **Configure MinIO client:**
+   ```bash
+   # For AWS S3
+   mc alias set aws https://s3.amazonaws.com your-access-key your-secret-key
+
+   # For MinIO server
+   mc alias set minio https://your-minio-server.com your-access-key your-secret-key
+   ```
+
+3. **List and verify backups:**
+   ```bash
+   # List all backups
+   mc ls aws/your-backup-bucket/
+
+   # List with details
+   mc ls --recursive --summarize aws/your-backup-bucket/
+
+   # Find backups by date
+   mc find aws/your-backup-bucket/ --name "*2024-01*" --print
+   ```
+
+4. **Download and verify backup content:**
+   ```bash
+   # Download a backup
+   mc cp aws/your-backup-bucket/postgres/database-2024-01-15.sql.gz ./
+
+   # Compare backup sizes
+   mc stat aws/your-backup-bucket/postgres/database-2024-01-15.sql.gz
+   ```
+
+5. **Monitor backup health:**
+   ```bash
+   # Check for recent backups (last 7 days)
+   mc find aws/your-backup-bucket/ --newer-than 7d --print
+
+   # Verify backup integrity with checksums
+   mc cat aws/your-backup-bucket/postgres/database-2024-01-15.sql.gz | md5sum
+   ```
+
+### Backup Verification Checklist
+
+- ✅ Backups are created on schedule
+- ✅ Backup files are properly named with timestamps
+- ✅ Backup files are not empty (check file sizes)
+- ✅ Recent backups exist (within expected time frame)
+- ✅ Backup files can be downloaded successfully
+- ✅ Backup content is valid (can be opened/restored)
+- ✅ Old backups are cleaned up according to retention policy
+
+## Development Setup
+
+### Setting up for Development
+
+1. **Clone and install in development mode:**
+   ```bash
+   git clone https://github.com/calypr/backup-service.git
+   cd backup-service
+   python3 -m venv venv
+   source venv/bin/activate
+   pip install --upgrade pip
+   pip install -r requirements.txt
+   pip install -e .
+   ```
+
+2. **Run tests:**
+   ```bash
+   # Run all tests
+   pytest
+
+   # Run with verbose output
+   pytest -v
+
+   # Run specific test file
+   pytest tests/test_backups.py
+
+   # Run with debug logging
+   pytest -v --log-cli-level=DEBUG
+   ```
+
+### Code Structure
+
+```
+backup-service/
+├── src/backup/           # Main package
+│   ├── main.py          # CLI entry point
+│   ├── options.py       # Click command options
+│   ├── postgres/        # PostgreSQL backup logic
+│   ├── s3/             # S3 upload/download logic
+│   └── grip/           # GRIP database backup logic
+├── tests/              # Test suite
+├── examples/           # Usage examples
+├── Dockerfile          # Container image
+└── pyproject.toml      # Package configuration
+```
+
+### Testing with Docker
+
+```bash
+# Build development image
+docker build -t backup-service:dev .
+
+# Run tests in container
+docker run --rm backup-service:dev pytest
+
+# Interactive development
+docker run -it --rm \
+  -v $(pwd):/app \
+  backup-service:dev bash
+```
+
+## Contributing Guidelines
+
+### Code Style
+
+- Follow **PEP 8** Python style guidelines
+- Use **type hints** where possible
+- Add **docstrings** for public functions and classes
+- Keep functions focused and well-named
+
+### Making Changes
+
+1. **Fork the repository** and create a feature branch
+2. **Write tests** for new functionality
+3. **Ensure all tests pass** before submitting
+4. **Update documentation** if needed
+5. **Submit a pull request** with a clear description
+
+### Testing Requirements
+
+- All new features must include tests
+- Tests should use **testcontainers** for integration testing
+- Maintain or improve test coverage
+- Test both success and failure scenarios
+
+### Pull Request Process
+
+1. Create a descriptive PR title and description
+2. Reference any related issues
+3. Ensure CI/CD pipelines pass
+4. Request review from maintainers
+5. Address any feedback promptly
+
+### Release Process
+
+This project uses **semantic-release** for automated versioning and releases:
+
+- Commits follow [Conventional Commits](https://conventionalcommits.org/)
+- Releases are automatically created on merge to main
+- Docker images are automatically built and published
+
+---
+
+For questions or support, please open an issue in the [GitHub repository](https://github.com/calypr/backup-service/issues).
\ No newline at end of file
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