mcp

type BuiltInTool struct {
	Tool    mcp.Tool
	Handler server.ToolHandlerFunc
	// ReadOnly is true if the tool only reads: it never changes data on the platform.
	ReadOnly bool
	// Instruction is an optional line of server instructions that tells the model when to use the tool.
	Instruction string
}

type Config struct {
	Logger *log.Logger

	// Version is reported to MCP clients as the server's version (serverInfo.version).
	// The CLI should set this to match the ivcap-cli build version.
	Version string

	// ToolSchema is the schema URN prefix used when discovering tool aspects.
	ToolSchema string

	// TimeoutSec is used both for adapter construction and request timeouts.
	TimeoutSec int

	// ChunkSize is used by artifact uploads.
	ChunkSize int64

	// CreateAdapter must return an authenticated adapter.
	CreateAdapter func(timeoutSec int) (*a.Adapter, error)

	// WithLogging enables JSON-RPC request/response logging to a file.
	WithLogging bool

	// LogDir specifies the directory for MCP log files (defaults to /tmp).
	LogDir string
}

type GenomeImportArgs struct {
	Accession       string   `json:"accession"`
	Include         []string `json:"include,omitempty"`
	Chromosomes     []string `json:"chromosomes,omitempty"`
	AssemblyVersion string   `json:"assembly_version,omitempty"`
	Name            string   `json:"name,omitempty"`
	Policy          string   `json:"policy,omitempty"`
	License         string   `json:"license,omitempty"`
}

type GenomeImportFunc func(ctxt context.Context, adapter *a.Adapter, args GenomeImportArgs) (any, error)

type GenomeListArgs struct {
	Limit int    `json:"limit,omitempty"`
	Page  string `json:"page,omitempty"`
}

type GenomeListFunc func(ctxt context.Context, adapter *a.Adapter, args GenomeListArgs) (any, error)

type JobWaitResult struct {
	JobID      string
	Status     string
	Result     map[string]any
	IsComplete bool
	Message    string
}

type ToolDefinition struct {
	Name        string         `json:"name"`
	Description string         `json:"description"`
	Schema      map[string]any `json:"fn_schema"`
}