feat: add Extensions Manager

[pavelnikonorov]

Summary by Sourcery

Add an Extensions Manager to manage extensions within the application, including new CLI commands for extension management. Enhance the Configuration and Transport structs to support extensions and TLS verification. Update dependencies to support these new features.

New Features:

• Introduce an Extensions Manager to handle the loading, enabling, and management of extensions within the application.
• Add new CLI subcommands for managing extensions, including listing, adding, removing, and enabling extensions.

Enhancements:

• Enhance the Configuration struct to support extensions and integrate with the new Extensions Manager.
• Improve the Transport struct to support TLS verification using extensions.

Build:

• Add new dependencies for handling extensions, including libloading and base64.

[sourcery-ai[bot]]

Reviewer's Guide by Sourcery

This PR introduces an Extensions Manager system that enables dynamic loading and management of extensions in the GA4GH SDK. The implementation includes configuration handling, extension loading/unloading, and TLS verification capabilities. The changes primarily affect the configuration and transport layers, with additional CLI commands for extension management.

Sequence diagram for loading extensions

sequenceDiagram
    participant CLI
    participant Configuration
    participant ExtensionManager
    participant Extension
    CLI->>Configuration: from_file()
    Configuration->>ExtensionManager: new(installed_extensions, service_config)
    ExtensionManager->>Extension: new(config)
    Extension->>Extension: load(service_config)
    ExtensionManager-->>Configuration: ExtensionManager instance
    Configuration-->>CLI: Configuration instance

Class diagram for the new Extensions Manager

classDiagram
    class Configuration {
        +String base_path
        +Option<String> user_agent
        +Option<BasicAuth> basic_auth
        +Option<String> oauth_access_token
        +Option<String> bearer_access_token
        +Option<ApiKey> api_key
        +Option<ServiceExtensionsConfiguration> extensions
        +ExtensionManager extensions_manager
        +from_file(service_type: Option<ServiceType>, service_config_path: &String, extensions_config_path: &String) Result<Self, Box<dyn std::error::Error>>
    }

    class ExtensionManager {
        +Vec<Extension> extensions
        +new(installed_extensions: InstalledExtensions, service_config: Option<ServiceExtensionsConfiguration>) Result<Self, Box<dyn Error>>
        +get_extensions() &Vec<Extension>
        +lookup_extension_methods(unified_method_name: &str) Vec<&ExtensionMethod>
    }

    class Extension {
        +String name
        +String version
        +Option<String> path
        +Option<String> description
        +bool enabled
        +bool loaded
        +Option<Library> library
        +HashMap<String, Vec<ExtensionMethod>> methods
        +new(config: InstalledExtension) Result<Self, Box<dyn Error>>
        +load(service_config: Value)
    }

    class Transport {
        +Configuration config
        +reqwest::Client client
        +new(config: &Configuration) Result<Self, Box<dyn Error>>
    }

    Configuration --> ExtensionManager
    ExtensionManager --> Extension
    Transport --> Configuration

File-Level Changes

Change	Details	Files
Implemented an Extension Manager system for dynamic extension loading	Added ExtensionManager struct to handle extension lifecycle Created Extension struct to represent individual extensions Implemented methods for loading, enabling, and unloading extensions Added support for extension method lookup and invocation	lib/src/utils/extension_manager.rs lib/src/utils/extension.rs
Enhanced Configuration struct to support extensions	Added extension-related fields to Configuration struct Implemented serialization/deserialization for Configuration Added support for installed extensions configuration Created new structs for extension configuration	lib/src/utils/configuration.rs
Updated Transport layer to support TLS verification through extensions	Added TLS verification support using extension methods Implemented certificate handling for secure connections Added security mode support (enforce/permissive) Enhanced error handling and logging	lib/src/utils/transport.rs
Added CLI commands for extension management	Added extension subcommands (list, add, remove, enable) Updated main CLI structure to include extension commands Enhanced CLI documentation and help messages	cli/src/main.rs

Possibly linked issues

• #1: The PR implements the Extensions Manager, addressing the issue's requirement for extension support.

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