SNPseek Datasource

A SNP data source that exposes and organizes variant data from the SNPseek backend database, supporting the SNPseek web application and related analytical and integration use cases.

Overview

SNPseek Datasource is a Java-based application built on the Spring Framework that provides data access layers for managing and querying SNP-related genomic information. It is based on the CHADO database schema, with targeted modifications and extensions to tailor the model to the specific requirements of the SNPseek system, and exposes a robust API for genomic data operations.

Features

• Data Access Layer: Comprehensive DAO (Data Access Object) implementations for genomic data
• Spring Integration: Built on Spring Framework for dependency injection and transaction management
• CHADO Schema Support: Integration with CHADO database schema for biological data
• Modular Architecture: Organized into logical packages for maintainability
• Configuration Management: Flexible XML-based Spring configuration

Project Structure

snpseek-datasource/
├── src/
│   ├── main/
│   │   ├── java/
│   │   │   └── org/trri/tric/ds/chado/
│   │   │       ├── dao/           # Data Access Objects
│   │   │       │  └── impl/    # DAO implementations
│   │   │       └── domain/        # Domain models
│   │   │          └── impl/       # implementations
│   │   └── resources/
│   │       ├── META-INF/
│   │       └── *.xml              # Spring configuration files
│   └── test/
├── lib/                           # External libraries
├── pom.xml                        # Maven configuration
└── README.md

Prerequisites

• Java 8 or higher
• Maven 3.x
• Spring Framework 3.2.x
• Database server (PostgreSQL recommended for CHADO)
• Eclipse IDE or similar Java IDE

Installation

1. Clone the repository

   git clone <repository-url>
   cd snpseek-datasource

2. Configure database connection

   • Configure database connection and data source properties
   • Review and adjust connection-related settings as needed
   • Credentials are read from environment variables by default
     • Values defined in the configuration file may override the environment variables if explicitly provided

3. Build the project

   mvn clean install

4. Run tests

   mvn test

Configuration

Database Configuration

Update your database connection settings in the Spring configuration files:

<!-- Example configuration in incDS_prod_crud-dao-context.xml -->
<bean class="org.apache.commons.dbcp.BasicDataSource"
		destroy-method="close" name="IRIC_ProductionDS_PG">
		<property name="driverClassName"
			value="org.postgresql.Driver" />
		<property name="username" value="${DB_USERNAME}" />
		<property name="password" value="${DB_PASSWORD}" />
		<property name="url" value="${DB_URL}" />
		<property name="maxIdle" value="1" />
		<property name="maxActive" value="10" />
	</bean>

Spring Context

The application uses Spring XML configuration for:

• Component scanning
• Transaction management
• Data source configuration
• DAO bean definitions

Usage

Basic DAO Operations

// Example usage of DAO classes
@Autowired
private YourDao yourDao;

// Perform database operations
List<Entity> results = yourDao.findAll();

Integration

Include SNPseek Datasource as a dependency in your project:

<dependency>
    <groupId>org.trri.tric</groupId>
    <artifactId>snpseek-datasource</artifactId>
    <version>1.0.0</version>
</dependency>

Development

Setting Up Development Environment

1. Import project into Eclipse:

   • File → Import → Maven → Existing Maven Projects
   • Select the project directory
   • Eclipse will automatically configure the build path

2. Configure application servers if needed

3. Run the application or tests from Eclipse

Code Structure

• DAO Layer: org.irri.tric.ds.chado.dao
• Implementation: org.irri.tric.ds.chado.dao.impl
• Domain Models: org.irri.tric.ds.chado.domain
• Configuration: src/resources/*.xml

Testing

Run the test suite:

# Run all tests
mvn test

# Run specific test class
mvn test -Dtest=YourTestClass

# Run with coverage
mvn clean test jacoco:report

Troubleshooting

Common Issues

Issue: XML Configuration Errors

• Ensure all Spring schema locations are correctly defined
• Verify namespace declarations in XML files
• Check that external resources can be downloaded

Issue: Database Connection Failures

• Verify database credentials
• Check network connectivity
• Ensure database server is running

Issue: Maven Build Failures

• Clear Maven cache: mvn clean
• Update dependencies: mvn dependency:resolve
• Check for conflicting library versions

Contributing

1. Fork the repository
2. Create a feature branch (git checkout -b feature/your-feature)
3. Commit your changes (git commit -am 'Add new feature')
4. Push to the branch (git push origin feature/your-feature)
5. Create a Pull Request

Coding Standards

• Follow Java naming conventions
• Write unit tests for new features
• Document public APIs with Javadoc
• Keep commits atomic and well-described

Contact

• Developer: [Lord Hendrix Barboza]
• Email: [l.h.barboza@cgiar.org]
• Organization: IRRI/Bioinformatics

Acknowledgments

• Built with Spring Framework
• Uses CHADO database schema

---

Note: This is an active development project. Please refer to the issue tracker for known issues and planned features.